From sotirisnik at gmail.com Fri Aug 2 07:57:42 2019 From: sotirisnik at gmail.com (Sotirios Nikoloutsopoulos) Date: Fri, 2 Aug 2019 14:57:42 +0300 Subject: [Loris-dev] Import mri - scripts In-Reply-To: References: Message-ID: Hi Christine, In the candidate_list page i can see this patient [image: image.png] If i press the link under PSCID i get to see [image: image.png] and if i press the link under Scan Done it redirects me to imaging_browser [image: image.png] At the mri_violations page i also see No results ( neither on resolved / not resolved ). At the imaging_uploader i can see the record that failed. [image: image.png] If i click on the tarchive info i get to see the Protocol Name which i think is the acquisition we wanted? [image: image.png] Also my mri_protocol table is empty. Furthermore i would like to ask about the defaced, native, selected. What exactly is native and selected? And where are the qc comments stored? [image: image.png] Finally a walkthrough would be helpful. Thanks, Sotirios ???? ???, 30 ???? 2019 ???? 8:29 ?.?., ?/? Christine Rogers, Ms. < christine.rogers at mcgill.ca> ??????: > Hi Sotirios, > Glad to hear you're making progress with the visit labels. To follow up > on your last few emails: > > a- The Wiki's Setup Guide contains Sample insert statements for the Visit > Windows table > > . > > As Cecile mentioned, the consistency of visit label format is important: > V01, v01, V1, 01 -- whichever you select to use is fine; we use V01 by > default across all documentation. > > b- For Password reset, there is a script in the tools/ directory so that a > back-end administrator can reset any front-end user password, including > Admin. (See info on setting up / resetting User passwords in the Wiki's > Setup Guide > > ) > > c- The minc file not being registered -- due to AcquisitionProtocol > unknown. > This means the SeriesDescription (Acquisition Protocol) in you Dicom > header was not matched to any scan listed in the mri_protocol database > table. > (In the online Loris-MRI Troubleshooting Guide, > this > is Table 3, 2nd-last item "no MINCs inserted"). > > The MRI Violations module (Readme here) > will show > you the details of this mismatch -- > Go to the module (under the Imaging menu), find your scan and click the > link "Could not identify scan type" -- in the next subpage you can compare > the scan's actual parameters against the mri_protocol table. > > To resolve this, adjust your mri_protocol table values or perhaps ensure > your DICOMs are labelled consistently. > > Let us know if this works for you -- we can also walk you through an > example of non-identified scans on Demo.loris.ca (MRI Violations module). > > Best, > Christine > > The LORIS team > > > On Tue, Jul 30, 2019 at 10:47 AM Sotirios Nikoloutsopoulos < > sotirisnik at gmail.com> wrote: > >> I hope this is sufficient as the error for the visit label disappeared. >> [image: image.png] >> >> Please see the attached file. Also something i found. >> >> lorisadmin at hbp:/data/loris/bin/mri$ cat >> /data/loris/data//logs/TarLoad-17-39-xubBdv.log >> >> ==> Loading file from disk >> /tmp/TarLoad-17-39-UyQcG2/dcc0000_258024_v1_20121205_102108_501e1_mri.mnc >> >> --> mapping DICOM parameter for >> /tmp/TarLoad-17-39-UyQcG2/dcc0000_258024_v1_20121205_102108_501e1_mri.mnc >> >> ==> computing md5 hash for MINC body. >> >> --> md5: 6b1202fd63e29de4c9be1cd9925888a5 >> >> ==> verifying acquisition protocol >> >> Acquisition protocol is unknown >> >> --> The minc file cannot be registered since the AcquisitionProtocol is >> unknown >> >> ???? ???, 30 ???? 2019 ???? 4:58 ?.?., ?/? Sotirios Nikoloutsopoulos < >> sotirisnik at gmail.com> ??????: >> >>> Ok I fixed the login problem by using a known hash and by deleting the >>> rows from the login_history i was able to login. >>> >>> ???? ???, 30 ???? 2019 ???? 4:50 ?.?., ?/? Sotirios Nikoloutsopoulos < >>> sotirisnik at gmail.com> ??????: >>> >>>> Hi, >>>> >>>> there was no visit label 01 in the Visit_Windows table and i don't know >>>> how to insert it because the record requires lots of attributes. Also the >>>> system for a reason asked me to update my password and now i don't remember >>>> it and my account got suspended. Is there a way to reset it or set a simple >>>> password? I updated the password hash in the users table by using the hash >>>> from another LORIS setup we had and i still couldn't login ( also the >>>> attribute password is always NULL and the expiration date is 1999-01-01 for >>>> some reason ). >>>> >>>> Thanks >>>> >>>> >>>> >>>> ???? ???, 29 ???? 2019 ???? 5:21 ?.?., ?/? Cecile Madjar < >>>> cecile.madjar at mcin.ca> ??????: >>>> >>>>> Hi Sotirios, >>>>> >>>>> Can you try adding the visit label v01 to the Visit_Windows table? >>>>> >>>>> However, I noticed that in a previous dataset, the label was V1. Does >>>>> that refer to the same visit? If so, you might want to harmonize the visit >>>>> labels so they are all the same across datasets for a given timepoint, >>>>> meaning you will need to relabel scans when the visit label is different >>>>> but referring to the same visit label (v01 = V1 etc...). >>>>> >>>>> Hope this helps, >>>>> >>>>> C?cile >>>>> >>>>> On Mon, Jul 29, 2019 at 10:15 AM Sotirios Nikoloutsopoulos < >>>>> sotirisnik at gmail.com> wrote: >>>>> >>>>>> Hi, >>>>>> >>>>>> Could you help me with the "Visit label does not exist"? I had >>>>>> changed $subjectID{'createVisitLabel'} to 1 as you had suggested but it >>>>>> appears that this problem hasn't been resolved yet. >>>>>> >>>>>> lorisadmin at hbp:/data/loris/bin/mri$ cat >>>>>> /data/loris/data//logs/TarLoad-14-58-9Xog7H.log >>>>>> >>>>>> ==> Loading file from disk >>>>>> /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc >>>>>> >>>>>> --> mapping DICOM parameter for >>>>>> /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc >>>>>> >>>>>> --> using user-defined filterParameters for >>>>>> /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc >>>>>> >>>>>> Candidate Mismatch Error is Visit label does not exist >>>>>> -> WARNING: This candidate was invalid. Logging to >>>>>> MRICandidateErrors table with reason Visit label does >>>>>> not exist >>>>>> >>>>>> Thank you, >>>>>> >>>>>> Sotirios >>>>>> >>>>>> ???? ???, 26 ???? 2019 ???? 3:02 ?.?., ?/? Sotirios Nikoloutsopoulos < >>>>>> sotirisnik at gmail.com> ??????: >>>>>> >>>>>>> Hi Cecile, >>>>>>> >>>>>>> The Center error was fixed. Still the insertion of mincs fails. >>>>>>> Please see the output.txt file i attached. Also is there something else i >>>>>>> need to change at the paths configuration? >>>>>>> >>>>>>> Thank you, >>>>>>> >>>>>>> Sotirios >>>>>>> >>>>>>> ???? ???, 25 ???? 2019 ???? 6:55 ?.?., ?/? Cecile Madjar < >>>>>>> cecile.madjar at mcin.ca> ??????: >>>>>>> >>>>>>>> Hi Sotirios, >>>>>>>> >>>>>>>> We are making progress! >>>>>>>> >>>>>>>> I have a feeling this error comes from the fact that your psc table >>>>>>>> does not have the MRI_alias populated for the DCC site. Running the >>>>>>>> following query in the mysql database should fix this: >>>>>>>> UPDATE psc SET MRI_alias="DCC", Alias="DCC" WHERE Name="Data >>>>>>>> Coordinating Center"; >>>>>>>> Repeat the same with all your sites (make sure to change the >>>>>>>> Aliases between sites, they should all be unique). >>>>>>>> >>>>>>>> Let me know how it goes! >>>>>>>> Best, >>>>>>>> >>>>>>>> C?cile >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> On Thu, Jul 25, 2019 at 11:43 AM Sotirios Nikoloutsopoulos < >>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>> >>>>>>>>> Dear Cecile, >>>>>>>>> You were right about your guesses. I did the modifications you >>>>>>>>> suggested, i still get the "no mincs inserted" error, now i am getting the >>>>>>>>> "No center found this candidate" error ( how do i fix that? from what i see >>>>>>>>> the .dcm files contains a 'Institution Name', is that the center? ), so i >>>>>>>>> guess that's why the validation fails, but i changed the force variable of >>>>>>>>> tarchiveLoader to 1, shouldn't it have inserted the mincs then? Also it is >>>>>>>>> optional to have a mail server, right? ( from what i see the mail error >>>>>>>>> does not affect the $valid_study, so i assume we are okay with that ) >>>>>>>>> Thank you a lot, >>>>>>>>> Sotirios >>>>>>>>> >>>>>>>>> ???? ???, 25 ???? 2019 ???? 5:48 ?.?., ?/? Cecile Madjar < >>>>>>>>> cecile.madjar at mcin.ca> ??????: >>>>>>>>> >>>>>>>>>> Hi Sotirios, >>>>>>>>>> >>>>>>>>>> From what I understand, I believe you just need to update a few >>>>>>>>>> config settings from the frontend in the Config module (under the Admin >>>>>>>>>> menu). >>>>>>>>>> [image: Screen Shot 2019-07-25 at 10.31.35 AM.png] >>>>>>>>>> >>>>>>>>>> Then go to the Paths section of the config module and update the >>>>>>>>>> "LORIS-MRI code" config setting to /data/loris/bin/mri (my guess is that >>>>>>>>>> currently, it is set to /data/LORIS/data) and click on the submit button. >>>>>>>>>> [image: Screen Shot 2019-07-25 at 10.32.50 AM.png] >>>>>>>>>> >>>>>>>>>> Then, go to Imaging Pipeline section of the Configuration module >>>>>>>>>> and update the "Loris-MRI Data Directory" to /data/loris/data/ (my guess is >>>>>>>>>> that it is empty at the moment in your database which is why $data_dir is >>>>>>>>>> not defined when you run the tarchiveLoader step of the insertion pipeline). >>>>>>>>>> [image: Screen Shot 2019-07-25 at 10.40.52 AM.png] >>>>>>>>>> >>>>>>>>>> Finally, I took a look at your environment file and it might be a >>>>>>>>>> good idea to update your PERL5LIB variable to the following (it has been >>>>>>>>>> added to the code a few releases ago as we realized this was needed for the >>>>>>>>>> libraries. Not sure which version of LORIS-MRI you are using but it does >>>>>>>>>> not hurt to update this variable to what I suggest below): >>>>>>>>>> export >>>>>>>>>> PERL5LIB=/data/loris/bin/mri/uploadNeuroDB:/data/loris/bin/mri/dicom-archive:$PERL5LIB >>>>>>>>>> >>>>>>>>>> Hope this helps. Sorry you are experiencing so much trouble >>>>>>>>>> setting things up. We probably need to update our WIKI. >>>>>>>>>> >>>>>>>>>> Best, >>>>>>>>>> >>>>>>>>>> C?cile >>>>>>>>>> >>>>>>>>>> On Thu, Jul 25, 2019 at 9:48 AM Sotirios Nikoloutsopoulos < >>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>> >>>>>>>>>>> The "Loris-MRI Data Directory" should be in the environment >>>>>>>>>>> file? >>>>>>>>>>> >>>>>>>>>>> ???? ???, 25 ???? 2019 ???? 12:59 ?.?., ?/? Sotirios >>>>>>>>>>> Nikoloutsopoulos ??????: >>>>>>>>>>> >>>>>>>>>>>> The scripts are located in /data/loris/bin/mri/. Somewhere I >>>>>>>>>>>> might have messed something up but i remember following the instructions in >>>>>>>>>>>> the wiki.For example when i tried to execute the >>>>>>>>>>>> batch_uploads_imageuploader perl script the line >>>>>>>>>>>> >>>>>>>>>>>> my $command = "$bin_dir/uploadNeuroDB/imaging_upload_file.pl " >>>>>>>>>>>> >>>>>>>>>>>> was pointing to an invalid path, for example: it was repeating >>>>>>>>>>>> a pattern and had LORIS instead of loris ( i think the mistake was that in >>>>>>>>>>>> the wiki it suggested to use $PROJECT for the name of the folder and i >>>>>>>>>>>> choosed 'loris' >>>>>>>>>>>> https://github.com/aces/Loris/wiki/Imaging-Database ). See >>>>>>>>>>>> also the in image for the modification i did. Also i didn't find the >>>>>>>>>>>> section to config the $data_dir variable. >>>>>>>>>>>> >>>>>>>>>>>> Thank you, >>>>>>>>>>>> >>>>>>>>>>>> Sotirios >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> ???? ???, 24 ???? 2019 ???? 6:05 ?.?., ?/? Cecile Madjar < >>>>>>>>>>>> cecile.madjar at mcin.ca> ??????: >>>>>>>>>>>> >>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>> >>>>>>>>>>>>> It looks like you have one Config setting not set (based on >>>>>>>>>>>>> the first error message you got when running it the first time). You need >>>>>>>>>>>>> to set a value for "Loris-MRI Data Directory" in the Config module under >>>>>>>>>>>>> the Imaging pipeline section (from what I can see, it would be >>>>>>>>>>>>> /data/loris/data/ for your setup). >>>>>>>>>>>>> >>>>>>>>>>>>> The reason you got that error message the second time is that >>>>>>>>>>>>> the pipeline checks if the DICOM study was already inserted in the tarchive >>>>>>>>>>>>> table. Since you ran the study once already, the study is inserted into the >>>>>>>>>>>>> tarchive, hence the message. However, the pipeline did not complete as the >>>>>>>>>>>>> MINC files were not created and inserted into the files/parameter_file >>>>>>>>>>>>> table. In order to continue the insertion, you will then need to run the >>>>>>>>>>>>> tarchiveLoader command suggested in the terminal during the second run: >>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader -globLocation >>>>>>>>>>>>> -profile prod >>>>>>>>>>>>> /data/loris/data/tarchive//2012/DCM_2012-12-05_ImagingUpload-17-43-ZUEFjb.tar >>>>>>>>>>>>> -verbose >>>>>>>>>>>>> >>>>>>>>>>>>> Finally, I am a bit confused by your setup. Where are the >>>>>>>>>>>>> scripts located? In /data/loris/bin/mri or /data/loris/data? It feels like >>>>>>>>>>>>> the Config setting "LORIS-MRI code" in the Paths section was set to >>>>>>>>>>>>> "/data/LORIS/data" but it should have been set to the directory where the >>>>>>>>>>>>> scripts are located (most probably /data/loris/bin/mri). >>>>>>>>>>>>> >>>>>>>>>>>>> Hope this helps, >>>>>>>>>>>>> >>>>>>>>>>>>> C?cile >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> On Wed, Jul 24, 2019 at 10:55 AM Sotirios Nikoloutsopoulos < >>>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>> >>>>>>>>>>>>>> Ok first i execute this command: >>>>>>>>>>>>>> >>>>>>>>>>>>>> "lorisadmin at hbp:/data/loris/bin/mri$ >>>>>>>>>>>>>> ./batch_uploads_imageuploader -profile prod < ~/Desktop/input.txt > log.txt >>>>>>>>>>>>>> Use of uninitialized value $data_dir in concatenation (.) or >>>>>>>>>>>>>> string at ./batch_uploads_imageuploader line 143. >>>>>>>>>>>>>> Use of uninitialized value $data_dir in concatenation (.) or >>>>>>>>>>>>>> string at ./batch_uploads_imageuploader line 143. >>>>>>>>>>>>>> Use of uninitialized value $_ in pattern match (m//) at >>>>>>>>>>>>>> ./batch_uploads_imageuploader line 147. >>>>>>>>>>>>>> base is DCC0000_258024_V01 >>>>>>>>>>>>>> path is /data/incoming/ >>>>>>>>>>>>>> type is .tar.gz >>>>>>>>>>>>>> fullpath is /data/incoming/DCC0000_258024_V01.tar.gz >>>>>>>>>>>>>> >>>>>>>>>>>>>> source /tmp/ImagingUpload-17-43-ZUEFjb >>>>>>>>>>>>>> targetlocation /data/loris/data/tarchive >>>>>>>>>>>>>> >>>>>>>>>>>>>> Use of uninitialized value $data_dir in concatenation (.) or >>>>>>>>>>>>>> string at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 256. >>>>>>>>>>>>>> Use of uninitialized value $data_dir in concatenation (.) or >>>>>>>>>>>>>> string at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 284. >>>>>>>>>>>>>> Use of uninitialized value $data_dir in concatenation (.) or >>>>>>>>>>>>>> string at /data/loris/bin/mri/uploadNeuroDB/ >>>>>>>>>>>>>> tarchive_validation.pl line 219. >>>>>>>>>>>>>> Use of uninitialized value $data_dir in concatenation (.) or >>>>>>>>>>>>>> string at /data/loris/bin/mri/uploadNeuroDB/minc_insertion.pl >>>>>>>>>>>>>> line 270. >>>>>>>>>>>>>> Use of uninitialized value $data_dir in concatenation (.) or >>>>>>>>>>>>>> string at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 711. >>>>>>>>>>>>>> Can't exec "mail": No such file or directory at >>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 721. >>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 722. >>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 723. >>>>>>>>>>>>>> Use of uninitialized value $data_dir in concatenation (.) or >>>>>>>>>>>>>> string at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 724. >>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 724. >>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 725. >>>>>>>>>>>>>> Use of uninitialized value $data_dir in concatenation (.) or >>>>>>>>>>>>>> string at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 735. >>>>>>>>>>>>>> >>>>>>>>>>>>>> No Mincs inserted >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> The tarchiveLoader insertion script has failed. >>>>>>>>>>>>>> Running now the following command: >>>>>>>>>>>>>> /data/loris/data/uploadNeuroDB/imaging_upload_file.pl >>>>>>>>>>>>>> -profile prod -upload_id 3 /data/incoming/DCC0000_258024_V01.tar.gz >>>>>>>>>>>>>> -verbose" >>>>>>>>>>>>>> >>>>>>>>>>>>>> I inserted the VisitLabel, but still the Mincs are not >>>>>>>>>>>>>> inserted and i am getting this error >>>>>>>>>>>>>> >>>>>>>>>>>>>> "lorisadmin at hbp:/data/loris/bin/mri$ >>>>>>>>>>>>>> /data/loris/data/uploadNeuroDB/imaging_upload_file.pl >>>>>>>>>>>>>> -profile prod -upload_id 3 /data/incoming/DCC0000_258024_V01.tar.gz -verbose >>>>>>>>>>>>>> >>>>>>>>>>>>>> find -path \/tmp\/ImagingUpload\-17\-45\-5MsWEd -name >>>>>>>>>>>>>> '__MACOSX' -delete >>>>>>>>>>>>>> Spool message is: >>>>>>>>>>>>>> The Scan for the uploadID 3 has already been run with >>>>>>>>>>>>>> tarchiveID: 7. >>>>>>>>>>>>>> To continue with the rest of the insertion pipeline, please >>>>>>>>>>>>>> run tarchiveLoader from a terminal as follows: >>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader -globLocation -profile prod >>>>>>>>>>>>>> /data/loris/data/tarchive//2012/DCM_2012-12-05_ImagingUpload-17-43-ZUEFjb.tar >>>>>>>>>>>>>> -verbose" >>>>>>>>>>>>>> >>>>>>>>>>>>>> Which files should i delete? I thought that deleting the >>>>>>>>>>>>>> files from the tarchive was enough. And i executed the last proposed >>>>>>>>>>>>>> command to continue to rest of the insertion pipeline ( check the image ). >>>>>>>>>>>>>> >>>>>>>>>>>>>> Thank you >>>>>>>>>>>>>> >>>>>>>>>>>>>> ???? ???, 24 ???? 2019 ???? 5:05 ?.?., ?/? Cecile Madjar < >>>>>>>>>>>>>> cecile.madjar at mcin.ca> ??????: >>>>>>>>>>>>>> >>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> Sorry I was not clear before. Every visits of candidates are >>>>>>>>>>>>>>> created in the session table with one entry per CandID/VisitLabel. So if >>>>>>>>>>>>>>> the imaging pipeline created visits in the session table (that are not >>>>>>>>>>>>>>> attached to instruments) and you want to clean your database completely, >>>>>>>>>>>>>>> you can delete entries in that table as well. >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> Regarding your point 2, the imaging pipeline can create the >>>>>>>>>>>>>>> visit in the session table as long as the visit label is present in the >>>>>>>>>>>>>>> Visit_Windows table (which means the visit label stored in the PatientName >>>>>>>>>>>>>>> is a valid visit label). >>>>>>>>>>>>>>> However, in your prod file, if the >>>>>>>>>>>>>>> variable $subjectID{'createVisitLabel'} is set to 1 for candidates, the >>>>>>>>>>>>>>> visit label should be created in the Visit_Windows table I believe. Here >>>>>>>>>>>>>>> is the line of the prod file you would need to change >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> . >>>>>>>>>>>>>>> In general, we prefer populating the Visit_Windows table and >>>>>>>>>>>>>>> set the $subjectID{'createVisitLabel'} to 0 for candidate data to avoid >>>>>>>>>>>>>>> insertion of badly labelled MRI data that are complex to relabel. >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> Finally, regarding the candidate creation, if you execute >>>>>>>>>>>>>>> the following steps, the pipeline should be able to create candidates: >>>>>>>>>>>>>>> - set in the Imaging Pipeline section of the config module >>>>>>>>>>>>>>> the config setting "Upload creation of candidates" to Yes >>>>>>>>>>>>>>> - manually transfer the scans to the LORIS server instead of >>>>>>>>>>>>>>> uploading it via the imaging browser >>>>>>>>>>>>>>> - run batch_imaging_upload.pl as you did until now. >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> Hope this helps! >>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> On Wed, Jul 24, 2019 at 8:47 AM Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> About my second question i replaced the name of the patient >>>>>>>>>>>>>>>> in the .dcm files and now i am getting an error that the visit label does >>>>>>>>>>>>>>>> not exist. >>>>>>>>>>>>>>>> I thought it was supposed to be automatically created. >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> "Done adding archive info into database >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader >>>>>>>>>>>>>>>> -globLocation -profile prod >>>>>>>>>>>>>>>> /data/loris/data/tarchive//DCM_2012-12-05_ImagingUpload-15-42-yUwQQV.tar >>>>>>>>>>>>>>>> -verbose >>>>>>>>>>>>>>>> md5sum >>>>>>>>>>>>>>>> /data/loris/data/tarchive/DCM_2012-12-05_ImagingUpload-15-42-yUwQQV.tar >>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>> candidate id 258024 >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> => No Visit labelVisit label does not exist >>>>>>>>>>>>>>>> Set centerID = 1 >>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Number of MINC files that will be considered for inserting >>>>>>>>>>>>>>>> into the database: 1 >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> log dir is /logs and log file is >>>>>>>>>>>>>>>> /logs/TarLoad-15-42-L6pocU.log >>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>> candidate id 258024 >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> => No Visit label >>>>>>>>>>>>>>>> Cleaning up temp files: rm -rf >>>>>>>>>>>>>>>> /tmp/TarLoad-15-42-J2rQms/ImagingUpload-15-42-yUwQQV*" >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> ???? ???, 24 ???? 2019 ???? 3:38 ?.?., ?/? Sotirios >>>>>>>>>>>>>>>> Nikoloutsopoulos ??????: >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> 1) What are the records in the session table? >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> 2) I tried to upload a non-phantom file like this >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> input_file.txt: >>>>>>>>>>>>>>>>> /data/incoming/DCC0000_258024_V1.tar.gz N DCC0000_258024_V1 >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Terminal: >>>>>>>>>>>>>>>>> ./batch_uploads_imageuploader -profile prod < >>>>>>>>>>>>>>>>> ~/Desktop/input.txt > log.txt >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> and i get the following error in the log.txt file >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> "Running now the following command: >>>>>>>>>>>>>>>>> /data/loris/data/uploadNeuroDB/imaging_upload_file.pl >>>>>>>>>>>>>>>>> -profile prod -upload_id 7 /data/incoming/DCC0000_258024_V1.tar.gz -verbose >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> find -path \/tmp\/ImagingUpload\-14\-56\-FeLCB4 -name >>>>>>>>>>>>>>>>> '__MACOSX' -delete >>>>>>>>>>>>>>>>> Spool message is: >>>>>>>>>>>>>>>>> The PatientName read from the DICOM header does not start >>>>>>>>>>>>>>>>> with DCC0000_258024_V1 from the mri_upload table >>>>>>>>>>>>>>>>> " >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> and the spool message is repeated for each .dcm file. >>>>>>>>>>>>>>>>> Should i preprocess every .dcm file and change the PatientName to >>>>>>>>>>>>>>>>> "DCC0000_258024_V1"? >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> 3) As far as it concerns the candidate profile i have to >>>>>>>>>>>>>>>>> create a new one each time before i try to upload a file? Is there already >>>>>>>>>>>>>>>>> a way to create a candidate profile and get the DCCID and PSCID without the >>>>>>>>>>>>>>>>> user interface? >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> ???? ???, 18 ???? 2019 ???? 5:00 ?.?., ?/? Cecile Madjar < >>>>>>>>>>>>>>>>> cecile.madjar at mcin.ca> ??????: >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> See answers to your questions below. >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> About the 1st case we had a dicom with a blank studyUID, >>>>>>>>>>>>>>>>>>> maybe someone accidentally removed it. >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> That is strange. Something must have been done to the >>>>>>>>>>>>>>>>>> DICOM files. I have never seen a study with no StudyUID out of the scanner. >>>>>>>>>>>>>>>>>> Usually, you need to manually erase it with some tool. However, DICOMs >>>>>>>>>>>>>>>>>> never cease to surprise me... >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Some other questions: >>>>>>>>>>>>>>>>>>> 1) What are the steps to remove all of my patients and >>>>>>>>>>>>>>>>>>> uploads?: because i want to try to reupload all the testing dicoms we had >>>>>>>>>>>>>>>>>>> with a clean database. >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Release 21.0 of LORIS-MRI will offer a script to remove >>>>>>>>>>>>>>>>>> all the entries and files specific to an upload. However, this release is >>>>>>>>>>>>>>>>>> not yet out. Hopefully in the next few weeks. >>>>>>>>>>>>>>>>>> In the meantime, since your case is particular and that >>>>>>>>>>>>>>>>>> you just want to start with a clean database, the following deletes should >>>>>>>>>>>>>>>>>> work (hopefully I won't forget any tables): >>>>>>>>>>>>>>>>>> delete from mri_violations_log; >>>>>>>>>>>>>>>>>> delete from mri_protocol_violated_scans; >>>>>>>>>>>>>>>>>> delete from MRICandidateErrors; >>>>>>>>>>>>>>>>>> delete from parameter_file; >>>>>>>>>>>>>>>>>> delete from files_qcstatus; # (if you played with the QC >>>>>>>>>>>>>>>>>> part of the imaging browser for testing) >>>>>>>>>>>>>>>>>> delete from feedback_mri_comments; # (if you played with >>>>>>>>>>>>>>>>>> the QC part of the imaging browser for testing) >>>>>>>>>>>>>>>>>> delete from tarchive_series; >>>>>>>>>>>>>>>>>> delete from tarchive_files; >>>>>>>>>>>>>>>>>> delete from mri_upload; >>>>>>>>>>>>>>>>>> delete from tarchive; >>>>>>>>>>>>>>>>>> delete from mri_scanner; >>>>>>>>>>>>>>>>>> delete from candidate where PSCID="scanner"; >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> I don't know if you want to also delete entries in the >>>>>>>>>>>>>>>>>> session and candidate table too? >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> 2) We do not need to create the profile of a patient ( >>>>>>>>>>>>>>>>>>> are the patients stored in the candidate table? because i can't see the >>>>>>>>>>>>>>>>>>> ghosts ), because will it automatically be created when importing a dicom? >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> I am not sure I understand fully this question. All >>>>>>>>>>>>>>>>>> candidates are stored in the candidate table. The phantom scans however are >>>>>>>>>>>>>>>>>> attached to a scanner candidate depending on where the scan happened. It is >>>>>>>>>>>>>>>>>> a bit of a weird concept that we have to redesign eventually but never got >>>>>>>>>>>>>>>>>> a chance to get to it. >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Hopefully this answered your question, otherwise, don't >>>>>>>>>>>>>>>>>> hesitate to let me know. >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> 3) What is the difference between uploading a dicom as >>>>>>>>>>>>>>>>>>> phantom instead of importing as PSCCID_DCCID_VisitLabel? >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> When you upload the scan as PSCID_DCCID_VisitLabel, there >>>>>>>>>>>>>>>>>> is a check that makes sure the candidate IDs and visit label are valid at >>>>>>>>>>>>>>>>>> the time of upload. >>>>>>>>>>>>>>>>>> When you upload a scan as phantom, it expects that the >>>>>>>>>>>>>>>>>> DICOM field PatientName and uploaded filename contains the string >>>>>>>>>>>>>>>>>> "phantom". We enforced this behaviour on the imaging uploader side in >>>>>>>>>>>>>>>>>> recent releases but I can't remember which one. Probably the upcoming 21.0 >>>>>>>>>>>>>>>>>> release. >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> All those verifications might seem cumbersome but they >>>>>>>>>>>>>>>>>> are here to ensure that the files inserted are all valid and labelled >>>>>>>>>>>>>>>>>> properly as it is a bit messy to have to delete files that were wrongly >>>>>>>>>>>>>>>>>> labelled. At least, the delete script present in release 21.0 will make >>>>>>>>>>>>>>>>>> this process easier but it is still good practice to verify those things. >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> With pleasure. Hopefully the answers to your questions >>>>>>>>>>>>>>>>>> will be helpful. >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> PS: loris-dev mailing list: you will find the initial >>>>>>>>>>>>>>>>>> answer I gave Sotirios below. I forgot to cc the loris-dev in my earlier >>>>>>>>>>>>>>>>>> reply... >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> ???? ???, 16 ???? 2019 ???? 12:02 ?.?., ?/? Cecile Madjar >>>>>>>>>>>>>>>>>>> ??????: >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Dear Sotirios, >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Thank you for reaching out. Since your email was >>>>>>>>>>>>>>>>>>>> already organized in points, I will reply directly below your questions >>>>>>>>>>>>>>>>>>>> below. >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> 1) What do we do when the StudyUID is blank on the >>>>>>>>>>>>>>>>>>>>> header? >>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/minor/docs/AppendixA-Troubleshooting_guideline.md >>>>>>>>>>>>>>>>>>>>> There solution provided at the table 3 does not guide us how to find the >>>>>>>>>>>>>>>>>>>>> information ( is possible ). >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> The StudyUID is the field used in our pipeline at the >>>>>>>>>>>>>>>>>>>> moment to check whether a DICOM study was already inserted into LORIS with >>>>>>>>>>>>>>>>>>>> that same StudyUID since it is supposed to be unique for every single >>>>>>>>>>>>>>>>>>>> study. Currently, we do not support insertion of DICOM studies if they do >>>>>>>>>>>>>>>>>>>> not have a StudyUID associated with them. >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Is there a specific reason why the StudyUID is blank in >>>>>>>>>>>>>>>>>>>> the DICOM headers in your DICOM files? Did they go through some processes >>>>>>>>>>>>>>>>>>>> before upload to LORIS? >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> 2) When i am about to upload a non-phanton case i need >>>>>>>>>>>>>>>>>>>>> a 'Visit Label'. Is there already a script that can create a new visit >>>>>>>>>>>>>>>>>>>>> label for a specific Candidate, so i can provide it as input afterwards to >>>>>>>>>>>>>>>>>>>>> the >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> batch_uploads_imageuploader ( See option 5.1.3 https://github.com/aces/Loris-MRI/blob/minor/docs/05-PipelineLaunchOptions.md ) >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> I am not sure if the front-end allows for it but if you >>>>>>>>>>>>>>>>>>>> use batch_uploads_imageuploader, the insertion scripts could create the >>>>>>>>>>>>>>>>>>>> visit label for you. However, it does need to be included in the patient >>>>>>>>>>>>>>>>>>>> name in order for the script to know which label it should use. >>>>>>>>>>>>>>>>>>>> For example: you upload V02 for MTL0123 (DCCID: >>>>>>>>>>>>>>>>>>>> 456789) but V02 was not yet created for MTL0123; the insertion scripts >>>>>>>>>>>>>>>>>>>> will create a V02 visit for MTL0123 if the PatientName field for the >>>>>>>>>>>>>>>>>>>> dataset is MTL0123_456789_V02 with Stage marked as "Not Started". >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> However, *note that for the script to create the visit >>>>>>>>>>>>>>>>>>>> for the candidate, you have to make sure that all the visit label of your >>>>>>>>>>>>>>>>>>>> projects were inserted in the Visit_Windows table* >>>>>>>>>>>>>>>>>>>> (otherwise, the visit will never be created as they were not specified as >>>>>>>>>>>>>>>>>>>> being part of the list of visit label to expect). So in the example above, >>>>>>>>>>>>>>>>>>>> you should have one row in Visit_Windows with Visit_label="V02" set. >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> 3) Section 4.3 >>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/minor/docs/04-Scripts.md >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> What do we do when the folder contains multiple mnc files? >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> This is a case by case. Most of the time, the MINC >>>>>>>>>>>>>>>>>>>> files that failed insertion into the imaging browser end up in the MRI >>>>>>>>>>>>>>>>>>>> violation module where you can see what went wrong with the acquisitions >>>>>>>>>>>>>>>>>>>> not inserted. If you notice that the MINC file should be inserted as a >>>>>>>>>>>>>>>>>>>> specific protocol, you can force the insertion as explained in section 4.3. >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> In your case, I have a feeling that you want to be able >>>>>>>>>>>>>>>>>>>> to insert MINC files that did not go through the whole pipeline insertion >>>>>>>>>>>>>>>>>>>> (DICOM archival, then dcm2mnc, then protocol identification, then >>>>>>>>>>>>>>>>>>>> insertion...). In theory, you could call >>>>>>>>>>>>>>>>>>>> minc_insertion.pl on any MINC file, provided you have >>>>>>>>>>>>>>>>>>>> at least the following information: >>>>>>>>>>>>>>>>>>>> - path to the MINC file >>>>>>>>>>>>>>>>>>>> - uploadID associated with the MINC files or DICOM >>>>>>>>>>>>>>>>>>>> archive path from which those MINC files were created from >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Then the minc_insertion.pl script will do the subject >>>>>>>>>>>>>>>>>>>> information and protocol validation etc... >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> If all the MINC files come from the same uploadID or >>>>>>>>>>>>>>>>>>>> TarchiveID, then you could run a loop in bash calling the >>>>>>>>>>>>>>>>>>>> minc_insertion.pl script like this for files deriving >>>>>>>>>>>>>>>>>>>> from uploadID=1: >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> ls /path/to/mnc/folder/* | while read f; do >>>>>>>>>>>>>>>>>>>> minc_insertion.pl -profile prod -uploadID 1 -mincPath >>>>>>>>>>>>>>>>>>>> $f; done >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Hope this helped! >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> _______________________________________________ >> Loris-dev mailing list >> Loris-dev at bic.mni.mcgill.ca >> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >> > > > -- > > christine.rogers at mcgill.ca > McGill Centre for Integrative Neuroscience | MCIN.ca > Montreal Neurological Institute > McGill University | Montreal | Canada > -------------- next part -------------- An HTML attachment was scrubbed... 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Name: image.png Type: image/png Size: 9670 bytes Desc: not available URL: From christine.rogers at mcgill.ca Fri Aug 2 18:08:05 2019 From: christine.rogers at mcgill.ca (Christine Rogers, Ms.) Date: Fri, 2 Aug 2019 22:08:05 +0000 Subject: [Loris-dev] Import mri - scripts In-Reply-To: <65ad2b70c3084ffdb1e4a9dcdad948cd@YTOPR0101MB1803.CANPRD01.PROD.OUTLOOK.COM> References: <65ad2b70c3084ffdb1e4a9dcdad948cd@YTOPR0101MB1803.CANPRD01.PROD.OUTLOOK.COM> Message-ID: Hi Sotirios, First, just a note: we've released LORIS 21 this week with some major new features and cleanup -- especially if you are early in your setup phase, check out the Release notes for both the LORIS and Loris-MRI repos. Thanks for your screenshots -- your empty mri_protocol table should be at the root of these issues : The mri_protocol table must be populated in order for your scans to be registered in LORIS -- it serves as a whitelist for the insertion pipeline which filters out scans that aren't identified or matched to scan types in this table. By default, this table is populated with entries for t1, t2, fMRI and DTI (Insert statements for 21 release branch are here) Feel free to restore our default records and broaden their parameters to match all your scan types. re Defaced, native, selected -- these filter the scans displayed as you move to the next page (View Session), instead of viewing "all types" of scans from a given session : * "defaced" means that a defacing script has masked the subject's face in the volume (for patient privacy) * "native" means that no pre-processing has been performed on the scan (it's raw data), * "selected" will show only volumes that have been QC'd and "selected" as the best of their type -- used to display only the best quality T1 image instead of all T1s acquired in a session, e.g. re QC Comments -- Once you have successfully loaded scans (matched to the mri_protocol table), you'll be able to use the Imaging Browser's View Session subpage to enter/view QC comments on each volume, or for each visit. These are stored directly in the database, and linked to each scan. (Table name: feedback_mri_comments) (Visit-level QC comments are linked to the session.) For a walkthrough of the Imaging setup - please see the Imaging Setup guide - An old LORIS walkthrough video can also walk you through some of the Imaging front-end features, starting at 8:00 LORIS' imaging modules have been updated many times since this video, but the functionality and workflow is similar. Let us know how it goes once you have entries in your mri_protocol table - Best, Christine On Fri, Aug 2, 2019 at 7:58 AM Sotirios Nikoloutsopoulos > wrote: Hi Christine, In the candidate_list page i can see this patient [image.png] If i press the link under PSCID i get to see [image.png] and if i press the link under Scan Done it redirects me to imaging_browser [image.png] At the mri_violations page i also see No results ( neither on resolved / not resolved ). At the imaging_uploader i can see the record that failed. [image.png] If i click on the tarchive info i get to see the Protocol Name which i think is the acquisition we wanted? [image.png] Also my mri_protocol table is empty. Furthermore i would like to ask about the defaced, native, selected. What exactly is native and selected? And where are the qc comments stored? [image.png] Finally a walkthrough would be helpful. Thanks, Sotirios ???? ???, 30 ???? 2019 ???? 8:29 ?.?., ?/? Christine Rogers, Ms. > ??????: Hi Sotirios, Glad to hear you're making progress with the visit labels. To follow up on your last few emails: a- The Wiki's Setup Guide contains Sample insert statements for the Visit Windows table. As Cecile mentioned, the consistency of visit label format is important: V01, v01, V1, 01 -- whichever you select to use is fine; we use V01 by default across all documentation. b- For Password reset, there is a script in the tools/ directory so that a back-end administrator can reset any front-end user password, including Admin. (See info on setting up / resetting User passwords in the Wiki's Setup Guide) c- The minc file not being registered -- due to AcquisitionProtocol unknown. This means the SeriesDescription (Acquisition Protocol) in you Dicom header was not matched to any scan listed in the mri_protocol database table. (In the online Loris-MRI Troubleshooting Guide, this is Table 3, 2nd-last item "no MINCs inserted"). The MRI Violations module (Readme here) will show you the details of this mismatch -- Go to the module (under the Imaging menu), find your scan and click the link "Could not identify scan type" -- in the next subpage you can compare the scan's actual parameters against the mri_protocol table. To resolve this, adjust your mri_protocol table values or perhaps ensure your DICOMs are labelled consistently. Let us know if this works for you -- we can also walk you through an example of non-identified scans on Demo.loris.ca (MRI Violations module). Best, Christine The LORIS team On Tue, Jul 30, 2019 at 10:47 AM Sotirios Nikoloutsopoulos > wrote: I hope this is sufficient as the error for the visit label disappeared. [image.png] Please see the attached file. Also something i found. lorisadmin at hbp:/data/loris/bin/mri$ cat /data/loris/data//logs/TarLoad-17-39-xubBdv.log ==> Loading file from disk /tmp/TarLoad-17-39-UyQcG2/dcc0000_258024_v1_20121205_102108_501e1_mri.mnc --> mapping DICOM parameter for /tmp/TarLoad-17-39-UyQcG2/dcc0000_258024_v1_20121205_102108_501e1_mri.mnc ==> computing md5 hash for MINC body. --> md5: 6b1202fd63e29de4c9be1cd9925888a5 ==> verifying acquisition protocol Acquisition protocol is unknown --> The minc file cannot be registered since the AcquisitionProtocol is unknown ???? ???, 30 ???? 2019 ???? 4:58 ?.?., ?/? Sotirios Nikoloutsopoulos > ??????: Ok I fixed the login problem by using a known hash and by deleting the rows from the login_history i was able to login. ???? ???, 30 ???? 2019 ???? 4:50 ?.?., ?/? Sotirios Nikoloutsopoulos > ??????: Hi, there was no visit label 01 in the Visit_Windows table and i don't know how to insert it because the record requires lots of attributes. Also the system for a reason asked me to update my password and now i don't remember it and my account got suspended. Is there a way to reset it or set a simple password? I updated the password hash in the users table by using the hash from another LORIS setup we had and i still couldn't login ( also the attribute password is always NULL and the expiration date is 1999-01-01 for some reason ). Thanks ???? ???, 29 ???? 2019 ???? 5:21 ?.?., ?/? Cecile Madjar > ??????: Hi Sotirios, Can you try adding the visit label v01 to the Visit_Windows table? However, I noticed that in a previous dataset, the label was V1. Does that refer to the same visit? If so, you might want to harmonize the visit labels so they are all the same across datasets for a given timepoint, meaning you will need to relabel scans when the visit label is different but referring to the same visit label (v01 = V1 etc...). Hope this helps, C?cile On Mon, Jul 29, 2019 at 10:15 AM Sotirios Nikoloutsopoulos > wrote: Hi, Could you help me with the "Visit label does not exist"? I had changed $subjectID{'createVisitLabel'} to 1 as you had suggested but it appears that this problem hasn't been resolved yet. lorisadmin at hbp:/data/loris/bin/mri$ cat /data/loris/data//logs/TarLoad-14-58-9Xog7H.log ==> Loading file from disk /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc --> mapping DICOM parameter for /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc --> using user-defined filterParameters for /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc Candidate Mismatch Error is Visit label does not exist -> WARNING: This candidate was invalid. Logging to MRICandidateErrors table with reason Visit label does not exist Thank you, Sotirios ???? ???, 26 ???? 2019 ???? 3:02 ?.?., ?/? Sotirios Nikoloutsopoulos > ??????: Hi Cecile, The Center error was fixed. Still the insertion of mincs fails. Please see the output.txt file i attached. Also is there something else i need to change at the paths configuration? Thank you, Sotirios ???? ???, 25 ???? 2019 ???? 6:55 ?.?., ?/? Cecile Madjar > ??????: Hi Sotirios, We are making progress! I have a feeling this error comes from the fact that your psc table does not have the MRI_alias populated for the DCC site. Running the following query in the mysql database should fix this: UPDATE psc SET MRI_alias="DCC", Alias="DCC" WHERE Name="Data Coordinating Center"; Repeat the same with all your sites (make sure to change the Aliases between sites, they should all be unique). Let me know how it goes! Best, C?cile On Thu, Jul 25, 2019 at 11:43 AM Sotirios Nikoloutsopoulos > wrote: Dear Cecile, You were right about your guesses. I did the modifications you suggested, i still get the "no mincs inserted" error, now i am getting the "No center found this candidate" error ( how do i fix that? from what i see the .dcm files contains a 'Institution Name', is that the center? ), so i guess that's why the validation fails, but i changed the force variable of tarchiveLoader to 1, shouldn't it have inserted the mincs then? Also it is optional to have a mail server, right? ( from what i see the mail error does not affect the $valid_study, so i assume we are okay with that ) Thank you a lot, Sotirios ???? ???, 25 ???? 2019 ???? 5:48 ?.?., ?/? Cecile Madjar > ??????: Hi Sotirios, From what I understand, I believe you just need to update a few config settings from the frontend in the Config module (under the Admin menu). [Screen Shot 2019-07-25 at 10.31.35 AM.png] Then go to the Paths section of the config module and update the "LORIS-MRI code" config setting to /data/loris/bin/mri (my guess is that currently, it is set to /data/LORIS/data) and click on the submit button. [Screen Shot 2019-07-25 at 10.32.50 AM.png] Then, go to Imaging Pipeline section of the Configuration module and update the "Loris-MRI Data Directory" to /data/loris/data/ (my guess is that it is empty at the moment in your database which is why $data_dir is not defined when you run the tarchiveLoader step of the insertion pipeline). [Screen Shot 2019-07-25 at 10.40.52 AM.png] Finally, I took a look at your environment file and it might be a good idea to update your PERL5LIB variable to the following (it has been added to the code a few releases ago as we realized this was needed for the libraries. Not sure which version of LORIS-MRI you are using but it does not hurt to update this variable to what I suggest below): export PERL5LIB=/data/loris/bin/mri/uploadNeuroDB:/data/loris/bin/mri/dicom-archive:$PERL5LIB Hope this helps. Sorry you are experiencing so much trouble setting things up. We probably need to update our WIKI. Best, C?cile On Thu, Jul 25, 2019 at 9:48 AM Sotirios Nikoloutsopoulos > wrote: The "Loris-MRI Data Directory" should be in the environment file? ???? ???, 25 ???? 2019 ???? 12:59 ?.?., ?/? Sotirios Nikoloutsopoulos > ??????: The scripts are located in /data/loris/bin/mri/. Somewhere I might have messed something up but i remember following the instructions in the wiki.For example when i tried to execute the batch_uploads_imageuploader perl script the line my $command = "$bin_dir/uploadNeuroDB/imaging_upload_file.pl " was pointing to an invalid path, for example: it was repeating a pattern and had LORIS instead of loris ( i think the mistake was that in the wiki it suggested to use $PROJECT for the name of the folder and i choosed 'loris' https://github.com/aces/Loris/wiki/Imaging-Database ). See also the in image for the modification i did. Also i didn't find the section to config the $data_dir variable. Thank you, Sotirios ???? ???, 24 ???? 2019 ???? 6:05 ?.?., ?/? Cecile Madjar > ??????: Hi Sotirios, It looks like you have one Config setting not set (based on the first error message you got when running it the first time). You need to set a value for "Loris-MRI Data Directory" in the Config module under the Imaging pipeline section (from what I can see, it would be /data/loris/data/ for your setup). The reason you got that error message the second time is that the pipeline checks if the DICOM study was already inserted in the tarchive table. Since you ran the study once already, the study is inserted into the tarchive, hence the message. However, the pipeline did not complete as the MINC files were not created and inserted into the files/parameter_file table. In order to continue the insertion, you will then need to run the tarchiveLoader command suggested in the terminal during the second run: /data/LORIS/data//uploadNeuroDB/tarchiveLoader -globLocation -profile prod /data/loris/data/tarchive//2012/DCM_2012-12-05_ImagingUpload-17-43-ZUEFjb.tar -verbose Finally, I am a bit confused by your setup. Where are the scripts located? In /data/loris/bin/mri or /data/loris/data? It feels like the Config setting "LORIS-MRI code" in the Paths section was set to "/data/LORIS/data" but it should have been set to the directory where the scripts are located (most probably /data/loris/bin/mri). Hope this helps, C?cile On Wed, Jul 24, 2019 at 10:55 AM Sotirios Nikoloutsopoulos > wrote: Ok first i execute this command: "lorisadmin at hbp:/data/loris/bin/mri$ ./batch_uploads_imageuploader -profile prod < ~/Desktop/input.txt > log.txt Use of uninitialized value $data_dir in concatenation (.) or string at ./batch_uploads_imageuploader line 143. Use of uninitialized value $data_dir in concatenation (.) or string at ./batch_uploads_imageuploader line 143. Use of uninitialized value $_ in pattern match (m//) at ./batch_uploads_imageuploader line 147. base is DCC0000_258024_V01 path is /data/incoming/ type is .tar.gz fullpath is /data/incoming/DCC0000_258024_V01.tar.gz source /tmp/ImagingUpload-17-43-ZUEFjb targetlocation /data/loris/data/tarchive Use of uninitialized value $data_dir in concatenation (.) or string at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 256. Use of uninitialized value $data_dir in concatenation (.) or string at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 284. Use of uninitialized value $data_dir in concatenation (.) or string at /data/loris/bin/mri/uploadNeuroDB/tarchive_validation.pl line 219. Use of uninitialized value $data_dir in concatenation (.) or string at /data/loris/bin/mri/uploadNeuroDB/minc_insertion.pl line 270. Use of uninitialized value $data_dir in concatenation (.) or string at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 711. Can't exec "mail": No such file or directory at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 721. print() on closed filehandle MAIL at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 722. print() on closed filehandle MAIL at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 723. Use of uninitialized value $data_dir in concatenation (.) or string at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 724. print() on closed filehandle MAIL at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 724. print() on closed filehandle MAIL at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 725. Use of uninitialized value $data_dir in concatenation (.) or string at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 735. No Mincs inserted The tarchiveLoader insertion script has failed. Running now the following command: /data/loris/data/uploadNeuroDB/imaging_upload_file.pl -profile prod -upload_id 3 /data/incoming/DCC0000_258024_V01.tar.gz -verbose" I inserted the VisitLabel, but still the Mincs are not inserted and i am getting this error "lorisadmin at hbp:/data/loris/bin/mri$ /data/loris/data/uploadNeuroDB/imaging_upload_file.pl -profile prod -upload_id 3 /data/incoming/DCC0000_258024_V01.tar.gz -verbose find -path \/tmp\/ImagingUpload\-17\-45\-5MsWEd -name '__MACOSX' -delete Spool message is: The Scan for the uploadID 3 has already been run with tarchiveID: 7. To continue with the rest of the insertion pipeline, please run tarchiveLoader from a terminal as follows: /data/LORIS/data//uploadNeuroDB/tarchiveLoader -globLocation -profile prod /data/loris/data/tarchive//2012/DCM_2012-12-05_ImagingUpload-17-43-ZUEFjb.tar -verbose" Which files should i delete? I thought that deleting the files from the tarchive was enough. And i executed the last proposed command to continue to rest of the insertion pipeline ( check the image ). Thank you ???? ???, 24 ???? 2019 ???? 5:05 ?.?., ?/? Cecile Madjar > ??????: Hi Sotirios, Sorry I was not clear before. Every visits of candidates are created in the session table with one entry per CandID/VisitLabel. So if the imaging pipeline created visits in the session table (that are not attached to instruments) and you want to clean your database completely, you can delete entries in that table as well. Regarding your point 2, the imaging pipeline can create the visit in the session table as long as the visit label is present in the Visit_Windows table (which means the visit label stored in the PatientName is a valid visit label). However, in your prod file, if the variable $subjectID{'createVisitLabel'} is set to 1 for candidates, the visit label should be created in the Visit_Windows table I believe. Here is the line of the prod file you would need to change. In general, we prefer populating the Visit_Windows table and set the $subjectID{'createVisitLabel'} to 0 for candidate data to avoid insertion of badly labelled MRI data that are complex to relabel. Finally, regarding the candidate creation, if you execute the following steps, the pipeline should be able to create candidates: - set in the Imaging Pipeline section of the config module the config setting "Upload creation of candidates" to Yes - manually transfer the scans to the LORIS server instead of uploading it via the imaging browser - run batch_imaging_upload.pl as you did until now. Hope this helps! Best, C?cile On Wed, Jul 24, 2019 at 8:47 AM Sotirios Nikoloutsopoulos > wrote: About my second question i replaced the name of the patient in the .dcm files and now i am getting an error that the visit label does not exist. I thought it was supposed to be automatically created. "Done adding archive info into database /data/LORIS/data//uploadNeuroDB/tarchiveLoader -globLocation -profile prod /data/loris/data/tarchive//DCM_2012-12-05_ImagingUpload-15-42-yUwQQV.tar -verbose md5sum /data/loris/data/tarchive/DCM_2012-12-05_ImagingUpload-15-42-yUwQQV.tar PSCID is: DCC0000 CandID id: 258024 visit_label is: V1 PSCID is: DCC0000 CandID id: 258024 visit_label is: V1 candidate id 258024 => No Visit labelVisit label does not exist Set centerID = 1 PSCID is: DCC0000 CandID id: 258024 visit_label is: V1 PSCID is: DCC0000 CandID id: 258024 visit_label is: V1 Number of MINC files that will be considered for inserting into the database: 1 log dir is /logs and log file is /logs/TarLoad-15-42-L6pocU.log PSCID is: DCC0000 CandID id: 258024 visit_label is: V1 PSCID is: DCC0000 CandID id: 258024 visit_label is: V1 candidate id 258024 => No Visit label Cleaning up temp files: rm -rf /tmp/TarLoad-15-42-J2rQms/ImagingUpload-15-42-yUwQQV*" ???? ???, 24 ???? 2019 ???? 3:38 ?.?., ?/? Sotirios Nikoloutsopoulos > ??????: Hi, 1) What are the records in the session table? 2) I tried to upload a non-phantom file like this input_file.txt: /data/incoming/DCC0000_258024_V1.tar.gz N DCC0000_258024_V1 Terminal: ./batch_uploads_imageuploader -profile prod < ~/Desktop/input.txt > log.txt and i get the following error in the log.txt file "Running now the following command: /data/loris/data/uploadNeuroDB/imaging_upload_file.pl -profile prod -upload_id 7 /data/incoming/DCC0000_258024_V1.tar.gz -verbose find -path \/tmp\/ImagingUpload\-14\-56\-FeLCB4 -name '__MACOSX' -delete Spool message is: The PatientName read from the DICOM header does not start with DCC0000_258024_V1 from the mri_upload table " and the spool message is repeated for each .dcm file. Should i preprocess every .dcm file and change the PatientName to "DCC0000_258024_V1"? 3) As far as it concerns the candidate profile i have to create a new one each time before i try to upload a file? Is there already a way to create a candidate profile and get the DCCID and PSCID without the user interface? Thank you, Sotirios ???? ???, 18 ???? 2019 ???? 5:00 ?.?., ?/? Cecile Madjar > ??????: Hi Sotirios, See answers to your questions below. About the 1st case we had a dicom with a blank studyUID, maybe someone accidentally removed it. That is strange. Something must have been done to the DICOM files. I have never seen a study with no StudyUID out of the scanner. Usually, you need to manually erase it with some tool. However, DICOMs never cease to surprise me... Some other questions: 1) What are the steps to remove all of my patients and uploads?: because i want to try to reupload all the testing dicoms we had with a clean database. Release 21.0 of LORIS-MRI will offer a script to remove all the entries and files specific to an upload. However, this release is not yet out. Hopefully in the next few weeks. In the meantime, since your case is particular and that you just want to start with a clean database, the following deletes should work (hopefully I won't forget any tables): delete from mri_violations_log; delete from mri_protocol_violated_scans; delete from MRICandidateErrors; delete from parameter_file; delete from files_qcstatus; # (if you played with the QC part of the imaging browser for testing) delete from feedback_mri_comments; # (if you played with the QC part of the imaging browser for testing) delete from tarchive_series; delete from tarchive_files; delete from mri_upload; delete from tarchive; delete from mri_scanner; delete from candidate where PSCID="scanner"; I don't know if you want to also delete entries in the session and candidate table too? 2) We do not need to create the profile of a patient ( are the patients stored in the candidate table? because i can't see the ghosts ), because will it automatically be created when importing a dicom? I am not sure I understand fully this question. All candidates are stored in the candidate table. The phantom scans however are attached to a scanner candidate depending on where the scan happened. It is a bit of a weird concept that we have to redesign eventually but never got a chance to get to it. Hopefully this answered your question, otherwise, don't hesitate to let me know. 3) What is the difference between uploading a dicom as phantom instead of importing as PSCCID_DCCID_VisitLabel? When you upload the scan as PSCID_DCCID_VisitLabel, there is a check that makes sure the candidate IDs and visit label are valid at the time of upload. When you upload a scan as phantom, it expects that the DICOM field PatientName and uploaded filename contains the string "phantom". We enforced this behaviour on the imaging uploader side in recent releases but I can't remember which one. Probably the upcoming 21.0 release. All those verifications might seem cumbersome but they are here to ensure that the files inserted are all valid and labelled properly as it is a bit messy to have to delete files that were wrongly labelled. At least, the delete script present in release 21.0 will make this process easier but it is still good practice to verify those things. Thank you, With pleasure. Hopefully the answers to your questions will be helpful. Best, C?cile PS: loris-dev mailing list: you will find the initial answer I gave Sotirios below. I forgot to cc the loris-dev in my earlier reply... ???? ???, 16 ???? 2019 ???? 12:02 ?.?., ?/? Cecile Madjar > ??????: Dear Sotirios, Thank you for reaching out. Since your email was already organized in points, I will reply directly below your questions below. Best, C?cile 1) What do we do when the StudyUID is blank on the header? https://github.com/aces/Loris-MRI/blob/minor/docs/AppendixA-Troubleshooting_guideline.md There solution provided at the table 3 does not guide us how to find the information ( is possible ). The StudyUID is the field used in our pipeline at the moment to check whether a DICOM study was already inserted into LORIS with that same StudyUID since it is supposed to be unique for every single study. Currently, we do not support insertion of DICOM studies if they do not have a StudyUID associated with them. Is there a specific reason why the StudyUID is blank in the DICOM headers in your DICOM files? Did they go through some processes before upload to LORIS? 2) When i am about to upload a non-phanton case i need a 'Visit Label'. Is there already a script that can create a new visit label for a specific Candidate, so i can provide it as input afterwards to the batch_uploads_imageuploader ( See option 5.1.3 https://github.com/aces/Loris-MRI/blob/minor/docs/05-PipelineLaunchOptions.md ) I am not sure if the front-end allows for it but if you use batch_uploads_imageuploader, the insertion scripts could create the visit label for you. However, it does need to be included in the patient name in order for the script to know which label it should use. For example: you upload V02 for MTL0123 (DCCID: 456789) but V02 was not yet created for MTL0123; the insertion scripts will create a V02 visit for MTL0123 if the PatientName field for the dataset is MTL0123_456789_V02 with Stage marked as "Not Started". However, note that for the script to create the visit for the candidate, you have to make sure that all the visit label of your projects were inserted in the Visit_Windows table (otherwise, the visit will never be created as they were not specified as being part of the list of visit label to expect). So in the example above, you should have one row in Visit_Windows with Visit_label="V02" set. 3) Section 4.3 https://github.com/aces/Loris-MRI/blob/minor/docs/04-Scripts.md What do we do when the folder contains multiple mnc files? This is a case by case. Most of the time, the MINC files that failed insertion into the imaging browser end up in the MRI violation module where you can see what went wrong with the acquisitions not inserted. If you notice that the MINC file should be inserted as a specific protocol, you can force the insertion as explained in section 4.3. In your case, I have a feeling that you want to be able to insert MINC files that did not go through the whole pipeline insertion (DICOM archival, then dcm2mnc, then protocol identification, then insertion...). In theory, you could call minc_insertion.pl on any MINC file, provided you have at least the following information: - path to the MINC file - uploadID associated with the MINC files or DICOM archive path from which those MINC files were created from Then the minc_insertion.pl script will do the subject information and protocol validation etc... If all the MINC files come from the same uploadID or TarchiveID, then you could run a loop in bash calling the minc_insertion.pl script like this for files deriving from uploadID=1: ls /path/to/mnc/folder/* | while read f; do minc_insertion.pl -profile prod -uploadID 1 -mincPath $f; done Thank you, Hope this helped! _______________________________________________ Loris-dev mailing list Loris-dev at bic.mni.mcgill.ca https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev -- christine.rogers at mcgill.ca McGill Centre for Integrative Neuroscience | MCIN.ca Montreal Neurological Institute McGill University | Montreal | Canada -- christine.rogers at mcgill.ca McGill Centre for Integrative Neuroscience | MCIN.ca Montreal Neurological Institute McGill University | Montreal | Canada -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... 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Name: image.png Type: image/png Size: 9670 bytes Desc: image.png URL: From sotirisnik at gmail.com Mon Aug 5 08:19:24 2019 From: sotirisnik at gmail.com (Sotirios Nikoloutsopoulos) Date: Mon, 5 Aug 2019 15:19:24 +0300 Subject: [Loris-dev] Import mri - scripts In-Reply-To: References: <65ad2b70c3084ffdb1e4a9dcdad948cd@YTOPR0101MB1803.CANPRD01.PROD.OUTLOOK.COM> Message-ID: Hi, Is it easy to upgrade to Loris 21? Also the following fails because the line 1985 of NeuroDB/MRIProcessingUtility.pm query mri_protocol which doesn't have TR_range https://github.com/aces/Loris/blob/21.0-release/SQL/0000-00-00-schema.sql#L556 [image: image.png] lorisadmin at hbp:/data/loris/bin/mri$ ./batch_uploads_imageuploader -profile prod < ~/Desktop/input.txt > log.txt Use of uninitialized value $_ in pattern match (m//) at ./batch_uploads_imageuploader line 147. base is DCC0000_258024_V1 path is /data/incoming/ type is .tar.gz fullpath is /data/incoming/DCC0000_258024_V1.tar.gz DBD::mysql::st execute failed: Unknown column 'TR_range' in 'where clause' at /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line 1985. DBD::mysql::st fetchrow_array failed: fetch() without execute() at /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line 1986. Use of uninitialized value $count_mri_protocol in numeric gt (>) at /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line 1995. DBD::mysql::st execute failed: Unknown column 'TR_range' in 'field list' at /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 562. Can't exec "mail": No such file or directory at /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 721. print() on closed filehandle MAIL at /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 722. print() on closed filehandle MAIL at /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 723. print() on closed filehandle MAIL at /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 724. print() on closed filehandle MAIL at /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 725. No Mincs inserted Thanks, Sotirios ???? ???, 3 ??? 2019 ???? 1:08 ?.?., ?/? Christine Rogers, Ms. < christine.rogers at mcgill.ca> ??????: > Hi Sotirios, > > First, just a note: we've released LORIS 21 this week with some major new > features and cleanup -- especially if you are early in your setup phase, > check out the Release notes for both the LORIS > and Loris-MRI > repos. > > Thanks for your screenshots -- your empty mri_protocol table should be at > the root of these issues : > > The mri_protocol table must be populated > > in order for your scans to be registered in LORIS -- it serves as a > whitelist for the insertion pipeline which filters out scans that aren't > identified or matched to scan types in this table. > > By default, this table is populated with entries for t1, t2, fMRI and DTI (Insert > statements for 21 release branch are here > > ) > Feel free to restore our default records and broaden their parameters to > match all your scan types. > > re Defaced, native, selected -- these filter the scans displayed as you > move to the next page (View Session), instead of viewing "all types" of > scans from a given session : > > - "defaced" means that a defacing script > > has masked the subject's face in the volume (for patient privacy) > - "native" means that no pre-processing has been performed on the scan > (it's raw data), > - "selected" will show only volumes that have been QC'd and > "selected" as the best of their type -- used to display only the best > quality T1 image instead of all T1s acquired in a session, e.g. > > re QC Comments -- > Once you have successfully loaded scans (matched to the mri_protocol > table), you'll be able to use the Imaging Browser's View Session subpage to > enter/view QC comments on each volume, or for each visit. > These are stored directly in the database, and linked to each scan. > (Table name: feedback_mri_comments) > (Visit-level QC comments are linked to the session.) > > For a walkthrough of the Imaging setup - please see the Imaging Setup > guide > - > > An old LORIS walkthrough video > can also walk you through > some of the Imaging front-end features, starting at 8:00 > LORIS' imaging modules have been updated many times since this video, but > the functionality and workflow is similar. > > Let us know how it goes once you have entries in your mri_protocol table - > Best, > Christine > > > > > On Fri, Aug 2, 2019 at 7:58 AM Sotirios Nikoloutsopoulos < > sotirisnik at gmail.com> wrote: > >> Hi Christine, >> >> In the candidate_list page i can see this patient >> >> [image: image.png] >> >> If i press the link under PSCID i get to see >> [image: image.png] >> >> and if i press the link under Scan Done it redirects me to imaging_browser >> >> [image: image.png] >> >> At the mri_violations page i also see No results ( neither on resolved / >> not resolved ). >> >> At the imaging_uploader i can see the record that failed. >> >> [image: image.png] >> >> If i click on the tarchive info i get to see the Protocol Name which i >> think is the acquisition we wanted? >> [image: image.png] >> >> Also my mri_protocol table is empty. >> >> Furthermore i would like to ask about the defaced, native, selected. What >> exactly is native and selected? And where are the qc comments stored? >> >> [image: image.png] >> >> Finally a walkthrough would be helpful. >> >> Thanks, >> >> Sotirios >> >> ???? ???, 30 ???? 2019 ???? 8:29 ?.?., ?/? Christine Rogers, Ms. < >> christine.rogers at mcgill.ca> ??????: >> >>> Hi Sotirios, >>> Glad to hear you're making progress with the visit labels. To follow up >>> on your last few emails: >>> >>> a- The Wiki's Setup Guide contains Sample insert statements for the >>> Visit Windows table >>> >>> . >>> >>> As Cecile mentioned, the consistency of visit label format is important: >>> V01, v01, V1, 01 -- whichever you select to use is fine; we use V01 by >>> default across all documentation. >>> >>> b- For Password reset, there is a script in the tools/ directory so that >>> a back-end administrator can reset any front-end user password, including >>> Admin. (See info on setting up / resetting User passwords in the Wiki's >>> Setup Guide >>> >>> ) >>> >>> c- The minc file not being registered -- due to AcquisitionProtocol >>> unknown. >>> This means the SeriesDescription (Acquisition Protocol) in you Dicom >>> header was not matched to any scan listed in the mri_protocol database >>> table. >>> (In the online Loris-MRI Troubleshooting Guide, >>> this >>> is Table 3, 2nd-last item "no MINCs inserted"). >>> >>> The MRI Violations module (Readme here) >>> will show >>> you the details of this mismatch -- >>> Go to the module (under the Imaging menu), find your scan and click the >>> link "Could not identify scan type" -- in the next subpage you can compare >>> the scan's actual parameters against the mri_protocol table. >>> >>> To resolve this, adjust your mri_protocol table values or perhaps ensure >>> your DICOMs are labelled consistently. >>> >>> Let us know if this works for you -- we can also walk you through an >>> example of non-identified scans on Demo.loris.ca (MRI Violations >>> module). >>> >>> Best, >>> Christine >>> >>> The LORIS team >>> >>> >>> On Tue, Jul 30, 2019 at 10:47 AM Sotirios Nikoloutsopoulos < >>> sotirisnik at gmail.com> wrote: >>> >>>> I hope this is sufficient as the error for the visit label disappeared. >>>> [image: image.png] >>>> >>>> Please see the attached file. Also something i found. >>>> >>>> lorisadmin at hbp:/data/loris/bin/mri$ cat >>>> /data/loris/data//logs/TarLoad-17-39-xubBdv.log >>>> >>>> ==> Loading file from disk >>>> /tmp/TarLoad-17-39-UyQcG2/dcc0000_258024_v1_20121205_102108_501e1_mri.mnc >>>> >>>> --> mapping DICOM parameter for >>>> /tmp/TarLoad-17-39-UyQcG2/dcc0000_258024_v1_20121205_102108_501e1_mri.mnc >>>> >>>> ==> computing md5 hash for MINC body. >>>> >>>> --> md5: 6b1202fd63e29de4c9be1cd9925888a5 >>>> >>>> ==> verifying acquisition protocol >>>> >>>> Acquisition protocol is unknown >>>> >>>> --> The minc file cannot be registered since the AcquisitionProtocol >>>> is unknown >>>> >>>> ???? ???, 30 ???? 2019 ???? 4:58 ?.?., ?/? Sotirios Nikoloutsopoulos < >>>> sotirisnik at gmail.com> ??????: >>>> >>>>> Ok I fixed the login problem by using a known hash and by deleting the >>>>> rows from the login_history i was able to login. >>>>> >>>>> ???? ???, 30 ???? 2019 ???? 4:50 ?.?., ?/? Sotirios Nikoloutsopoulos < >>>>> sotirisnik at gmail.com> ??????: >>>>> >>>>>> Hi, >>>>>> >>>>>> there was no visit label 01 in the Visit_Windows table and i don't >>>>>> know how to insert it because the record requires lots of attributes. Also >>>>>> the system for a reason asked me to update my password and now i don't >>>>>> remember it and my account got suspended. Is there a way to reset it or set >>>>>> a simple password? I updated the password hash in the users table by using >>>>>> the hash from another LORIS setup we had and i still couldn't login ( also >>>>>> the attribute password is always NULL and the expiration date is 1999-01-01 >>>>>> for some reason ). >>>>>> >>>>>> Thanks >>>>>> >>>>>> >>>>>> >>>>>> ???? ???, 29 ???? 2019 ???? 5:21 ?.?., ?/? Cecile Madjar < >>>>>> cecile.madjar at mcin.ca> ??????: >>>>>> >>>>>>> Hi Sotirios, >>>>>>> >>>>>>> Can you try adding the visit label v01 to the Visit_Windows table? >>>>>>> >>>>>>> However, I noticed that in a previous dataset, the label was V1. >>>>>>> Does that refer to the same visit? If so, you might want to harmonize the >>>>>>> visit labels so they are all the same across datasets for a given >>>>>>> timepoint, meaning you will need to relabel scans when the visit label is >>>>>>> different but referring to the same visit label (v01 = V1 etc...). >>>>>>> >>>>>>> Hope this helps, >>>>>>> >>>>>>> C?cile >>>>>>> >>>>>>> On Mon, Jul 29, 2019 at 10:15 AM Sotirios Nikoloutsopoulos < >>>>>>> sotirisnik at gmail.com> wrote: >>>>>>> >>>>>>>> Hi, >>>>>>>> >>>>>>>> Could you help me with the "Visit label does not exist"? I had >>>>>>>> changed $subjectID{'createVisitLabel'} to 1 as you had suggested but it >>>>>>>> appears that this problem hasn't been resolved yet. >>>>>>>> >>>>>>>> lorisadmin at hbp:/data/loris/bin/mri$ cat >>>>>>>> /data/loris/data//logs/TarLoad-14-58-9Xog7H.log >>>>>>>> >>>>>>>> ==> Loading file from disk >>>>>>>> /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc >>>>>>>> >>>>>>>> --> mapping DICOM parameter for >>>>>>>> /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc >>>>>>>> >>>>>>>> --> using user-defined filterParameters for >>>>>>>> /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc >>>>>>>> >>>>>>>> Candidate Mismatch Error is Visit label does not exist >>>>>>>> -> WARNING: This candidate was invalid. Logging to >>>>>>>> MRICandidateErrors table with reason Visit label does >>>>>>>> not exist >>>>>>>> >>>>>>>> Thank you, >>>>>>>> >>>>>>>> Sotirios >>>>>>>> >>>>>>>> ???? ???, 26 ???? 2019 ???? 3:02 ?.?., ?/? Sotirios >>>>>>>> Nikoloutsopoulos ??????: >>>>>>>> >>>>>>>>> Hi Cecile, >>>>>>>>> >>>>>>>>> The Center error was fixed. Still the insertion of mincs fails. >>>>>>>>> Please see the output.txt file i attached. Also is there something else i >>>>>>>>> need to change at the paths configuration? >>>>>>>>> >>>>>>>>> Thank you, >>>>>>>>> >>>>>>>>> Sotirios >>>>>>>>> >>>>>>>>> ???? ???, 25 ???? 2019 ???? 6:55 ?.?., ?/? Cecile Madjar < >>>>>>>>> cecile.madjar at mcin.ca> ??????: >>>>>>>>> >>>>>>>>>> Hi Sotirios, >>>>>>>>>> >>>>>>>>>> We are making progress! >>>>>>>>>> >>>>>>>>>> I have a feeling this error comes from the fact that your psc >>>>>>>>>> table does not have the MRI_alias populated for the DCC site. Running the >>>>>>>>>> following query in the mysql database should fix this: >>>>>>>>>> UPDATE psc SET MRI_alias="DCC", Alias="DCC" WHERE Name="Data >>>>>>>>>> Coordinating Center"; >>>>>>>>>> Repeat the same with all your sites (make sure to change the >>>>>>>>>> Aliases between sites, they should all be unique). >>>>>>>>>> >>>>>>>>>> Let me know how it goes! >>>>>>>>>> Best, >>>>>>>>>> >>>>>>>>>> C?cile >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> On Thu, Jul 25, 2019 at 11:43 AM Sotirios Nikoloutsopoulos < >>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>> >>>>>>>>>>> Dear Cecile, >>>>>>>>>>> You were right about your guesses. I did the modifications you >>>>>>>>>>> suggested, i still get the "no mincs inserted" error, now i am getting the >>>>>>>>>>> "No center found this candidate" error ( how do i fix that? from what i see >>>>>>>>>>> the .dcm files contains a 'Institution Name', is that the center? ), so i >>>>>>>>>>> guess that's why the validation fails, but i changed the force variable of >>>>>>>>>>> tarchiveLoader to 1, shouldn't it have inserted the mincs then? Also it is >>>>>>>>>>> optional to have a mail server, right? ( from what i see the mail error >>>>>>>>>>> does not affect the $valid_study, so i assume we are okay with that ) >>>>>>>>>>> Thank you a lot, >>>>>>>>>>> Sotirios >>>>>>>>>>> >>>>>>>>>>> ???? ???, 25 ???? 2019 ???? 5:48 ?.?., ?/? Cecile Madjar < >>>>>>>>>>> cecile.madjar at mcin.ca> ??????: >>>>>>>>>>> >>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>> >>>>>>>>>>>> From what I understand, I believe you just need to update a few >>>>>>>>>>>> config settings from the frontend in the Config module (under the Admin >>>>>>>>>>>> menu). >>>>>>>>>>>> [image: Screen Shot 2019-07-25 at 10.31.35 AM.png] >>>>>>>>>>>> >>>>>>>>>>>> Then go to the Paths section of the config module and update >>>>>>>>>>>> the "LORIS-MRI code" config setting to /data/loris/bin/mri (my guess is >>>>>>>>>>>> that currently, it is set to /data/LORIS/data) and click on the submit >>>>>>>>>>>> button. >>>>>>>>>>>> [image: Screen Shot 2019-07-25 at 10.32.50 AM.png] >>>>>>>>>>>> >>>>>>>>>>>> Then, go to Imaging Pipeline section of the Configuration >>>>>>>>>>>> module and update the "Loris-MRI Data Directory" to /data/loris/data/ (my >>>>>>>>>>>> guess is that it is empty at the moment in your database which is why >>>>>>>>>>>> $data_dir is not defined when you run the tarchiveLoader step of the >>>>>>>>>>>> insertion pipeline). >>>>>>>>>>>> [image: Screen Shot 2019-07-25 at 10.40.52 AM.png] >>>>>>>>>>>> >>>>>>>>>>>> Finally, I took a look at your environment file and it might be >>>>>>>>>>>> a good idea to update your PERL5LIB variable to the following (it has been >>>>>>>>>>>> added to the code a few releases ago as we realized this was needed for the >>>>>>>>>>>> libraries. Not sure which version of LORIS-MRI you are using but it does >>>>>>>>>>>> not hurt to update this variable to what I suggest below): >>>>>>>>>>>> export >>>>>>>>>>>> PERL5LIB=/data/loris/bin/mri/uploadNeuroDB:/data/loris/bin/mri/dicom-archive:$PERL5LIB >>>>>>>>>>>> >>>>>>>>>>>> Hope this helps. Sorry you are experiencing so much trouble >>>>>>>>>>>> setting things up. We probably need to update our WIKI. >>>>>>>>>>>> >>>>>>>>>>>> Best, >>>>>>>>>>>> >>>>>>>>>>>> C?cile >>>>>>>>>>>> >>>>>>>>>>>> On Thu, Jul 25, 2019 at 9:48 AM Sotirios Nikoloutsopoulos < >>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>> >>>>>>>>>>>>> The "Loris-MRI Data Directory" should be in the environment >>>>>>>>>>>>> file? >>>>>>>>>>>>> >>>>>>>>>>>>> ???? ???, 25 ???? 2019 ???? 12:59 ?.?., ?/? Sotirios >>>>>>>>>>>>> Nikoloutsopoulos ??????: >>>>>>>>>>>>> >>>>>>>>>>>>>> The scripts are located in /data/loris/bin/mri/. Somewhere I >>>>>>>>>>>>>> might have messed something up but i remember following the instructions in >>>>>>>>>>>>>> the wiki.For example when i tried to execute the >>>>>>>>>>>>>> batch_uploads_imageuploader perl script the line >>>>>>>>>>>>>> >>>>>>>>>>>>>> my $command = "$bin_dir/uploadNeuroDB/imaging_upload_file.pl >>>>>>>>>>>>>> " >>>>>>>>>>>>>> >>>>>>>>>>>>>> was pointing to an invalid path, for example: it was >>>>>>>>>>>>>> repeating a pattern and had LORIS instead of loris ( i think the mistake >>>>>>>>>>>>>> was that in the wiki it suggested to use $PROJECT for the name of the >>>>>>>>>>>>>> folder and i choosed 'loris' >>>>>>>>>>>>>> https://github.com/aces/Loris/wiki/Imaging-Database ). See >>>>>>>>>>>>>> also the in image for the modification i did. Also i didn't find the >>>>>>>>>>>>>> section to config the $data_dir variable. >>>>>>>>>>>>>> >>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>> >>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> ???? ???, 24 ???? 2019 ???? 6:05 ?.?., ?/? Cecile Madjar < >>>>>>>>>>>>>> cecile.madjar at mcin.ca> ??????: >>>>>>>>>>>>>> >>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> It looks like you have one Config setting not set (based on >>>>>>>>>>>>>>> the first error message you got when running it the first time). You need >>>>>>>>>>>>>>> to set a value for "Loris-MRI Data Directory" in the Config module under >>>>>>>>>>>>>>> the Imaging pipeline section (from what I can see, it would be >>>>>>>>>>>>>>> /data/loris/data/ for your setup). >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> The reason you got that error message the second time is >>>>>>>>>>>>>>> that the pipeline checks if the DICOM study was already inserted in the >>>>>>>>>>>>>>> tarchive table. Since you ran the study once already, the study is inserted >>>>>>>>>>>>>>> into the tarchive, hence the message. However, the pipeline did not >>>>>>>>>>>>>>> complete as the MINC files were not created and inserted into the >>>>>>>>>>>>>>> files/parameter_file table. In order to continue the insertion, you will >>>>>>>>>>>>>>> then need to run the tarchiveLoader command suggested in the terminal >>>>>>>>>>>>>>> during the second run: >>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader -globLocation >>>>>>>>>>>>>>> -profile prod >>>>>>>>>>>>>>> /data/loris/data/tarchive//2012/DCM_2012-12-05_ImagingUpload-17-43-ZUEFjb.tar >>>>>>>>>>>>>>> -verbose >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> Finally, I am a bit confused by your setup. Where are the >>>>>>>>>>>>>>> scripts located? In /data/loris/bin/mri or /data/loris/data? It feels like >>>>>>>>>>>>>>> the Config setting "LORIS-MRI code" in the Paths section was set to >>>>>>>>>>>>>>> "/data/LORIS/data" but it should have been set to the directory where the >>>>>>>>>>>>>>> scripts are located (most probably /data/loris/bin/mri). >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> Hope this helps, >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> On Wed, Jul 24, 2019 at 10:55 AM Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Ok first i execute this command: >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> "lorisadmin at hbp:/data/loris/bin/mri$ >>>>>>>>>>>>>>>> ./batch_uploads_imageuploader -profile prod < ~/Desktop/input.txt > log.txt >>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in concatenation (.) >>>>>>>>>>>>>>>> or string at ./batch_uploads_imageuploader line 143. >>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in concatenation (.) >>>>>>>>>>>>>>>> or string at ./batch_uploads_imageuploader line 143. >>>>>>>>>>>>>>>> Use of uninitialized value $_ in pattern match (m//) at >>>>>>>>>>>>>>>> ./batch_uploads_imageuploader line 147. >>>>>>>>>>>>>>>> base is DCC0000_258024_V01 >>>>>>>>>>>>>>>> path is /data/incoming/ >>>>>>>>>>>>>>>> type is .tar.gz >>>>>>>>>>>>>>>> fullpath is /data/incoming/DCC0000_258024_V01.tar.gz >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> source /tmp/ImagingUpload-17-43-ZUEFjb >>>>>>>>>>>>>>>> targetlocation /data/loris/data/tarchive >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in concatenation (.) >>>>>>>>>>>>>>>> or string at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 256. >>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in concatenation (.) >>>>>>>>>>>>>>>> or string at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 284. >>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in concatenation (.) >>>>>>>>>>>>>>>> or string at /data/loris/bin/mri/uploadNeuroDB/ >>>>>>>>>>>>>>>> tarchive_validation.pl line 219. >>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in concatenation (.) >>>>>>>>>>>>>>>> or string at /data/loris/bin/mri/uploadNeuroDB/ >>>>>>>>>>>>>>>> minc_insertion.pl line 270. >>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in concatenation (.) >>>>>>>>>>>>>>>> or string at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 711. >>>>>>>>>>>>>>>> Can't exec "mail": No such file or directory at >>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 721. >>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 722. >>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 723. >>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in concatenation (.) >>>>>>>>>>>>>>>> or string at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 724. >>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 724. >>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 725. >>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in concatenation (.) >>>>>>>>>>>>>>>> or string at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 735. >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> No Mincs inserted >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> The tarchiveLoader insertion script has failed. >>>>>>>>>>>>>>>> Running now the following command: >>>>>>>>>>>>>>>> /data/loris/data/uploadNeuroDB/imaging_upload_file.pl >>>>>>>>>>>>>>>> -profile prod -upload_id 3 /data/incoming/DCC0000_258024_V01.tar.gz >>>>>>>>>>>>>>>> -verbose" >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> I inserted the VisitLabel, but still the Mincs are not >>>>>>>>>>>>>>>> inserted and i am getting this error >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> "lorisadmin at hbp:/data/loris/bin/mri$ >>>>>>>>>>>>>>>> /data/loris/data/uploadNeuroDB/imaging_upload_file.pl >>>>>>>>>>>>>>>> -profile prod -upload_id 3 /data/incoming/DCC0000_258024_V01.tar.gz -verbose >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> find -path \/tmp\/ImagingUpload\-17\-45\-5MsWEd -name >>>>>>>>>>>>>>>> '__MACOSX' -delete >>>>>>>>>>>>>>>> Spool message is: >>>>>>>>>>>>>>>> The Scan for the uploadID 3 has already been run with >>>>>>>>>>>>>>>> tarchiveID: 7. >>>>>>>>>>>>>>>> To continue with the rest of the insertion pipeline, please >>>>>>>>>>>>>>>> run tarchiveLoader from a terminal as follows: >>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader -globLocation -profile prod >>>>>>>>>>>>>>>> /data/loris/data/tarchive//2012/DCM_2012-12-05_ImagingUpload-17-43-ZUEFjb.tar >>>>>>>>>>>>>>>> -verbose" >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Which files should i delete? I thought that deleting the >>>>>>>>>>>>>>>> files from the tarchive was enough. And i executed the last proposed >>>>>>>>>>>>>>>> command to continue to rest of the insertion pipeline ( check the image ). >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Thank you >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> ???? ???, 24 ???? 2019 ???? 5:05 ?.?., ?/? Cecile Madjar < >>>>>>>>>>>>>>>> cecile.madjar at mcin.ca> ??????: >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Sorry I was not clear before. Every visits of candidates >>>>>>>>>>>>>>>>> are created in the session table with one entry per CandID/VisitLabel. So >>>>>>>>>>>>>>>>> if the imaging pipeline created visits in the session table (that are not >>>>>>>>>>>>>>>>> attached to instruments) and you want to clean your database completely, >>>>>>>>>>>>>>>>> you can delete entries in that table as well. >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Regarding your point 2, the imaging pipeline can create >>>>>>>>>>>>>>>>> the visit in the session table as long as the visit label is present in the >>>>>>>>>>>>>>>>> Visit_Windows table (which means the visit label stored in the PatientName >>>>>>>>>>>>>>>>> is a valid visit label). >>>>>>>>>>>>>>>>> However, in your prod file, if the >>>>>>>>>>>>>>>>> variable $subjectID{'createVisitLabel'} is set to 1 for candidates, the >>>>>>>>>>>>>>>>> visit label should be created in the Visit_Windows table I believe. Here >>>>>>>>>>>>>>>>> is the line of the prod file you would need to change >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> . >>>>>>>>>>>>>>>>> In general, we prefer populating the Visit_Windows table >>>>>>>>>>>>>>>>> and set the $subjectID{'createVisitLabel'} to 0 for candidate data to avoid >>>>>>>>>>>>>>>>> insertion of badly labelled MRI data that are complex to relabel. >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Finally, regarding the candidate creation, if you execute >>>>>>>>>>>>>>>>> the following steps, the pipeline should be able to create candidates: >>>>>>>>>>>>>>>>> - set in the Imaging Pipeline section of the config module >>>>>>>>>>>>>>>>> the config setting "Upload creation of candidates" to Yes >>>>>>>>>>>>>>>>> - manually transfer the scans to the LORIS server instead >>>>>>>>>>>>>>>>> of uploading it via the imaging browser >>>>>>>>>>>>>>>>> - run batch_imaging_upload.pl as you did until now. >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Hope this helps! >>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> On Wed, Jul 24, 2019 at 8:47 AM Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> About my second question i replaced the name of the >>>>>>>>>>>>>>>>>> patient in the .dcm files and now i am getting an error that the visit >>>>>>>>>>>>>>>>>> label does not exist. >>>>>>>>>>>>>>>>>> I thought it was supposed to be automatically created. >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> "Done adding archive info into database >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader >>>>>>>>>>>>>>>>>> -globLocation -profile prod >>>>>>>>>>>>>>>>>> /data/loris/data/tarchive//DCM_2012-12-05_ImagingUpload-15-42-yUwQQV.tar >>>>>>>>>>>>>>>>>> -verbose >>>>>>>>>>>>>>>>>> md5sum >>>>>>>>>>>>>>>>>> /data/loris/data/tarchive/DCM_2012-12-05_ImagingUpload-15-42-yUwQQV.tar >>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>> candidate id 258024 >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> => No Visit labelVisit label does not exist >>>>>>>>>>>>>>>>>> Set centerID = 1 >>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Number of MINC files that will be considered for >>>>>>>>>>>>>>>>>> inserting into the database: 1 >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> log dir is /logs and log file is >>>>>>>>>>>>>>>>>> /logs/TarLoad-15-42-L6pocU.log >>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>> candidate id 258024 >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> => No Visit label >>>>>>>>>>>>>>>>>> Cleaning up temp files: rm -rf >>>>>>>>>>>>>>>>>> /tmp/TarLoad-15-42-J2rQms/ImagingUpload-15-42-yUwQQV*" >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> ???? ???, 24 ???? 2019 ???? 3:38 ?.?., ?/? Sotirios >>>>>>>>>>>>>>>>>> Nikoloutsopoulos ??????: >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> 1) What are the records in the session table? >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> 2) I tried to upload a non-phantom file like this >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> input_file.txt: >>>>>>>>>>>>>>>>>>> /data/incoming/DCC0000_258024_V1.tar.gz N >>>>>>>>>>>>>>>>>>> DCC0000_258024_V1 >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Terminal: >>>>>>>>>>>>>>>>>>> ./batch_uploads_imageuploader -profile prod < >>>>>>>>>>>>>>>>>>> ~/Desktop/input.txt > log.txt >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> and i get the following error in the log.txt file >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> "Running now the following command: >>>>>>>>>>>>>>>>>>> /data/loris/data/uploadNeuroDB/imaging_upload_file.pl >>>>>>>>>>>>>>>>>>> -profile prod -upload_id 7 /data/incoming/DCC0000_258024_V1.tar.gz -verbose >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> find -path \/tmp\/ImagingUpload\-14\-56\-FeLCB4 -name >>>>>>>>>>>>>>>>>>> '__MACOSX' -delete >>>>>>>>>>>>>>>>>>> Spool message is: >>>>>>>>>>>>>>>>>>> The PatientName read from the DICOM header does not >>>>>>>>>>>>>>>>>>> start with DCC0000_258024_V1 from the mri_upload table >>>>>>>>>>>>>>>>>>> " >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> and the spool message is repeated for each .dcm file. >>>>>>>>>>>>>>>>>>> Should i preprocess every .dcm file and change the PatientName to >>>>>>>>>>>>>>>>>>> "DCC0000_258024_V1"? >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> 3) As far as it concerns the candidate profile i have to >>>>>>>>>>>>>>>>>>> create a new one each time before i try to upload a file? Is there already >>>>>>>>>>>>>>>>>>> a way to create a candidate profile and get the DCCID and PSCID without the >>>>>>>>>>>>>>>>>>> user interface? >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> ???? ???, 18 ???? 2019 ???? 5:00 ?.?., ?/? Cecile Madjar >>>>>>>>>>>>>>>>>>> ??????: >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> See answers to your questions below. >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> About the 1st case we had a dicom with a blank >>>>>>>>>>>>>>>>>>>>> studyUID, maybe someone accidentally removed it. >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> That is strange. Something must have been done to the >>>>>>>>>>>>>>>>>>>> DICOM files. I have never seen a study with no StudyUID out of the scanner. >>>>>>>>>>>>>>>>>>>> Usually, you need to manually erase it with some tool. However, DICOMs >>>>>>>>>>>>>>>>>>>> never cease to surprise me... >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> Some other questions: >>>>>>>>>>>>>>>>>>>>> 1) What are the steps to remove all of my patients and >>>>>>>>>>>>>>>>>>>>> uploads?: because i want to try to reupload all the testing dicoms we had >>>>>>>>>>>>>>>>>>>>> with a clean database. >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Release 21.0 of LORIS-MRI will offer a script to remove >>>>>>>>>>>>>>>>>>>> all the entries and files specific to an upload. However, this release is >>>>>>>>>>>>>>>>>>>> not yet out. Hopefully in the next few weeks. >>>>>>>>>>>>>>>>>>>> In the meantime, since your case is particular and that >>>>>>>>>>>>>>>>>>>> you just want to start with a clean database, the following deletes should >>>>>>>>>>>>>>>>>>>> work (hopefully I won't forget any tables): >>>>>>>>>>>>>>>>>>>> delete from mri_violations_log; >>>>>>>>>>>>>>>>>>>> delete from mri_protocol_violated_scans; >>>>>>>>>>>>>>>>>>>> delete from MRICandidateErrors; >>>>>>>>>>>>>>>>>>>> delete from parameter_file; >>>>>>>>>>>>>>>>>>>> delete from files_qcstatus; # (if you played with the >>>>>>>>>>>>>>>>>>>> QC part of the imaging browser for testing) >>>>>>>>>>>>>>>>>>>> delete from feedback_mri_comments; # (if you played >>>>>>>>>>>>>>>>>>>> with the QC part of the imaging browser for testing) >>>>>>>>>>>>>>>>>>>> delete from tarchive_series; >>>>>>>>>>>>>>>>>>>> delete from tarchive_files; >>>>>>>>>>>>>>>>>>>> delete from mri_upload; >>>>>>>>>>>>>>>>>>>> delete from tarchive; >>>>>>>>>>>>>>>>>>>> delete from mri_scanner; >>>>>>>>>>>>>>>>>>>> delete from candidate where PSCID="scanner"; >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> I don't know if you want to also delete entries in the >>>>>>>>>>>>>>>>>>>> session and candidate table too? >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> 2) We do not need to create the profile of a patient ( >>>>>>>>>>>>>>>>>>>>> are the patients stored in the candidate table? because i can't see the >>>>>>>>>>>>>>>>>>>>> ghosts ), because will it automatically be created when importing a dicom? >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> I am not sure I understand fully this question. All >>>>>>>>>>>>>>>>>>>> candidates are stored in the candidate table. The phantom scans however are >>>>>>>>>>>>>>>>>>>> attached to a scanner candidate depending on where the scan happened. It is >>>>>>>>>>>>>>>>>>>> a bit of a weird concept that we have to redesign eventually but never got >>>>>>>>>>>>>>>>>>>> a chance to get to it. >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Hopefully this answered your question, otherwise, don't >>>>>>>>>>>>>>>>>>>> hesitate to let me know. >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> 3) What is the difference between uploading a dicom as >>>>>>>>>>>>>>>>>>>>> phantom instead of importing as PSCCID_DCCID_VisitLabel? >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> When you upload the scan as PSCID_DCCID_VisitLabel, >>>>>>>>>>>>>>>>>>>> there is a check that makes sure the candidate IDs and visit label are >>>>>>>>>>>>>>>>>>>> valid at the time of upload. >>>>>>>>>>>>>>>>>>>> When you upload a scan as phantom, it expects that the >>>>>>>>>>>>>>>>>>>> DICOM field PatientName and uploaded filename contains the string >>>>>>>>>>>>>>>>>>>> "phantom". We enforced this behaviour on the imaging uploader side in >>>>>>>>>>>>>>>>>>>> recent releases but I can't remember which one. Probably the upcoming 21.0 >>>>>>>>>>>>>>>>>>>> release. >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> All those verifications might seem cumbersome but they >>>>>>>>>>>>>>>>>>>> are here to ensure that the files inserted are all valid and labelled >>>>>>>>>>>>>>>>>>>> properly as it is a bit messy to have to delete files that were wrongly >>>>>>>>>>>>>>>>>>>> labelled. At least, the delete script present in release 21.0 will make >>>>>>>>>>>>>>>>>>>> this process easier but it is still good practice to verify those things. >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> With pleasure. Hopefully the answers to your questions >>>>>>>>>>>>>>>>>>>> will be helpful. >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> PS: loris-dev mailing list: you will find the initial >>>>>>>>>>>>>>>>>>>> answer I gave Sotirios below. I forgot to cc the loris-dev in my earlier >>>>>>>>>>>>>>>>>>>> reply... >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> ???? ???, 16 ???? 2019 ???? 12:02 ?.?., ?/? Cecile >>>>>>>>>>>>>>>>>>>>> Madjar ??????: >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> Dear Sotirios, >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> Thank you for reaching out. Since your email was >>>>>>>>>>>>>>>>>>>>>> already organized in points, I will reply directly below your questions >>>>>>>>>>>>>>>>>>>>>> below. >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> 1) What do we do when the StudyUID is blank on the >>>>>>>>>>>>>>>>>>>>>>> header? >>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/minor/docs/AppendixA-Troubleshooting_guideline.md >>>>>>>>>>>>>>>>>>>>>>> There solution provided at the table 3 does not guide us how to find the >>>>>>>>>>>>>>>>>>>>>>> information ( is possible ). >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> The StudyUID is the field used in our pipeline at the >>>>>>>>>>>>>>>>>>>>>> moment to check whether a DICOM study was already inserted into LORIS with >>>>>>>>>>>>>>>>>>>>>> that same StudyUID since it is supposed to be unique for every single >>>>>>>>>>>>>>>>>>>>>> study. Currently, we do not support insertion of DICOM studies if they do >>>>>>>>>>>>>>>>>>>>>> not have a StudyUID associated with them. >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> Is there a specific reason why the StudyUID is blank >>>>>>>>>>>>>>>>>>>>>> in the DICOM headers in your DICOM files? Did they go through some >>>>>>>>>>>>>>>>>>>>>> processes before upload to LORIS? >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> 2) When i am about to upload a non-phanton case i >>>>>>>>>>>>>>>>>>>>>>> need a 'Visit Label'. Is there already a script that can create a new visit >>>>>>>>>>>>>>>>>>>>>>> label for a specific Candidate, so i can provide it as input afterwards to >>>>>>>>>>>>>>>>>>>>>>> the >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> batch_uploads_imageuploader ( See option 5.1.3 https://github.com/aces/Loris-MRI/blob/minor/docs/05-PipelineLaunchOptions.md ) >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> I am not sure if the front-end allows for it but if >>>>>>>>>>>>>>>>>>>>>> you use batch_uploads_imageuploader, the insertion scripts could create the >>>>>>>>>>>>>>>>>>>>>> visit label for you. However, it does need to be included in the patient >>>>>>>>>>>>>>>>>>>>>> name in order for the script to know which label it should use. >>>>>>>>>>>>>>>>>>>>>> For example: you upload V02 for MTL0123 (DCCID: >>>>>>>>>>>>>>>>>>>>>> 456789) but V02 was not yet created for MTL0123; the insertion scripts >>>>>>>>>>>>>>>>>>>>>> will create a V02 visit for MTL0123 if the PatientName field for the >>>>>>>>>>>>>>>>>>>>>> dataset is MTL0123_456789_V02 with Stage marked as "Not Started". >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> However, *note that for the script to create the >>>>>>>>>>>>>>>>>>>>>> visit for the candidate, you have to make sure that all the visit label of >>>>>>>>>>>>>>>>>>>>>> your projects were inserted in the Visit_Windows table* >>>>>>>>>>>>>>>>>>>>>> (otherwise, the visit will never be created as they were not specified as >>>>>>>>>>>>>>>>>>>>>> being part of the list of visit label to expect). So in the example above, >>>>>>>>>>>>>>>>>>>>>> you should have one row in Visit_Windows with Visit_label="V02" set. >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> 3) Section 4.3 >>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/minor/docs/04-Scripts.md >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> What do we do when the folder contains multiple mnc files? >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> This is a case by case. Most of the time, the MINC >>>>>>>>>>>>>>>>>>>>>> files that failed insertion into the imaging browser end up in the MRI >>>>>>>>>>>>>>>>>>>>>> violation module where you can see what went wrong with the acquisitions >>>>>>>>>>>>>>>>>>>>>> not inserted. If you notice that the MINC file should be inserted as a >>>>>>>>>>>>>>>>>>>>>> specific protocol, you can force the insertion as explained in section 4.3. >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> In your case, I have a feeling that you want to be >>>>>>>>>>>>>>>>>>>>>> able to insert MINC files that did not go through the whole pipeline >>>>>>>>>>>>>>>>>>>>>> insertion (DICOM archival, then dcm2mnc, then protocol identification, then >>>>>>>>>>>>>>>>>>>>>> insertion...). In theory, you could call >>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl on any MINC file, provided you >>>>>>>>>>>>>>>>>>>>>> have at least the following information: >>>>>>>>>>>>>>>>>>>>>> - path to the MINC file >>>>>>>>>>>>>>>>>>>>>> - uploadID associated with the MINC files or DICOM >>>>>>>>>>>>>>>>>>>>>> archive path from which those MINC files were created from >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> Then the minc_insertion.pl script will do the >>>>>>>>>>>>>>>>>>>>>> subject information and protocol validation etc... >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> If all the MINC files come from the same uploadID or >>>>>>>>>>>>>>>>>>>>>> TarchiveID, then you could run a loop in bash calling the >>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl script like this for files >>>>>>>>>>>>>>>>>>>>>> deriving from uploadID=1: >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> ls /path/to/mnc/folder/* | while read f; do >>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl -profile prod -uploadID 1 >>>>>>>>>>>>>>>>>>>>>> -mincPath $f; done >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> Hope this helped! >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> _______________________________________________ >>>> Loris-dev mailing list >>>> Loris-dev at bic.mni.mcgill.ca >>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>> >>> >>> >>> -- >>> >>> christine.rogers at mcgill.ca >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>> Montreal Neurological Institute >>> McGill University | Montreal | Canada >>> >> > > -- > > christine.rogers at mcgill.ca > McGill Centre for Integrative Neuroscience | MCIN.ca > Montreal Neurological Institute > McGill University | Montreal | Canada > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 78176 bytes Desc: not available URL: From sotirisnik at gmail.com Mon Aug 5 09:05:34 2019 From: sotirisnik at gmail.com (Sotirios Nikoloutsopoulos) Date: Mon, 5 Aug 2019 16:05:34 +0300 Subject: [Loris-dev] Import mri - scripts In-Reply-To: References: <65ad2b70c3084ffdb1e4a9dcdad948cd@YTOPR0101MB1803.CANPRD01.PROD.OUTLOOK.COM> Message-ID: I reinstalled LORIS to 21 version and now the content is not visible at all at most pages. [image: image.png] ???? ???, 5 ??? 2019 ???? 3:19 ?.?., ?/? Sotirios Nikoloutsopoulos < sotirisnik at gmail.com> ??????: > Hi, > > Is it easy to upgrade to Loris 21? Also the following fails because the > line 1985 of NeuroDB/MRIProcessingUtility.pm query mri_protocol which > doesn't have TR_range > https://github.com/aces/Loris/blob/21.0-release/SQL/0000-00-00-schema.sql#L556 > > [image: image.png] > > lorisadmin at hbp:/data/loris/bin/mri$ ./batch_uploads_imageuploader > -profile prod < ~/Desktop/input.txt > log.txt > Use of uninitialized value $_ in pattern match (m//) at > ./batch_uploads_imageuploader line 147. > base is DCC0000_258024_V1 > path is /data/incoming/ > type is .tar.gz > fullpath is /data/incoming/DCC0000_258024_V1.tar.gz > DBD::mysql::st execute failed: Unknown column 'TR_range' in 'where clause' > at /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line > 1985. > DBD::mysql::st fetchrow_array failed: fetch() without execute() at > /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line 1986. > Use of uninitialized value $count_mri_protocol in numeric gt (>) at > /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line 1995. > DBD::mysql::st execute failed: Unknown column 'TR_range' in 'field list' > at /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 562. > Can't exec "mail": No such file or directory at > /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 721. > print() on closed filehandle MAIL at > /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 722. > print() on closed filehandle MAIL at > /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 723. > print() on closed filehandle MAIL at > /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 724. > print() on closed filehandle MAIL at > /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 725. > > No Mincs inserted > > Thanks, > > Sotirios > > ???? ???, 3 ??? 2019 ???? 1:08 ?.?., ?/? Christine Rogers, Ms. < > christine.rogers at mcgill.ca> ??????: > >> Hi Sotirios, >> >> First, just a note: we've released LORIS 21 this week with some major >> new features and cleanup -- especially if you are early in your setup >> phase, check out the Release notes for both the LORIS >> and Loris-MRI >> repos. >> >> Thanks for your screenshots -- your empty mri_protocol table should be at >> the root of these issues : >> >> The mri_protocol table must be populated >> >> in order for your scans to be registered in LORIS -- it serves as a >> whitelist for the insertion pipeline which filters out scans that aren't >> identified or matched to scan types in this table. >> >> By default, this table is populated with entries for t1, t2, fMRI and DTI >> (Insert statements for 21 release branch are here >> >> ) >> Feel free to restore our default records and broaden their parameters to >> match all your scan types. >> >> re Defaced, native, selected -- these filter the scans displayed as you >> move to the next page (View Session), instead of viewing "all types" of >> scans from a given session : >> >> - "defaced" means that a defacing script >> >> has masked the subject's face in the volume (for patient privacy) >> - "native" means that no pre-processing has been performed on the >> scan (it's raw data), >> - "selected" will show only volumes that have been QC'd and >> "selected" as the best of their type -- used to display only the best >> quality T1 image instead of all T1s acquired in a session, e.g. >> >> re QC Comments -- >> Once you have successfully loaded scans (matched to the mri_protocol >> table), you'll be able to use the Imaging Browser's View Session subpage to >> enter/view QC comments on each volume, or for each visit. >> These are stored directly in the database, and linked to each scan. >> (Table name: feedback_mri_comments) >> (Visit-level QC comments are linked to the session.) >> >> For a walkthrough of the Imaging setup - please see the Imaging Setup >> guide >> - >> >> An old LORIS walkthrough video >> can also walk you through >> some of the Imaging front-end features, starting at 8:00 >> LORIS' imaging modules have been updated many times since this video, but >> the functionality and workflow is similar. >> >> Let us know how it goes once you have entries in your mri_protocol table >> - >> Best, >> Christine >> >> >> >> >> On Fri, Aug 2, 2019 at 7:58 AM Sotirios Nikoloutsopoulos < >> sotirisnik at gmail.com> wrote: >> >>> Hi Christine, >>> >>> In the candidate_list page i can see this patient >>> >>> [image: image.png] >>> >>> If i press the link under PSCID i get to see >>> [image: image.png] >>> >>> and if i press the link under Scan Done it redirects me to >>> imaging_browser >>> >>> [image: image.png] >>> >>> At the mri_violations page i also see No results ( neither on resolved / >>> not resolved ). >>> >>> At the imaging_uploader i can see the record that failed. >>> >>> [image: image.png] >>> >>> If i click on the tarchive info i get to see the Protocol Name which i >>> think is the acquisition we wanted? >>> [image: image.png] >>> >>> Also my mri_protocol table is empty. >>> >>> Furthermore i would like to ask about the defaced, native, selected. >>> What exactly is native and selected? And where are the qc comments stored? >>> >>> [image: image.png] >>> >>> Finally a walkthrough would be helpful. >>> >>> Thanks, >>> >>> Sotirios >>> >>> ???? ???, 30 ???? 2019 ???? 8:29 ?.?., ?/? Christine Rogers, Ms. < >>> christine.rogers at mcgill.ca> ??????: >>> >>>> Hi Sotirios, >>>> Glad to hear you're making progress with the visit labels. To follow >>>> up on your last few emails: >>>> >>>> a- The Wiki's Setup Guide contains Sample insert statements for the >>>> Visit Windows table >>>> >>>> . >>>> >>>> As Cecile mentioned, the consistency of visit label format is >>>> important: V01, v01, V1, 01 -- whichever you select to use is fine; we use >>>> V01 by default across all documentation. >>>> >>>> b- For Password reset, there is a script in the tools/ directory so >>>> that a back-end administrator can reset any front-end user password, >>>> including Admin. (See info on setting up / resetting User passwords in the Wiki's >>>> Setup Guide >>>> >>>> ) >>>> >>>> c- The minc file not being registered -- due to AcquisitionProtocol >>>> unknown. >>>> This means the SeriesDescription (Acquisition Protocol) in you Dicom >>>> header was not matched to any scan listed in the mri_protocol database >>>> table. >>>> (In the online Loris-MRI Troubleshooting Guide, >>>> this >>>> is Table 3, 2nd-last item "no MINCs inserted"). >>>> >>>> The MRI Violations module (Readme here) >>>> will show >>>> you the details of this mismatch -- >>>> Go to the module (under the Imaging menu), find your scan and click the >>>> link "Could not identify scan type" -- in the next subpage you can compare >>>> the scan's actual parameters against the mri_protocol table. >>>> >>>> To resolve this, adjust your mri_protocol table values or perhaps >>>> ensure your DICOMs are labelled consistently. >>>> >>>> Let us know if this works for you -- we can also walk you through an >>>> example of non-identified scans on Demo.loris.ca (MRI Violations >>>> module). >>>> >>>> Best, >>>> Christine >>>> >>>> The LORIS team >>>> >>>> >>>> On Tue, Jul 30, 2019 at 10:47 AM Sotirios Nikoloutsopoulos < >>>> sotirisnik at gmail.com> wrote: >>>> >>>>> I hope this is sufficient as the error for the visit label disappeared. >>>>> [image: image.png] >>>>> >>>>> Please see the attached file. Also something i found. >>>>> >>>>> lorisadmin at hbp:/data/loris/bin/mri$ cat >>>>> /data/loris/data//logs/TarLoad-17-39-xubBdv.log >>>>> >>>>> ==> Loading file from disk >>>>> /tmp/TarLoad-17-39-UyQcG2/dcc0000_258024_v1_20121205_102108_501e1_mri.mnc >>>>> >>>>> --> mapping DICOM parameter for >>>>> /tmp/TarLoad-17-39-UyQcG2/dcc0000_258024_v1_20121205_102108_501e1_mri.mnc >>>>> >>>>> ==> computing md5 hash for MINC body. >>>>> >>>>> --> md5: 6b1202fd63e29de4c9be1cd9925888a5 >>>>> >>>>> ==> verifying acquisition protocol >>>>> >>>>> Acquisition protocol is unknown >>>>> >>>>> --> The minc file cannot be registered since the AcquisitionProtocol >>>>> is unknown >>>>> >>>>> ???? ???, 30 ???? 2019 ???? 4:58 ?.?., ?/? Sotirios Nikoloutsopoulos < >>>>> sotirisnik at gmail.com> ??????: >>>>> >>>>>> Ok I fixed the login problem by using a known hash and by deleting >>>>>> the rows from the login_history i was able to login. >>>>>> >>>>>> ???? ???, 30 ???? 2019 ???? 4:50 ?.?., ?/? Sotirios Nikoloutsopoulos < >>>>>> sotirisnik at gmail.com> ??????: >>>>>> >>>>>>> Hi, >>>>>>> >>>>>>> there was no visit label 01 in the Visit_Windows table and i don't >>>>>>> know how to insert it because the record requires lots of attributes. Also >>>>>>> the system for a reason asked me to update my password and now i don't >>>>>>> remember it and my account got suspended. Is there a way to reset it or set >>>>>>> a simple password? I updated the password hash in the users table by using >>>>>>> the hash from another LORIS setup we had and i still couldn't login ( also >>>>>>> the attribute password is always NULL and the expiration date is 1999-01-01 >>>>>>> for some reason ). >>>>>>> >>>>>>> Thanks >>>>>>> >>>>>>> >>>>>>> >>>>>>> ???? ???, 29 ???? 2019 ???? 5:21 ?.?., ?/? Cecile Madjar < >>>>>>> cecile.madjar at mcin.ca> ??????: >>>>>>> >>>>>>>> Hi Sotirios, >>>>>>>> >>>>>>>> Can you try adding the visit label v01 to the Visit_Windows table? >>>>>>>> >>>>>>>> However, I noticed that in a previous dataset, the label was V1. >>>>>>>> Does that refer to the same visit? If so, you might want to harmonize the >>>>>>>> visit labels so they are all the same across datasets for a given >>>>>>>> timepoint, meaning you will need to relabel scans when the visit label is >>>>>>>> different but referring to the same visit label (v01 = V1 etc...). >>>>>>>> >>>>>>>> Hope this helps, >>>>>>>> >>>>>>>> C?cile >>>>>>>> >>>>>>>> On Mon, Jul 29, 2019 at 10:15 AM Sotirios Nikoloutsopoulos < >>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>> >>>>>>>>> Hi, >>>>>>>>> >>>>>>>>> Could you help me with the "Visit label does not exist"? I had >>>>>>>>> changed $subjectID{'createVisitLabel'} to 1 as you had suggested but it >>>>>>>>> appears that this problem hasn't been resolved yet. >>>>>>>>> >>>>>>>>> lorisadmin at hbp:/data/loris/bin/mri$ cat >>>>>>>>> /data/loris/data//logs/TarLoad-14-58-9Xog7H.log >>>>>>>>> >>>>>>>>> ==> Loading file from disk >>>>>>>>> /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc >>>>>>>>> >>>>>>>>> --> mapping DICOM parameter for >>>>>>>>> /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc >>>>>>>>> >>>>>>>>> --> using user-defined filterParameters for >>>>>>>>> /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc >>>>>>>>> >>>>>>>>> Candidate Mismatch Error is Visit label does not exist >>>>>>>>> -> WARNING: This candidate was invalid. Logging to >>>>>>>>> MRICandidateErrors table with reason Visit label >>>>>>>>> does not exist >>>>>>>>> >>>>>>>>> Thank you, >>>>>>>>> >>>>>>>>> Sotirios >>>>>>>>> >>>>>>>>> ???? ???, 26 ???? 2019 ???? 3:02 ?.?., ?/? Sotirios >>>>>>>>> Nikoloutsopoulos ??????: >>>>>>>>> >>>>>>>>>> Hi Cecile, >>>>>>>>>> >>>>>>>>>> The Center error was fixed. Still the insertion of mincs fails. >>>>>>>>>> Please see the output.txt file i attached. Also is there something else i >>>>>>>>>> need to change at the paths configuration? >>>>>>>>>> >>>>>>>>>> Thank you, >>>>>>>>>> >>>>>>>>>> Sotirios >>>>>>>>>> >>>>>>>>>> ???? ???, 25 ???? 2019 ???? 6:55 ?.?., ?/? Cecile Madjar < >>>>>>>>>> cecile.madjar at mcin.ca> ??????: >>>>>>>>>> >>>>>>>>>>> Hi Sotirios, >>>>>>>>>>> >>>>>>>>>>> We are making progress! >>>>>>>>>>> >>>>>>>>>>> I have a feeling this error comes from the fact that your psc >>>>>>>>>>> table does not have the MRI_alias populated for the DCC site. Running the >>>>>>>>>>> following query in the mysql database should fix this: >>>>>>>>>>> UPDATE psc SET MRI_alias="DCC", Alias="DCC" WHERE Name="Data >>>>>>>>>>> Coordinating Center"; >>>>>>>>>>> Repeat the same with all your sites (make sure to change the >>>>>>>>>>> Aliases between sites, they should all be unique). >>>>>>>>>>> >>>>>>>>>>> Let me know how it goes! >>>>>>>>>>> Best, >>>>>>>>>>> >>>>>>>>>>> C?cile >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> On Thu, Jul 25, 2019 at 11:43 AM Sotirios Nikoloutsopoulos < >>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>> >>>>>>>>>>>> Dear Cecile, >>>>>>>>>>>> You were right about your guesses. I did the modifications you >>>>>>>>>>>> suggested, i still get the "no mincs inserted" error, now i am getting the >>>>>>>>>>>> "No center found this candidate" error ( how do i fix that? from what i see >>>>>>>>>>>> the .dcm files contains a 'Institution Name', is that the center? ), so i >>>>>>>>>>>> guess that's why the validation fails, but i changed the force variable of >>>>>>>>>>>> tarchiveLoader to 1, shouldn't it have inserted the mincs then? Also it is >>>>>>>>>>>> optional to have a mail server, right? ( from what i see the mail error >>>>>>>>>>>> does not affect the $valid_study, so i assume we are okay with that ) >>>>>>>>>>>> Thank you a lot, >>>>>>>>>>>> Sotirios >>>>>>>>>>>> >>>>>>>>>>>> ???? ???, 25 ???? 2019 ???? 5:48 ?.?., ?/? Cecile Madjar < >>>>>>>>>>>> cecile.madjar at mcin.ca> ??????: >>>>>>>>>>>> >>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>> >>>>>>>>>>>>> From what I understand, I believe you just need to update a >>>>>>>>>>>>> few config settings from the frontend in the Config module (under the Admin >>>>>>>>>>>>> menu). >>>>>>>>>>>>> [image: Screen Shot 2019-07-25 at 10.31.35 AM.png] >>>>>>>>>>>>> >>>>>>>>>>>>> Then go to the Paths section of the config module and update >>>>>>>>>>>>> the "LORIS-MRI code" config setting to /data/loris/bin/mri (my guess is >>>>>>>>>>>>> that currently, it is set to /data/LORIS/data) and click on the submit >>>>>>>>>>>>> button. >>>>>>>>>>>>> [image: Screen Shot 2019-07-25 at 10.32.50 AM.png] >>>>>>>>>>>>> >>>>>>>>>>>>> Then, go to Imaging Pipeline section of the Configuration >>>>>>>>>>>>> module and update the "Loris-MRI Data Directory" to /data/loris/data/ (my >>>>>>>>>>>>> guess is that it is empty at the moment in your database which is why >>>>>>>>>>>>> $data_dir is not defined when you run the tarchiveLoader step of the >>>>>>>>>>>>> insertion pipeline). >>>>>>>>>>>>> [image: Screen Shot 2019-07-25 at 10.40.52 AM.png] >>>>>>>>>>>>> >>>>>>>>>>>>> Finally, I took a look at your environment file and it might >>>>>>>>>>>>> be a good idea to update your PERL5LIB variable to the following (it has >>>>>>>>>>>>> been added to the code a few releases ago as we realized this was needed >>>>>>>>>>>>> for the libraries. Not sure which version of LORIS-MRI you are using but it >>>>>>>>>>>>> does not hurt to update this variable to what I suggest below): >>>>>>>>>>>>> export >>>>>>>>>>>>> PERL5LIB=/data/loris/bin/mri/uploadNeuroDB:/data/loris/bin/mri/dicom-archive:$PERL5LIB >>>>>>>>>>>>> >>>>>>>>>>>>> Hope this helps. Sorry you are experiencing so much trouble >>>>>>>>>>>>> setting things up. We probably need to update our WIKI. >>>>>>>>>>>>> >>>>>>>>>>>>> Best, >>>>>>>>>>>>> >>>>>>>>>>>>> C?cile >>>>>>>>>>>>> >>>>>>>>>>>>> On Thu, Jul 25, 2019 at 9:48 AM Sotirios Nikoloutsopoulos < >>>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>> >>>>>>>>>>>>>> The "Loris-MRI Data Directory" should be in the environment >>>>>>>>>>>>>> file? >>>>>>>>>>>>>> >>>>>>>>>>>>>> ???? ???, 25 ???? 2019 ???? 12:59 ?.?., ?/? Sotirios >>>>>>>>>>>>>> Nikoloutsopoulos ??????: >>>>>>>>>>>>>> >>>>>>>>>>>>>>> The scripts are located in /data/loris/bin/mri/. Somewhere >>>>>>>>>>>>>>> I might have messed something up but i remember following the instructions >>>>>>>>>>>>>>> in the wiki.For example when i tried to execute the >>>>>>>>>>>>>>> batch_uploads_imageuploader perl script the line >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> my $command = "$bin_dir/uploadNeuroDB/imaging_upload_file.pl >>>>>>>>>>>>>>> " >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> was pointing to an invalid path, for example: it was >>>>>>>>>>>>>>> repeating a pattern and had LORIS instead of loris ( i think the mistake >>>>>>>>>>>>>>> was that in the wiki it suggested to use $PROJECT for the name of the >>>>>>>>>>>>>>> folder and i choosed 'loris' >>>>>>>>>>>>>>> https://github.com/aces/Loris/wiki/Imaging-Database ). See >>>>>>>>>>>>>>> also the in image for the modification i did. Also i didn't find the >>>>>>>>>>>>>>> section to config the $data_dir variable. >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> ???? ???, 24 ???? 2019 ???? 6:05 ?.?., ?/? Cecile Madjar < >>>>>>>>>>>>>>> cecile.madjar at mcin.ca> ??????: >>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> It looks like you have one Config setting not set (based on >>>>>>>>>>>>>>>> the first error message you got when running it the first time). You need >>>>>>>>>>>>>>>> to set a value for "Loris-MRI Data Directory" in the Config module under >>>>>>>>>>>>>>>> the Imaging pipeline section (from what I can see, it would be >>>>>>>>>>>>>>>> /data/loris/data/ for your setup). >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> The reason you got that error message the second time is >>>>>>>>>>>>>>>> that the pipeline checks if the DICOM study was already inserted in the >>>>>>>>>>>>>>>> tarchive table. Since you ran the study once already, the study is inserted >>>>>>>>>>>>>>>> into the tarchive, hence the message. However, the pipeline did not >>>>>>>>>>>>>>>> complete as the MINC files were not created and inserted into the >>>>>>>>>>>>>>>> files/parameter_file table. In order to continue the insertion, you will >>>>>>>>>>>>>>>> then need to run the tarchiveLoader command suggested in the terminal >>>>>>>>>>>>>>>> during the second run: >>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader >>>>>>>>>>>>>>>> -globLocation -profile prod >>>>>>>>>>>>>>>> /data/loris/data/tarchive//2012/DCM_2012-12-05_ImagingUpload-17-43-ZUEFjb.tar >>>>>>>>>>>>>>>> -verbose >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Finally, I am a bit confused by your setup. Where are the >>>>>>>>>>>>>>>> scripts located? In /data/loris/bin/mri or /data/loris/data? It feels like >>>>>>>>>>>>>>>> the Config setting "LORIS-MRI code" in the Paths section was set to >>>>>>>>>>>>>>>> "/data/LORIS/data" but it should have been set to the directory where the >>>>>>>>>>>>>>>> scripts are located (most probably /data/loris/bin/mri). >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Hope this helps, >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> On Wed, Jul 24, 2019 at 10:55 AM Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Ok first i execute this command: >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> "lorisadmin at hbp:/data/loris/bin/mri$ >>>>>>>>>>>>>>>>> ./batch_uploads_imageuploader -profile prod < ~/Desktop/input.txt > log.txt >>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in concatenation (.) >>>>>>>>>>>>>>>>> or string at ./batch_uploads_imageuploader line 143. >>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in concatenation (.) >>>>>>>>>>>>>>>>> or string at ./batch_uploads_imageuploader line 143. >>>>>>>>>>>>>>>>> Use of uninitialized value $_ in pattern match (m//) at >>>>>>>>>>>>>>>>> ./batch_uploads_imageuploader line 147. >>>>>>>>>>>>>>>>> base is DCC0000_258024_V01 >>>>>>>>>>>>>>>>> path is /data/incoming/ >>>>>>>>>>>>>>>>> type is .tar.gz >>>>>>>>>>>>>>>>> fullpath is /data/incoming/DCC0000_258024_V01.tar.gz >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> source /tmp/ImagingUpload-17-43-ZUEFjb >>>>>>>>>>>>>>>>> targetlocation /data/loris/data/tarchive >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in concatenation (.) >>>>>>>>>>>>>>>>> or string at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 256. >>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in concatenation (.) >>>>>>>>>>>>>>>>> or string at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 284. >>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in concatenation (.) >>>>>>>>>>>>>>>>> or string at /data/loris/bin/mri/uploadNeuroDB/ >>>>>>>>>>>>>>>>> tarchive_validation.pl line 219. >>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in concatenation (.) >>>>>>>>>>>>>>>>> or string at /data/loris/bin/mri/uploadNeuroDB/ >>>>>>>>>>>>>>>>> minc_insertion.pl line 270. >>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in concatenation (.) >>>>>>>>>>>>>>>>> or string at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 711. >>>>>>>>>>>>>>>>> Can't exec "mail": No such file or directory at >>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 721. >>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 722. >>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 723. >>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in concatenation (.) >>>>>>>>>>>>>>>>> or string at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 724. >>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 724. >>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 725. >>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in concatenation (.) >>>>>>>>>>>>>>>>> or string at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 735. >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> No Mincs inserted >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> The tarchiveLoader insertion script has failed. >>>>>>>>>>>>>>>>> Running now the following command: >>>>>>>>>>>>>>>>> /data/loris/data/uploadNeuroDB/imaging_upload_file.pl >>>>>>>>>>>>>>>>> -profile prod -upload_id 3 /data/incoming/DCC0000_258024_V01.tar.gz >>>>>>>>>>>>>>>>> -verbose" >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> I inserted the VisitLabel, but still the Mincs are not >>>>>>>>>>>>>>>>> inserted and i am getting this error >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> "lorisadmin at hbp:/data/loris/bin/mri$ >>>>>>>>>>>>>>>>> /data/loris/data/uploadNeuroDB/imaging_upload_file.pl >>>>>>>>>>>>>>>>> -profile prod -upload_id 3 /data/incoming/DCC0000_258024_V01.tar.gz -verbose >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> find -path \/tmp\/ImagingUpload\-17\-45\-5MsWEd -name >>>>>>>>>>>>>>>>> '__MACOSX' -delete >>>>>>>>>>>>>>>>> Spool message is: >>>>>>>>>>>>>>>>> The Scan for the uploadID 3 has already been run with >>>>>>>>>>>>>>>>> tarchiveID: 7. >>>>>>>>>>>>>>>>> To continue with the rest of the insertion pipeline, >>>>>>>>>>>>>>>>> please run tarchiveLoader from a terminal as follows: >>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader -globLocation -profile prod >>>>>>>>>>>>>>>>> /data/loris/data/tarchive//2012/DCM_2012-12-05_ImagingUpload-17-43-ZUEFjb.tar >>>>>>>>>>>>>>>>> -verbose" >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Which files should i delete? I thought that deleting the >>>>>>>>>>>>>>>>> files from the tarchive was enough. And i executed the last proposed >>>>>>>>>>>>>>>>> command to continue to rest of the insertion pipeline ( check the image ). >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Thank you >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> ???? ???, 24 ???? 2019 ???? 5:05 ?.?., ?/? Cecile Madjar < >>>>>>>>>>>>>>>>> cecile.madjar at mcin.ca> ??????: >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Sorry I was not clear before. Every visits of candidates >>>>>>>>>>>>>>>>>> are created in the session table with one entry per CandID/VisitLabel. So >>>>>>>>>>>>>>>>>> if the imaging pipeline created visits in the session table (that are not >>>>>>>>>>>>>>>>>> attached to instruments) and you want to clean your database completely, >>>>>>>>>>>>>>>>>> you can delete entries in that table as well. >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Regarding your point 2, the imaging pipeline can create >>>>>>>>>>>>>>>>>> the visit in the session table as long as the visit label is present in the >>>>>>>>>>>>>>>>>> Visit_Windows table (which means the visit label stored in the PatientName >>>>>>>>>>>>>>>>>> is a valid visit label). >>>>>>>>>>>>>>>>>> However, in your prod file, if the >>>>>>>>>>>>>>>>>> variable $subjectID{'createVisitLabel'} is set to 1 for candidates, the >>>>>>>>>>>>>>>>>> visit label should be created in the Visit_Windows table I believe. Here >>>>>>>>>>>>>>>>>> is the line of the prod file you would need to change >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> . >>>>>>>>>>>>>>>>>> In general, we prefer populating the Visit_Windows table >>>>>>>>>>>>>>>>>> and set the $subjectID{'createVisitLabel'} to 0 for candidate data to avoid >>>>>>>>>>>>>>>>>> insertion of badly labelled MRI data that are complex to relabel. >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Finally, regarding the candidate creation, if you execute >>>>>>>>>>>>>>>>>> the following steps, the pipeline should be able to create candidates: >>>>>>>>>>>>>>>>>> - set in the Imaging Pipeline section of the config >>>>>>>>>>>>>>>>>> module the config setting "Upload creation of candidates" to Yes >>>>>>>>>>>>>>>>>> - manually transfer the scans to the LORIS server instead >>>>>>>>>>>>>>>>>> of uploading it via the imaging browser >>>>>>>>>>>>>>>>>> - run batch_imaging_upload.pl as you did until now. >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Hope this helps! >>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> On Wed, Jul 24, 2019 at 8:47 AM Sotirios Nikoloutsopoulos >>>>>>>>>>>>>>>>>> wrote: >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> About my second question i replaced the name of the >>>>>>>>>>>>>>>>>>> patient in the .dcm files and now i am getting an error that the visit >>>>>>>>>>>>>>>>>>> label does not exist. >>>>>>>>>>>>>>>>>>> I thought it was supposed to be automatically created. >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> "Done adding archive info into database >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader >>>>>>>>>>>>>>>>>>> -globLocation -profile prod >>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive//DCM_2012-12-05_ImagingUpload-15-42-yUwQQV.tar >>>>>>>>>>>>>>>>>>> -verbose >>>>>>>>>>>>>>>>>>> md5sum >>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive/DCM_2012-12-05_ImagingUpload-15-42-yUwQQV.tar >>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>> candidate id 258024 >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> => No Visit labelVisit label does not exist >>>>>>>>>>>>>>>>>>> Set centerID = 1 >>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Number of MINC files that will be considered for >>>>>>>>>>>>>>>>>>> inserting into the database: 1 >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> log dir is /logs and log file is >>>>>>>>>>>>>>>>>>> /logs/TarLoad-15-42-L6pocU.log >>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>> candidate id 258024 >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> => No Visit label >>>>>>>>>>>>>>>>>>> Cleaning up temp files: rm -rf >>>>>>>>>>>>>>>>>>> /tmp/TarLoad-15-42-J2rQms/ImagingUpload-15-42-yUwQQV*" >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> ???? ???, 24 ???? 2019 ???? 3:38 ?.?., ?/? Sotirios >>>>>>>>>>>>>>>>>>> Nikoloutsopoulos ??????: >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> 1) What are the records in the session table? >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> 2) I tried to upload a non-phantom file like this >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> input_file.txt: >>>>>>>>>>>>>>>>>>>> /data/incoming/DCC0000_258024_V1.tar.gz N >>>>>>>>>>>>>>>>>>>> DCC0000_258024_V1 >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Terminal: >>>>>>>>>>>>>>>>>>>> ./batch_uploads_imageuploader -profile prod < >>>>>>>>>>>>>>>>>>>> ~/Desktop/input.txt > log.txt >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> and i get the following error in the log.txt file >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> "Running now the following command: >>>>>>>>>>>>>>>>>>>> /data/loris/data/uploadNeuroDB/imaging_upload_file.pl >>>>>>>>>>>>>>>>>>>> -profile prod -upload_id 7 /data/incoming/DCC0000_258024_V1.tar.gz -verbose >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> find -path \/tmp\/ImagingUpload\-14\-56\-FeLCB4 -name >>>>>>>>>>>>>>>>>>>> '__MACOSX' -delete >>>>>>>>>>>>>>>>>>>> Spool message is: >>>>>>>>>>>>>>>>>>>> The PatientName read from the DICOM header does not >>>>>>>>>>>>>>>>>>>> start with DCC0000_258024_V1 from the mri_upload table >>>>>>>>>>>>>>>>>>>> " >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> and the spool message is repeated for each .dcm file. >>>>>>>>>>>>>>>>>>>> Should i preprocess every .dcm file and change the PatientName to >>>>>>>>>>>>>>>>>>>> "DCC0000_258024_V1"? >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> 3) As far as it concerns the candidate profile i have >>>>>>>>>>>>>>>>>>>> to create a new one each time before i try to upload a file? Is there >>>>>>>>>>>>>>>>>>>> already a way to create a candidate profile and get the DCCID and PSCID >>>>>>>>>>>>>>>>>>>> without the user interface? >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> ???? ???, 18 ???? 2019 ???? 5:00 ?.?., ?/? Cecile >>>>>>>>>>>>>>>>>>>> Madjar ??????: >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> See answers to your questions below. >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> About the 1st case we had a dicom with a blank >>>>>>>>>>>>>>>>>>>>>> studyUID, maybe someone accidentally removed it. >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> That is strange. Something must have been done to the >>>>>>>>>>>>>>>>>>>>> DICOM files. I have never seen a study with no StudyUID out of the scanner. >>>>>>>>>>>>>>>>>>>>> Usually, you need to manually erase it with some tool. However, DICOMs >>>>>>>>>>>>>>>>>>>>> never cease to surprise me... >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> Some other questions: >>>>>>>>>>>>>>>>>>>>>> 1) What are the steps to remove all of my patients >>>>>>>>>>>>>>>>>>>>>> and uploads?: because i want to try to reupload all the testing dicoms we >>>>>>>>>>>>>>>>>>>>>> had with a clean database. >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> Release 21.0 of LORIS-MRI will offer a script to >>>>>>>>>>>>>>>>>>>>> remove all the entries and files specific to an upload. However, this >>>>>>>>>>>>>>>>>>>>> release is not yet out. Hopefully in the next few weeks. >>>>>>>>>>>>>>>>>>>>> In the meantime, since your case is particular and >>>>>>>>>>>>>>>>>>>>> that you just want to start with a clean database, the following deletes >>>>>>>>>>>>>>>>>>>>> should work (hopefully I won't forget any tables): >>>>>>>>>>>>>>>>>>>>> delete from mri_violations_log; >>>>>>>>>>>>>>>>>>>>> delete from mri_protocol_violated_scans; >>>>>>>>>>>>>>>>>>>>> delete from MRICandidateErrors; >>>>>>>>>>>>>>>>>>>>> delete from parameter_file; >>>>>>>>>>>>>>>>>>>>> delete from files_qcstatus; # (if you played with the >>>>>>>>>>>>>>>>>>>>> QC part of the imaging browser for testing) >>>>>>>>>>>>>>>>>>>>> delete from feedback_mri_comments; # (if you played >>>>>>>>>>>>>>>>>>>>> with the QC part of the imaging browser for testing) >>>>>>>>>>>>>>>>>>>>> delete from tarchive_series; >>>>>>>>>>>>>>>>>>>>> delete from tarchive_files; >>>>>>>>>>>>>>>>>>>>> delete from mri_upload; >>>>>>>>>>>>>>>>>>>>> delete from tarchive; >>>>>>>>>>>>>>>>>>>>> delete from mri_scanner; >>>>>>>>>>>>>>>>>>>>> delete from candidate where PSCID="scanner"; >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> I don't know if you want to also delete entries in the >>>>>>>>>>>>>>>>>>>>> session and candidate table too? >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> 2) We do not need to create the profile of a patient ( >>>>>>>>>>>>>>>>>>>>>> are the patients stored in the candidate table? because i can't see the >>>>>>>>>>>>>>>>>>>>>> ghosts ), because will it automatically be created when importing a dicom? >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> I am not sure I understand fully this question. All >>>>>>>>>>>>>>>>>>>>> candidates are stored in the candidate table. The phantom scans however are >>>>>>>>>>>>>>>>>>>>> attached to a scanner candidate depending on where the scan happened. It is >>>>>>>>>>>>>>>>>>>>> a bit of a weird concept that we have to redesign eventually but never got >>>>>>>>>>>>>>>>>>>>> a chance to get to it. >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> Hopefully this answered your question, otherwise, >>>>>>>>>>>>>>>>>>>>> don't hesitate to let me know. >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> 3) What is the difference between uploading a dicom as >>>>>>>>>>>>>>>>>>>>>> phantom instead of importing as PSCCID_DCCID_VisitLabel? >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> When you upload the scan as PSCID_DCCID_VisitLabel, >>>>>>>>>>>>>>>>>>>>> there is a check that makes sure the candidate IDs and visit label are >>>>>>>>>>>>>>>>>>>>> valid at the time of upload. >>>>>>>>>>>>>>>>>>>>> When you upload a scan as phantom, it expects that the >>>>>>>>>>>>>>>>>>>>> DICOM field PatientName and uploaded filename contains the string >>>>>>>>>>>>>>>>>>>>> "phantom". We enforced this behaviour on the imaging uploader side in >>>>>>>>>>>>>>>>>>>>> recent releases but I can't remember which one. Probably the upcoming 21.0 >>>>>>>>>>>>>>>>>>>>> release. >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> All those verifications might seem cumbersome but they >>>>>>>>>>>>>>>>>>>>> are here to ensure that the files inserted are all valid and labelled >>>>>>>>>>>>>>>>>>>>> properly as it is a bit messy to have to delete files that were wrongly >>>>>>>>>>>>>>>>>>>>> labelled. At least, the delete script present in release 21.0 will make >>>>>>>>>>>>>>>>>>>>> this process easier but it is still good practice to verify those things. >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> With pleasure. Hopefully the answers to your questions >>>>>>>>>>>>>>>>>>>>> will be helpful. >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> PS: loris-dev mailing list: you will find the initial >>>>>>>>>>>>>>>>>>>>> answer I gave Sotirios below. I forgot to cc the loris-dev in my earlier >>>>>>>>>>>>>>>>>>>>> reply... >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> ???? ???, 16 ???? 2019 ???? 12:02 ?.?., ?/? Cecile >>>>>>>>>>>>>>>>>>>>>> Madjar ??????: >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> Dear Sotirios, >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> Thank you for reaching out. Since your email was >>>>>>>>>>>>>>>>>>>>>>> already organized in points, I will reply directly below your questions >>>>>>>>>>>>>>>>>>>>>>> below. >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> 1) What do we do when the StudyUID is blank on the >>>>>>>>>>>>>>>>>>>>>>>> header? >>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/minor/docs/AppendixA-Troubleshooting_guideline.md >>>>>>>>>>>>>>>>>>>>>>>> There solution provided at the table 3 does not guide us how to find the >>>>>>>>>>>>>>>>>>>>>>>> information ( is possible ). >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> The StudyUID is the field used in our pipeline at >>>>>>>>>>>>>>>>>>>>>>> the moment to check whether a DICOM study was already inserted into LORIS >>>>>>>>>>>>>>>>>>>>>>> with that same StudyUID since it is supposed to be unique for every single >>>>>>>>>>>>>>>>>>>>>>> study. Currently, we do not support insertion of DICOM studies if they do >>>>>>>>>>>>>>>>>>>>>>> not have a StudyUID associated with them. >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> Is there a specific reason why the StudyUID is blank >>>>>>>>>>>>>>>>>>>>>>> in the DICOM headers in your DICOM files? Did they go through some >>>>>>>>>>>>>>>>>>>>>>> processes before upload to LORIS? >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> 2) When i am about to upload a non-phanton case i >>>>>>>>>>>>>>>>>>>>>>>> need a 'Visit Label'. Is there already a script that can create a new visit >>>>>>>>>>>>>>>>>>>>>>>> label for a specific Candidate, so i can provide it as input afterwards to >>>>>>>>>>>>>>>>>>>>>>>> the >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> batch_uploads_imageuploader ( See option 5.1.3 https://github.com/aces/Loris-MRI/blob/minor/docs/05-PipelineLaunchOptions.md ) >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> I am not sure if the front-end allows for it but if >>>>>>>>>>>>>>>>>>>>>>> you use batch_uploads_imageuploader, the insertion scripts could create the >>>>>>>>>>>>>>>>>>>>>>> visit label for you. However, it does need to be included in the patient >>>>>>>>>>>>>>>>>>>>>>> name in order for the script to know which label it should use. >>>>>>>>>>>>>>>>>>>>>>> For example: you upload V02 for MTL0123 (DCCID: >>>>>>>>>>>>>>>>>>>>>>> 456789) but V02 was not yet created for MTL0123; the insertion scripts >>>>>>>>>>>>>>>>>>>>>>> will create a V02 visit for MTL0123 if the PatientName field for the >>>>>>>>>>>>>>>>>>>>>>> dataset is MTL0123_456789_V02 with Stage marked as "Not Started". >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> However, *note that for the script to create the >>>>>>>>>>>>>>>>>>>>>>> visit for the candidate, you have to make sure that all the visit label of >>>>>>>>>>>>>>>>>>>>>>> your projects were inserted in the Visit_Windows table* >>>>>>>>>>>>>>>>>>>>>>> (otherwise, the visit will never be created as they were not specified as >>>>>>>>>>>>>>>>>>>>>>> being part of the list of visit label to expect). So in the example above, >>>>>>>>>>>>>>>>>>>>>>> you should have one row in Visit_Windows with Visit_label="V02" set. >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> 3) Section 4.3 >>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/minor/docs/04-Scripts.md >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> What do we do when the folder contains multiple mnc files? >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> This is a case by case. Most of the time, the MINC >>>>>>>>>>>>>>>>>>>>>>> files that failed insertion into the imaging browser end up in the MRI >>>>>>>>>>>>>>>>>>>>>>> violation module where you can see what went wrong with the acquisitions >>>>>>>>>>>>>>>>>>>>>>> not inserted. If you notice that the MINC file should be inserted as a >>>>>>>>>>>>>>>>>>>>>>> specific protocol, you can force the insertion as explained in section 4.3. >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> In your case, I have a feeling that you want to be >>>>>>>>>>>>>>>>>>>>>>> able to insert MINC files that did not go through the whole pipeline >>>>>>>>>>>>>>>>>>>>>>> insertion (DICOM archival, then dcm2mnc, then protocol identification, then >>>>>>>>>>>>>>>>>>>>>>> insertion...). In theory, you could call >>>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl on any MINC file, provided you >>>>>>>>>>>>>>>>>>>>>>> have at least the following information: >>>>>>>>>>>>>>>>>>>>>>> - path to the MINC file >>>>>>>>>>>>>>>>>>>>>>> - uploadID associated with the MINC files or DICOM >>>>>>>>>>>>>>>>>>>>>>> archive path from which those MINC files were created from >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> Then the minc_insertion.pl script will do the >>>>>>>>>>>>>>>>>>>>>>> subject information and protocol validation etc... >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> If all the MINC files come from the same uploadID or >>>>>>>>>>>>>>>>>>>>>>> TarchiveID, then you could run a loop in bash calling the >>>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl script like this for files >>>>>>>>>>>>>>>>>>>>>>> deriving from uploadID=1: >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> ls /path/to/mnc/folder/* | while read f; do >>>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl -profile prod -uploadID 1 >>>>>>>>>>>>>>>>>>>>>>> -mincPath $f; done >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> Hope this helped! >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> _______________________________________________ >>>>> Loris-dev mailing list >>>>> Loris-dev at bic.mni.mcgill.ca >>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>> >>>> >>>> >>>> -- >>>> >>>> christine.rogers at mcgill.ca >>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>> Montreal Neurological Institute >>>> McGill University | Montreal | Canada >>>> >>> >> >> -- >> >> christine.rogers at mcgill.ca >> McGill Centre for Integrative Neuroscience | MCIN.ca >> Montreal Neurological Institute >> McGill University | Montreal | Canada >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 78176 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 20518 bytes Desc: not available URL: From christine.rogers at mcgill.ca Mon Aug 5 10:22:09 2019 From: christine.rogers at mcgill.ca (Christine Rogers, Ms.) Date: Mon, 5 Aug 2019 14:22:09 +0000 Subject: [Loris-dev] Import mri - scripts In-Reply-To: References: <65ad2b70c3084ffdb1e4a9dcdad948cd@YTOPR0101MB1803.CANPRD01.PROD.OUTLOOK.COM> Message-ID: Hi Sotorios, Thanks - when you re-installed did you start on a fresh root path / VM or might some of your old system setting still apply? (And if you did any steps similar to an upgrade, did you follow the Upgrade steps in the Release Notes, from both repos?) About the TR_range column - it was recently split (MRI pr339) split into TR_min and _max columns. Given the code was trying to query TR_range which does not exist in your mri_protocol table, double-check which version of the Loris repo (tables) and the Loris-MRI repo (code) you have installed to ensure they match. Christine On Mon, Aug 5, 2019 at 9:06 AM Sotirios Nikoloutsopoulos > wrote: I reinstalled LORIS to 21 version and now the content is not visible at all at most pages. [image.png] ???? ???, 5 ??? 2019 ???? 3:19 ?.?., ?/? Sotirios Nikoloutsopoulos > ??????: Hi, Is it easy to upgrade to Loris 21? Also the following fails because the line 1985 of NeuroDB/MRIProcessingUtility.pm query mri_protocol which doesn't have TR_range https://github.com/aces/Loris/blob/21.0-release/SQL/0000-00-00-schema.sql#L556 [image.png] lorisadmin at hbp:/data/loris/bin/mri$ ./batch_uploads_imageuploader -profile prod < ~/Desktop/input.txt > log.txt Use of uninitialized value $_ in pattern match (m//) at ./batch_uploads_imageuploader line 147. base is DCC0000_258024_V1 path is /data/incoming/ type is .tar.gz fullpath is /data/incoming/DCC0000_258024_V1.tar.gz DBD::mysql::st execute failed: Unknown column 'TR_range' in 'where clause' at /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line 1985. DBD::mysql::st fetchrow_array failed: fetch() without execute() at /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line 1986. Use of uninitialized value $count_mri_protocol in numeric gt (>) at /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line 1995. DBD::mysql::st execute failed: Unknown column 'TR_range' in 'field list' at /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 562. Can't exec "mail": No such file or directory at /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 721. print() on closed filehandle MAIL at /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 722. print() on closed filehandle MAIL at /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 723. print() on closed filehandle MAIL at /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 724. print() on closed filehandle MAIL at /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 725. No Mincs inserted Thanks, Sotirios ???? ???, 3 ??? 2019 ???? 1:08 ?.?., ?/? Christine Rogers, Ms. > ??????: Hi Sotirios, First, just a note: we've released LORIS 21 this week with some major new features and cleanup -- especially if you are early in your setup phase, check out the Release notes for both the LORIS and Loris-MRI repos. Thanks for your screenshots -- your empty mri_protocol table should be at the root of these issues : The mri_protocol table must be populated in order for your scans to be registered in LORIS -- it serves as a whitelist for the insertion pipeline which filters out scans that aren't identified or matched to scan types in this table. By default, this table is populated with entries for t1, t2, fMRI and DTI (Insert statements for 21 release branch are here) Feel free to restore our default records and broaden their parameters to match all your scan types. re Defaced, native, selected -- these filter the scans displayed as you move to the next page (View Session), instead of viewing "all types" of scans from a given session : * "defaced" means that a defacing script has masked the subject's face in the volume (for patient privacy) * "native" means that no pre-processing has been performed on the scan (it's raw data), * "selected" will show only volumes that have been QC'd and "selected" as the best of their type -- used to display only the best quality T1 image instead of all T1s acquired in a session, e.g. re QC Comments -- Once you have successfully loaded scans (matched to the mri_protocol table), you'll be able to use the Imaging Browser's View Session subpage to enter/view QC comments on each volume, or for each visit. These are stored directly in the database, and linked to each scan. (Table name: feedback_mri_comments) (Visit-level QC comments are linked to the session.) For a walkthrough of the Imaging setup - please see the Imaging Setup guide - An old LORIS walkthrough video can also walk you through some of the Imaging front-end features, starting at 8:00 LORIS' imaging modules have been updated many times since this video, but the functionality and workflow is similar. Let us know how it goes once you have entries in your mri_protocol table - Best, Christine On Fri, Aug 2, 2019 at 7:58 AM Sotirios Nikoloutsopoulos > wrote: Hi Christine, In the candidate_list page i can see this patient [image.png] If i press the link under PSCID i get to see [image.png] and if i press the link under Scan Done it redirects me to imaging_browser [image.png] At the mri_violations page i also see No results ( neither on resolved / not resolved ). At the imaging_uploader i can see the record that failed. [image.png] If i click on the tarchive info i get to see the Protocol Name which i think is the acquisition we wanted? [image.png] Also my mri_protocol table is empty. Furthermore i would like to ask about the defaced, native, selected. What exactly is native and selected? And where are the qc comments stored? [image.png] Finally a walkthrough would be helpful. Thanks, Sotirios ???? ???, 30 ???? 2019 ???? 8:29 ?.?., ?/? Christine Rogers, Ms. > ??????: Hi Sotirios, Glad to hear you're making progress with the visit labels. To follow up on your last few emails: a- The Wiki's Setup Guide contains Sample insert statements for the Visit Windows table. As Cecile mentioned, the consistency of visit label format is important: V01, v01, V1, 01 -- whichever you select to use is fine; we use V01 by default across all documentation. b- For Password reset, there is a script in the tools/ directory so that a back-end administrator can reset any front-end user password, including Admin. (See info on setting up / resetting User passwords in the Wiki's Setup Guide) c- The minc file not being registered -- due to AcquisitionProtocol unknown. This means the SeriesDescription (Acquisition Protocol) in you Dicom header was not matched to any scan listed in the mri_protocol database table. (In the online Loris-MRI Troubleshooting Guide, this is Table 3, 2nd-last item "no MINCs inserted"). The MRI Violations module (Readme here) will show you the details of this mismatch -- Go to the module (under the Imaging menu), find your scan and click the link "Could not identify scan type" -- in the next subpage you can compare the scan's actual parameters against the mri_protocol table. To resolve this, adjust your mri_protocol table values or perhaps ensure your DICOMs are labelled consistently. Let us know if this works for you -- we can also walk you through an example of non-identified scans on Demo.loris.ca (MRI Violations module). Best, Christine The LORIS team On Tue, Jul 30, 2019 at 10:47 AM Sotirios Nikoloutsopoulos > wrote: I hope this is sufficient as the error for the visit label disappeared. [image.png] Please see the attached file. Also something i found. lorisadmin at hbp:/data/loris/bin/mri$ cat /data/loris/data//logs/TarLoad-17-39-xubBdv.log ==> Loading file from disk /tmp/TarLoad-17-39-UyQcG2/dcc0000_258024_v1_20121205_102108_501e1_mri.mnc --> mapping DICOM parameter for /tmp/TarLoad-17-39-UyQcG2/dcc0000_258024_v1_20121205_102108_501e1_mri.mnc ==> computing md5 hash for MINC body. --> md5: 6b1202fd63e29de4c9be1cd9925888a5 ==> verifying acquisition protocol Acquisition protocol is unknown --> The minc file cannot be registered since the AcquisitionProtocol is unknown ???? ???, 30 ???? 2019 ???? 4:58 ?.?., ?/? Sotirios Nikoloutsopoulos > ??????: Ok I fixed the login problem by using a known hash and by deleting the rows from the login_history i was able to login. ???? ???, 30 ???? 2019 ???? 4:50 ?.?., ?/? Sotirios Nikoloutsopoulos > ??????: Hi, there was no visit label 01 in the Visit_Windows table and i don't know how to insert it because the record requires lots of attributes. Also the system for a reason asked me to update my password and now i don't remember it and my account got suspended. Is there a way to reset it or set a simple password? I updated the password hash in the users table by using the hash from another LORIS setup we had and i still couldn't login ( also the attribute password is always NULL and the expiration date is 1999-01-01 for some reason ). Thanks ???? ???, 29 ???? 2019 ???? 5:21 ?.?., ?/? Cecile Madjar > ??????: Hi Sotirios, Can you try adding the visit label v01 to the Visit_Windows table? However, I noticed that in a previous dataset, the label was V1. Does that refer to the same visit? If so, you might want to harmonize the visit labels so they are all the same across datasets for a given timepoint, meaning you will need to relabel scans when the visit label is different but referring to the same visit label (v01 = V1 etc...). Hope this helps, C?cile On Mon, Jul 29, 2019 at 10:15 AM Sotirios Nikoloutsopoulos > wrote: Hi, Could you help me with the "Visit label does not exist"? I had changed $subjectID{'createVisitLabel'} to 1 as you had suggested but it appears that this problem hasn't been resolved yet. lorisadmin at hbp:/data/loris/bin/mri$ cat /data/loris/data//logs/TarLoad-14-58-9Xog7H.log ==> Loading file from disk /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc --> mapping DICOM parameter for /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc --> using user-defined filterParameters for /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc Candidate Mismatch Error is Visit label does not exist -> WARNING: This candidate was invalid. Logging to MRICandidateErrors table with reason Visit label does not exist Thank you, Sotirios ???? ???, 26 ???? 2019 ???? 3:02 ?.?., ?/? Sotirios Nikoloutsopoulos > ??????: Hi Cecile, The Center error was fixed. Still the insertion of mincs fails. Please see the output.txt file i attached. Also is there something else i need to change at the paths configuration? Thank you, Sotirios ???? ???, 25 ???? 2019 ???? 6:55 ?.?., ?/? Cecile Madjar > ??????: Hi Sotirios, We are making progress! I have a feeling this error comes from the fact that your psc table does not have the MRI_alias populated for the DCC site. Running the following query in the mysql database should fix this: UPDATE psc SET MRI_alias="DCC", Alias="DCC" WHERE Name="Data Coordinating Center"; Repeat the same with all your sites (make sure to change the Aliases between sites, they should all be unique). Let me know how it goes! Best, C?cile On Thu, Jul 25, 2019 at 11:43 AM Sotirios Nikoloutsopoulos > wrote: Dear Cecile, You were right about your guesses. I did the modifications you suggested, i still get the "no mincs inserted" error, now i am getting the "No center found this candidate" error ( how do i fix that? from what i see the .dcm files contains a 'Institution Name', is that the center? ), so i guess that's why the validation fails, but i changed the force variable of tarchiveLoader to 1, shouldn't it have inserted the mincs then? Also it is optional to have a mail server, right? ( from what i see the mail error does not affect the $valid_study, so i assume we are okay with that ) Thank you a lot, Sotirios ???? ???, 25 ???? 2019 ???? 5:48 ?.?., ?/? Cecile Madjar > ??????: Hi Sotirios, From what I understand, I believe you just need to update a few config settings from the frontend in the Config module (under the Admin menu). [Screen Shot 2019-07-25 at 10.31.35 AM.png] Then go to the Paths section of the config module and update the "LORIS-MRI code" config setting to /data/loris/bin/mri (my guess is that currently, it is set to /data/LORIS/data) and click on the submit button. [Screen Shot 2019-07-25 at 10.32.50 AM.png] Then, go to Imaging Pipeline section of the Configuration module and update the "Loris-MRI Data Directory" to /data/loris/data/ (my guess is that it is empty at the moment in your database which is why $data_dir is not defined when you run the tarchiveLoader step of the insertion pipeline). [Screen Shot 2019-07-25 at 10.40.52 AM.png] Finally, I took a look at your environment file and it might be a good idea to update your PERL5LIB variable to the following (it has been added to the code a few releases ago as we realized this was needed for the libraries. Not sure which version of LORIS-MRI you are using but it does not hurt to update this variable to what I suggest below): export PERL5LIB=/data/loris/bin/mri/uploadNeuroDB:/data/loris/bin/mri/dicom-archive:$PERL5LIB Hope this helps. Sorry you are experiencing so much trouble setting things up. We probably need to update our WIKI. Best, C?cile On Thu, Jul 25, 2019 at 9:48 AM Sotirios Nikoloutsopoulos > wrote: The "Loris-MRI Data Directory" should be in the environment file? ???? ???, 25 ???? 2019 ???? 12:59 ?.?., ?/? Sotirios Nikoloutsopoulos > ??????: The scripts are located in /data/loris/bin/mri/. Somewhere I might have messed something up but i remember following the instructions in the wiki.For example when i tried to execute the batch_uploads_imageuploader perl script the line my $command = "$bin_dir/uploadNeuroDB/imaging_upload_file.pl " was pointing to an invalid path, for example: it was repeating a pattern and had LORIS instead of loris ( i think the mistake was that in the wiki it suggested to use $PROJECT for the name of the folder and i choosed 'loris' https://github.com/aces/Loris/wiki/Imaging-Database ). See also the in image for the modification i did. Also i didn't find the section to config the $data_dir variable. Thank you, Sotirios ???? ???, 24 ???? 2019 ???? 6:05 ?.?., ?/? Cecile Madjar > ??????: Hi Sotirios, It looks like you have one Config setting not set (based on the first error message you got when running it the first time). You need to set a value for "Loris-MRI Data Directory" in the Config module under the Imaging pipeline section (from what I can see, it would be /data/loris/data/ for your setup). The reason you got that error message the second time is that the pipeline checks if the DICOM study was already inserted in the tarchive table. Since you ran the study once already, the study is inserted into the tarchive, hence the message. However, the pipeline did not complete as the MINC files were not created and inserted into the files/parameter_file table. In order to continue the insertion, you will then need to run the tarchiveLoader command suggested in the terminal during the second run: /data/LORIS/data//uploadNeuroDB/tarchiveLoader -globLocation -profile prod /data/loris/data/tarchive//2012/DCM_2012-12-05_ImagingUpload-17-43-ZUEFjb.tar -verbose Finally, I am a bit confused by your setup. Where are the scripts located? In /data/loris/bin/mri or /data/loris/data? It feels like the Config setting "LORIS-MRI code" in the Paths section was set to "/data/LORIS/data" but it should have been set to the directory where the scripts are located (most probably /data/loris/bin/mri). Hope this helps, C?cile On Wed, Jul 24, 2019 at 10:55 AM Sotirios Nikoloutsopoulos > wrote: Ok first i execute this command: "lorisadmin at hbp:/data/loris/bin/mri$ ./batch_uploads_imageuploader -profile prod < ~/Desktop/input.txt > log.txt Use of uninitialized value $data_dir in concatenation (.) or string at ./batch_uploads_imageuploader line 143. Use of uninitialized value $data_dir in concatenation (.) or string at ./batch_uploads_imageuploader line 143. Use of uninitialized value $_ in pattern match (m//) at ./batch_uploads_imageuploader line 147. base is DCC0000_258024_V01 path is /data/incoming/ type is .tar.gz fullpath is /data/incoming/DCC0000_258024_V01.tar.gz source /tmp/ImagingUpload-17-43-ZUEFjb targetlocation /data/loris/data/tarchive Use of uninitialized value $data_dir in concatenation (.) or string at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 256. Use of uninitialized value $data_dir in concatenation (.) or string at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 284. Use of uninitialized value $data_dir in concatenation (.) or string at /data/loris/bin/mri/uploadNeuroDB/tarchive_validation.pl line 219. Use of uninitialized value $data_dir in concatenation (.) or string at /data/loris/bin/mri/uploadNeuroDB/minc_insertion.pl line 270. Use of uninitialized value $data_dir in concatenation (.) or string at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 711. Can't exec "mail": No such file or directory at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 721. print() on closed filehandle MAIL at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 722. print() on closed filehandle MAIL at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 723. Use of uninitialized value $data_dir in concatenation (.) or string at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 724. print() on closed filehandle MAIL at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 724. print() on closed filehandle MAIL at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 725. Use of uninitialized value $data_dir in concatenation (.) or string at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 735. No Mincs inserted The tarchiveLoader insertion script has failed. Running now the following command: /data/loris/data/uploadNeuroDB/imaging_upload_file.pl -profile prod -upload_id 3 /data/incoming/DCC0000_258024_V01.tar.gz -verbose" I inserted the VisitLabel, but still the Mincs are not inserted and i am getting this error "lorisadmin at hbp:/data/loris/bin/mri$ /data/loris/data/uploadNeuroDB/imaging_upload_file.pl -profile prod -upload_id 3 /data/incoming/DCC0000_258024_V01.tar.gz -verbose find -path \/tmp\/ImagingUpload\-17\-45\-5MsWEd -name '__MACOSX' -delete Spool message is: The Scan for the uploadID 3 has already been run with tarchiveID: 7. To continue with the rest of the insertion pipeline, please run tarchiveLoader from a terminal as follows: /data/LORIS/data//uploadNeuroDB/tarchiveLoader -globLocation -profile prod /data/loris/data/tarchive//2012/DCM_2012-12-05_ImagingUpload-17-43-ZUEFjb.tar -verbose" Which files should i delete? I thought that deleting the files from the tarchive was enough. And i executed the last proposed command to continue to rest of the insertion pipeline ( check the image ). Thank you ???? ???, 24 ???? 2019 ???? 5:05 ?.?., ?/? Cecile Madjar > ??????: Hi Sotirios, Sorry I was not clear before. Every visits of candidates are created in the session table with one entry per CandID/VisitLabel. So if the imaging pipeline created visits in the session table (that are not attached to instruments) and you want to clean your database completely, you can delete entries in that table as well. Regarding your point 2, the imaging pipeline can create the visit in the session table as long as the visit label is present in the Visit_Windows table (which means the visit label stored in the PatientName is a valid visit label). However, in your prod file, if the variable $subjectID{'createVisitLabel'} is set to 1 for candidates, the visit label should be created in the Visit_Windows table I believe. Here is the line of the prod file you would need to change. In general, we prefer populating the Visit_Windows table and set the $subjectID{'createVisitLabel'} to 0 for candidate data to avoid insertion of badly labelled MRI data that are complex to relabel. Finally, regarding the candidate creation, if you execute the following steps, the pipeline should be able to create candidates: - set in the Imaging Pipeline section of the config module the config setting "Upload creation of candidates" to Yes - manually transfer the scans to the LORIS server instead of uploading it via the imaging browser - run batch_imaging_upload.pl as you did until now. Hope this helps! Best, C?cile On Wed, Jul 24, 2019 at 8:47 AM Sotirios Nikoloutsopoulos > wrote: About my second question i replaced the name of the patient in the .dcm files and now i am getting an error that the visit label does not exist. I thought it was supposed to be automatically created. "Done adding archive info into database /data/LORIS/data//uploadNeuroDB/tarchiveLoader -globLocation -profile prod /data/loris/data/tarchive//DCM_2012-12-05_ImagingUpload-15-42-yUwQQV.tar -verbose md5sum /data/loris/data/tarchive/DCM_2012-12-05_ImagingUpload-15-42-yUwQQV.tar PSCID is: DCC0000 CandID id: 258024 visit_label is: V1 PSCID is: DCC0000 CandID id: 258024 visit_label is: V1 candidate id 258024 => No Visit labelVisit label does not exist Set centerID = 1 PSCID is: DCC0000 CandID id: 258024 visit_label is: V1 PSCID is: DCC0000 CandID id: 258024 visit_label is: V1 Number of MINC files that will be considered for inserting into the database: 1 log dir is /logs and log file is /logs/TarLoad-15-42-L6pocU.log PSCID is: DCC0000 CandID id: 258024 visit_label is: V1 PSCID is: DCC0000 CandID id: 258024 visit_label is: V1 candidate id 258024 => No Visit label Cleaning up temp files: rm -rf /tmp/TarLoad-15-42-J2rQms/ImagingUpload-15-42-yUwQQV*" ???? ???, 24 ???? 2019 ???? 3:38 ?.?., ?/? Sotirios Nikoloutsopoulos > ??????: Hi, 1) What are the records in the session table? 2) I tried to upload a non-phantom file like this input_file.txt: /data/incoming/DCC0000_258024_V1.tar.gz N DCC0000_258024_V1 Terminal: ./batch_uploads_imageuploader -profile prod < ~/Desktop/input.txt > log.txt and i get the following error in the log.txt file "Running now the following command: /data/loris/data/uploadNeuroDB/imaging_upload_file.pl -profile prod -upload_id 7 /data/incoming/DCC0000_258024_V1.tar.gz -verbose find -path \/tmp\/ImagingUpload\-14\-56\-FeLCB4 -name '__MACOSX' -delete Spool message is: The PatientName read from the DICOM header does not start with DCC0000_258024_V1 from the mri_upload table " and the spool message is repeated for each .dcm file. Should i preprocess every .dcm file and change the PatientName to "DCC0000_258024_V1"? 3) As far as it concerns the candidate profile i have to create a new one each time before i try to upload a file? Is there already a way to create a candidate profile and get the DCCID and PSCID without the user interface? Thank you, Sotirios ???? ???, 18 ???? 2019 ???? 5:00 ?.?., ?/? Cecile Madjar > ??????: Hi Sotirios, See answers to your questions below. About the 1st case we had a dicom with a blank studyUID, maybe someone accidentally removed it. That is strange. Something must have been done to the DICOM files. I have never seen a study with no StudyUID out of the scanner. Usually, you need to manually erase it with some tool. However, DICOMs never cease to surprise me... Some other questions: 1) What are the steps to remove all of my patients and uploads?: because i want to try to reupload all the testing dicoms we had with a clean database. Release 21.0 of LORIS-MRI will offer a script to remove all the entries and files specific to an upload. However, this release is not yet out. Hopefully in the next few weeks. In the meantime, since your case is particular and that you just want to start with a clean database, the following deletes should work (hopefully I won't forget any tables): delete from mri_violations_log; delete from mri_protocol_violated_scans; delete from MRICandidateErrors; delete from parameter_file; delete from files_qcstatus; # (if you played with the QC part of the imaging browser for testing) delete from feedback_mri_comments; # (if you played with the QC part of the imaging browser for testing) delete from tarchive_series; delete from tarchive_files; delete from mri_upload; delete from tarchive; delete from mri_scanner; delete from candidate where PSCID="scanner"; I don't know if you want to also delete entries in the session and candidate table too? 2) We do not need to create the profile of a patient ( are the patients stored in the candidate table? because i can't see the ghosts ), because will it automatically be created when importing a dicom? I am not sure I understand fully this question. All candidates are stored in the candidate table. The phantom scans however are attached to a scanner candidate depending on where the scan happened. It is a bit of a weird concept that we have to redesign eventually but never got a chance to get to it. Hopefully this answered your question, otherwise, don't hesitate to let me know. 3) What is the difference between uploading a dicom as phantom instead of importing as PSCCID_DCCID_VisitLabel? When you upload the scan as PSCID_DCCID_VisitLabel, there is a check that makes sure the candidate IDs and visit label are valid at the time of upload. When you upload a scan as phantom, it expects that the DICOM field PatientName and uploaded filename contains the string "phantom". We enforced this behaviour on the imaging uploader side in recent releases but I can't remember which one. Probably the upcoming 21.0 release. All those verifications might seem cumbersome but they are here to ensure that the files inserted are all valid and labelled properly as it is a bit messy to have to delete files that were wrongly labelled. At least, the delete script present in release 21.0 will make this process easier but it is still good practice to verify those things. Thank you, With pleasure. Hopefully the answers to your questions will be helpful. Best, C?cile PS: loris-dev mailing list: you will find the initial answer I gave Sotirios below. I forgot to cc the loris-dev in my earlier reply... ???? ???, 16 ???? 2019 ???? 12:02 ?.?., ?/? Cecile Madjar > ??????: Dear Sotirios, Thank you for reaching out. Since your email was already organized in points, I will reply directly below your questions below. Best, C?cile 1) What do we do when the StudyUID is blank on the header? https://github.com/aces/Loris-MRI/blob/minor/docs/AppendixA-Troubleshooting_guideline.md There solution provided at the table 3 does not guide us how to find the information ( is possible ). The StudyUID is the field used in our pipeline at the moment to check whether a DICOM study was already inserted into LORIS with that same StudyUID since it is supposed to be unique for every single study. Currently, we do not support insertion of DICOM studies if they do not have a StudyUID associated with them. Is there a specific reason why the StudyUID is blank in the DICOM headers in your DICOM files? Did they go through some processes before upload to LORIS? 2) When i am about to upload a non-phanton case i need a 'Visit Label'. Is there already a script that can create a new visit label for a specific Candidate, so i can provide it as input afterwards to the batch_uploads_imageuploader ( See option 5.1.3 https://github.com/aces/Loris-MRI/blob/minor/docs/05-PipelineLaunchOptions.md ) I am not sure if the front-end allows for it but if you use batch_uploads_imageuploader, the insertion scripts could create the visit label for you. However, it does need to be included in the patient name in order for the script to know which label it should use. For example: you upload V02 for MTL0123 (DCCID: 456789) but V02 was not yet created for MTL0123; the insertion scripts will create a V02 visit for MTL0123 if the PatientName field for the dataset is MTL0123_456789_V02 with Stage marked as "Not Started". However, note that for the script to create the visit for the candidate, you have to make sure that all the visit label of your projects were inserted in the Visit_Windows table (otherwise, the visit will never be created as they were not specified as being part of the list of visit label to expect). So in the example above, you should have one row in Visit_Windows with Visit_label="V02" set. 3) Section 4.3 https://github.com/aces/Loris-MRI/blob/minor/docs/04-Scripts.md What do we do when the folder contains multiple mnc files? This is a case by case. Most of the time, the MINC files that failed insertion into the imaging browser end up in the MRI violation module where you can see what went wrong with the acquisitions not inserted. If you notice that the MINC file should be inserted as a specific protocol, you can force the insertion as explained in section 4.3. In your case, I have a feeling that you want to be able to insert MINC files that did not go through the whole pipeline insertion (DICOM archival, then dcm2mnc, then protocol identification, then insertion...). In theory, you could call minc_insertion.pl on any MINC file, provided you have at least the following information: - path to the MINC file - uploadID associated with the MINC files or DICOM archive path from which those MINC files were created from Then the minc_insertion.pl script will do the subject information and protocol validation etc... If all the MINC files come from the same uploadID or TarchiveID, then you could run a loop in bash calling the minc_insertion.pl script like this for files deriving from uploadID=1: ls /path/to/mnc/folder/* | while read f; do minc_insertion.pl -profile prod -uploadID 1 -mincPath $f; done Thank you, Hope this helped! _______________________________________________ Loris-dev mailing list Loris-dev at bic.mni.mcgill.ca https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev -- christine.rogers at mcgill.ca McGill Centre for Integrative Neuroscience | MCIN.ca Montreal Neurological Institute McGill University | Montreal | Canada -- christine.rogers at mcgill.ca McGill Centre for Integrative Neuroscience | MCIN.ca Montreal Neurological Institute McGill University | Montreal | Canada _______________________________________________ Loris-dev mailing list Loris-dev at bic.mni.mcgill.ca https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev -- christine.rogers at mcgill.ca McGill Centre for Integrative Neuroscience | MCIN.ca Montreal Neurological Institute McGill University | Montreal | Canada -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 78176 bytes Desc: image.png URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 20518 bytes Desc: image.png URL: From sotirisnik at gmail.com Tue Aug 6 07:53:08 2019 From: sotirisnik at gmail.com (Sotirios Nikoloutsopoulos) Date: Tue, 6 Aug 2019 14:53:08 +0300 Subject: [Loris-dev] Import mri - scripts In-Reply-To: References: <65ad2b70c3084ffdb1e4a9dcdad948cd@YTOPR0101MB1803.CANPRD01.PROD.OUTLOOK.COM> Message-ID: I am using a VM. What i did was: 1) Download the files from https://github.com/aces/Loris and replace them to my existing /vaw/www/loris folder. 2) Execute the composer install --no-dev and then composer dump-autoload as mentioned here https://github.com/aces/Loris/wiki/Updating-your-LORIS. 3) Execute install.sh from /var/www/loris/tools and because LORIS already existed i moved a .config file, then re-executed the install.sh successfully 4 ) As for the database, i dropped the schema and i executed the installdb.php ???? ???, 5 ??? 2019 ???? 5:22 ?.?., ?/? Christine Rogers, Ms. < christine.rogers at mcgill.ca> ??????: > Hi Sotorios, > > Thanks - when you re-installed did you start on a fresh root path / VM or > might some of your old system setting still apply? > (And if you did any steps similar to an upgrade, did you follow the > Upgrade steps in the Release Notes, from both repos?) > > About the TR_range column - it was recently split (MRI pr339 > ) split into TR_min and _max > columns. Given the code was trying to query TR_range which does not exist > in your mri_protocol table, double-check which version of the Loris repo > (tables) and the Loris-MRI repo (code) you have installed to ensure they > match. > > Christine > > > On Mon, Aug 5, 2019 at 9:06 AM Sotirios Nikoloutsopoulos < > sotirisnik at gmail.com> wrote: > >> I reinstalled LORIS to 21 version and now the content is not visible at >> all at most pages. >> >> [image: image.png] >> >> ???? ???, 5 ??? 2019 ???? 3:19 ?.?., ?/? Sotirios Nikoloutsopoulos < >> sotirisnik at gmail.com> ??????: >> >>> Hi, >>> >>> Is it easy to upgrade to Loris 21? Also the following fails because the >>> line 1985 of NeuroDB/MRIProcessingUtility.pm query mri_protocol which >>> doesn't have TR_range >>> https://github.com/aces/Loris/blob/21.0-release/SQL/0000-00-00-schema.sql#L556 >>> >>> [image: image.png] >>> >>> lorisadmin at hbp:/data/loris/bin/mri$ ./batch_uploads_imageuploader >>> -profile prod < ~/Desktop/input.txt > log.txt >>> Use of uninitialized value $_ in pattern match (m//) at >>> ./batch_uploads_imageuploader line 147. >>> base is DCC0000_258024_V1 >>> path is /data/incoming/ >>> type is .tar.gz >>> fullpath is /data/incoming/DCC0000_258024_V1.tar.gz >>> DBD::mysql::st execute failed: Unknown column 'TR_range' in 'where >>> clause' at >>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line 1985. >>> DBD::mysql::st fetchrow_array failed: fetch() without execute() at >>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line 1986. >>> Use of uninitialized value $count_mri_protocol in numeric gt (>) at >>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line 1995. >>> DBD::mysql::st execute failed: Unknown column 'TR_range' in 'field list' >>> at /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 562. >>> Can't exec "mail": No such file or directory at >>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 721. >>> print() on closed filehandle MAIL at >>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 722. >>> print() on closed filehandle MAIL at >>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 723. >>> print() on closed filehandle MAIL at >>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 724. >>> print() on closed filehandle MAIL at >>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 725. >>> >>> No Mincs inserted >>> >>> Thanks, >>> >>> Sotirios >>> >>> ???? ???, 3 ??? 2019 ???? 1:08 ?.?., ?/? Christine Rogers, Ms. < >>> christine.rogers at mcgill.ca> ??????: >>> >>>> Hi Sotirios, >>>> >>>> First, just a note: we've released LORIS 21 this week with some major >>>> new features and cleanup -- especially if you are early in your setup >>>> phase, check out the Release notes for both the LORIS >>>> and Loris-MRI >>>> repos. >>>> >>>> Thanks for your screenshots -- your empty mri_protocol table should be >>>> at the root of these issues : >>>> >>>> The mri_protocol table must be populated >>>> >>>> in order for your scans to be registered in LORIS -- it serves as a >>>> whitelist for the insertion pipeline which filters out scans that aren't >>>> identified or matched to scan types in this table. >>>> >>>> By default, this table is populated with entries for t1, t2, fMRI and >>>> DTI (Insert statements for 21 release branch are here >>>> >>>> ) >>>> Feel free to restore our default records and broaden their parameters >>>> to match all your scan types. >>>> >>>> re Defaced, native, selected -- these filter the scans displayed as you >>>> move to the next page (View Session), instead of viewing "all types" of >>>> scans from a given session : >>>> >>>> - "defaced" means that a defacing script >>>> >>>> has masked the subject's face in the volume (for patient privacy) >>>> - "native" means that no pre-processing has been performed on the >>>> scan (it's raw data), >>>> - "selected" will show only volumes that have been QC'd and >>>> "selected" as the best of their type -- used to display only the best >>>> quality T1 image instead of all T1s acquired in a session, e.g. >>>> >>>> re QC Comments -- >>>> Once you have successfully loaded scans (matched to the mri_protocol >>>> table), you'll be able to use the Imaging Browser's View Session subpage to >>>> enter/view QC comments on each volume, or for each visit. >>>> These are stored directly in the database, and linked to each scan. >>>> (Table name: feedback_mri_comments) >>>> (Visit-level QC comments are linked to the session.) >>>> >>>> For a walkthrough of the Imaging setup - please see the Imaging Setup >>>> guide >>>> >>>> - >>>> >>>> An old LORIS walkthrough video >>>> can also walk you >>>> through some of the Imaging front-end features, starting at 8:00 >>>> LORIS' imaging modules have been updated many times since this video, >>>> but the functionality and workflow is similar. >>>> >>>> Let us know how it goes once you have entries in your mri_protocol >>>> table - >>>> Best, >>>> Christine >>>> >>>> >>>> >>>> >>>> On Fri, Aug 2, 2019 at 7:58 AM Sotirios Nikoloutsopoulos < >>>> sotirisnik at gmail.com> wrote: >>>> >>>>> Hi Christine, >>>>> >>>>> In the candidate_list page i can see this patient >>>>> >>>>> [image: image.png] >>>>> >>>>> If i press the link under PSCID i get to see >>>>> [image: image.png] >>>>> >>>>> and if i press the link under Scan Done it redirects me to >>>>> imaging_browser >>>>> >>>>> [image: image.png] >>>>> >>>>> At the mri_violations page i also see No results ( neither on resolved >>>>> / not resolved ). >>>>> >>>>> At the imaging_uploader i can see the record that failed. >>>>> >>>>> [image: image.png] >>>>> >>>>> If i click on the tarchive info i get to see the Protocol Name which i >>>>> think is the acquisition we wanted? >>>>> [image: image.png] >>>>> >>>>> Also my mri_protocol table is empty. >>>>> >>>>> Furthermore i would like to ask about the defaced, native, selected. >>>>> What exactly is native and selected? And where are the qc comments stored? >>>>> >>>>> [image: image.png] >>>>> >>>>> Finally a walkthrough would be helpful. >>>>> >>>>> Thanks, >>>>> >>>>> Sotirios >>>>> >>>>> ???? ???, 30 ???? 2019 ???? 8:29 ?.?., ?/? Christine Rogers, Ms. < >>>>> christine.rogers at mcgill.ca> ??????: >>>>> >>>>>> Hi Sotirios, >>>>>> Glad to hear you're making progress with the visit labels. To follow >>>>>> up on your last few emails: >>>>>> >>>>>> a- The Wiki's Setup Guide contains Sample insert statements for the >>>>>> Visit Windows table >>>>>> >>>>>> . >>>>>> >>>>>> As Cecile mentioned, the consistency of visit label format is >>>>>> important: V01, v01, V1, 01 -- whichever you select to use is fine; we use >>>>>> V01 by default across all documentation. >>>>>> >>>>>> b- For Password reset, there is a script in the tools/ directory so >>>>>> that a back-end administrator can reset any front-end user password, >>>>>> including Admin. (See info on setting up / resetting User passwords in the Wiki's >>>>>> Setup Guide >>>>>> >>>>>> ) >>>>>> >>>>>> c- The minc file not being registered -- due to AcquisitionProtocol >>>>>> unknown. >>>>>> This means the SeriesDescription (Acquisition Protocol) in you Dicom >>>>>> header was not matched to any scan listed in the mri_protocol database >>>>>> table. >>>>>> (In the online Loris-MRI Troubleshooting Guide, >>>>>> this >>>>>> is Table 3, 2nd-last item "no MINCs inserted"). >>>>>> >>>>>> The MRI Violations module (Readme here) >>>>>> will show >>>>>> you the details of this mismatch -- >>>>>> Go to the module (under the Imaging menu), find your scan and click >>>>>> the link "Could not identify scan type" -- in the next subpage you can >>>>>> compare the scan's actual parameters against the mri_protocol table. >>>>>> >>>>>> To resolve this, adjust your mri_protocol table values or perhaps >>>>>> ensure your DICOMs are labelled consistently. >>>>>> >>>>>> Let us know if this works for you -- we can also walk you through an >>>>>> example of non-identified scans on Demo.loris.ca (MRI Violations >>>>>> module). >>>>>> >>>>>> Best, >>>>>> Christine >>>>>> >>>>>> The LORIS team >>>>>> >>>>>> >>>>>> On Tue, Jul 30, 2019 at 10:47 AM Sotirios Nikoloutsopoulos < >>>>>> sotirisnik at gmail.com> wrote: >>>>>> >>>>>>> I hope this is sufficient as the error for the visit label >>>>>>> disappeared. >>>>>>> [image: image.png] >>>>>>> >>>>>>> Please see the attached file. Also something i found. >>>>>>> >>>>>>> lorisadmin at hbp:/data/loris/bin/mri$ cat >>>>>>> /data/loris/data//logs/TarLoad-17-39-xubBdv.log >>>>>>> >>>>>>> ==> Loading file from disk >>>>>>> /tmp/TarLoad-17-39-UyQcG2/dcc0000_258024_v1_20121205_102108_501e1_mri.mnc >>>>>>> >>>>>>> --> mapping DICOM parameter for >>>>>>> /tmp/TarLoad-17-39-UyQcG2/dcc0000_258024_v1_20121205_102108_501e1_mri.mnc >>>>>>> >>>>>>> ==> computing md5 hash for MINC body. >>>>>>> >>>>>>> --> md5: 6b1202fd63e29de4c9be1cd9925888a5 >>>>>>> >>>>>>> ==> verifying acquisition protocol >>>>>>> >>>>>>> Acquisition protocol is unknown >>>>>>> >>>>>>> --> The minc file cannot be registered since the >>>>>>> AcquisitionProtocol is unknown >>>>>>> >>>>>>> ???? ???, 30 ???? 2019 ???? 4:58 ?.?., ?/? Sotirios Nikoloutsopoulos >>>>>>> ??????: >>>>>>> >>>>>>>> Ok I fixed the login problem by using a known hash and by deleting >>>>>>>> the rows from the login_history i was able to login. >>>>>>>> >>>>>>>> ???? ???, 30 ???? 2019 ???? 4:50 ?.?., ?/? Sotirios >>>>>>>> Nikoloutsopoulos ??????: >>>>>>>> >>>>>>>>> Hi, >>>>>>>>> >>>>>>>>> there was no visit label 01 in the Visit_Windows table and i don't >>>>>>>>> know how to insert it because the record requires lots of attributes. Also >>>>>>>>> the system for a reason asked me to update my password and now i don't >>>>>>>>> remember it and my account got suspended. Is there a way to reset it or set >>>>>>>>> a simple password? I updated the password hash in the users table by using >>>>>>>>> the hash from another LORIS setup we had and i still couldn't login ( also >>>>>>>>> the attribute password is always NULL and the expiration date is 1999-01-01 >>>>>>>>> for some reason ). >>>>>>>>> >>>>>>>>> Thanks >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> ???? ???, 29 ???? 2019 ???? 5:21 ?.?., ?/? Cecile Madjar < >>>>>>>>> cecile.madjar at mcin.ca> ??????: >>>>>>>>> >>>>>>>>>> Hi Sotirios, >>>>>>>>>> >>>>>>>>>> Can you try adding the visit label v01 to the Visit_Windows >>>>>>>>>> table? >>>>>>>>>> >>>>>>>>>> However, I noticed that in a previous dataset, the label was V1. >>>>>>>>>> Does that refer to the same visit? If so, you might want to harmonize the >>>>>>>>>> visit labels so they are all the same across datasets for a given >>>>>>>>>> timepoint, meaning you will need to relabel scans when the visit label is >>>>>>>>>> different but referring to the same visit label (v01 = V1 etc...). >>>>>>>>>> >>>>>>>>>> Hope this helps, >>>>>>>>>> >>>>>>>>>> C?cile >>>>>>>>>> >>>>>>>>>> On Mon, Jul 29, 2019 at 10:15 AM Sotirios Nikoloutsopoulos < >>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>> >>>>>>>>>>> Hi, >>>>>>>>>>> >>>>>>>>>>> Could you help me with the "Visit label does not exist"? I had >>>>>>>>>>> changed $subjectID{'createVisitLabel'} to 1 as you had suggested but it >>>>>>>>>>> appears that this problem hasn't been resolved yet. >>>>>>>>>>> >>>>>>>>>>> lorisadmin at hbp:/data/loris/bin/mri$ cat >>>>>>>>>>> /data/loris/data//logs/TarLoad-14-58-9Xog7H.log >>>>>>>>>>> >>>>>>>>>>> ==> Loading file from disk >>>>>>>>>>> /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc >>>>>>>>>>> >>>>>>>>>>> --> mapping DICOM parameter for >>>>>>>>>>> /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc >>>>>>>>>>> >>>>>>>>>>> --> using user-defined filterParameters for >>>>>>>>>>> /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc >>>>>>>>>>> >>>>>>>>>>> Candidate Mismatch Error is Visit label does not exist >>>>>>>>>>> -> WARNING: This candidate was invalid. Logging to >>>>>>>>>>> MRICandidateErrors table with reason Visit label >>>>>>>>>>> does not exist >>>>>>>>>>> >>>>>>>>>>> Thank you, >>>>>>>>>>> >>>>>>>>>>> Sotirios >>>>>>>>>>> >>>>>>>>>>> ???? ???, 26 ???? 2019 ???? 3:02 ?.?., ?/? Sotirios >>>>>>>>>>> Nikoloutsopoulos ??????: >>>>>>>>>>> >>>>>>>>>>>> Hi Cecile, >>>>>>>>>>>> >>>>>>>>>>>> The Center error was fixed. Still the insertion of mincs fails. >>>>>>>>>>>> Please see the output.txt file i attached. Also is there something else i >>>>>>>>>>>> need to change at the paths configuration? >>>>>>>>>>>> >>>>>>>>>>>> Thank you, >>>>>>>>>>>> >>>>>>>>>>>> Sotirios >>>>>>>>>>>> >>>>>>>>>>>> ???? ???, 25 ???? 2019 ???? 6:55 ?.?., ?/? Cecile Madjar < >>>>>>>>>>>> cecile.madjar at mcin.ca> ??????: >>>>>>>>>>>> >>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>> >>>>>>>>>>>>> We are making progress! >>>>>>>>>>>>> >>>>>>>>>>>>> I have a feeling this error comes from the fact that your psc >>>>>>>>>>>>> table does not have the MRI_alias populated for the DCC site. Running the >>>>>>>>>>>>> following query in the mysql database should fix this: >>>>>>>>>>>>> UPDATE psc SET MRI_alias="DCC", Alias="DCC" WHERE Name="Data >>>>>>>>>>>>> Coordinating Center"; >>>>>>>>>>>>> Repeat the same with all your sites (make sure to change the >>>>>>>>>>>>> Aliases between sites, they should all be unique). >>>>>>>>>>>>> >>>>>>>>>>>>> Let me know how it goes! >>>>>>>>>>>>> Best, >>>>>>>>>>>>> >>>>>>>>>>>>> C?cile >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> On Thu, Jul 25, 2019 at 11:43 AM Sotirios Nikoloutsopoulos < >>>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>> >>>>>>>>>>>>>> Dear Cecile, >>>>>>>>>>>>>> You were right about your guesses. I did the modifications >>>>>>>>>>>>>> you suggested, i still get the "no mincs inserted" error, now i am getting >>>>>>>>>>>>>> the "No center found this candidate" error ( how do i fix that? from what i >>>>>>>>>>>>>> see the .dcm files contains a 'Institution Name', is that the center? ), so >>>>>>>>>>>>>> i guess that's why the validation fails, but i changed the force variable >>>>>>>>>>>>>> of tarchiveLoader to 1, shouldn't it have inserted the mincs then? Also it >>>>>>>>>>>>>> is optional to have a mail server, right? ( from what i see the mail error >>>>>>>>>>>>>> does not affect the $valid_study, so i assume we are okay with that ) >>>>>>>>>>>>>> Thank you a lot, >>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>> >>>>>>>>>>>>>> ???? ???, 25 ???? 2019 ???? 5:48 ?.?., ?/? Cecile Madjar < >>>>>>>>>>>>>> cecile.madjar at mcin.ca> ??????: >>>>>>>>>>>>>> >>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> From what I understand, I believe you just need to update a >>>>>>>>>>>>>>> few config settings from the frontend in the Config module (under the Admin >>>>>>>>>>>>>>> menu). >>>>>>>>>>>>>>> [image: Screen Shot 2019-07-25 at 10.31.35 AM.png] >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> Then go to the Paths section of the config module and update >>>>>>>>>>>>>>> the "LORIS-MRI code" config setting to /data/loris/bin/mri (my guess is >>>>>>>>>>>>>>> that currently, it is set to /data/LORIS/data) and click on the submit >>>>>>>>>>>>>>> button. >>>>>>>>>>>>>>> [image: Screen Shot 2019-07-25 at 10.32.50 AM.png] >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> Then, go to Imaging Pipeline section of the Configuration >>>>>>>>>>>>>>> module and update the "Loris-MRI Data Directory" to /data/loris/data/ (my >>>>>>>>>>>>>>> guess is that it is empty at the moment in your database which is why >>>>>>>>>>>>>>> $data_dir is not defined when you run the tarchiveLoader step of the >>>>>>>>>>>>>>> insertion pipeline). >>>>>>>>>>>>>>> [image: Screen Shot 2019-07-25 at 10.40.52 AM.png] >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> Finally, I took a look at your environment file and it might >>>>>>>>>>>>>>> be a good idea to update your PERL5LIB variable to the following (it has >>>>>>>>>>>>>>> been added to the code a few releases ago as we realized this was needed >>>>>>>>>>>>>>> for the libraries. Not sure which version of LORIS-MRI you are using but it >>>>>>>>>>>>>>> does not hurt to update this variable to what I suggest below): >>>>>>>>>>>>>>> export >>>>>>>>>>>>>>> PERL5LIB=/data/loris/bin/mri/uploadNeuroDB:/data/loris/bin/mri/dicom-archive:$PERL5LIB >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> Hope this helps. Sorry you are experiencing so much trouble >>>>>>>>>>>>>>> setting things up. We probably need to update our WIKI. >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> On Thu, Jul 25, 2019 at 9:48 AM Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> The "Loris-MRI Data Directory" should be in the environment >>>>>>>>>>>>>>>> file? >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> ???? ???, 25 ???? 2019 ???? 12:59 ?.?., ?/? Sotirios >>>>>>>>>>>>>>>> Nikoloutsopoulos ??????: >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> The scripts are located in /data/loris/bin/mri/. >>>>>>>>>>>>>>>>> Somewhere I might have messed something up but i remember following the >>>>>>>>>>>>>>>>> instructions in the wiki.For example when i tried to execute the >>>>>>>>>>>>>>>>> batch_uploads_imageuploader perl script the line >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> my $command = "$bin_dir/uploadNeuroDB/ >>>>>>>>>>>>>>>>> imaging_upload_file.pl " >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> was pointing to an invalid path, for example: it was >>>>>>>>>>>>>>>>> repeating a pattern and had LORIS instead of loris ( i think the mistake >>>>>>>>>>>>>>>>> was that in the wiki it suggested to use $PROJECT for the name of the >>>>>>>>>>>>>>>>> folder and i choosed 'loris' >>>>>>>>>>>>>>>>> https://github.com/aces/Loris/wiki/Imaging-Database ). >>>>>>>>>>>>>>>>> See also the in image for the modification i did. Also i didn't find the >>>>>>>>>>>>>>>>> section to config the $data_dir variable. >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> ???? ???, 24 ???? 2019 ???? 6:05 ?.?., ?/? Cecile Madjar < >>>>>>>>>>>>>>>>> cecile.madjar at mcin.ca> ??????: >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> It looks like you have one Config setting not set (based >>>>>>>>>>>>>>>>>> on the first error message you got when running it the first time). You >>>>>>>>>>>>>>>>>> need to set a value for "Loris-MRI Data Directory" in the Config module >>>>>>>>>>>>>>>>>> under the Imaging pipeline section (from what I can see, it would be >>>>>>>>>>>>>>>>>> /data/loris/data/ for your setup). >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> The reason you got that error message the second time is >>>>>>>>>>>>>>>>>> that the pipeline checks if the DICOM study was already inserted in the >>>>>>>>>>>>>>>>>> tarchive table. Since you ran the study once already, the study is inserted >>>>>>>>>>>>>>>>>> into the tarchive, hence the message. However, the pipeline did not >>>>>>>>>>>>>>>>>> complete as the MINC files were not created and inserted into the >>>>>>>>>>>>>>>>>> files/parameter_file table. In order to continue the insertion, you will >>>>>>>>>>>>>>>>>> then need to run the tarchiveLoader command suggested in the terminal >>>>>>>>>>>>>>>>>> during the second run: >>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader >>>>>>>>>>>>>>>>>> -globLocation -profile prod >>>>>>>>>>>>>>>>>> /data/loris/data/tarchive//2012/DCM_2012-12-05_ImagingUpload-17-43-ZUEFjb.tar >>>>>>>>>>>>>>>>>> -verbose >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Finally, I am a bit confused by your setup. Where are the >>>>>>>>>>>>>>>>>> scripts located? In /data/loris/bin/mri or /data/loris/data? It feels like >>>>>>>>>>>>>>>>>> the Config setting "LORIS-MRI code" in the Paths section was set to >>>>>>>>>>>>>>>>>> "/data/LORIS/data" but it should have been set to the directory where the >>>>>>>>>>>>>>>>>> scripts are located (most probably /data/loris/bin/mri). >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Hope this helps, >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> On Wed, Jul 24, 2019 at 10:55 AM Sotirios >>>>>>>>>>>>>>>>>> Nikoloutsopoulos wrote: >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Ok first i execute this command: >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> "lorisadmin at hbp:/data/loris/bin/mri$ >>>>>>>>>>>>>>>>>>> ./batch_uploads_imageuploader -profile prod < ~/Desktop/input.txt > log.txt >>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in concatenation >>>>>>>>>>>>>>>>>>> (.) or string at ./batch_uploads_imageuploader line 143. >>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in concatenation >>>>>>>>>>>>>>>>>>> (.) or string at ./batch_uploads_imageuploader line 143. >>>>>>>>>>>>>>>>>>> Use of uninitialized value $_ in pattern match (m//) at >>>>>>>>>>>>>>>>>>> ./batch_uploads_imageuploader line 147. >>>>>>>>>>>>>>>>>>> base is DCC0000_258024_V01 >>>>>>>>>>>>>>>>>>> path is /data/incoming/ >>>>>>>>>>>>>>>>>>> type is .tar.gz >>>>>>>>>>>>>>>>>>> fullpath is /data/incoming/DCC0000_258024_V01.tar.gz >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> source /tmp/ImagingUpload-17-43-ZUEFjb >>>>>>>>>>>>>>>>>>> targetlocation /data/loris/data/tarchive >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in concatenation >>>>>>>>>>>>>>>>>>> (.) or string at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 256. >>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in concatenation >>>>>>>>>>>>>>>>>>> (.) or string at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 284. >>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in concatenation >>>>>>>>>>>>>>>>>>> (.) or string at /data/loris/bin/mri/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>> tarchive_validation.pl line 219. >>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in concatenation >>>>>>>>>>>>>>>>>>> (.) or string at /data/loris/bin/mri/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>> minc_insertion.pl line 270. >>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in concatenation >>>>>>>>>>>>>>>>>>> (.) or string at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 711. >>>>>>>>>>>>>>>>>>> Can't exec "mail": No such file or directory at >>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 721. >>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 722. >>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 723. >>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in concatenation >>>>>>>>>>>>>>>>>>> (.) or string at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 724. >>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 724. >>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 725. >>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in concatenation >>>>>>>>>>>>>>>>>>> (.) or string at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 735. >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> No Mincs inserted >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> The tarchiveLoader insertion script has failed. >>>>>>>>>>>>>>>>>>> Running now the following command: >>>>>>>>>>>>>>>>>>> /data/loris/data/uploadNeuroDB/imaging_upload_file.pl >>>>>>>>>>>>>>>>>>> -profile prod -upload_id 3 /data/incoming/DCC0000_258024_V01.tar.gz >>>>>>>>>>>>>>>>>>> -verbose" >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> I inserted the VisitLabel, but still the Mincs are not >>>>>>>>>>>>>>>>>>> inserted and i am getting this error >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> "lorisadmin at hbp:/data/loris/bin/mri$ >>>>>>>>>>>>>>>>>>> /data/loris/data/uploadNeuroDB/imaging_upload_file.pl >>>>>>>>>>>>>>>>>>> -profile prod -upload_id 3 /data/incoming/DCC0000_258024_V01.tar.gz -verbose >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> find -path \/tmp\/ImagingUpload\-17\-45\-5MsWEd -name >>>>>>>>>>>>>>>>>>> '__MACOSX' -delete >>>>>>>>>>>>>>>>>>> Spool message is: >>>>>>>>>>>>>>>>>>> The Scan for the uploadID 3 has already been run with >>>>>>>>>>>>>>>>>>> tarchiveID: 7. >>>>>>>>>>>>>>>>>>> To continue with the rest of the insertion pipeline, >>>>>>>>>>>>>>>>>>> please run tarchiveLoader from a terminal as follows: >>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader -globLocation -profile prod >>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive//2012/DCM_2012-12-05_ImagingUpload-17-43-ZUEFjb.tar >>>>>>>>>>>>>>>>>>> -verbose" >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Which files should i delete? I thought that deleting the >>>>>>>>>>>>>>>>>>> files from the tarchive was enough. And i executed the last proposed >>>>>>>>>>>>>>>>>>> command to continue to rest of the insertion pipeline ( check the image ). >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Thank you >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> ???? ???, 24 ???? 2019 ???? 5:05 ?.?., ?/? Cecile Madjar >>>>>>>>>>>>>>>>>>> ??????: >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Sorry I was not clear before. Every visits of >>>>>>>>>>>>>>>>>>>> candidates are created in the session table with one entry per >>>>>>>>>>>>>>>>>>>> CandID/VisitLabel. So if the imaging pipeline created visits in the session >>>>>>>>>>>>>>>>>>>> table (that are not attached to instruments) and you want to clean your >>>>>>>>>>>>>>>>>>>> database completely, you can delete entries in that table as well. >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Regarding your point 2, the imaging pipeline can create >>>>>>>>>>>>>>>>>>>> the visit in the session table as long as the visit label is present in the >>>>>>>>>>>>>>>>>>>> Visit_Windows table (which means the visit label stored in the PatientName >>>>>>>>>>>>>>>>>>>> is a valid visit label). >>>>>>>>>>>>>>>>>>>> However, in your prod file, if the >>>>>>>>>>>>>>>>>>>> variable $subjectID{'createVisitLabel'} is set to 1 for candidates, the >>>>>>>>>>>>>>>>>>>> visit label should be created in the Visit_Windows table I believe. Here >>>>>>>>>>>>>>>>>>>> is the line of the prod file you would need to change >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> . >>>>>>>>>>>>>>>>>>>> In general, we prefer populating the Visit_Windows >>>>>>>>>>>>>>>>>>>> table and set the $subjectID{'createVisitLabel'} to 0 for candidate data to >>>>>>>>>>>>>>>>>>>> avoid insertion of badly labelled MRI data that are complex to relabel. >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Finally, regarding the candidate creation, if you >>>>>>>>>>>>>>>>>>>> execute the following steps, the pipeline should be able to create >>>>>>>>>>>>>>>>>>>> candidates: >>>>>>>>>>>>>>>>>>>> - set in the Imaging Pipeline section of the config >>>>>>>>>>>>>>>>>>>> module the config setting "Upload creation of candidates" to Yes >>>>>>>>>>>>>>>>>>>> - manually transfer the scans to the LORIS server >>>>>>>>>>>>>>>>>>>> instead of uploading it via the imaging browser >>>>>>>>>>>>>>>>>>>> - run batch_imaging_upload.pl as you did until now. >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Hope this helps! >>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> On Wed, Jul 24, 2019 at 8:47 AM Sotirios >>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos wrote: >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> About my second question i replaced the name of the >>>>>>>>>>>>>>>>>>>>> patient in the .dcm files and now i am getting an error that the visit >>>>>>>>>>>>>>>>>>>>> label does not exist. >>>>>>>>>>>>>>>>>>>>> I thought it was supposed to be automatically created. >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> "Done adding archive info into database >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader >>>>>>>>>>>>>>>>>>>>> -globLocation -profile prod >>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive//DCM_2012-12-05_ImagingUpload-15-42-yUwQQV.tar >>>>>>>>>>>>>>>>>>>>> -verbose >>>>>>>>>>>>>>>>>>>>> md5sum >>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive/DCM_2012-12-05_ImagingUpload-15-42-yUwQQV.tar >>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>> candidate id 258024 >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> => No Visit labelVisit label does not exist >>>>>>>>>>>>>>>>>>>>> Set centerID = 1 >>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> Number of MINC files that will be considered for >>>>>>>>>>>>>>>>>>>>> inserting into the database: 1 >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> log dir is /logs and log file is >>>>>>>>>>>>>>>>>>>>> /logs/TarLoad-15-42-L6pocU.log >>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>> candidate id 258024 >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> => No Visit label >>>>>>>>>>>>>>>>>>>>> Cleaning up temp files: rm -rf >>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-15-42-J2rQms/ImagingUpload-15-42-yUwQQV*" >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> ???? ???, 24 ???? 2019 ???? 3:38 ?.?., ?/? Sotirios >>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos ??????: >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> 1) What are the records in the session table? >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> 2) I tried to upload a non-phantom file like this >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> input_file.txt: >>>>>>>>>>>>>>>>>>>>>> /data/incoming/DCC0000_258024_V1.tar.gz N >>>>>>>>>>>>>>>>>>>>>> DCC0000_258024_V1 >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> Terminal: >>>>>>>>>>>>>>>>>>>>>> ./batch_uploads_imageuploader -profile prod < >>>>>>>>>>>>>>>>>>>>>> ~/Desktop/input.txt > log.txt >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> and i get the following error in the log.txt file >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> "Running now the following command: >>>>>>>>>>>>>>>>>>>>>> /data/loris/data/uploadNeuroDB/imaging_upload_file.pl >>>>>>>>>>>>>>>>>>>>>> -profile prod -upload_id 7 /data/incoming/DCC0000_258024_V1.tar.gz -verbose >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> find -path \/tmp\/ImagingUpload\-14\-56\-FeLCB4 >>>>>>>>>>>>>>>>>>>>>> -name '__MACOSX' -delete >>>>>>>>>>>>>>>>>>>>>> Spool message is: >>>>>>>>>>>>>>>>>>>>>> The PatientName read from the DICOM header does not >>>>>>>>>>>>>>>>>>>>>> start with DCC0000_258024_V1 from the mri_upload table >>>>>>>>>>>>>>>>>>>>>> " >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> and the spool message is repeated for each .dcm file. >>>>>>>>>>>>>>>>>>>>>> Should i preprocess every .dcm file and change the PatientName to >>>>>>>>>>>>>>>>>>>>>> "DCC0000_258024_V1"? >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> 3) As far as it concerns the candidate profile i have >>>>>>>>>>>>>>>>>>>>>> to create a new one each time before i try to upload a file? Is there >>>>>>>>>>>>>>>>>>>>>> already a way to create a candidate profile and get the DCCID and PSCID >>>>>>>>>>>>>>>>>>>>>> without the user interface? >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> ???? ???, 18 ???? 2019 ???? 5:00 ?.?., ?/? Cecile >>>>>>>>>>>>>>>>>>>>>> Madjar ??????: >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> See answers to your questions below. >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> About the 1st case we had a dicom with a blank >>>>>>>>>>>>>>>>>>>>>>>> studyUID, maybe someone accidentally removed it. >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> That is strange. Something must have been done to >>>>>>>>>>>>>>>>>>>>>>> the DICOM files. I have never seen a study with no StudyUID out of the >>>>>>>>>>>>>>>>>>>>>>> scanner. Usually, you need to manually erase it with some tool. However, >>>>>>>>>>>>>>>>>>>>>>> DICOMs never cease to surprise me... >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> Some other questions: >>>>>>>>>>>>>>>>>>>>>>>> 1) What are the steps to remove all of my patients >>>>>>>>>>>>>>>>>>>>>>>> and uploads?: because i want to try to reupload all the testing dicoms we >>>>>>>>>>>>>>>>>>>>>>>> had with a clean database. >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> Release 21.0 of LORIS-MRI will offer a script to >>>>>>>>>>>>>>>>>>>>>>> remove all the entries and files specific to an upload. However, this >>>>>>>>>>>>>>>>>>>>>>> release is not yet out. Hopefully in the next few weeks. >>>>>>>>>>>>>>>>>>>>>>> In the meantime, since your case is particular and >>>>>>>>>>>>>>>>>>>>>>> that you just want to start with a clean database, the following deletes >>>>>>>>>>>>>>>>>>>>>>> should work (hopefully I won't forget any tables): >>>>>>>>>>>>>>>>>>>>>>> delete from mri_violations_log; >>>>>>>>>>>>>>>>>>>>>>> delete from mri_protocol_violated_scans; >>>>>>>>>>>>>>>>>>>>>>> delete from MRICandidateErrors; >>>>>>>>>>>>>>>>>>>>>>> delete from parameter_file; >>>>>>>>>>>>>>>>>>>>>>> delete from files_qcstatus; # (if you played with >>>>>>>>>>>>>>>>>>>>>>> the QC part of the imaging browser for testing) >>>>>>>>>>>>>>>>>>>>>>> delete from feedback_mri_comments; # (if you played >>>>>>>>>>>>>>>>>>>>>>> with the QC part of the imaging browser for testing) >>>>>>>>>>>>>>>>>>>>>>> delete from tarchive_series; >>>>>>>>>>>>>>>>>>>>>>> delete from tarchive_files; >>>>>>>>>>>>>>>>>>>>>>> delete from mri_upload; >>>>>>>>>>>>>>>>>>>>>>> delete from tarchive; >>>>>>>>>>>>>>>>>>>>>>> delete from mri_scanner; >>>>>>>>>>>>>>>>>>>>>>> delete from candidate where PSCID="scanner"; >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> I don't know if you want to also delete entries in >>>>>>>>>>>>>>>>>>>>>>> the session and candidate table too? >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> 2) We do not need to create the profile of a patient >>>>>>>>>>>>>>>>>>>>>>>> ( are the patients stored in the candidate table? because i can't see the >>>>>>>>>>>>>>>>>>>>>>>> ghosts ), because will it automatically be created when importing a dicom? >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> I am not sure I understand fully this question. All >>>>>>>>>>>>>>>>>>>>>>> candidates are stored in the candidate table. The phantom scans however are >>>>>>>>>>>>>>>>>>>>>>> attached to a scanner candidate depending on where the scan happened. It is >>>>>>>>>>>>>>>>>>>>>>> a bit of a weird concept that we have to redesign eventually but never got >>>>>>>>>>>>>>>>>>>>>>> a chance to get to it. >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> Hopefully this answered your question, otherwise, >>>>>>>>>>>>>>>>>>>>>>> don't hesitate to let me know. >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> 3) What is the difference between uploading a dicom >>>>>>>>>>>>>>>>>>>>>>>> as phantom instead of importing as PSCCID_DCCID_VisitLabel? >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> When you upload the scan as PSCID_DCCID_VisitLabel, >>>>>>>>>>>>>>>>>>>>>>> there is a check that makes sure the candidate IDs and visit label are >>>>>>>>>>>>>>>>>>>>>>> valid at the time of upload. >>>>>>>>>>>>>>>>>>>>>>> When you upload a scan as phantom, it expects that >>>>>>>>>>>>>>>>>>>>>>> the DICOM field PatientName and uploaded filename contains the string >>>>>>>>>>>>>>>>>>>>>>> "phantom". We enforced this behaviour on the imaging uploader side in >>>>>>>>>>>>>>>>>>>>>>> recent releases but I can't remember which one. Probably the upcoming 21.0 >>>>>>>>>>>>>>>>>>>>>>> release. >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> All those verifications might seem cumbersome but >>>>>>>>>>>>>>>>>>>>>>> they are here to ensure that the files inserted are all valid and labelled >>>>>>>>>>>>>>>>>>>>>>> properly as it is a bit messy to have to delete files that were wrongly >>>>>>>>>>>>>>>>>>>>>>> labelled. At least, the delete script present in release 21.0 will make >>>>>>>>>>>>>>>>>>>>>>> this process easier but it is still good practice to verify those things. >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> With pleasure. Hopefully the answers to your >>>>>>>>>>>>>>>>>>>>>>> questions will be helpful. >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> PS: loris-dev mailing list: you will find the >>>>>>>>>>>>>>>>>>>>>>> initial answer I gave Sotirios below. I forgot to cc the loris-dev in my >>>>>>>>>>>>>>>>>>>>>>> earlier reply... >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> ???? ???, 16 ???? 2019 ???? 12:02 ?.?., ?/? Cecile >>>>>>>>>>>>>>>>>>>>>>>> Madjar ??????: >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> Dear Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> Thank you for reaching out. Since your email was >>>>>>>>>>>>>>>>>>>>>>>>> already organized in points, I will reply directly below your questions >>>>>>>>>>>>>>>>>>>>>>>>> below. >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> 1) What do we do when the StudyUID is blank on the >>>>>>>>>>>>>>>>>>>>>>>>>> header? >>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/minor/docs/AppendixA-Troubleshooting_guideline.md >>>>>>>>>>>>>>>>>>>>>>>>>> There solution provided at the table 3 does not guide us how to find the >>>>>>>>>>>>>>>>>>>>>>>>>> information ( is possible ). >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> The StudyUID is the field used in our pipeline at >>>>>>>>>>>>>>>>>>>>>>>>> the moment to check whether a DICOM study was already inserted into LORIS >>>>>>>>>>>>>>>>>>>>>>>>> with that same StudyUID since it is supposed to be unique for every single >>>>>>>>>>>>>>>>>>>>>>>>> study. Currently, we do not support insertion of DICOM studies if they do >>>>>>>>>>>>>>>>>>>>>>>>> not have a StudyUID associated with them. >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> Is there a specific reason why the StudyUID is >>>>>>>>>>>>>>>>>>>>>>>>> blank in the DICOM headers in your DICOM files? Did they go through some >>>>>>>>>>>>>>>>>>>>>>>>> processes before upload to LORIS? >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> 2) When i am about to upload a non-phanton case i >>>>>>>>>>>>>>>>>>>>>>>>>> need a 'Visit Label'. Is there already a script that can create a new visit >>>>>>>>>>>>>>>>>>>>>>>>>> label for a specific Candidate, so i can provide it as input afterwards to >>>>>>>>>>>>>>>>>>>>>>>>>> the >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> batch_uploads_imageuploader ( See option 5.1.3 https://github.com/aces/Loris-MRI/blob/minor/docs/05-PipelineLaunchOptions.md ) >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> I am not sure if the front-end allows for it but >>>>>>>>>>>>>>>>>>>>>>>>> if you use batch_uploads_imageuploader, the insertion scripts could create >>>>>>>>>>>>>>>>>>>>>>>>> the visit label for you. However, it does need to be included in the >>>>>>>>>>>>>>>>>>>>>>>>> patient name in order for the script to know which label it should use. >>>>>>>>>>>>>>>>>>>>>>>>> For example: you upload V02 for MTL0123 (DCCID: >>>>>>>>>>>>>>>>>>>>>>>>> 456789) but V02 was not yet created for MTL0123; the insertion scripts >>>>>>>>>>>>>>>>>>>>>>>>> will create a V02 visit for MTL0123 if the PatientName field for the >>>>>>>>>>>>>>>>>>>>>>>>> dataset is MTL0123_456789_V02 with Stage marked as "Not Started". >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> However, *note that for the script to create the >>>>>>>>>>>>>>>>>>>>>>>>> visit for the candidate, you have to make sure that all the visit label of >>>>>>>>>>>>>>>>>>>>>>>>> your projects were inserted in the Visit_Windows table* >>>>>>>>>>>>>>>>>>>>>>>>> (otherwise, the visit will never be created as they were not specified as >>>>>>>>>>>>>>>>>>>>>>>>> being part of the list of visit label to expect). So in the example above, >>>>>>>>>>>>>>>>>>>>>>>>> you should have one row in Visit_Windows with Visit_label="V02" set. >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> 3) Section 4.3 >>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/minor/docs/04-Scripts.md >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> What do we do when the folder contains multiple mnc files? >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> This is a case by case. Most of the time, the >>>>>>>>>>>>>>>>>>>>>>>>> MINC files that failed insertion into the imaging browser end up in the MRI >>>>>>>>>>>>>>>>>>>>>>>>> violation module where you can see what went wrong with the acquisitions >>>>>>>>>>>>>>>>>>>>>>>>> not inserted. If you notice that the MINC file should be inserted as a >>>>>>>>>>>>>>>>>>>>>>>>> specific protocol, you can force the insertion as explained in section 4.3. >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> In your case, I have a feeling that you want to be >>>>>>>>>>>>>>>>>>>>>>>>> able to insert MINC files that did not go through the whole pipeline >>>>>>>>>>>>>>>>>>>>>>>>> insertion (DICOM archival, then dcm2mnc, then protocol identification, then >>>>>>>>>>>>>>>>>>>>>>>>> insertion...). In theory, you could call >>>>>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl on any MINC file, provided you >>>>>>>>>>>>>>>>>>>>>>>>> have at least the following information: >>>>>>>>>>>>>>>>>>>>>>>>> - path to the MINC file >>>>>>>>>>>>>>>>>>>>>>>>> - uploadID associated with the MINC files or DICOM >>>>>>>>>>>>>>>>>>>>>>>>> archive path from which those MINC files were created from >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> Then the minc_insertion.pl script will do the >>>>>>>>>>>>>>>>>>>>>>>>> subject information and protocol validation etc... >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> If all the MINC files come from the same uploadID >>>>>>>>>>>>>>>>>>>>>>>>> or TarchiveID, then you could run a loop in bash calling the >>>>>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl script like this for files >>>>>>>>>>>>>>>>>>>>>>>>> deriving from uploadID=1: >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> ls /path/to/mnc/folder/* | while read f; do >>>>>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl -profile prod -uploadID 1 >>>>>>>>>>>>>>>>>>>>>>>>> -mincPath $f; done >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> Hope this helped! >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________ >>>>>>> Loris-dev mailing list >>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>> >>>>>> >>>>>> >>>>>> -- >>>>>> >>>>>> christine.rogers at mcgill.ca >>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>> Montreal Neurological Institute >>>>>> McGill University | Montreal | Canada >>>>>> >>>>> >>>> >>>> -- >>>> >>>> christine.rogers at mcgill.ca >>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>> Montreal Neurological Institute >>>> McGill University | Montreal | Canada >>>> >>> _______________________________________________ >> Loris-dev mailing list >> Loris-dev at bic.mni.mcgill.ca >> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >> > > > -- > > christine.rogers at mcgill.ca > McGill Centre for Integrative Neuroscience | MCIN.ca > Montreal Neurological Institute > McGill University | Montreal | Canada > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 78176 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 20518 bytes Desc: not available URL: From christine.rogers at mcgill.ca Tue Aug 6 09:53:45 2019 From: christine.rogers at mcgill.ca (Christine Rogers, Ms.) Date: Tue, 6 Aug 2019 13:53:45 +0000 Subject: [Loris-dev] Import mri - scripts In-Reply-To: References: <65ad2b70c3084ffdb1e4a9dcdad948cd@YTOPR0101MB1803.CANPRD01.PROD.OUTLOOK.COM> Message-ID: Thanks Sotirios, That's good to know. It sounds like you've checked that your /var/www/loris/project/config.xml file get populated properly. Please send us the last few errors you're seeing in your apache error log file, and your config paths and we can see what's happening with your front end -- Run these Troubleshooting Queries to get your config path settings, given your front end is not displaying fully. The Loris-MRI repo 21 install/upgrade would then be your next steps. Best, Christine On Tue, Aug 6, 2019 at 7:53 AM Sotirios Nikoloutsopoulos > wrote: I am using a VM. What i did was: 1) Download the files from https://github.com/aces/Loris and replace them to my existing /vaw/www/loris folder. 2) Execute the composer install --no-dev and then composer dump-autoload as mentioned here https://github.com/aces/Loris/wiki/Updating-your-LORIS. 3) Execute install.sh from /var/www/loris/tools and because LORIS already existed i moved a .config file, then re-executed the install.sh successfully 4 ) As for the database, i dropped the schema and i executed the installdb.php ???? ???, 5 ??? 2019 ???? 5:22 ?.?., ?/? Christine Rogers, Ms. > ??????: Hi Sotorios, Thanks - when you re-installed did you start on a fresh root path / VM or might some of your old system setting still apply? (And if you did any steps similar to an upgrade, did you follow the Upgrade steps in the Release Notes, from both repos?) About the TR_range column - it was recently split (MRI pr339) split into TR_min and _max columns. Given the code was trying to query TR_range which does not exist in your mri_protocol table, double-check which version of the Loris repo (tables) and the Loris-MRI repo (code) you have installed to ensure they match. Christine On Mon, Aug 5, 2019 at 9:06 AM Sotirios Nikoloutsopoulos > wrote: I reinstalled LORIS to 21 version and now the content is not visible at all at most pages. [image.png] ???? ???, 5 ??? 2019 ???? 3:19 ?.?., ?/? Sotirios Nikoloutsopoulos > ??????: Hi, Is it easy to upgrade to Loris 21? Also the following fails because the line 1985 of NeuroDB/MRIProcessingUtility.pm query mri_protocol which doesn't have TR_range https://github.com/aces/Loris/blob/21.0-release/SQL/0000-00-00-schema.sql#L556 [image.png] lorisadmin at hbp:/data/loris/bin/mri$ ./batch_uploads_imageuploader -profile prod < ~/Desktop/input.txt > log.txt Use of uninitialized value $_ in pattern match (m//) at ./batch_uploads_imageuploader line 147. base is DCC0000_258024_V1 path is /data/incoming/ type is .tar.gz fullpath is /data/incoming/DCC0000_258024_V1.tar.gz DBD::mysql::st execute failed: Unknown column 'TR_range' in 'where clause' at /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line 1985. DBD::mysql::st fetchrow_array failed: fetch() without execute() at /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line 1986. Use of uninitialized value $count_mri_protocol in numeric gt (>) at /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line 1995. DBD::mysql::st execute failed: Unknown column 'TR_range' in 'field list' at /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 562. Can't exec "mail": No such file or directory at /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 721. print() on closed filehandle MAIL at /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 722. print() on closed filehandle MAIL at /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 723. print() on closed filehandle MAIL at /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 724. print() on closed filehandle MAIL at /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 725. No Mincs inserted Thanks, Sotirios ???? ???, 3 ??? 2019 ???? 1:08 ?.?., ?/? Christine Rogers, Ms. > ??????: Hi Sotirios, First, just a note: we've released LORIS 21 this week with some major new features and cleanup -- especially if you are early in your setup phase, check out the Release notes for both the LORIS and Loris-MRI repos. Thanks for your screenshots -- your empty mri_protocol table should be at the root of these issues : The mri_protocol table must be populated in order for your scans to be registered in LORIS -- it serves as a whitelist for the insertion pipeline which filters out scans that aren't identified or matched to scan types in this table. By default, this table is populated with entries for t1, t2, fMRI and DTI (Insert statements for 21 release branch are here) Feel free to restore our default records and broaden their parameters to match all your scan types. re Defaced, native, selected -- these filter the scans displayed as you move to the next page (View Session), instead of viewing "all types" of scans from a given session : * "defaced" means that a defacing script has masked the subject's face in the volume (for patient privacy) * "native" means that no pre-processing has been performed on the scan (it's raw data), * "selected" will show only volumes that have been QC'd and "selected" as the best of their type -- used to display only the best quality T1 image instead of all T1s acquired in a session, e.g. re QC Comments -- Once you have successfully loaded scans (matched to the mri_protocol table), you'll be able to use the Imaging Browser's View Session subpage to enter/view QC comments on each volume, or for each visit. These are stored directly in the database, and linked to each scan. (Table name: feedback_mri_comments) (Visit-level QC comments are linked to the session.) For a walkthrough of the Imaging setup - please see the Imaging Setup guide - An old LORIS walkthrough video can also walk you through some of the Imaging front-end features, starting at 8:00 LORIS' imaging modules have been updated many times since this video, but the functionality and workflow is similar. Let us know how it goes once you have entries in your mri_protocol table - Best, Christine On Fri, Aug 2, 2019 at 7:58 AM Sotirios Nikoloutsopoulos > wrote: Hi Christine, In the candidate_list page i can see this patient [image.png] If i press the link under PSCID i get to see [image.png] and if i press the link under Scan Done it redirects me to imaging_browser [image.png] At the mri_violations page i also see No results ( neither on resolved / not resolved ). At the imaging_uploader i can see the record that failed. [image.png] If i click on the tarchive info i get to see the Protocol Name which i think is the acquisition we wanted? [image.png] Also my mri_protocol table is empty. Furthermore i would like to ask about the defaced, native, selected. What exactly is native and selected? And where are the qc comments stored? [image.png] Finally a walkthrough would be helpful. Thanks, Sotirios ???? ???, 30 ???? 2019 ???? 8:29 ?.?., ?/? Christine Rogers, Ms. > ??????: Hi Sotirios, Glad to hear you're making progress with the visit labels. To follow up on your last few emails: a- The Wiki's Setup Guide contains Sample insert statements for the Visit Windows table. As Cecile mentioned, the consistency of visit label format is important: V01, v01, V1, 01 -- whichever you select to use is fine; we use V01 by default across all documentation. b- For Password reset, there is a script in the tools/ directory so that a back-end administrator can reset any front-end user password, including Admin. (See info on setting up / resetting User passwords in the Wiki's Setup Guide) c- The minc file not being registered -- due to AcquisitionProtocol unknown. This means the SeriesDescription (Acquisition Protocol) in you Dicom header was not matched to any scan listed in the mri_protocol database table. (In the online Loris-MRI Troubleshooting Guide, this is Table 3, 2nd-last item "no MINCs inserted"). The MRI Violations module (Readme here) will show you the details of this mismatch -- Go to the module (under the Imaging menu), find your scan and click the link "Could not identify scan type" -- in the next subpage you can compare the scan's actual parameters against the mri_protocol table. To resolve this, adjust your mri_protocol table values or perhaps ensure your DICOMs are labelled consistently. Let us know if this works for you -- we can also walk you through an example of non-identified scans on Demo.loris.ca (MRI Violations module). Best, Christine The LORIS team On Tue, Jul 30, 2019 at 10:47 AM Sotirios Nikoloutsopoulos > wrote: I hope this is sufficient as the error for the visit label disappeared. [image.png] Please see the attached file. Also something i found. lorisadmin at hbp:/data/loris/bin/mri$ cat /data/loris/data//logs/TarLoad-17-39-xubBdv.log ==> Loading file from disk /tmp/TarLoad-17-39-UyQcG2/dcc0000_258024_v1_20121205_102108_501e1_mri.mnc --> mapping DICOM parameter for /tmp/TarLoad-17-39-UyQcG2/dcc0000_258024_v1_20121205_102108_501e1_mri.mnc ==> computing md5 hash for MINC body. --> md5: 6b1202fd63e29de4c9be1cd9925888a5 ==> verifying acquisition protocol Acquisition protocol is unknown --> The minc file cannot be registered since the AcquisitionProtocol is unknown ???? ???, 30 ???? 2019 ???? 4:58 ?.?., ?/? Sotirios Nikoloutsopoulos > ??????: Ok I fixed the login problem by using a known hash and by deleting the rows from the login_history i was able to login. ???? ???, 30 ???? 2019 ???? 4:50 ?.?., ?/? Sotirios Nikoloutsopoulos > ??????: Hi, there was no visit label 01 in the Visit_Windows table and i don't know how to insert it because the record requires lots of attributes. Also the system for a reason asked me to update my password and now i don't remember it and my account got suspended. Is there a way to reset it or set a simple password? I updated the password hash in the users table by using the hash from another LORIS setup we had and i still couldn't login ( also the attribute password is always NULL and the expiration date is 1999-01-01 for some reason ). Thanks ???? ???, 29 ???? 2019 ???? 5:21 ?.?., ?/? Cecile Madjar > ??????: Hi Sotirios, Can you try adding the visit label v01 to the Visit_Windows table? However, I noticed that in a previous dataset, the label was V1. Does that refer to the same visit? If so, you might want to harmonize the visit labels so they are all the same across datasets for a given timepoint, meaning you will need to relabel scans when the visit label is different but referring to the same visit label (v01 = V1 etc...). Hope this helps, C?cile On Mon, Jul 29, 2019 at 10:15 AM Sotirios Nikoloutsopoulos > wrote: Hi, Could you help me with the "Visit label does not exist"? I had changed $subjectID{'createVisitLabel'} to 1 as you had suggested but it appears that this problem hasn't been resolved yet. lorisadmin at hbp:/data/loris/bin/mri$ cat /data/loris/data//logs/TarLoad-14-58-9Xog7H.log ==> Loading file from disk /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc --> mapping DICOM parameter for /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc --> using user-defined filterParameters for /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc Candidate Mismatch Error is Visit label does not exist -> WARNING: This candidate was invalid. Logging to MRICandidateErrors table with reason Visit label does not exist Thank you, Sotirios ???? ???, 26 ???? 2019 ???? 3:02 ?.?., ?/? Sotirios Nikoloutsopoulos > ??????: Hi Cecile, The Center error was fixed. Still the insertion of mincs fails. Please see the output.txt file i attached. Also is there something else i need to change at the paths configuration? Thank you, Sotirios ???? ???, 25 ???? 2019 ???? 6:55 ?.?., ?/? Cecile Madjar > ??????: Hi Sotirios, We are making progress! I have a feeling this error comes from the fact that your psc table does not have the MRI_alias populated for the DCC site. Running the following query in the mysql database should fix this: UPDATE psc SET MRI_alias="DCC", Alias="DCC" WHERE Name="Data Coordinating Center"; Repeat the same with all your sites (make sure to change the Aliases between sites, they should all be unique). Let me know how it goes! Best, C?cile On Thu, Jul 25, 2019 at 11:43 AM Sotirios Nikoloutsopoulos > wrote: Dear Cecile, You were right about your guesses. I did the modifications you suggested, i still get the "no mincs inserted" error, now i am getting the "No center found this candidate" error ( how do i fix that? from what i see the .dcm files contains a 'Institution Name', is that the center? ), so i guess that's why the validation fails, but i changed the force variable of tarchiveLoader to 1, shouldn't it have inserted the mincs then? Also it is optional to have a mail server, right? ( from what i see the mail error does not affect the $valid_study, so i assume we are okay with that ) Thank you a lot, Sotirios ???? ???, 25 ???? 2019 ???? 5:48 ?.?., ?/? Cecile Madjar > ??????: Hi Sotirios, From what I understand, I believe you just need to update a few config settings from the frontend in the Config module (under the Admin menu). [Screen Shot 2019-07-25 at 10.31.35 AM.png] Then go to the Paths section of the config module and update the "LORIS-MRI code" config setting to /data/loris/bin/mri (my guess is that currently, it is set to /data/LORIS/data) and click on the submit button. [Screen Shot 2019-07-25 at 10.32.50 AM.png] Then, go to Imaging Pipeline section of the Configuration module and update the "Loris-MRI Data Directory" to /data/loris/data/ (my guess is that it is empty at the moment in your database which is why $data_dir is not defined when you run the tarchiveLoader step of the insertion pipeline). [Screen Shot 2019-07-25 at 10.40.52 AM.png] Finally, I took a look at your environment file and it might be a good idea to update your PERL5LIB variable to the following (it has been added to the code a few releases ago as we realized this was needed for the libraries. Not sure which version of LORIS-MRI you are using but it does not hurt to update this variable to what I suggest below): export PERL5LIB=/data/loris/bin/mri/uploadNeuroDB:/data/loris/bin/mri/dicom-archive:$PERL5LIB Hope this helps. Sorry you are experiencing so much trouble setting things up. We probably need to update our WIKI. Best, C?cile On Thu, Jul 25, 2019 at 9:48 AM Sotirios Nikoloutsopoulos > wrote: The "Loris-MRI Data Directory" should be in the environment file? ???? ???, 25 ???? 2019 ???? 12:59 ?.?., ?/? Sotirios Nikoloutsopoulos > ??????: The scripts are located in /data/loris/bin/mri/. Somewhere I might have messed something up but i remember following the instructions in the wiki.For example when i tried to execute the batch_uploads_imageuploader perl script the line my $command = "$bin_dir/uploadNeuroDB/imaging_upload_file.pl " was pointing to an invalid path, for example: it was repeating a pattern and had LORIS instead of loris ( i think the mistake was that in the wiki it suggested to use $PROJECT for the name of the folder and i choosed 'loris' https://github.com/aces/Loris/wiki/Imaging-Database ). See also the in image for the modification i did. Also i didn't find the section to config the $data_dir variable. Thank you, Sotirios ???? ???, 24 ???? 2019 ???? 6:05 ?.?., ?/? Cecile Madjar > ??????: Hi Sotirios, It looks like you have one Config setting not set (based on the first error message you got when running it the first time). You need to set a value for "Loris-MRI Data Directory" in the Config module under the Imaging pipeline section (from what I can see, it would be /data/loris/data/ for your setup). The reason you got that error message the second time is that the pipeline checks if the DICOM study was already inserted in the tarchive table. Since you ran the study once already, the study is inserted into the tarchive, hence the message. However, the pipeline did not complete as the MINC files were not created and inserted into the files/parameter_file table. In order to continue the insertion, you will then need to run the tarchiveLoader command suggested in the terminal during the second run: /data/LORIS/data//uploadNeuroDB/tarchiveLoader -globLocation -profile prod /data/loris/data/tarchive//2012/DCM_2012-12-05_ImagingUpload-17-43-ZUEFjb.tar -verbose Finally, I am a bit confused by your setup. Where are the scripts located? In /data/loris/bin/mri or /data/loris/data? It feels like the Config setting "LORIS-MRI code" in the Paths section was set to "/data/LORIS/data" but it should have been set to the directory where the scripts are located (most probably /data/loris/bin/mri). Hope this helps, C?cile On Wed, Jul 24, 2019 at 10:55 AM Sotirios Nikoloutsopoulos > wrote: Ok first i execute this command: "lorisadmin at hbp:/data/loris/bin/mri$ ./batch_uploads_imageuploader -profile prod < ~/Desktop/input.txt > log.txt Use of uninitialized value $data_dir in concatenation (.) or string at ./batch_uploads_imageuploader line 143. Use of uninitialized value $data_dir in concatenation (.) or string at ./batch_uploads_imageuploader line 143. Use of uninitialized value $_ in pattern match (m//) at ./batch_uploads_imageuploader line 147. base is DCC0000_258024_V01 path is /data/incoming/ type is .tar.gz fullpath is /data/incoming/DCC0000_258024_V01.tar.gz source /tmp/ImagingUpload-17-43-ZUEFjb targetlocation /data/loris/data/tarchive Use of uninitialized value $data_dir in concatenation (.) or string at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 256. Use of uninitialized value $data_dir in concatenation (.) or string at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 284. Use of uninitialized value $data_dir in concatenation (.) or string at /data/loris/bin/mri/uploadNeuroDB/tarchive_validation.pl line 219. Use of uninitialized value $data_dir in concatenation (.) or string at /data/loris/bin/mri/uploadNeuroDB/minc_insertion.pl line 270. Use of uninitialized value $data_dir in concatenation (.) or string at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 711. Can't exec "mail": No such file or directory at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 721. print() on closed filehandle MAIL at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 722. print() on closed filehandle MAIL at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 723. Use of uninitialized value $data_dir in concatenation (.) or string at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 724. print() on closed filehandle MAIL at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 724. print() on closed filehandle MAIL at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 725. Use of uninitialized value $data_dir in concatenation (.) or string at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 735. No Mincs inserted The tarchiveLoader insertion script has failed. Running now the following command: /data/loris/data/uploadNeuroDB/imaging_upload_file.pl -profile prod -upload_id 3 /data/incoming/DCC0000_258024_V01.tar.gz -verbose" I inserted the VisitLabel, but still the Mincs are not inserted and i am getting this error "lorisadmin at hbp:/data/loris/bin/mri$ /data/loris/data/uploadNeuroDB/imaging_upload_file.pl -profile prod -upload_id 3 /data/incoming/DCC0000_258024_V01.tar.gz -verbose find -path \/tmp\/ImagingUpload\-17\-45\-5MsWEd -name '__MACOSX' -delete Spool message is: The Scan for the uploadID 3 has already been run with tarchiveID: 7. To continue with the rest of the insertion pipeline, please run tarchiveLoader from a terminal as follows: /data/LORIS/data//uploadNeuroDB/tarchiveLoader -globLocation -profile prod /data/loris/data/tarchive//2012/DCM_2012-12-05_ImagingUpload-17-43-ZUEFjb.tar -verbose" Which files should i delete? I thought that deleting the files from the tarchive was enough. And i executed the last proposed command to continue to rest of the insertion pipeline ( check the image ). Thank you ???? ???, 24 ???? 2019 ???? 5:05 ?.?., ?/? Cecile Madjar > ??????: Hi Sotirios, Sorry I was not clear before. Every visits of candidates are created in the session table with one entry per CandID/VisitLabel. So if the imaging pipeline created visits in the session table (that are not attached to instruments) and you want to clean your database completely, you can delete entries in that table as well. Regarding your point 2, the imaging pipeline can create the visit in the session table as long as the visit label is present in the Visit_Windows table (which means the visit label stored in the PatientName is a valid visit label). However, in your prod file, if the variable $subjectID{'createVisitLabel'} is set to 1 for candidates, the visit label should be created in the Visit_Windows table I believe. Here is the line of the prod file you would need to change. In general, we prefer populating the Visit_Windows table and set the $subjectID{'createVisitLabel'} to 0 for candidate data to avoid insertion of badly labelled MRI data that are complex to relabel. Finally, regarding the candidate creation, if you execute the following steps, the pipeline should be able to create candidates: - set in the Imaging Pipeline section of the config module the config setting "Upload creation of candidates" to Yes - manually transfer the scans to the LORIS server instead of uploading it via the imaging browser - run batch_imaging_upload.pl as you did until now. Hope this helps! Best, C?cile On Wed, Jul 24, 2019 at 8:47 AM Sotirios Nikoloutsopoulos > wrote: About my second question i replaced the name of the patient in the .dcm files and now i am getting an error that the visit label does not exist. I thought it was supposed to be automatically created. "Done adding archive info into database /data/LORIS/data//uploadNeuroDB/tarchiveLoader -globLocation -profile prod /data/loris/data/tarchive//DCM_2012-12-05_ImagingUpload-15-42-yUwQQV.tar -verbose md5sum /data/loris/data/tarchive/DCM_2012-12-05_ImagingUpload-15-42-yUwQQV.tar PSCID is: DCC0000 CandID id: 258024 visit_label is: V1 PSCID is: DCC0000 CandID id: 258024 visit_label is: V1 candidate id 258024 => No Visit labelVisit label does not exist Set centerID = 1 PSCID is: DCC0000 CandID id: 258024 visit_label is: V1 PSCID is: DCC0000 CandID id: 258024 visit_label is: V1 Number of MINC files that will be considered for inserting into the database: 1 log dir is /logs and log file is /logs/TarLoad-15-42-L6pocU.log PSCID is: DCC0000 CandID id: 258024 visit_label is: V1 PSCID is: DCC0000 CandID id: 258024 visit_label is: V1 candidate id 258024 => No Visit label Cleaning up temp files: rm -rf /tmp/TarLoad-15-42-J2rQms/ImagingUpload-15-42-yUwQQV*" ???? ???, 24 ???? 2019 ???? 3:38 ?.?., ?/? Sotirios Nikoloutsopoulos > ??????: Hi, 1) What are the records in the session table? 2) I tried to upload a non-phantom file like this input_file.txt: /data/incoming/DCC0000_258024_V1.tar.gz N DCC0000_258024_V1 Terminal: ./batch_uploads_imageuploader -profile prod < ~/Desktop/input.txt > log.txt and i get the following error in the log.txt file "Running now the following command: /data/loris/data/uploadNeuroDB/imaging_upload_file.pl -profile prod -upload_id 7 /data/incoming/DCC0000_258024_V1.tar.gz -verbose find -path \/tmp\/ImagingUpload\-14\-56\-FeLCB4 -name '__MACOSX' -delete Spool message is: The PatientName read from the DICOM header does not start with DCC0000_258024_V1 from the mri_upload table " and the spool message is repeated for each .dcm file. Should i preprocess every .dcm file and change the PatientName to "DCC0000_258024_V1"? 3) As far as it concerns the candidate profile i have to create a new one each time before i try to upload a file? Is there already a way to create a candidate profile and get the DCCID and PSCID without the user interface? Thank you, Sotirios ???? ???, 18 ???? 2019 ???? 5:00 ?.?., ?/? Cecile Madjar > ??????: Hi Sotirios, See answers to your questions below. About the 1st case we had a dicom with a blank studyUID, maybe someone accidentally removed it. That is strange. Something must have been done to the DICOM files. I have never seen a study with no StudyUID out of the scanner. Usually, you need to manually erase it with some tool. However, DICOMs never cease to surprise me... Some other questions: 1) What are the steps to remove all of my patients and uploads?: because i want to try to reupload all the testing dicoms we had with a clean database. Release 21.0 of LORIS-MRI will offer a script to remove all the entries and files specific to an upload. However, this release is not yet out. Hopefully in the next few weeks. In the meantime, since your case is particular and that you just want to start with a clean database, the following deletes should work (hopefully I won't forget any tables): delete from mri_violations_log; delete from mri_protocol_violated_scans; delete from MRICandidateErrors; delete from parameter_file; delete from files_qcstatus; # (if you played with the QC part of the imaging browser for testing) delete from feedback_mri_comments; # (if you played with the QC part of the imaging browser for testing) delete from tarchive_series; delete from tarchive_files; delete from mri_upload; delete from tarchive; delete from mri_scanner; delete from candidate where PSCID="scanner"; I don't know if you want to also delete entries in the session and candidate table too? 2) We do not need to create the profile of a patient ( are the patients stored in the candidate table? because i can't see the ghosts ), because will it automatically be created when importing a dicom? I am not sure I understand fully this question. All candidates are stored in the candidate table. The phantom scans however are attached to a scanner candidate depending on where the scan happened. It is a bit of a weird concept that we have to redesign eventually but never got a chance to get to it. Hopefully this answered your question, otherwise, don't hesitate to let me know. 3) What is the difference between uploading a dicom as phantom instead of importing as PSCCID_DCCID_VisitLabel? When you upload the scan as PSCID_DCCID_VisitLabel, there is a check that makes sure the candidate IDs and visit label are valid at the time of upload. When you upload a scan as phantom, it expects that the DICOM field PatientName and uploaded filename contains the string "phantom". We enforced this behaviour on the imaging uploader side in recent releases but I can't remember which one. Probably the upcoming 21.0 release. All those verifications might seem cumbersome but they are here to ensure that the files inserted are all valid and labelled properly as it is a bit messy to have to delete files that were wrongly labelled. At least, the delete script present in release 21.0 will make this process easier but it is still good practice to verify those things. Thank you, With pleasure. Hopefully the answers to your questions will be helpful. Best, C?cile PS: loris-dev mailing list: you will find the initial answer I gave Sotirios below. I forgot to cc the loris-dev in my earlier reply... ???? ???, 16 ???? 2019 ???? 12:02 ?.?., ?/? Cecile Madjar > ??????: Dear Sotirios, Thank you for reaching out. Since your email was already organized in points, I will reply directly below your questions below. Best, C?cile 1) What do we do when the StudyUID is blank on the header? https://github.com/aces/Loris-MRI/blob/minor/docs/AppendixA-Troubleshooting_guideline.md There solution provided at the table 3 does not guide us how to find the information ( is possible ). The StudyUID is the field used in our pipeline at the moment to check whether a DICOM study was already inserted into LORIS with that same StudyUID since it is supposed to be unique for every single study. Currently, we do not support insertion of DICOM studies if they do not have a StudyUID associated with them. Is there a specific reason why the StudyUID is blank in the DICOM headers in your DICOM files? Did they go through some processes before upload to LORIS? 2) When i am about to upload a non-phanton case i need a 'Visit Label'. Is there already a script that can create a new visit label for a specific Candidate, so i can provide it as input afterwards to the batch_uploads_imageuploader ( See option 5.1.3 https://github.com/aces/Loris-MRI/blob/minor/docs/05-PipelineLaunchOptions.md ) I am not sure if the front-end allows for it but if you use batch_uploads_imageuploader, the insertion scripts could create the visit label for you. However, it does need to be included in the patient name in order for the script to know which label it should use. For example: you upload V02 for MTL0123 (DCCID: 456789) but V02 was not yet created for MTL0123; the insertion scripts will create a V02 visit for MTL0123 if the PatientName field for the dataset is MTL0123_456789_V02 with Stage marked as "Not Started". However, note that for the script to create the visit for the candidate, you have to make sure that all the visit label of your projects were inserted in the Visit_Windows table (otherwise, the visit will never be created as they were not specified as being part of the list of visit label to expect). So in the example above, you should have one row in Visit_Windows with Visit_label="V02" set. 3) Section 4.3 https://github.com/aces/Loris-MRI/blob/minor/docs/04-Scripts.md What do we do when the folder contains multiple mnc files? This is a case by case. Most of the time, the MINC files that failed insertion into the imaging browser end up in the MRI violation module where you can see what went wrong with the acquisitions not inserted. If you notice that the MINC file should be inserted as a specific protocol, you can force the insertion as explained in section 4.3. In your case, I have a feeling that you want to be able to insert MINC files that did not go through the whole pipeline insertion (DICOM archival, then dcm2mnc, then protocol identification, then insertion...). In theory, you could call minc_insertion.pl on any MINC file, provided you have at least the following information: - path to the MINC file - uploadID associated with the MINC files or DICOM archive path from which those MINC files were created from Then the minc_insertion.pl script will do the subject information and protocol validation etc... If all the MINC files come from the same uploadID or TarchiveID, then you could run a loop in bash calling the minc_insertion.pl script like this for files deriving from uploadID=1: ls /path/to/mnc/folder/* | while read f; do minc_insertion.pl -profile prod -uploadID 1 -mincPath $f; done Thank you, Hope this helped! _______________________________________________ Loris-dev mailing list Loris-dev at bic.mni.mcgill.ca https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev -- christine.rogers at mcgill.ca McGill Centre for Integrative Neuroscience | MCIN.ca Montreal Neurological Institute McGill University | Montreal | Canada -- christine.rogers at mcgill.ca McGill Centre for Integrative Neuroscience | MCIN.ca Montreal Neurological Institute McGill University | Montreal | Canada _______________________________________________ Loris-dev mailing list Loris-dev at bic.mni.mcgill.ca https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev -- christine.rogers at mcgill.ca McGill Centre for Integrative Neuroscience | MCIN.ca Montreal Neurological Institute McGill University | Montreal | Canada _______________________________________________ Loris-dev mailing list Loris-dev at bic.mni.mcgill.ca https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev -- christine.rogers at mcgill.ca McGill Centre for Integrative Neuroscience | MCIN.ca Montreal Neurological Institute McGill University | Montreal | Canada -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 78176 bytes Desc: image.png URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 20518 bytes Desc: image.png URL: From christine.rogers at mcgill.ca Tue Aug 6 10:09:01 2019 From: christine.rogers at mcgill.ca (Christine Rogers, Ms.) Date: Tue, 6 Aug 2019 14:09:01 +0000 Subject: [Loris-dev] Import mri - scripts In-Reply-To: References: <65ad2b70c3084ffdb1e4a9dcdad948cd@YTOPR0101MB1803.CANPRD01.PROD.OUTLOOK.COM> Message-ID: Hi Sotirios, Could you also let us know -- on which pages is content visible, and on which pages/modules is content not visible for you? Thanks, Christine On Tue, Aug 6, 2019 at 9:54 AM Christine Rogers, Ms. > wrote: Thanks Sotirios, That's good to know. It sounds like you've checked that your /var/www/loris/project/config.xml file get populated properly. Please send us the last few errors you're seeing in your apache error log file, and your config paths and we can see what's happening with your front end -- Run these Troubleshooting Queries to get your config path settings, given your front end is not displaying fully. The Loris-MRI repo 21 install/upgrade would then be your next steps. Best, Christine On Tue, Aug 6, 2019 at 7:53 AM Sotirios Nikoloutsopoulos > wrote: I am using a VM. What i did was: 1) Download the files from https://github.com/aces/Loris and replace them to my existing /vaw/www/loris folder. 2) Execute the composer install --no-dev and then composer dump-autoload as mentioned here https://github.com/aces/Loris/wiki/Updating-your-LORIS. 3) Execute install.sh from /var/www/loris/tools and because LORIS already existed i moved a .config file, then re-executed the install.sh successfully 4 ) As for the database, i dropped the schema and i executed the installdb.php ???? ???, 5 ??? 2019 ???? 5:22 ?.?., ?/? Christine Rogers, Ms. > ??????: Hi Sotorios, Thanks - when you re-installed did you start on a fresh root path / VM or might some of your old system setting still apply? (And if you did any steps similar to an upgrade, did you follow the Upgrade steps in the Release Notes, from both repos?) About the TR_range column - it was recently split (MRI pr339) split into TR_min and _max columns. Given the code was trying to query TR_range which does not exist in your mri_protocol table, double-check which version of the Loris repo (tables) and the Loris-MRI repo (code) you have installed to ensure they match. Christine On Mon, Aug 5, 2019 at 9:06 AM Sotirios Nikoloutsopoulos > wrote: I reinstalled LORIS to 21 version and now the content is not visible at all at most pages. [image.png] ???? ???, 5 ??? 2019 ???? 3:19 ?.?., ?/? Sotirios Nikoloutsopoulos > ??????: Hi, Is it easy to upgrade to Loris 21? Also the following fails because the line 1985 of NeuroDB/MRIProcessingUtility.pm query mri_protocol which doesn't have TR_range https://github.com/aces/Loris/blob/21.0-release/SQL/0000-00-00-schema.sql#L556 [image.png] lorisadmin at hbp:/data/loris/bin/mri$ ./batch_uploads_imageuploader -profile prod < ~/Desktop/input.txt > log.txt Use of uninitialized value $_ in pattern match (m//) at ./batch_uploads_imageuploader line 147. base is DCC0000_258024_V1 path is /data/incoming/ type is .tar.gz fullpath is /data/incoming/DCC0000_258024_V1.tar.gz DBD::mysql::st execute failed: Unknown column 'TR_range' in 'where clause' at /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line 1985. DBD::mysql::st fetchrow_array failed: fetch() without execute() at /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line 1986. Use of uninitialized value $count_mri_protocol in numeric gt (>) at /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line 1995. DBD::mysql::st execute failed: Unknown column 'TR_range' in 'field list' at /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 562. Can't exec "mail": No such file or directory at /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 721. print() on closed filehandle MAIL at /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 722. print() on closed filehandle MAIL at /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 723. print() on closed filehandle MAIL at /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 724. print() on closed filehandle MAIL at /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 725. No Mincs inserted Thanks, Sotirios ???? ???, 3 ??? 2019 ???? 1:08 ?.?., ?/? Christine Rogers, Ms. > ??????: Hi Sotirios, First, just a note: we've released LORIS 21 this week with some major new features and cleanup -- especially if you are early in your setup phase, check out the Release notes for both the LORIS and Loris-MRI repos. Thanks for your screenshots -- your empty mri_protocol table should be at the root of these issues : The mri_protocol table must be populated in order for your scans to be registered in LORIS -- it serves as a whitelist for the insertion pipeline which filters out scans that aren't identified or matched to scan types in this table. By default, this table is populated with entries for t1, t2, fMRI and DTI (Insert statements for 21 release branch are here) Feel free to restore our default records and broaden their parameters to match all your scan types. re Defaced, native, selected -- these filter the scans displayed as you move to the next page (View Session), instead of viewing "all types" of scans from a given session : * "defaced" means that a defacing script has masked the subject's face in the volume (for patient privacy) * "native" means that no pre-processing has been performed on the scan (it's raw data), * "selected" will show only volumes that have been QC'd and "selected" as the best of their type -- used to display only the best quality T1 image instead of all T1s acquired in a session, e.g. re QC Comments -- Once you have successfully loaded scans (matched to the mri_protocol table), you'll be able to use the Imaging Browser's View Session subpage to enter/view QC comments on each volume, or for each visit. These are stored directly in the database, and linked to each scan. (Table name: feedback_mri_comments) (Visit-level QC comments are linked to the session.) For a walkthrough of the Imaging setup - please see the Imaging Setup guide - An old LORIS walkthrough video can also walk you through some of the Imaging front-end features, starting at 8:00 LORIS' imaging modules have been updated many times since this video, but the functionality and workflow is similar. Let us know how it goes once you have entries in your mri_protocol table - Best, Christine On Fri, Aug 2, 2019 at 7:58 AM Sotirios Nikoloutsopoulos > wrote: Hi Christine, In the candidate_list page i can see this patient [image.png] If i press the link under PSCID i get to see [image.png] and if i press the link under Scan Done it redirects me to imaging_browser [image.png] At the mri_violations page i also see No results ( neither on resolved / not resolved ). At the imaging_uploader i can see the record that failed. [image.png] If i click on the tarchive info i get to see the Protocol Name which i think is the acquisition we wanted? [image.png] Also my mri_protocol table is empty. Furthermore i would like to ask about the defaced, native, selected. What exactly is native and selected? And where are the qc comments stored? [image.png] Finally a walkthrough would be helpful. Thanks, Sotirios ???? ???, 30 ???? 2019 ???? 8:29 ?.?., ?/? Christine Rogers, Ms. > ??????: Hi Sotirios, Glad to hear you're making progress with the visit labels. To follow up on your last few emails: a- The Wiki's Setup Guide contains Sample insert statements for the Visit Windows table. As Cecile mentioned, the consistency of visit label format is important: V01, v01, V1, 01 -- whichever you select to use is fine; we use V01 by default across all documentation. b- For Password reset, there is a script in the tools/ directory so that a back-end administrator can reset any front-end user password, including Admin. (See info on setting up / resetting User passwords in the Wiki's Setup Guide) c- The minc file not being registered -- due to AcquisitionProtocol unknown. This means the SeriesDescription (Acquisition Protocol) in you Dicom header was not matched to any scan listed in the mri_protocol database table. (In the online Loris-MRI Troubleshooting Guide, this is Table 3, 2nd-last item "no MINCs inserted"). The MRI Violations module (Readme here) will show you the details of this mismatch -- Go to the module (under the Imaging menu), find your scan and click the link "Could not identify scan type" -- in the next subpage you can compare the scan's actual parameters against the mri_protocol table. To resolve this, adjust your mri_protocol table values or perhaps ensure your DICOMs are labelled consistently. Let us know if this works for you -- we can also walk you through an example of non-identified scans on Demo.loris.ca (MRI Violations module). Best, Christine The LORIS team On Tue, Jul 30, 2019 at 10:47 AM Sotirios Nikoloutsopoulos > wrote: I hope this is sufficient as the error for the visit label disappeared. [image.png] Please see the attached file. Also something i found. lorisadmin at hbp:/data/loris/bin/mri$ cat /data/loris/data//logs/TarLoad-17-39-xubBdv.log ==> Loading file from disk /tmp/TarLoad-17-39-UyQcG2/dcc0000_258024_v1_20121205_102108_501e1_mri.mnc --> mapping DICOM parameter for /tmp/TarLoad-17-39-UyQcG2/dcc0000_258024_v1_20121205_102108_501e1_mri.mnc ==> computing md5 hash for MINC body. --> md5: 6b1202fd63e29de4c9be1cd9925888a5 ==> verifying acquisition protocol Acquisition protocol is unknown --> The minc file cannot be registered since the AcquisitionProtocol is unknown ???? ???, 30 ???? 2019 ???? 4:58 ?.?., ?/? Sotirios Nikoloutsopoulos > ??????: Ok I fixed the login problem by using a known hash and by deleting the rows from the login_history i was able to login. ???? ???, 30 ???? 2019 ???? 4:50 ?.?., ?/? Sotirios Nikoloutsopoulos > ??????: Hi, there was no visit label 01 in the Visit_Windows table and i don't know how to insert it because the record requires lots of attributes. Also the system for a reason asked me to update my password and now i don't remember it and my account got suspended. Is there a way to reset it or set a simple password? I updated the password hash in the users table by using the hash from another LORIS setup we had and i still couldn't login ( also the attribute password is always NULL and the expiration date is 1999-01-01 for some reason ). Thanks ???? ???, 29 ???? 2019 ???? 5:21 ?.?., ?/? Cecile Madjar > ??????: Hi Sotirios, Can you try adding the visit label v01 to the Visit_Windows table? However, I noticed that in a previous dataset, the label was V1. Does that refer to the same visit? If so, you might want to harmonize the visit labels so they are all the same across datasets for a given timepoint, meaning you will need to relabel scans when the visit label is different but referring to the same visit label (v01 = V1 etc...). Hope this helps, C?cile On Mon, Jul 29, 2019 at 10:15 AM Sotirios Nikoloutsopoulos > wrote: Hi, Could you help me with the "Visit label does not exist"? I had changed $subjectID{'createVisitLabel'} to 1 as you had suggested but it appears that this problem hasn't been resolved yet. lorisadmin at hbp:/data/loris/bin/mri$ cat /data/loris/data//logs/TarLoad-14-58-9Xog7H.log ==> Loading file from disk /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc --> mapping DICOM parameter for /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc --> using user-defined filterParameters for /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc Candidate Mismatch Error is Visit label does not exist -> WARNING: This candidate was invalid. Logging to MRICandidateErrors table with reason Visit label does not exist Thank you, Sotirios ???? ???, 26 ???? 2019 ???? 3:02 ?.?., ?/? Sotirios Nikoloutsopoulos > ??????: Hi Cecile, The Center error was fixed. Still the insertion of mincs fails. Please see the output.txt file i attached. Also is there something else i need to change at the paths configuration? Thank you, Sotirios ???? ???, 25 ???? 2019 ???? 6:55 ?.?., ?/? Cecile Madjar > ??????: Hi Sotirios, We are making progress! I have a feeling this error comes from the fact that your psc table does not have the MRI_alias populated for the DCC site. Running the following query in the mysql database should fix this: UPDATE psc SET MRI_alias="DCC", Alias="DCC" WHERE Name="Data Coordinating Center"; Repeat the same with all your sites (make sure to change the Aliases between sites, they should all be unique). Let me know how it goes! Best, C?cile On Thu, Jul 25, 2019 at 11:43 AM Sotirios Nikoloutsopoulos > wrote: Dear Cecile, You were right about your guesses. I did the modifications you suggested, i still get the "no mincs inserted" error, now i am getting the "No center found this candidate" error ( how do i fix that? from what i see the .dcm files contains a 'Institution Name', is that the center? ), so i guess that's why the validation fails, but i changed the force variable of tarchiveLoader to 1, shouldn't it have inserted the mincs then? Also it is optional to have a mail server, right? ( from what i see the mail error does not affect the $valid_study, so i assume we are okay with that ) Thank you a lot, Sotirios ???? ???, 25 ???? 2019 ???? 5:48 ?.?., ?/? Cecile Madjar > ??????: Hi Sotirios, From what I understand, I believe you just need to update a few config settings from the frontend in the Config module (under the Admin menu). [Screen Shot 2019-07-25 at 10.31.35 AM.png] Then go to the Paths section of the config module and update the "LORIS-MRI code" config setting to /data/loris/bin/mri (my guess is that currently, it is set to /data/LORIS/data) and click on the submit button. [Screen Shot 2019-07-25 at 10.32.50 AM.png] Then, go to Imaging Pipeline section of the Configuration module and update the "Loris-MRI Data Directory" to /data/loris/data/ (my guess is that it is empty at the moment in your database which is why $data_dir is not defined when you run the tarchiveLoader step of the insertion pipeline). [Screen Shot 2019-07-25 at 10.40.52 AM.png] Finally, I took a look at your environment file and it might be a good idea to update your PERL5LIB variable to the following (it has been added to the code a few releases ago as we realized this was needed for the libraries. Not sure which version of LORIS-MRI you are using but it does not hurt to update this variable to what I suggest below): export PERL5LIB=/data/loris/bin/mri/uploadNeuroDB:/data/loris/bin/mri/dicom-archive:$PERL5LIB Hope this helps. Sorry you are experiencing so much trouble setting things up. We probably need to update our WIKI. Best, C?cile On Thu, Jul 25, 2019 at 9:48 AM Sotirios Nikoloutsopoulos > wrote: The "Loris-MRI Data Directory" should be in the environment file? ???? ???, 25 ???? 2019 ???? 12:59 ?.?., ?/? Sotirios Nikoloutsopoulos > ??????: The scripts are located in /data/loris/bin/mri/. Somewhere I might have messed something up but i remember following the instructions in the wiki.For example when i tried to execute the batch_uploads_imageuploader perl script the line my $command = "$bin_dir/uploadNeuroDB/imaging_upload_file.pl " was pointing to an invalid path, for example: it was repeating a pattern and had LORIS instead of loris ( i think the mistake was that in the wiki it suggested to use $PROJECT for the name of the folder and i choosed 'loris' https://github.com/aces/Loris/wiki/Imaging-Database ). See also the in image for the modification i did. Also i didn't find the section to config the $data_dir variable. Thank you, Sotirios ???? ???, 24 ???? 2019 ???? 6:05 ?.?., ?/? Cecile Madjar > ??????: Hi Sotirios, It looks like you have one Config setting not set (based on the first error message you got when running it the first time). You need to set a value for "Loris-MRI Data Directory" in the Config module under the Imaging pipeline section (from what I can see, it would be /data/loris/data/ for your setup). The reason you got that error message the second time is that the pipeline checks if the DICOM study was already inserted in the tarchive table. Since you ran the study once already, the study is inserted into the tarchive, hence the message. However, the pipeline did not complete as the MINC files were not created and inserted into the files/parameter_file table. In order to continue the insertion, you will then need to run the tarchiveLoader command suggested in the terminal during the second run: /data/LORIS/data//uploadNeuroDB/tarchiveLoader -globLocation -profile prod /data/loris/data/tarchive//2012/DCM_2012-12-05_ImagingUpload-17-43-ZUEFjb.tar -verbose Finally, I am a bit confused by your setup. Where are the scripts located? In /data/loris/bin/mri or /data/loris/data? It feels like the Config setting "LORIS-MRI code" in the Paths section was set to "/data/LORIS/data" but it should have been set to the directory where the scripts are located (most probably /data/loris/bin/mri). Hope this helps, C?cile On Wed, Jul 24, 2019 at 10:55 AM Sotirios Nikoloutsopoulos > wrote: Ok first i execute this command: "lorisadmin at hbp:/data/loris/bin/mri$ ./batch_uploads_imageuploader -profile prod < ~/Desktop/input.txt > log.txt Use of uninitialized value $data_dir in concatenation (.) or string at ./batch_uploads_imageuploader line 143. Use of uninitialized value $data_dir in concatenation (.) or string at ./batch_uploads_imageuploader line 143. Use of uninitialized value $_ in pattern match (m//) at ./batch_uploads_imageuploader line 147. base is DCC0000_258024_V01 path is /data/incoming/ type is .tar.gz fullpath is /data/incoming/DCC0000_258024_V01.tar.gz source /tmp/ImagingUpload-17-43-ZUEFjb targetlocation /data/loris/data/tarchive Use of uninitialized value $data_dir in concatenation (.) or string at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 256. Use of uninitialized value $data_dir in concatenation (.) or string at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 284. Use of uninitialized value $data_dir in concatenation (.) or string at /data/loris/bin/mri/uploadNeuroDB/tarchive_validation.pl line 219. Use of uninitialized value $data_dir in concatenation (.) or string at /data/loris/bin/mri/uploadNeuroDB/minc_insertion.pl line 270. Use of uninitialized value $data_dir in concatenation (.) or string at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 711. Can't exec "mail": No such file or directory at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 721. print() on closed filehandle MAIL at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 722. print() on closed filehandle MAIL at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 723. Use of uninitialized value $data_dir in concatenation (.) or string at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 724. print() on closed filehandle MAIL at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 724. print() on closed filehandle MAIL at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 725. Use of uninitialized value $data_dir in concatenation (.) or string at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 735. No Mincs inserted The tarchiveLoader insertion script has failed. Running now the following command: /data/loris/data/uploadNeuroDB/imaging_upload_file.pl -profile prod -upload_id 3 /data/incoming/DCC0000_258024_V01.tar.gz -verbose" I inserted the VisitLabel, but still the Mincs are not inserted and i am getting this error "lorisadmin at hbp:/data/loris/bin/mri$ /data/loris/data/uploadNeuroDB/imaging_upload_file.pl -profile prod -upload_id 3 /data/incoming/DCC0000_258024_V01.tar.gz -verbose find -path \/tmp\/ImagingUpload\-17\-45\-5MsWEd -name '__MACOSX' -delete Spool message is: The Scan for the uploadID 3 has already been run with tarchiveID: 7. To continue with the rest of the insertion pipeline, please run tarchiveLoader from a terminal as follows: /data/LORIS/data//uploadNeuroDB/tarchiveLoader -globLocation -profile prod /data/loris/data/tarchive//2012/DCM_2012-12-05_ImagingUpload-17-43-ZUEFjb.tar -verbose" Which files should i delete? I thought that deleting the files from the tarchive was enough. And i executed the last proposed command to continue to rest of the insertion pipeline ( check the image ). Thank you ???? ???, 24 ???? 2019 ???? 5:05 ?.?., ?/? Cecile Madjar > ??????: Hi Sotirios, Sorry I was not clear before. Every visits of candidates are created in the session table with one entry per CandID/VisitLabel. So if the imaging pipeline created visits in the session table (that are not attached to instruments) and you want to clean your database completely, you can delete entries in that table as well. Regarding your point 2, the imaging pipeline can create the visit in the session table as long as the visit label is present in the Visit_Windows table (which means the visit label stored in the PatientName is a valid visit label). However, in your prod file, if the variable $subjectID{'createVisitLabel'} is set to 1 for candidates, the visit label should be created in the Visit_Windows table I believe. Here is the line of the prod file you would need to change. In general, we prefer populating the Visit_Windows table and set the $subjectID{'createVisitLabel'} to 0 for candidate data to avoid insertion of badly labelled MRI data that are complex to relabel. Finally, regarding the candidate creation, if you execute the following steps, the pipeline should be able to create candidates: - set in the Imaging Pipeline section of the config module the config setting "Upload creation of candidates" to Yes - manually transfer the scans to the LORIS server instead of uploading it via the imaging browser - run batch_imaging_upload.pl as you did until now. Hope this helps! Best, C?cile On Wed, Jul 24, 2019 at 8:47 AM Sotirios Nikoloutsopoulos > wrote: About my second question i replaced the name of the patient in the .dcm files and now i am getting an error that the visit label does not exist. I thought it was supposed to be automatically created. "Done adding archive info into database /data/LORIS/data//uploadNeuroDB/tarchiveLoader -globLocation -profile prod /data/loris/data/tarchive//DCM_2012-12-05_ImagingUpload-15-42-yUwQQV.tar -verbose md5sum /data/loris/data/tarchive/DCM_2012-12-05_ImagingUpload-15-42-yUwQQV.tar PSCID is: DCC0000 CandID id: 258024 visit_label is: V1 PSCID is: DCC0000 CandID id: 258024 visit_label is: V1 candidate id 258024 => No Visit labelVisit label does not exist Set centerID = 1 PSCID is: DCC0000 CandID id: 258024 visit_label is: V1 PSCID is: DCC0000 CandID id: 258024 visit_label is: V1 Number of MINC files that will be considered for inserting into the database: 1 log dir is /logs and log file is /logs/TarLoad-15-42-L6pocU.log PSCID is: DCC0000 CandID id: 258024 visit_label is: V1 PSCID is: DCC0000 CandID id: 258024 visit_label is: V1 candidate id 258024 => No Visit label Cleaning up temp files: rm -rf /tmp/TarLoad-15-42-J2rQms/ImagingUpload-15-42-yUwQQV*" ???? ???, 24 ???? 2019 ???? 3:38 ?.?., ?/? Sotirios Nikoloutsopoulos > ??????: Hi, 1) What are the records in the session table? 2) I tried to upload a non-phantom file like this input_file.txt: /data/incoming/DCC0000_258024_V1.tar.gz N DCC0000_258024_V1 Terminal: ./batch_uploads_imageuploader -profile prod < ~/Desktop/input.txt > log.txt and i get the following error in the log.txt file "Running now the following command: /data/loris/data/uploadNeuroDB/imaging_upload_file.pl -profile prod -upload_id 7 /data/incoming/DCC0000_258024_V1.tar.gz -verbose find -path \/tmp\/ImagingUpload\-14\-56\-FeLCB4 -name '__MACOSX' -delete Spool message is: The PatientName read from the DICOM header does not start with DCC0000_258024_V1 from the mri_upload table " and the spool message is repeated for each .dcm file. Should i preprocess every .dcm file and change the PatientName to "DCC0000_258024_V1"? 3) As far as it concerns the candidate profile i have to create a new one each time before i try to upload a file? Is there already a way to create a candidate profile and get the DCCID and PSCID without the user interface? Thank you, Sotirios ???? ???, 18 ???? 2019 ???? 5:00 ?.?., ?/? Cecile Madjar > ??????: Hi Sotirios, See answers to your questions below. About the 1st case we had a dicom with a blank studyUID, maybe someone accidentally removed it. That is strange. Something must have been done to the DICOM files. I have never seen a study with no StudyUID out of the scanner. Usually, you need to manually erase it with some tool. However, DICOMs never cease to surprise me... Some other questions: 1) What are the steps to remove all of my patients and uploads?: because i want to try to reupload all the testing dicoms we had with a clean database. Release 21.0 of LORIS-MRI will offer a script to remove all the entries and files specific to an upload. However, this release is not yet out. Hopefully in the next few weeks. In the meantime, since your case is particular and that you just want to start with a clean database, the following deletes should work (hopefully I won't forget any tables): delete from mri_violations_log; delete from mri_protocol_violated_scans; delete from MRICandidateErrors; delete from parameter_file; delete from files_qcstatus; # (if you played with the QC part of the imaging browser for testing) delete from feedback_mri_comments; # (if you played with the QC part of the imaging browser for testing) delete from tarchive_series; delete from tarchive_files; delete from mri_upload; delete from tarchive; delete from mri_scanner; delete from candidate where PSCID="scanner"; I don't know if you want to also delete entries in the session and candidate table too? 2) We do not need to create the profile of a patient ( are the patients stored in the candidate table? because i can't see the ghosts ), because will it automatically be created when importing a dicom? I am not sure I understand fully this question. All candidates are stored in the candidate table. The phantom scans however are attached to a scanner candidate depending on where the scan happened. It is a bit of a weird concept that we have to redesign eventually but never got a chance to get to it. Hopefully this answered your question, otherwise, don't hesitate to let me know. 3) What is the difference between uploading a dicom as phantom instead of importing as PSCCID_DCCID_VisitLabel? When you upload the scan as PSCID_DCCID_VisitLabel, there is a check that makes sure the candidate IDs and visit label are valid at the time of upload. When you upload a scan as phantom, it expects that the DICOM field PatientName and uploaded filename contains the string "phantom". We enforced this behaviour on the imaging uploader side in recent releases but I can't remember which one. Probably the upcoming 21.0 release. All those verifications might seem cumbersome but they are here to ensure that the files inserted are all valid and labelled properly as it is a bit messy to have to delete files that were wrongly labelled. At least, the delete script present in release 21.0 will make this process easier but it is still good practice to verify those things. Thank you, With pleasure. Hopefully the answers to your questions will be helpful. Best, C?cile PS: loris-dev mailing list: you will find the initial answer I gave Sotirios below. I forgot to cc the loris-dev in my earlier reply... ???? ???, 16 ???? 2019 ???? 12:02 ?.?., ?/? Cecile Madjar > ??????: Dear Sotirios, Thank you for reaching out. Since your email was already organized in points, I will reply directly below your questions below. Best, C?cile 1) What do we do when the StudyUID is blank on the header? https://github.com/aces/Loris-MRI/blob/minor/docs/AppendixA-Troubleshooting_guideline.md There solution provided at the table 3 does not guide us how to find the information ( is possible ). The StudyUID is the field used in our pipeline at the moment to check whether a DICOM study was already inserted into LORIS with that same StudyUID since it is supposed to be unique for every single study. Currently, we do not support insertion of DICOM studies if they do not have a StudyUID associated with them. Is there a specific reason why the StudyUID is blank in the DICOM headers in your DICOM files? Did they go through some processes before upload to LORIS? 2) When i am about to upload a non-phanton case i need a 'Visit Label'. Is there already a script that can create a new visit label for a specific Candidate, so i can provide it as input afterwards to the batch_uploads_imageuploader ( See option 5.1.3 https://github.com/aces/Loris-MRI/blob/minor/docs/05-PipelineLaunchOptions.md ) I am not sure if the front-end allows for it but if you use batch_uploads_imageuploader, the insertion scripts could create the visit label for you. However, it does need to be included in the patient name in order for the script to know which label it should use. For example: you upload V02 for MTL0123 (DCCID: 456789) but V02 was not yet created for MTL0123; the insertion scripts will create a V02 visit for MTL0123 if the PatientName field for the dataset is MTL0123_456789_V02 with Stage marked as "Not Started". However, note that for the script to create the visit for the candidate, you have to make sure that all the visit label of your projects were inserted in the Visit_Windows table (otherwise, the visit will never be created as they were not specified as being part of the list of visit label to expect). So in the example above, you should have one row in Visit_Windows with Visit_label="V02" set. 3) Section 4.3 https://github.com/aces/Loris-MRI/blob/minor/docs/04-Scripts.md What do we do when the folder contains multiple mnc files? This is a case by case. Most of the time, the MINC files that failed insertion into the imaging browser end up in the MRI violation module where you can see what went wrong with the acquisitions not inserted. If you notice that the MINC file should be inserted as a specific protocol, you can force the insertion as explained in section 4.3. In your case, I have a feeling that you want to be able to insert MINC files that did not go through the whole pipeline insertion (DICOM archival, then dcm2mnc, then protocol identification, then insertion...). In theory, you could call minc_insertion.pl on any MINC file, provided you have at least the following information: - path to the MINC file - uploadID associated with the MINC files or DICOM archive path from which those MINC files were created from Then the minc_insertion.pl script will do the subject information and protocol validation etc... If all the MINC files come from the same uploadID or TarchiveID, then you could run a loop in bash calling the minc_insertion.pl script like this for files deriving from uploadID=1: ls /path/to/mnc/folder/* | while read f; do minc_insertion.pl -profile prod -uploadID 1 -mincPath $f; done Thank you, Hope this helped! _______________________________________________ Loris-dev mailing list Loris-dev at bic.mni.mcgill.ca https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev -- christine.rogers at mcgill.ca McGill Centre for Integrative Neuroscience | MCIN.ca Montreal Neurological Institute McGill University | Montreal | Canada -- christine.rogers at mcgill.ca McGill Centre for Integrative Neuroscience | MCIN.ca Montreal Neurological Institute McGill University | Montreal | Canada _______________________________________________ Loris-dev mailing list Loris-dev at bic.mni.mcgill.ca https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev -- christine.rogers at mcgill.ca McGill Centre for Integrative Neuroscience | MCIN.ca Montreal Neurological Institute McGill University | Montreal | Canada _______________________________________________ Loris-dev mailing list Loris-dev at bic.mni.mcgill.ca https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev -- christine.rogers at mcgill.ca McGill Centre for Integrative Neuroscience | MCIN.ca Montreal Neurological Institute McGill University | Montreal | Canada _______________________________________________ Loris-dev mailing list Loris-dev at bic.mni.mcgill.ca https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev -- christine.rogers at mcgill.ca McGill Centre for Integrative Neuroscience | MCIN.ca Montreal Neurological Institute McGill University | Montreal | Canada -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 78176 bytes Desc: image.png URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 20518 bytes Desc: image.png URL: From christine.rogers at mcgill.ca Tue Aug 6 15:13:42 2019 From: christine.rogers at mcgill.ca (Christine Rogers, Ms.) Date: Tue, 6 Aug 2019 19:13:42 +0000 Subject: [Loris-dev] Upgrading to Loris 21 - new make file In-Reply-To: Message-ID: Hi Sotirios and LORIS community -- When upgrading to brand-new release 21 -- just a reminder to follow the release notes and run the new make file to update your dependencies (instead of using composer commands). We've also updated the Wiki page to clarify that the release notes for each version will tell you what to run. If your current version is not the last release (20.3), it's still important to upgrade to each minor release increment (e.g. 20.2, 20.3) before making the leap to 21.0. If you're getting blank pages, post-upgrade -- Try clearing your cache. Got questions or feedback e.g. on the Release Notes? please don't hesitate to let us know. Thanks, Christine The LORIS team On Tue, Aug 6, 2019 at 10:09 AM Christine Rogers, Ms. > wrote: Hi Sotirios, Could you also let us know -- on which pages is content visible, and on which pages/modules is content not visible for you? Thanks, Christine On Tue, Aug 6, 2019 at 9:54 AM Christine Rogers, Ms. > wrote: Thanks Sotirios, That's good to know. It sounds like you've checked that your /var/www/loris/project/config.xml file get populated properly. Please send us the last few errors you're seeing in your apache error log file, and your config paths and we can see what's happening with your front end -- Run these Troubleshooting Queries to get your config path settings, given your front end is not displaying fully. The Loris-MRI repo 21 install/upgrade would then be your next steps. Best, Christine On Tue, Aug 6, 2019 at 7:53 AM Sotirios Nikoloutsopoulos > wrote: I am using a VM. What i did was: 1) Download the files from https://github.com/aces/Loris and replace them to my existing /vaw/www/loris folder. 2) Execute the composer install --no-dev and then composer dump-autoload as mentioned here https://github.com/aces/Loris/wiki/Updating-your-LORIS. 3) Execute install.sh from /var/www/loris/tools and because LORIS already existed i moved a .config file, then re-executed the install.sh successfully 4 ) As for the database, i dropped the schema and i executed the installdb.php ???? ???, 5 ??? 2019 ???? 5:22 ?.?., ?/? Christine Rogers, Ms. > ??????: Hi Sotorios, Thanks - when you re-installed did you start on a fresh root path / VM or might some of your old system setting still apply? (And if you did any steps similar to an upgrade, did you follow the Upgrade steps in the Release Notes, from both repos?) About the TR_range column - it was recently split (MRI pr339) split into TR_min and _max columns. Given the code was trying to query TR_range which does not exist in your mri_protocol table, double-check which version of the Loris repo (tables) and the Loris-MRI repo (code) you have installed to ensure they match. Christine On Mon, Aug 5, 2019 at 9:06 AM Sotirios Nikoloutsopoulos > wrote: I reinstalled LORIS to 21 version and now the content is not visible at all at most pages. [image.png] ???? ???, 5 ??? 2019 ???? 3:19 ?.?., ?/? Sotirios Nikoloutsopoulos > ??????: Hi, Is it easy to upgrade to Loris 21? Also the following fails because the line 1985 of NeuroDB/MRIProcessingUtility.pm query mri_protocol which doesn't have TR_range https://github.com/aces/Loris/blob/21.0-release/SQL/0000-00-00-schema.sql#L556 [image.png] lorisadmin at hbp:/data/loris/bin/mri$ ./batch_uploads_imageuploader -profile prod < ~/Desktop/input.txt > log.txt Use of uninitialized value $_ in pattern match (m//) at ./batch_uploads_imageuploader line 147. base is DCC0000_258024_V1 path is /data/incoming/ type is .tar.gz fullpath is /data/incoming/DCC0000_258024_V1.tar.gz DBD::mysql::st execute failed: Unknown column 'TR_range' in 'where clause' at /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line 1985. DBD::mysql::st fetchrow_array failed: fetch() without execute() at /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line 1986. Use of uninitialized value $count_mri_protocol in numeric gt (>) at /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line 1995. DBD::mysql::st execute failed: Unknown column 'TR_range' in 'field list' at /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 562. Can't exec "mail": No such file or directory at /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 721. print() on closed filehandle MAIL at /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 722. print() on closed filehandle MAIL at /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 723. print() on closed filehandle MAIL at /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 724. print() on closed filehandle MAIL at /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 725. No Mincs inserted Thanks, Sotirios ???? ???, 3 ??? 2019 ???? 1:08 ?.?., ?/? Christine Rogers, Ms. > ??????: Hi Sotirios, First, just a note: we've released LORIS 21 this week with some major new features and cleanup -- especially if you are early in your setup phase, check out the Release notes for both the LORIS and Loris-MRI repos. Thanks for your screenshots -- your empty mri_protocol table should be at the root of these issues : The mri_protocol table must be populated in order for your scans to be registered in LORIS -- it serves as a whitelist for the insertion pipeline which filters out scans that aren't identified or matched to scan types in this table. By default, this table is populated with entries for t1, t2, fMRI and DTI (Insert statements for 21 release branch are here) Feel free to restore our default records and broaden their parameters to match all your scan types. re Defaced, native, selected -- these filter the scans displayed as you move to the next page (View Session), instead of viewing "all types" of scans from a given session : * "defaced" means that a defacing script has masked the subject's face in the volume (for patient privacy) * "native" means that no pre-processing has been performed on the scan (it's raw data), * "selected" will show only volumes that have been QC'd and "selected" as the best of their type -- used to display only the best quality T1 image instead of all T1s acquired in a session, e.g. re QC Comments -- Once you have successfully loaded scans (matched to the mri_protocol table), you'll be able to use the Imaging Browser's View Session subpage to enter/view QC comments on each volume, or for each visit. These are stored directly in the database, and linked to each scan. (Table name: feedback_mri_comments) (Visit-level QC comments are linked to the session.) For a walkthrough of the Imaging setup - please see the Imaging Setup guide - An old LORIS walkthrough video can also walk you through some of the Imaging front-end features, starting at 8:00 LORIS' imaging modules have been updated many times since this video, but the functionality and workflow is similar. Let us know how it goes once you have entries in your mri_protocol table - Best, Christine On Fri, Aug 2, 2019 at 7:58 AM Sotirios Nikoloutsopoulos > wrote: Hi Christine, In the candidate_list page i can see this patient [image.png] If i press the link under PSCID i get to see [image.png] and if i press the link under Scan Done it redirects me to imaging_browser [image.png] At the mri_violations page i also see No results ( neither on resolved / not resolved ). At the imaging_uploader i can see the record that failed. [image.png] If i click on the tarchive info i get to see the Protocol Name which i think is the acquisition we wanted? [image.png] Also my mri_protocol table is empty. Furthermore i would like to ask about the defaced, native, selected. What exactly is native and selected? And where are the qc comments stored? [image.png] Finally a walkthrough would be helpful. Thanks, Sotirios ???? ???, 30 ???? 2019 ???? 8:29 ?.?., ?/? Christine Rogers, Ms. > ??????: Hi Sotirios, Glad to hear you're making progress with the visit labels. To follow up on your last few emails: a- The Wiki's Setup Guide contains Sample insert statements for the Visit Windows table. As Cecile mentioned, the consistency of visit label format is important: V01, v01, V1, 01 -- whichever you select to use is fine; we use V01 by default across all documentation. b- For Password reset, there is a script in the tools/ directory so that a back-end administrator can reset any front-end user password, including Admin. (See info on setting up / resetting User passwords in the Wiki's Setup Guide) c- The minc file not being registered -- due to AcquisitionProtocol unknown. This means the SeriesDescription (Acquisition Protocol) in you Dicom header was not matched to any scan listed in the mri_protocol database table. (In the online Loris-MRI Troubleshooting Guide, this is Table 3, 2nd-last item "no MINCs inserted"). The MRI Violations module (Readme here) will show you the details of this mismatch -- Go to the module (under the Imaging menu), find your scan and click the link "Could not identify scan type" -- in the next subpage you can compare the scan's actual parameters against the mri_protocol table. To resolve this, adjust your mri_protocol table values or perhaps ensure your DICOMs are labelled consistently. Let us know if this works for you -- we can also walk you through an example of non-identified scans on Demo.loris.ca (MRI Violations module). Best, Christine The LORIS team On Tue, Jul 30, 2019 at 10:47 AM Sotirios Nikoloutsopoulos > wrote: I hope this is sufficient as the error for the visit label disappeared. [image.png] Please see the attached file. Also something i found. lorisadmin at hbp:/data/loris/bin/mri$ cat /data/loris/data//logs/TarLoad-17-39-xubBdv.log ==> Loading file from disk /tmp/TarLoad-17-39-UyQcG2/dcc0000_258024_v1_20121205_102108_501e1_mri.mnc --> mapping DICOM parameter for /tmp/TarLoad-17-39-UyQcG2/dcc0000_258024_v1_20121205_102108_501e1_mri.mnc ==> computing md5 hash for MINC body. --> md5: 6b1202fd63e29de4c9be1cd9925888a5 ==> verifying acquisition protocol Acquisition protocol is unknown --> The minc file cannot be registered since the AcquisitionProtocol is unknown ???? ???, 30 ???? 2019 ???? 4:58 ?.?., ?/? Sotirios Nikoloutsopoulos > ??????: Ok I fixed the login problem by using a known hash and by deleting the rows from the login_history i was able to login. ???? ???, 30 ???? 2019 ???? 4:50 ?.?., ?/? Sotirios Nikoloutsopoulos > ??????: Hi, there was no visit label 01 in the Visit_Windows table and i don't know how to insert it because the record requires lots of attributes. Also the system for a reason asked me to update my password and now i don't remember it and my account got suspended. Is there a way to reset it or set a simple password? I updated the password hash in the users table by using the hash from another LORIS setup we had and i still couldn't login ( also the attribute password is always NULL and the expiration date is 1999-01-01 for some reason ). Thanks ???? ???, 29 ???? 2019 ???? 5:21 ?.?., ?/? Cecile Madjar > ??????: Hi Sotirios, Can you try adding the visit label v01 to the Visit_Windows table? However, I noticed that in a previous dataset, the label was V1. Does that refer to the same visit? If so, you might want to harmonize the visit labels so they are all the same across datasets for a given timepoint, meaning you will need to relabel scans when the visit label is different but referring to the same visit label (v01 = V1 etc...). Hope this helps, C?cile On Mon, Jul 29, 2019 at 10:15 AM Sotirios Nikoloutsopoulos > wrote: Hi, Could you help me with the "Visit label does not exist"? I had changed $subjectID{'createVisitLabel'} to 1 as you had suggested but it appears that this problem hasn't been resolved yet. lorisadmin at hbp:/data/loris/bin/mri$ cat /data/loris/data//logs/TarLoad-14-58-9Xog7H.log ==> Loading file from disk /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc --> mapping DICOM parameter for /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc --> using user-defined filterParameters for /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc Candidate Mismatch Error is Visit label does not exist -> WARNING: This candidate was invalid. Logging to MRICandidateErrors table with reason Visit label does not exist Thank you, Sotirios ???? ???, 26 ???? 2019 ???? 3:02 ?.?., ?/? Sotirios Nikoloutsopoulos > ??????: Hi Cecile, The Center error was fixed. Still the insertion of mincs fails. Please see the output.txt file i attached. Also is there something else i need to change at the paths configuration? Thank you, Sotirios ???? ???, 25 ???? 2019 ???? 6:55 ?.?., ?/? Cecile Madjar > ??????: Hi Sotirios, We are making progress! I have a feeling this error comes from the fact that your psc table does not have the MRI_alias populated for the DCC site. Running the following query in the mysql database should fix this: UPDATE psc SET MRI_alias="DCC", Alias="DCC" WHERE Name="Data Coordinating Center"; Repeat the same with all your sites (make sure to change the Aliases between sites, they should all be unique). Let me know how it goes! Best, C?cile On Thu, Jul 25, 2019 at 11:43 AM Sotirios Nikoloutsopoulos > wrote: Dear Cecile, You were right about your guesses. I did the modifications you suggested, i still get the "no mincs inserted" error, now i am getting the "No center found this candidate" error ( how do i fix that? from what i see the .dcm files contains a 'Institution Name', is that the center? ), so i guess that's why the validation fails, but i changed the force variable of tarchiveLoader to 1, shouldn't it have inserted the mincs then? Also it is optional to have a mail server, right? ( from what i see the mail error does not affect the $valid_study, so i assume we are okay with that ) Thank you a lot, Sotirios ???? ???, 25 ???? 2019 ???? 5:48 ?.?., ?/? Cecile Madjar > ??????: Hi Sotirios, From what I understand, I believe you just need to update a few config settings from the frontend in the Config module (under the Admin menu). [Screen Shot 2019-07-25 at 10.31.35 AM.png] Then go to the Paths section of the config module and update the "LORIS-MRI code" config setting to /data/loris/bin/mri (my guess is that currently, it is set to /data/LORIS/data) and click on the submit button. [Screen Shot 2019-07-25 at 10.32.50 AM.png] Then, go to Imaging Pipeline section of the Configuration module and update the "Loris-MRI Data Directory" to /data/loris/data/ (my guess is that it is empty at the moment in your database which is why $data_dir is not defined when you run the tarchiveLoader step of the insertion pipeline). [Screen Shot 2019-07-25 at 10.40.52 AM.png] Finally, I took a look at your environment file and it might be a good idea to update your PERL5LIB variable to the following (it has been added to the code a few releases ago as we realized this was needed for the libraries. Not sure which version of LORIS-MRI you are using but it does not hurt to update this variable to what I suggest below): export PERL5LIB=/data/loris/bin/mri/uploadNeuroDB:/data/loris/bin/mri/dicom-archive:$PERL5LIB Hope this helps. Sorry you are experiencing so much trouble setting things up. We probably need to update our WIKI. Best, C?cile On Thu, Jul 25, 2019 at 9:48 AM Sotirios Nikoloutsopoulos > wrote: The "Loris-MRI Data Directory" should be in the environment file? ???? ???, 25 ???? 2019 ???? 12:59 ?.?., ?/? Sotirios Nikoloutsopoulos > ??????: The scripts are located in /data/loris/bin/mri/. Somewhere I might have messed something up but i remember following the instructions in the wiki.For example when i tried to execute the batch_uploads_imageuploader perl script the line my $command = "$bin_dir/uploadNeuroDB/imaging_upload_file.pl " was pointing to an invalid path, for example: it was repeating a pattern and had LORIS instead of loris ( i think the mistake was that in the wiki it suggested to use $PROJECT for the name of the folder and i choosed 'loris' https://github.com/aces/Loris/wiki/Imaging-Database ). See also the in image for the modification i did. Also i didn't find the section to config the $data_dir variable. Thank you, Sotirios ???? ???, 24 ???? 2019 ???? 6:05 ?.?., ?/? Cecile Madjar > ??????: Hi Sotirios, It looks like you have one Config setting not set (based on the first error message you got when running it the first time). You need to set a value for "Loris-MRI Data Directory" in the Config module under the Imaging pipeline section (from what I can see, it would be /data/loris/data/ for your setup). The reason you got that error message the second time is that the pipeline checks if the DICOM study was already inserted in the tarchive table. Since you ran the study once already, the study is inserted into the tarchive, hence the message. However, the pipeline did not complete as the MINC files were not created and inserted into the files/parameter_file table. In order to continue the insertion, you will then need to run the tarchiveLoader command suggested in the terminal during the second run: /data/LORIS/data//uploadNeuroDB/tarchiveLoader -globLocation -profile prod /data/loris/data/tarchive//2012/DCM_2012-12-05_ImagingUpload-17-43-ZUEFjb.tar -verbose Finally, I am a bit confused by your setup. Where are the scripts located? In /data/loris/bin/mri or /data/loris/data? It feels like the Config setting "LORIS-MRI code" in the Paths section was set to "/data/LORIS/data" but it should have been set to the directory where the scripts are located (most probably /data/loris/bin/mri). Hope this helps, C?cile On Wed, Jul 24, 2019 at 10:55 AM Sotirios Nikoloutsopoulos > wrote: Ok first i execute this command: "lorisadmin at hbp:/data/loris/bin/mri$ ./batch_uploads_imageuploader -profile prod < ~/Desktop/input.txt > log.txt Use of uninitialized value $data_dir in concatenation (.) or string at ./batch_uploads_imageuploader line 143. Use of uninitialized value $data_dir in concatenation (.) or string at ./batch_uploads_imageuploader line 143. Use of uninitialized value $_ in pattern match (m//) at ./batch_uploads_imageuploader line 147. base is DCC0000_258024_V01 path is /data/incoming/ type is .tar.gz fullpath is /data/incoming/DCC0000_258024_V01.tar.gz source /tmp/ImagingUpload-17-43-ZUEFjb targetlocation /data/loris/data/tarchive Use of uninitialized value $data_dir in concatenation (.) or string at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 256. Use of uninitialized value $data_dir in concatenation (.) or string at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 284. Use of uninitialized value $data_dir in concatenation (.) or string at /data/loris/bin/mri/uploadNeuroDB/tarchive_validation.pl line 219. Use of uninitialized value $data_dir in concatenation (.) or string at /data/loris/bin/mri/uploadNeuroDB/minc_insertion.pl line 270. Use of uninitialized value $data_dir in concatenation (.) or string at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 711. Can't exec "mail": No such file or directory at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 721. print() on closed filehandle MAIL at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 722. print() on closed filehandle MAIL at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 723. Use of uninitialized value $data_dir in concatenation (.) or string at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 724. print() on closed filehandle MAIL at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 724. print() on closed filehandle MAIL at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 725. Use of uninitialized value $data_dir in concatenation (.) or string at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 735. No Mincs inserted The tarchiveLoader insertion script has failed. Running now the following command: /data/loris/data/uploadNeuroDB/imaging_upload_file.pl -profile prod -upload_id 3 /data/incoming/DCC0000_258024_V01.tar.gz -verbose" I inserted the VisitLabel, but still the Mincs are not inserted and i am getting this error "lorisadmin at hbp:/data/loris/bin/mri$ /data/loris/data/uploadNeuroDB/imaging_upload_file.pl -profile prod -upload_id 3 /data/incoming/DCC0000_258024_V01.tar.gz -verbose find -path \/tmp\/ImagingUpload\-17\-45\-5MsWEd -name '__MACOSX' -delete Spool message is: The Scan for the uploadID 3 has already been run with tarchiveID: 7. To continue with the rest of the insertion pipeline, please run tarchiveLoader from a terminal as follows: /data/LORIS/data//uploadNeuroDB/tarchiveLoader -globLocation -profile prod /data/loris/data/tarchive//2012/DCM_2012-12-05_ImagingUpload-17-43-ZUEFjb.tar -verbose" Which files should i delete? I thought that deleting the files from the tarchive was enough. And i executed the last proposed command to continue to rest of the insertion pipeline ( check the image ). Thank you ???? ???, 24 ???? 2019 ???? 5:05 ?.?., ?/? Cecile Madjar > ??????: Hi Sotirios, Sorry I was not clear before. Every visits of candidates are created in the session table with one entry per CandID/VisitLabel. So if the imaging pipeline created visits in the session table (that are not attached to instruments) and you want to clean your database completely, you can delete entries in that table as well. Regarding your point 2, the imaging pipeline can create the visit in the session table as long as the visit label is present in the Visit_Windows table (which means the visit label stored in the PatientName is a valid visit label). However, in your prod file, if the variable $subjectID{'createVisitLabel'} is set to 1 for candidates, the visit label should be created in the Visit_Windows table I believe. Here is the line of the prod file you would need to change. In general, we prefer populating the Visit_Windows table and set the $subjectID{'createVisitLabel'} to 0 for candidate data to avoid insertion of badly labelled MRI data that are complex to relabel. Finally, regarding the candidate creation, if you execute the following steps, the pipeline should be able to create candidates: - set in the Imaging Pipeline section of the config module the config setting "Upload creation of candidates" to Yes - manually transfer the scans to the LORIS server instead of uploading it via the imaging browser - run batch_imaging_upload.pl as you did until now. Hope this helps! Best, C?cile On Wed, Jul 24, 2019 at 8:47 AM Sotirios Nikoloutsopoulos > wrote: About my second question i replaced the name of the patient in the .dcm files and now i am getting an error that the visit label does not exist. I thought it was supposed to be automatically created. "Done adding archive info into database /data/LORIS/data//uploadNeuroDB/tarchiveLoader -globLocation -profile prod /data/loris/data/tarchive//DCM_2012-12-05_ImagingUpload-15-42-yUwQQV.tar -verbose md5sum /data/loris/data/tarchive/DCM_2012-12-05_ImagingUpload-15-42-yUwQQV.tar PSCID is: DCC0000 CandID id: 258024 visit_label is: V1 PSCID is: DCC0000 CandID id: 258024 visit_label is: V1 candidate id 258024 => No Visit labelVisit label does not exist Set centerID = 1 PSCID is: DCC0000 CandID id: 258024 visit_label is: V1 PSCID is: DCC0000 CandID id: 258024 visit_label is: V1 Number of MINC files that will be considered for inserting into the database: 1 log dir is /logs and log file is /logs/TarLoad-15-42-L6pocU.log PSCID is: DCC0000 CandID id: 258024 visit_label is: V1 PSCID is: DCC0000 CandID id: 258024 visit_label is: V1 candidate id 258024 => No Visit label Cleaning up temp files: rm -rf /tmp/TarLoad-15-42-J2rQms/ImagingUpload-15-42-yUwQQV*" ???? ???, 24 ???? 2019 ???? 3:38 ?.?., ?/? Sotirios Nikoloutsopoulos > ??????: Hi, 1) What are the records in the session table? 2) I tried to upload a non-phantom file like this input_file.txt: /data/incoming/DCC0000_258024_V1.tar.gz N DCC0000_258024_V1 Terminal: ./batch_uploads_imageuploader -profile prod < ~/Desktop/input.txt > log.txt and i get the following error in the log.txt file "Running now the following command: /data/loris/data/uploadNeuroDB/imaging_upload_file.pl -profile prod -upload_id 7 /data/incoming/DCC0000_258024_V1.tar.gz -verbose find -path \/tmp\/ImagingUpload\-14\-56\-FeLCB4 -name '__MACOSX' -delete Spool message is: The PatientName read from the DICOM header does not start with DCC0000_258024_V1 from the mri_upload table " and the spool message is repeated for each .dcm file. Should i preprocess every .dcm file and change the PatientName to "DCC0000_258024_V1"? 3) As far as it concerns the candidate profile i have to create a new one each time before i try to upload a file? Is there already a way to create a candidate profile and get the DCCID and PSCID without the user interface? Thank you, Sotirios ???? ???, 18 ???? 2019 ???? 5:00 ?.?., ?/? Cecile Madjar > ??????: Hi Sotirios, See answers to your questions below. About the 1st case we had a dicom with a blank studyUID, maybe someone accidentally removed it. That is strange. Something must have been done to the DICOM files. I have never seen a study with no StudyUID out of the scanner. Usually, you need to manually erase it with some tool. However, DICOMs never cease to surprise me... Some other questions: 1) What are the steps to remove all of my patients and uploads?: because i want to try to reupload all the testing dicoms we had with a clean database. Release 21.0 of LORIS-MRI will offer a script to remove all the entries and files specific to an upload. However, this release is not yet out. Hopefully in the next few weeks. In the meantime, since your case is particular and that you just want to start with a clean database, the following deletes should work (hopefully I won't forget any tables): delete from mri_violations_log; delete from mri_protocol_violated_scans; delete from MRICandidateErrors; delete from parameter_file; delete from files_qcstatus; # (if you played with the QC part of the imaging browser for testing) delete from feedback_mri_comments; # (if you played with the QC part of the imaging browser for testing) delete from tarchive_series; delete from tarchive_files; delete from mri_upload; delete from tarchive; delete from mri_scanner; delete from candidate where PSCID="scanner"; I don't know if you want to also delete entries in the session and candidate table too? 2) We do not need to create the profile of a patient ( are the patients stored in the candidate table? because i can't see the ghosts ), because will it automatically be created when importing a dicom? I am not sure I understand fully this question. All candidates are stored in the candidate table. The phantom scans however are attached to a scanner candidate depending on where the scan happened. It is a bit of a weird concept that we have to redesign eventually but never got a chance to get to it. Hopefully this answered your question, otherwise, don't hesitate to let me know. 3) What is the difference between uploading a dicom as phantom instead of importing as PSCCID_DCCID_VisitLabel? When you upload the scan as PSCID_DCCID_VisitLabel, there is a check that makes sure the candidate IDs and visit label are valid at the time of upload. When you upload a scan as phantom, it expects that the DICOM field PatientName and uploaded filename contains the string "phantom". We enforced this behaviour on the imaging uploader side in recent releases but I can't remember which one. Probably the upcoming 21.0 release. All those verifications might seem cumbersome but they are here to ensure that the files inserted are all valid and labelled properly as it is a bit messy to have to delete files that were wrongly labelled. At least, the delete script present in release 21.0 will make this process easier but it is still good practice to verify those things. Thank you, With pleasure. Hopefully the answers to your questions will be helpful. Best, C?cile PS: loris-dev mailing list: you will find the initial answer I gave Sotirios below. I forgot to cc the loris-dev in my earlier reply... ???? ???, 16 ???? 2019 ???? 12:02 ?.?., ?/? Cecile Madjar > ??????: Dear Sotirios, Thank you for reaching out. Since your email was already organized in points, I will reply directly below your questions below. Best, C?cile 1) What do we do when the StudyUID is blank on the header? https://github.com/aces/Loris-MRI/blob/minor/docs/AppendixA-Troubleshooting_guideline.md There solution provided at the table 3 does not guide us how to find the information ( is possible ). The StudyUID is the field used in our pipeline at the moment to check whether a DICOM study was already inserted into LORIS with that same StudyUID since it is supposed to be unique for every single study. Currently, we do not support insertion of DICOM studies if they do not have a StudyUID associated with them. Is there a specific reason why the StudyUID is blank in the DICOM headers in your DICOM files? Did they go through some processes before upload to LORIS? 2) When i am about to upload a non-phanton case i need a 'Visit Label'. Is there already a script that can create a new visit label for a specific Candidate, so i can provide it as input afterwards to the batch_uploads_imageuploader ( See option 5.1.3 https://github.com/aces/Loris-MRI/blob/minor/docs/05-PipelineLaunchOptions.md ) I am not sure if the front-end allows for it but if you use batch_uploads_imageuploader, the insertion scripts could create the visit label for you. However, it does need to be included in the patient name in order for the script to know which label it should use. For example: you upload V02 for MTL0123 (DCCID: 456789) but V02 was not yet created for MTL0123; the insertion scripts will create a V02 visit for MTL0123 if the PatientName field for the dataset is MTL0123_456789_V02 with Stage marked as "Not Started". However, note that for the script to create the visit for the candidate, you have to make sure that all the visit label of your projects were inserted in the Visit_Windows table (otherwise, the visit will never be created as they were not specified as being part of the list of visit label to expect). So in the example above, you should have one row in Visit_Windows with Visit_label="V02" set. 3) Section 4.3 https://github.com/aces/Loris-MRI/blob/minor/docs/04-Scripts.md What do we do when the folder contains multiple mnc files? This is a case by case. Most of the time, the MINC files that failed insertion into the imaging browser end up in the MRI violation module where you can see what went wrong with the acquisitions not inserted. If you notice that the MINC file should be inserted as a specific protocol, you can force the insertion as explained in section 4.3. In your case, I have a feeling that you want to be able to insert MINC files that did not go through the whole pipeline insertion (DICOM archival, then dcm2mnc, then protocol identification, then insertion...). In theory, you could call minc_insertion.pl on any MINC file, provided you have at least the following information: - path to the MINC file - uploadID associated with the MINC files or DICOM archive path from which those MINC files were created from Then the minc_insertion.pl script will do the subject information and protocol validation etc... If all the MINC files come from the same uploadID or TarchiveID, then you could run a loop in bash calling the minc_insertion.pl script like this for files deriving from uploadID=1: ls /path/to/mnc/folder/* | while read f; do minc_insertion.pl -profile prod -uploadID 1 -mincPath $f; done Thank you, Hope this helped! _______________________________________________ Loris-dev mailing list Loris-dev at bic.mni.mcgill.ca https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev -- christine.rogers at mcgill.ca McGill Centre for Integrative Neuroscience | MCIN.ca Montreal Neurological Institute McGill University | Montreal | Canada -- christine.rogers at mcgill.ca McGill Centre for Integrative Neuroscience | MCIN.ca Montreal Neurological Institute McGill University | Montreal | Canada _______________________________________________ Loris-dev mailing list Loris-dev at bic.mni.mcgill.ca https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev -- christine.rogers at mcgill.ca McGill Centre for Integrative Neuroscience | MCIN.ca Montreal Neurological Institute McGill University | Montreal | Canada _______________________________________________ Loris-dev mailing list Loris-dev at bic.mni.mcgill.ca https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev -- christine.rogers at mcgill.ca McGill Centre for Integrative Neuroscience | MCIN.ca Montreal Neurological Institute McGill University | Montreal | Canada _______________________________________________ Loris-dev mailing list Loris-dev at bic.mni.mcgill.ca https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev -- christine.rogers at mcgill.ca McGill Centre for Integrative Neuroscience | MCIN.ca Montreal Neurological Institute McGill University | Montreal | Canada _______________________________________________ Loris-dev mailing list Loris-dev at bic.mni.mcgill.ca https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev -- christine.rogers at mcgill.ca McGill Centre for Integrative Neuroscience | MCIN.ca Montreal Neurological Institute McGill University | Montreal | Canada -------------- next part -------------- An HTML attachment was scrubbed... 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Name: image.png Type: image/png Size: 20518 bytes Desc: image.png URL: From sotirisnik at gmail.com Wed Aug 7 08:01:01 2019 From: sotirisnik at gmail.com (Sotirios Nikoloutsopoulos) Date: Wed, 7 Aug 2019 15:01:01 +0300 Subject: [Loris-dev] Upgrading to Loris 21 - new make file In-Reply-To: References: Message-ID: Hi, lorisadmin at hbp:/var/www/loris$ sudo cat /var/log/apache2/error.log [Wed Aug 07 07:35:02.422501 2019] [mpm_prefork:notice] [pid 1267] AH00163: Apache/2.4.18 (Ubuntu) OpenSSL/1.0.2g configured -- resuming normal operations [Wed Aug 07 07:35:02.422514 2019] [core:notice] [pid 1267] AH00094: Command line: '/usr/sbin/apache2' And as for the access.log the content are empty lorisadmin at hbp:/var/www/loris$ sudo ls -l /var/log/apache2/access.log lorisadmin at hbp:/var/www/loris$ sudo ls -l /var/log/apache2/access.log -rw-r----- 1 root adm 0 ???? 28 14:09 /var/log/apache2/access.log Also i noticed a loris_access.log. The only non-blank pages are: mri_violations, dataquery does not exist at all, statistics, data_team_helper, genomic_browser, configuration and server_processes_manager/ prints "Required configuration settings for Server Processes Manager are missing. Cannot continue." Thanks, Sotirios ???? ???, 6 ??? 2019 ???? 10:13 ?.?., ?/? Christine Rogers, Ms. < christine.rogers at mcgill.ca> ??????: > Hi Sotirios and LORIS community -- > > When upgrading to brand-new release 21 -- just a reminder to follow the > release notes and run the new *make* file to update your dependencies > (instead of using *composer* commands). > We've also updated the Wiki page > to clarify that > the release notes for each version will tell you what to run. > > If your current version is not the last release (20.3), it's still > important to upgrade to each minor release increment (e.g. 20.2, 20.3) > before making the leap to 21.0. > > If you're getting blank pages, post-upgrade -- Try clearing your cache. > > Got questions or feedback e.g. on the Release Notes? please don't hesitate > to let us know. > Thanks, > Christine > The LORIS team > > > > On Tue, Aug 6, 2019 at 10:09 AM Christine Rogers, Ms. < > christine.rogers at mcgill.ca> wrote: > >> Hi Sotirios, >> Could you also let us know -- on which pages is content visible, and on >> which pages/modules is content not visible for you? >> Thanks, >> Christine >> >> On Tue, Aug 6, 2019 at 9:54 AM Christine Rogers, Ms. < >> christine.rogers at mcgill.ca> wrote: >> >>> Thanks Sotirios, >>> That's good to know. It sounds like you've checked that your >>> /var/www/loris/project/config.xml file get populated properly. >>> >>> Please send us the last few errors you're seeing in your apache error >>> log file, and your config paths and we can see what's happening with your >>> front end -- >>> Run these Troubleshooting Queries >>> >>> to get your config path settings, given your front end is not displaying >>> fully. >>> >>> The Loris-MRI repo >>> 21 >>> install/upgrade would then be your next steps. >>> Best, >>> Christine >>> >>> On Tue, Aug 6, 2019 at 7:53 AM Sotirios Nikoloutsopoulos < >>> sotirisnik at gmail.com> wrote: >>> >>>> I am using a VM. What i did was: >>>> 1) Download the files from https://github.com/aces/Loris and replace >>>> them to my existing /vaw/www/loris folder. >>>> 2) Execute the composer install --no-dev and then composer >>>> dump-autoload as mentioned here >>>> https://github.com/aces/Loris/wiki/Updating-your-LORIS. >>>> 3) Execute install.sh from /var/www/loris/tools and because LORIS >>>> already existed i moved a .config file, then re-executed the install.sh >>>> successfully >>>> 4 ) As for the database, i dropped the schema and i executed the >>>> installdb.php >>>> >>>> ???? ???, 5 ??? 2019 ???? 5:22 ?.?., ?/? Christine Rogers, Ms. < >>>> christine.rogers at mcgill.ca> ??????: >>>> >>>>> Hi Sotorios, >>>>> >>>>> Thanks - when you re-installed did you start on a fresh root path / VM >>>>> or might some of your old system setting still apply? >>>>> (And if you did any steps similar to an upgrade, did you follow the >>>>> Upgrade steps in the Release Notes, from both repos?) >>>>> >>>>> About the TR_range column - it was recently split (MRI pr339 >>>>> ) split into TR_min and >>>>> _max columns. Given the code was trying to query TR_range which does not >>>>> exist in your mri_protocol table, double-check which version of the Loris >>>>> repo (tables) and the Loris-MRI repo (code) you have installed to ensure >>>>> they match. >>>>> >>>>> Christine >>>>> >>>>> >>>>> On Mon, Aug 5, 2019 at 9:06 AM Sotirios Nikoloutsopoulos < >>>>> sotirisnik at gmail.com> wrote: >>>>> >>>>>> I reinstalled LORIS to 21 version and now the content is not visible >>>>>> at all at most pages. >>>>>> >>>>>> [image: image.png] >>>>>> >>>>>> ???? ???, 5 ??? 2019 ???? 3:19 ?.?., ?/? Sotirios Nikoloutsopoulos < >>>>>> sotirisnik at gmail.com> ??????: >>>>>> >>>>>>> Hi, >>>>>>> >>>>>>> Is it easy to upgrade to Loris 21? Also the following fails because >>>>>>> the line 1985 of NeuroDB/MRIProcessingUtility.pm query mri_protocol which >>>>>>> doesn't have TR_range >>>>>>> https://github.com/aces/Loris/blob/21.0-release/SQL/0000-00-00-schema.sql#L556 >>>>>>> >>>>>>> [image: image.png] >>>>>>> >>>>>>> lorisadmin at hbp:/data/loris/bin/mri$ ./batch_uploads_imageuploader >>>>>>> -profile prod < ~/Desktop/input.txt > log.txt >>>>>>> Use of uninitialized value $_ in pattern match (m//) at >>>>>>> ./batch_uploads_imageuploader line 147. >>>>>>> base is DCC0000_258024_V1 >>>>>>> path is /data/incoming/ >>>>>>> type is .tar.gz >>>>>>> fullpath is /data/incoming/DCC0000_258024_V1.tar.gz >>>>>>> DBD::mysql::st execute failed: Unknown column 'TR_range' in 'where >>>>>>> clause' at >>>>>>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line 1985. >>>>>>> DBD::mysql::st fetchrow_array failed: fetch() without execute() at >>>>>>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line 1986. >>>>>>> Use of uninitialized value $count_mri_protocol in numeric gt (>) at >>>>>>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line 1995. >>>>>>> DBD::mysql::st execute failed: Unknown column 'TR_range' in 'field >>>>>>> list' at /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 562. >>>>>>> Can't exec "mail": No such file or directory at >>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 721. >>>>>>> print() on closed filehandle MAIL at >>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 722. >>>>>>> print() on closed filehandle MAIL at >>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 723. >>>>>>> print() on closed filehandle MAIL at >>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 724. >>>>>>> print() on closed filehandle MAIL at >>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 725. >>>>>>> >>>>>>> No Mincs inserted >>>>>>> >>>>>>> Thanks, >>>>>>> >>>>>>> Sotirios >>>>>>> >>>>>>> ???? ???, 3 ??? 2019 ???? 1:08 ?.?., ?/? Christine Rogers, Ms. < >>>>>>> christine.rogers at mcgill.ca> ??????: >>>>>>> >>>>>>>> Hi Sotirios, >>>>>>>> >>>>>>>> First, just a note: we've released LORIS 21 this week with some >>>>>>>> major new features and cleanup -- especially if you are early in your setup >>>>>>>> phase, check out the Release notes for both the LORIS >>>>>>>> and Loris-MRI >>>>>>>> repos. >>>>>>>> >>>>>>>> Thanks for your screenshots -- your empty mri_protocol table should >>>>>>>> be at the root of these issues : >>>>>>>> >>>>>>>> The mri_protocol table must be populated >>>>>>>> >>>>>>>> in order for your scans to be registered in LORIS -- it serves as a >>>>>>>> whitelist for the insertion pipeline which filters out scans that aren't >>>>>>>> identified or matched to scan types in this table. >>>>>>>> >>>>>>>> By default, this table is populated with entries for t1, t2, fMRI >>>>>>>> and DTI (Insert statements for 21 release branch are here >>>>>>>> >>>>>>>> ) >>>>>>>> Feel free to restore our default records and broaden their >>>>>>>> parameters to match all your scan types. >>>>>>>> >>>>>>>> re Defaced, native, selected -- these filter the scans displayed as >>>>>>>> you move to the next page (View Session), instead of viewing "all types" of >>>>>>>> scans from a given session : >>>>>>>> >>>>>>>> - "defaced" means that a defacing script >>>>>>>> >>>>>>>> has masked the subject's face in the volume (for patient privacy) >>>>>>>> - "native" means that no pre-processing has been performed on >>>>>>>> the scan (it's raw data), >>>>>>>> - "selected" will show only volumes that have been QC'd and >>>>>>>> "selected" as the best of their type -- used to display only the best >>>>>>>> quality T1 image instead of all T1s acquired in a session, e.g. >>>>>>>> >>>>>>>> re QC Comments -- >>>>>>>> Once you have successfully loaded scans (matched to the >>>>>>>> mri_protocol table), you'll be able to use the Imaging Browser's View >>>>>>>> Session subpage to enter/view QC comments on each volume, or for each >>>>>>>> visit. >>>>>>>> These are stored directly in the database, and linked to each >>>>>>>> scan. (Table name: feedback_mri_comments) >>>>>>>> (Visit-level QC comments are linked to the session.) >>>>>>>> >>>>>>>> For a walkthrough of the Imaging setup - please see the Imaging >>>>>>>> Setup guide >>>>>>>> >>>>>>>> - >>>>>>>> >>>>>>>> An old LORIS walkthrough video >>>>>>>> can also walk you >>>>>>>> through some of the Imaging front-end features, starting at 8:00 >>>>>>>> LORIS' imaging modules have been updated many times since this >>>>>>>> video, but the functionality and workflow is similar. >>>>>>>> >>>>>>>> Let us know how it goes once you have entries in your mri_protocol >>>>>>>> table - >>>>>>>> Best, >>>>>>>> Christine >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> On Fri, Aug 2, 2019 at 7:58 AM Sotirios Nikoloutsopoulos < >>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>> >>>>>>>>> Hi Christine, >>>>>>>>> >>>>>>>>> In the candidate_list page i can see this patient >>>>>>>>> >>>>>>>>> [image: image.png] >>>>>>>>> >>>>>>>>> If i press the link under PSCID i get to see >>>>>>>>> [image: image.png] >>>>>>>>> >>>>>>>>> and if i press the link under Scan Done it redirects me to >>>>>>>>> imaging_browser >>>>>>>>> >>>>>>>>> [image: image.png] >>>>>>>>> >>>>>>>>> At the mri_violations page i also see No results ( neither on >>>>>>>>> resolved / not resolved ). >>>>>>>>> >>>>>>>>> At the imaging_uploader i can see the record that failed. >>>>>>>>> >>>>>>>>> [image: image.png] >>>>>>>>> >>>>>>>>> If i click on the tarchive info i get to see the Protocol Name >>>>>>>>> which i think is the acquisition we wanted? >>>>>>>>> [image: image.png] >>>>>>>>> >>>>>>>>> Also my mri_protocol table is empty. >>>>>>>>> >>>>>>>>> Furthermore i would like to ask about the defaced, native, >>>>>>>>> selected. What exactly is native and selected? And where are the qc >>>>>>>>> comments stored? >>>>>>>>> >>>>>>>>> [image: image.png] >>>>>>>>> >>>>>>>>> Finally a walkthrough would be helpful. >>>>>>>>> >>>>>>>>> Thanks, >>>>>>>>> >>>>>>>>> Sotirios >>>>>>>>> >>>>>>>>> ???? ???, 30 ???? 2019 ???? 8:29 ?.?., ?/? Christine Rogers, Ms. < >>>>>>>>> christine.rogers at mcgill.ca> ??????: >>>>>>>>> >>>>>>>>>> Hi Sotirios, >>>>>>>>>> Glad to hear you're making progress with the visit labels. To >>>>>>>>>> follow up on your last few emails: >>>>>>>>>> >>>>>>>>>> a- The Wiki's Setup Guide contains Sample insert statements for >>>>>>>>>> the Visit Windows table >>>>>>>>>> >>>>>>>>>> . >>>>>>>>>> >>>>>>>>>> As Cecile mentioned, the consistency of visit label format is >>>>>>>>>> important: V01, v01, V1, 01 -- whichever you select to use is fine; we use >>>>>>>>>> V01 by default across all documentation. >>>>>>>>>> >>>>>>>>>> b- For Password reset, there is a script in the tools/ directory >>>>>>>>>> so that a back-end administrator can reset any front-end user password, >>>>>>>>>> including Admin. (See info on setting up / resetting User passwords in the Wiki's >>>>>>>>>> Setup Guide >>>>>>>>>> >>>>>>>>>> ) >>>>>>>>>> >>>>>>>>>> c- The minc file not being registered -- due to >>>>>>>>>> AcquisitionProtocol unknown. >>>>>>>>>> This means the SeriesDescription (Acquisition Protocol) in you >>>>>>>>>> Dicom header was not matched to any scan listed in the mri_protocol >>>>>>>>>> database table. >>>>>>>>>> (In the online Loris-MRI Troubleshooting Guide, >>>>>>>>>> this >>>>>>>>>> is Table 3, 2nd-last item "no MINCs inserted"). >>>>>>>>>> >>>>>>>>>> The MRI Violations module (Readme here) >>>>>>>>>> will show >>>>>>>>>> you the details of this mismatch -- >>>>>>>>>> Go to the module (under the Imaging menu), find your scan and >>>>>>>>>> click the link "Could not identify scan type" -- in the next subpage you >>>>>>>>>> can compare the scan's actual parameters against the mri_protocol table. >>>>>>>>>> >>>>>>>>>> To resolve this, adjust your mri_protocol table values or perhaps >>>>>>>>>> ensure your DICOMs are labelled consistently. >>>>>>>>>> >>>>>>>>>> Let us know if this works for you -- we can also walk you through >>>>>>>>>> an example of non-identified scans on Demo.loris.ca (MRI >>>>>>>>>> Violations module). >>>>>>>>>> >>>>>>>>>> Best, >>>>>>>>>> Christine >>>>>>>>>> >>>>>>>>>> The LORIS team >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> On Tue, Jul 30, 2019 at 10:47 AM Sotirios Nikoloutsopoulos < >>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>> >>>>>>>>>>> I hope this is sufficient as the error for the visit label >>>>>>>>>>> disappeared. >>>>>>>>>>> [image: image.png] >>>>>>>>>>> >>>>>>>>>>> Please see the attached file. Also something i found. >>>>>>>>>>> >>>>>>>>>>> lorisadmin at hbp:/data/loris/bin/mri$ cat >>>>>>>>>>> /data/loris/data//logs/TarLoad-17-39-xubBdv.log >>>>>>>>>>> >>>>>>>>>>> ==> Loading file from disk >>>>>>>>>>> /tmp/TarLoad-17-39-UyQcG2/dcc0000_258024_v1_20121205_102108_501e1_mri.mnc >>>>>>>>>>> >>>>>>>>>>> --> mapping DICOM parameter for >>>>>>>>>>> /tmp/TarLoad-17-39-UyQcG2/dcc0000_258024_v1_20121205_102108_501e1_mri.mnc >>>>>>>>>>> >>>>>>>>>>> ==> computing md5 hash for MINC body. >>>>>>>>>>> >>>>>>>>>>> --> md5: 6b1202fd63e29de4c9be1cd9925888a5 >>>>>>>>>>> >>>>>>>>>>> ==> verifying acquisition protocol >>>>>>>>>>> >>>>>>>>>>> Acquisition protocol is unknown >>>>>>>>>>> >>>>>>>>>>> --> The minc file cannot be registered since the >>>>>>>>>>> AcquisitionProtocol is unknown >>>>>>>>>>> >>>>>>>>>>> ???? ???, 30 ???? 2019 ???? 4:58 ?.?., ?/? Sotirios >>>>>>>>>>> Nikoloutsopoulos ??????: >>>>>>>>>>> >>>>>>>>>>>> Ok I fixed the login problem by using a known hash and by >>>>>>>>>>>> deleting the rows from the login_history i was able to login. >>>>>>>>>>>> >>>>>>>>>>>> ???? ???, 30 ???? 2019 ???? 4:50 ?.?., ?/? Sotirios >>>>>>>>>>>> Nikoloutsopoulos ??????: >>>>>>>>>>>> >>>>>>>>>>>>> Hi, >>>>>>>>>>>>> >>>>>>>>>>>>> there was no visit label 01 in the Visit_Windows table and i >>>>>>>>>>>>> don't know how to insert it because the record requires lots of attributes. >>>>>>>>>>>>> Also the system for a reason asked me to update my password and now i don't >>>>>>>>>>>>> remember it and my account got suspended. Is there a way to reset it or set >>>>>>>>>>>>> a simple password? I updated the password hash in the users table by using >>>>>>>>>>>>> the hash from another LORIS setup we had and i still couldn't login ( also >>>>>>>>>>>>> the attribute password is always NULL and the expiration date is 1999-01-01 >>>>>>>>>>>>> for some reason ). >>>>>>>>>>>>> >>>>>>>>>>>>> Thanks >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> ???? ???, 29 ???? 2019 ???? 5:21 ?.?., ?/? Cecile Madjar < >>>>>>>>>>>>> cecile.madjar at mcin.ca> ??????: >>>>>>>>>>>>> >>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>> >>>>>>>>>>>>>> Can you try adding the visit label v01 to the Visit_Windows >>>>>>>>>>>>>> table? >>>>>>>>>>>>>> >>>>>>>>>>>>>> However, I noticed that in a previous dataset, the label was >>>>>>>>>>>>>> V1. Does that refer to the same visit? If so, you might want to harmonize >>>>>>>>>>>>>> the visit labels so they are all the same across datasets for a given >>>>>>>>>>>>>> timepoint, meaning you will need to relabel scans when the visit label is >>>>>>>>>>>>>> different but referring to the same visit label (v01 = V1 etc...). >>>>>>>>>>>>>> >>>>>>>>>>>>>> Hope this helps, >>>>>>>>>>>>>> >>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>> >>>>>>>>>>>>>> On Mon, Jul 29, 2019 at 10:15 AM Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>> >>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> Could you help me with the "Visit label does not exist"? I >>>>>>>>>>>>>>> had changed $subjectID{'createVisitLabel'} to 1 as you had suggested but >>>>>>>>>>>>>>> it appears that this problem hasn't been resolved yet. >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> lorisadmin at hbp:/data/loris/bin/mri$ cat >>>>>>>>>>>>>>> /data/loris/data//logs/TarLoad-14-58-9Xog7H.log >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> ==> Loading file from disk >>>>>>>>>>>>>>> /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> --> mapping DICOM parameter for >>>>>>>>>>>>>>> /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> --> using user-defined filterParameters for >>>>>>>>>>>>>>> /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> Candidate Mismatch Error is Visit label does not exist >>>>>>>>>>>>>>> -> WARNING: This candidate was invalid. Logging to >>>>>>>>>>>>>>> MRICandidateErrors table with reason Visit >>>>>>>>>>>>>>> label does not exist >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> ???? ???, 26 ???? 2019 ???? 3:02 ?.?., ?/? Sotirios >>>>>>>>>>>>>>> Nikoloutsopoulos ??????: >>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Hi Cecile, >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> The Center error was fixed. Still the insertion of mincs >>>>>>>>>>>>>>>> fails. Please see the output.txt file i attached. Also is there something >>>>>>>>>>>>>>>> else i need to change at the paths configuration? >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> ???? ???, 25 ???? 2019 ???? 6:55 ?.?., ?/? Cecile Madjar < >>>>>>>>>>>>>>>> cecile.madjar at mcin.ca> ??????: >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> We are making progress! >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> I have a feeling this error comes from the fact that your >>>>>>>>>>>>>>>>> psc table does not have the MRI_alias populated for the DCC site. Running >>>>>>>>>>>>>>>>> the following query in the mysql database should fix this: >>>>>>>>>>>>>>>>> UPDATE psc SET MRI_alias="DCC", Alias="DCC" WHERE >>>>>>>>>>>>>>>>> Name="Data Coordinating Center"; >>>>>>>>>>>>>>>>> Repeat the same with all your sites (make sure to change >>>>>>>>>>>>>>>>> the Aliases between sites, they should all be unique). >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Let me know how it goes! >>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> On Thu, Jul 25, 2019 at 11:43 AM Sotirios Nikoloutsopoulos >>>>>>>>>>>>>>>>> wrote: >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Dear Cecile, >>>>>>>>>>>>>>>>>> You were right about your guesses. I did the >>>>>>>>>>>>>>>>>> modifications you suggested, i still get the "no mincs inserted" error, now >>>>>>>>>>>>>>>>>> i am getting the "No center found this candidate" error ( how do i fix >>>>>>>>>>>>>>>>>> that? from what i see the .dcm files contains a 'Institution Name', is that >>>>>>>>>>>>>>>>>> the center? ), so i guess that's why the validation fails, but i changed >>>>>>>>>>>>>>>>>> the force variable of tarchiveLoader to 1, shouldn't it have inserted the >>>>>>>>>>>>>>>>>> mincs then? Also it is optional to have a mail server, right? ( from what i >>>>>>>>>>>>>>>>>> see the mail error does not affect the $valid_study, so i assume we are >>>>>>>>>>>>>>>>>> okay with that ) >>>>>>>>>>>>>>>>>> Thank you a lot, >>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> ???? ???, 25 ???? 2019 ???? 5:48 ?.?., ?/? Cecile Madjar < >>>>>>>>>>>>>>>>>> cecile.madjar at mcin.ca> ??????: >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> From what I understand, I believe you just need to >>>>>>>>>>>>>>>>>>> update a few config settings from the frontend in the Config module (under >>>>>>>>>>>>>>>>>>> the Admin menu). >>>>>>>>>>>>>>>>>>> [image: Screen Shot 2019-07-25 at 10.31.35 AM.png] >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Then go to the Paths section of the config module and >>>>>>>>>>>>>>>>>>> update the "LORIS-MRI code" config setting to /data/loris/bin/mri (my guess >>>>>>>>>>>>>>>>>>> is that currently, it is set to /data/LORIS/data) and click on the submit >>>>>>>>>>>>>>>>>>> button. >>>>>>>>>>>>>>>>>>> [image: Screen Shot 2019-07-25 at 10.32.50 AM.png] >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Then, go to Imaging Pipeline section of the >>>>>>>>>>>>>>>>>>> Configuration module and update the "Loris-MRI Data Directory" to >>>>>>>>>>>>>>>>>>> /data/loris/data/ (my guess is that it is empty at the moment in your >>>>>>>>>>>>>>>>>>> database which is why $data_dir is not defined when you run the >>>>>>>>>>>>>>>>>>> tarchiveLoader step of the insertion pipeline). >>>>>>>>>>>>>>>>>>> [image: Screen Shot 2019-07-25 at 10.40.52 AM.png] >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Finally, I took a look at your environment file and it >>>>>>>>>>>>>>>>>>> might be a good idea to update your PERL5LIB variable to the following (it >>>>>>>>>>>>>>>>>>> has been added to the code a few releases ago as we realized this was >>>>>>>>>>>>>>>>>>> needed for the libraries. Not sure which version of LORIS-MRI you are using >>>>>>>>>>>>>>>>>>> but it does not hurt to update this variable to what I suggest below): >>>>>>>>>>>>>>>>>>> export >>>>>>>>>>>>>>>>>>> PERL5LIB=/data/loris/bin/mri/uploadNeuroDB:/data/loris/bin/mri/dicom-archive:$PERL5LIB >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Hope this helps. Sorry you are experiencing so much >>>>>>>>>>>>>>>>>>> trouble setting things up. We probably need to update our WIKI. >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> On Thu, Jul 25, 2019 at 9:48 AM Sotirios >>>>>>>>>>>>>>>>>>> Nikoloutsopoulos wrote: >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> The "Loris-MRI Data Directory" should be in the >>>>>>>>>>>>>>>>>>>> environment file? >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> ???? ???, 25 ???? 2019 ???? 12:59 ?.?., ?/? Sotirios >>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos ??????: >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> The scripts are located in /data/loris/bin/mri/. >>>>>>>>>>>>>>>>>>>>> Somewhere I might have messed something up but i remember following the >>>>>>>>>>>>>>>>>>>>> instructions in the wiki.For example when i tried to execute the >>>>>>>>>>>>>>>>>>>>> batch_uploads_imageuploader perl script the line >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> my $command = "$bin_dir/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl " >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> was pointing to an invalid path, for example: it was >>>>>>>>>>>>>>>>>>>>> repeating a pattern and had LORIS instead of loris ( i think the mistake >>>>>>>>>>>>>>>>>>>>> was that in the wiki it suggested to use $PROJECT for the name of the >>>>>>>>>>>>>>>>>>>>> folder and i choosed 'loris' >>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris/wiki/Imaging-Database >>>>>>>>>>>>>>>>>>>>> ). See also the in image for the modification i did. Also i didn't find the >>>>>>>>>>>>>>>>>>>>> section to config the $data_dir variable. >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> ???? ???, 24 ???? 2019 ???? 6:05 ?.?., ?/? Cecile >>>>>>>>>>>>>>>>>>>>> Madjar ??????: >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> It looks like you have one Config setting not set >>>>>>>>>>>>>>>>>>>>>> (based on the first error message you got when running it the first time). >>>>>>>>>>>>>>>>>>>>>> You need to set a value for "Loris-MRI Data Directory" in the Config module >>>>>>>>>>>>>>>>>>>>>> under the Imaging pipeline section (from what I can see, it would be >>>>>>>>>>>>>>>>>>>>>> /data/loris/data/ for your setup). >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> The reason you got that error message the second time >>>>>>>>>>>>>>>>>>>>>> is that the pipeline checks if the DICOM study was already inserted in the >>>>>>>>>>>>>>>>>>>>>> tarchive table. Since you ran the study once already, the study is inserted >>>>>>>>>>>>>>>>>>>>>> into the tarchive, hence the message. However, the pipeline did not >>>>>>>>>>>>>>>>>>>>>> complete as the MINC files were not created and inserted into the >>>>>>>>>>>>>>>>>>>>>> files/parameter_file table. In order to continue the insertion, you will >>>>>>>>>>>>>>>>>>>>>> then need to run the tarchiveLoader command suggested in the terminal >>>>>>>>>>>>>>>>>>>>>> during the second run: >>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader >>>>>>>>>>>>>>>>>>>>>> -globLocation -profile prod >>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive//2012/DCM_2012-12-05_ImagingUpload-17-43-ZUEFjb.tar >>>>>>>>>>>>>>>>>>>>>> -verbose >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> Finally, I am a bit confused by your setup. Where are >>>>>>>>>>>>>>>>>>>>>> the scripts located? In /data/loris/bin/mri or /data/loris/data? It feels >>>>>>>>>>>>>>>>>>>>>> like the Config setting "LORIS-MRI code" in the Paths section was set to >>>>>>>>>>>>>>>>>>>>>> "/data/LORIS/data" but it should have been set to the directory where the >>>>>>>>>>>>>>>>>>>>>> scripts are located (most probably /data/loris/bin/mri). >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> Hope this helps, >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> On Wed, Jul 24, 2019 at 10:55 AM Sotirios >>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos wrote: >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> Ok first i execute this command: >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> "lorisadmin at hbp:/data/loris/bin/mri$ >>>>>>>>>>>>>>>>>>>>>>> ./batch_uploads_imageuploader -profile prod < ~/Desktop/input.txt > log.txt >>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at ./batch_uploads_imageuploader line 143. >>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at ./batch_uploads_imageuploader line 143. >>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $_ in pattern match (m//) >>>>>>>>>>>>>>>>>>>>>>> at ./batch_uploads_imageuploader line 147. >>>>>>>>>>>>>>>>>>>>>>> base is DCC0000_258024_V01 >>>>>>>>>>>>>>>>>>>>>>> path is /data/incoming/ >>>>>>>>>>>>>>>>>>>>>>> type is .tar.gz >>>>>>>>>>>>>>>>>>>>>>> fullpath is /data/incoming/DCC0000_258024_V01.tar.gz >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> source /tmp/ImagingUpload-17-43-ZUEFjb >>>>>>>>>>>>>>>>>>>>>>> targetlocation /data/loris/data/tarchive >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 256. >>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 284. >>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at /data/loris/bin/mri/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>> tarchive_validation.pl line 219. >>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at /data/loris/bin/mri/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl line 270. >>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 711. >>>>>>>>>>>>>>>>>>>>>>> Can't exec "mail": No such file or directory at >>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 721. >>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 722. >>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 723. >>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 724. >>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 724. >>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 725. >>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 735. >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> No Mincs inserted >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> The tarchiveLoader insertion script has failed. >>>>>>>>>>>>>>>>>>>>>>> Running now the following command: >>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl -profile prod -upload_id 3 >>>>>>>>>>>>>>>>>>>>>>> /data/incoming/DCC0000_258024_V01.tar.gz -verbose" >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> I inserted the VisitLabel, but still the Mincs are >>>>>>>>>>>>>>>>>>>>>>> not inserted and i am getting this error >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> "lorisadmin at hbp:/data/loris/bin/mri$ >>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl -profile prod -upload_id 3 >>>>>>>>>>>>>>>>>>>>>>> /data/incoming/DCC0000_258024_V01.tar.gz -verbose >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> find -path \/tmp\/ImagingUpload\-17\-45\-5MsWEd >>>>>>>>>>>>>>>>>>>>>>> -name '__MACOSX' -delete >>>>>>>>>>>>>>>>>>>>>>> Spool message is: >>>>>>>>>>>>>>>>>>>>>>> The Scan for the uploadID 3 has already been run >>>>>>>>>>>>>>>>>>>>>>> with tarchiveID: 7. >>>>>>>>>>>>>>>>>>>>>>> To continue with the rest of the insertion pipeline, >>>>>>>>>>>>>>>>>>>>>>> please run tarchiveLoader from a terminal as follows: >>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader -globLocation -profile prod >>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive//2012/DCM_2012-12-05_ImagingUpload-17-43-ZUEFjb.tar >>>>>>>>>>>>>>>>>>>>>>> -verbose" >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> Which files should i delete? I thought that deleting >>>>>>>>>>>>>>>>>>>>>>> the files from the tarchive was enough. And i executed the last proposed >>>>>>>>>>>>>>>>>>>>>>> command to continue to rest of the insertion pipeline ( check the image ). >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> Thank you >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> ???? ???, 24 ???? 2019 ???? 5:05 ?.?., ?/? Cecile >>>>>>>>>>>>>>>>>>>>>>> Madjar ??????: >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> Sorry I was not clear before. Every visits of >>>>>>>>>>>>>>>>>>>>>>>> candidates are created in the session table with one entry per >>>>>>>>>>>>>>>>>>>>>>>> CandID/VisitLabel. So if the imaging pipeline created visits in the session >>>>>>>>>>>>>>>>>>>>>>>> table (that are not attached to instruments) and you want to clean your >>>>>>>>>>>>>>>>>>>>>>>> database completely, you can delete entries in that table as well. >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> Regarding your point 2, the imaging pipeline can >>>>>>>>>>>>>>>>>>>>>>>> create the visit in the session table as long as the visit label is present >>>>>>>>>>>>>>>>>>>>>>>> in the Visit_Windows table (which means the visit label stored in the >>>>>>>>>>>>>>>>>>>>>>>> PatientName is a valid visit label). >>>>>>>>>>>>>>>>>>>>>>>> However, in your prod file, if the >>>>>>>>>>>>>>>>>>>>>>>> variable $subjectID{'createVisitLabel'} is set to 1 for candidates, the >>>>>>>>>>>>>>>>>>>>>>>> visit label should be created in the Visit_Windows table I believe. Here >>>>>>>>>>>>>>>>>>>>>>>> is the line of the prod file you would need to change >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> . >>>>>>>>>>>>>>>>>>>>>>>> In general, we prefer populating the Visit_Windows >>>>>>>>>>>>>>>>>>>>>>>> table and set the $subjectID{'createVisitLabel'} to 0 for candidate data to >>>>>>>>>>>>>>>>>>>>>>>> avoid insertion of badly labelled MRI data that are complex to relabel. >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> Finally, regarding the candidate creation, if you >>>>>>>>>>>>>>>>>>>>>>>> execute the following steps, the pipeline should be able to create >>>>>>>>>>>>>>>>>>>>>>>> candidates: >>>>>>>>>>>>>>>>>>>>>>>> - set in the Imaging Pipeline section of the config >>>>>>>>>>>>>>>>>>>>>>>> module the config setting "Upload creation of candidates" to Yes >>>>>>>>>>>>>>>>>>>>>>>> - manually transfer the scans to the LORIS server >>>>>>>>>>>>>>>>>>>>>>>> instead of uploading it via the imaging browser >>>>>>>>>>>>>>>>>>>>>>>> - run batch_imaging_upload.pl as you did until now. >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> Hope this helps! >>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> On Wed, Jul 24, 2019 at 8:47 AM Sotirios >>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos wrote: >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> About my second question i replaced the name of >>>>>>>>>>>>>>>>>>>>>>>>> the patient in the .dcm files and now i am getting an error that the visit >>>>>>>>>>>>>>>>>>>>>>>>> label does not exist. >>>>>>>>>>>>>>>>>>>>>>>>> I thought it was supposed to be automatically >>>>>>>>>>>>>>>>>>>>>>>>> created. >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> "Done adding archive info into database >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader >>>>>>>>>>>>>>>>>>>>>>>>> -globLocation -profile prod >>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive//DCM_2012-12-05_ImagingUpload-15-42-yUwQQV.tar >>>>>>>>>>>>>>>>>>>>>>>>> -verbose >>>>>>>>>>>>>>>>>>>>>>>>> md5sum >>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive/DCM_2012-12-05_ImagingUpload-15-42-yUwQQV.tar >>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>> candidate id 258024 >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> => No Visit labelVisit label does not exist >>>>>>>>>>>>>>>>>>>>>>>>> Set centerID = 1 >>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> Number of MINC files that will be considered for >>>>>>>>>>>>>>>>>>>>>>>>> inserting into the database: 1 >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> log dir is /logs and log file is >>>>>>>>>>>>>>>>>>>>>>>>> /logs/TarLoad-15-42-L6pocU.log >>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>> candidate id 258024 >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> => No Visit label >>>>>>>>>>>>>>>>>>>>>>>>> Cleaning up temp files: rm -rf >>>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-15-42-J2rQms/ImagingUpload-15-42-yUwQQV*" >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 24 ???? 2019 ???? 3:38 ?.?., ?/? >>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos >>>>>>>>>>>>>>>>>>>>>>>>> ??????: >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> 1) What are the records in the session table? >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> 2) I tried to upload a non-phantom file like this >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> input_file.txt: >>>>>>>>>>>>>>>>>>>>>>>>>> /data/incoming/DCC0000_258024_V1.tar.gz N >>>>>>>>>>>>>>>>>>>>>>>>>> DCC0000_258024_V1 >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> Terminal: >>>>>>>>>>>>>>>>>>>>>>>>>> ./batch_uploads_imageuploader -profile prod < >>>>>>>>>>>>>>>>>>>>>>>>>> ~/Desktop/input.txt > log.txt >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> and i get the following error in the log.txt file >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> "Running now the following command: >>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl -profile prod -upload_id >>>>>>>>>>>>>>>>>>>>>>>>>> 7 /data/incoming/DCC0000_258024_V1.tar.gz -verbose >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> find -path \/tmp\/ImagingUpload\-14\-56\-FeLCB4 >>>>>>>>>>>>>>>>>>>>>>>>>> -name '__MACOSX' -delete >>>>>>>>>>>>>>>>>>>>>>>>>> Spool message is: >>>>>>>>>>>>>>>>>>>>>>>>>> The PatientName read from the DICOM header does >>>>>>>>>>>>>>>>>>>>>>>>>> not start with DCC0000_258024_V1 from the mri_upload table >>>>>>>>>>>>>>>>>>>>>>>>>> " >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> and the spool message is repeated for each .dcm >>>>>>>>>>>>>>>>>>>>>>>>>> file. Should i preprocess every .dcm file and change the PatientName to >>>>>>>>>>>>>>>>>>>>>>>>>> "DCC0000_258024_V1"? >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> 3) As far as it concerns the candidate profile i >>>>>>>>>>>>>>>>>>>>>>>>>> have to create a new one each time before i try to upload a file? Is there >>>>>>>>>>>>>>>>>>>>>>>>>> already a way to create a candidate profile and get the DCCID and PSCID >>>>>>>>>>>>>>>>>>>>>>>>>> without the user interface? >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 18 ???? 2019 ???? 5:00 ?.?., ?/? Cecile >>>>>>>>>>>>>>>>>>>>>>>>>> Madjar ??????: >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> See answers to your questions below. >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> About the 1st case we had a dicom with a blank >>>>>>>>>>>>>>>>>>>>>>>>>>>> studyUID, maybe someone accidentally removed it. >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> That is strange. Something must have been done >>>>>>>>>>>>>>>>>>>>>>>>>>> to the DICOM files. I have never seen a study with no StudyUID out of the >>>>>>>>>>>>>>>>>>>>>>>>>>> scanner. Usually, you need to manually erase it with some tool. However, >>>>>>>>>>>>>>>>>>>>>>>>>>> DICOMs never cease to surprise me... >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> Some other questions: >>>>>>>>>>>>>>>>>>>>>>>>>>>> 1) What are the steps to remove all of my >>>>>>>>>>>>>>>>>>>>>>>>>>>> patients and uploads?: because i want to try to reupload all the testing >>>>>>>>>>>>>>>>>>>>>>>>>>>> dicoms we had with a clean database. >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> Release 21.0 of LORIS-MRI will offer a script to >>>>>>>>>>>>>>>>>>>>>>>>>>> remove all the entries and files specific to an upload. However, this >>>>>>>>>>>>>>>>>>>>>>>>>>> release is not yet out. Hopefully in the next few weeks. >>>>>>>>>>>>>>>>>>>>>>>>>>> In the meantime, since your case is particular >>>>>>>>>>>>>>>>>>>>>>>>>>> and that you just want to start with a clean database, the following >>>>>>>>>>>>>>>>>>>>>>>>>>> deletes should work (hopefully I won't forget any tables): >>>>>>>>>>>>>>>>>>>>>>>>>>> delete from mri_violations_log; >>>>>>>>>>>>>>>>>>>>>>>>>>> delete from mri_protocol_violated_scans; >>>>>>>>>>>>>>>>>>>>>>>>>>> delete from MRICandidateErrors; >>>>>>>>>>>>>>>>>>>>>>>>>>> delete from parameter_file; >>>>>>>>>>>>>>>>>>>>>>>>>>> delete from files_qcstatus; # (if you played >>>>>>>>>>>>>>>>>>>>>>>>>>> with the QC part of the imaging browser for testing) >>>>>>>>>>>>>>>>>>>>>>>>>>> delete from feedback_mri_comments; # (if you >>>>>>>>>>>>>>>>>>>>>>>>>>> played with the QC part of the imaging browser for testing) >>>>>>>>>>>>>>>>>>>>>>>>>>> delete from tarchive_series; >>>>>>>>>>>>>>>>>>>>>>>>>>> delete from tarchive_files; >>>>>>>>>>>>>>>>>>>>>>>>>>> delete from mri_upload; >>>>>>>>>>>>>>>>>>>>>>>>>>> delete from tarchive; >>>>>>>>>>>>>>>>>>>>>>>>>>> delete from mri_scanner; >>>>>>>>>>>>>>>>>>>>>>>>>>> delete from candidate where PSCID="scanner"; >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> I don't know if you want to also delete entries >>>>>>>>>>>>>>>>>>>>>>>>>>> in the session and candidate table too? >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> 2) We do not need to create the profile of a >>>>>>>>>>>>>>>>>>>>>>>>>>>> patient ( are the patients stored in the candidate table? because i can't >>>>>>>>>>>>>>>>>>>>>>>>>>>> see the ghosts ), because will it automatically be created when importing a >>>>>>>>>>>>>>>>>>>>>>>>>>>> dicom? >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> I am not sure I understand fully this question. >>>>>>>>>>>>>>>>>>>>>>>>>>> All candidates are stored in the candidate table. The phantom scans however >>>>>>>>>>>>>>>>>>>>>>>>>>> are attached to a scanner candidate depending on where the scan happened. >>>>>>>>>>>>>>>>>>>>>>>>>>> It is a bit of a weird concept that we have to redesign eventually but >>>>>>>>>>>>>>>>>>>>>>>>>>> never got a chance to get to it. >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> Hopefully this answered your question, >>>>>>>>>>>>>>>>>>>>>>>>>>> otherwise, don't hesitate to let me know. >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> 3) What is the difference between uploading a >>>>>>>>>>>>>>>>>>>>>>>>>>>> dicom as phantom instead of importing as PSCCID_DCCID_VisitLabel? >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> When you upload the scan as >>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID_DCCID_VisitLabel, there is a check that makes sure the candidate IDs >>>>>>>>>>>>>>>>>>>>>>>>>>> and visit label are valid at the time of upload. >>>>>>>>>>>>>>>>>>>>>>>>>>> When you upload a scan as phantom, it expects >>>>>>>>>>>>>>>>>>>>>>>>>>> that the DICOM field PatientName and uploaded filename contains the string >>>>>>>>>>>>>>>>>>>>>>>>>>> "phantom". We enforced this behaviour on the imaging uploader side in >>>>>>>>>>>>>>>>>>>>>>>>>>> recent releases but I can't remember which one. Probably the upcoming 21.0 >>>>>>>>>>>>>>>>>>>>>>>>>>> release. >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> All those verifications might seem cumbersome >>>>>>>>>>>>>>>>>>>>>>>>>>> but they are here to ensure that the files inserted are all valid and >>>>>>>>>>>>>>>>>>>>>>>>>>> labelled properly as it is a bit messy to have to delete files that were >>>>>>>>>>>>>>>>>>>>>>>>>>> wrongly labelled. At least, the delete script present in release 21.0 will >>>>>>>>>>>>>>>>>>>>>>>>>>> make this process easier but it is still good practice to verify those >>>>>>>>>>>>>>>>>>>>>>>>>>> things. >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> With pleasure. Hopefully the answers to your >>>>>>>>>>>>>>>>>>>>>>>>>>> questions will be helpful. >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> PS: loris-dev mailing list: you will find the >>>>>>>>>>>>>>>>>>>>>>>>>>> initial answer I gave Sotirios below. I forgot to cc the loris-dev in my >>>>>>>>>>>>>>>>>>>>>>>>>>> earlier reply... >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 16 ???? 2019 ???? 12:02 ?.?., ?/? >>>>>>>>>>>>>>>>>>>>>>>>>>>> Cecile Madjar ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Dear Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you for reaching out. Since your email >>>>>>>>>>>>>>>>>>>>>>>>>>>>> was already organized in points, I will reply directly below your questions >>>>>>>>>>>>>>>>>>>>>>>>>>>>> below. >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> 1) What do we do when the StudyUID is blank on >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the header? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/minor/docs/AppendixA-Troubleshooting_guideline.md >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> There solution provided at the table 3 does not guide us how to find the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> information ( is possible ). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> The StudyUID is the field used in our pipeline >>>>>>>>>>>>>>>>>>>>>>>>>>>>> at the moment to check whether a DICOM study was already inserted into >>>>>>>>>>>>>>>>>>>>>>>>>>>>> LORIS with that same StudyUID since it is supposed to be unique for every >>>>>>>>>>>>>>>>>>>>>>>>>>>>> single study. Currently, we do not support insertion of DICOM studies if >>>>>>>>>>>>>>>>>>>>>>>>>>>>> they do not have a StudyUID associated with them. >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Is there a specific reason why the StudyUID is >>>>>>>>>>>>>>>>>>>>>>>>>>>>> blank in the DICOM headers in your DICOM files? Did they go through some >>>>>>>>>>>>>>>>>>>>>>>>>>>>> processes before upload to LORIS? >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> 2) When i am about to upload a non-phanton >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> case i need a 'Visit Label'. Is there already a script that can create a >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> new visit label for a specific Candidate, so i can provide it as input >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> afterwards to the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> batch_uploads_imageuploader ( See option 5.1.3 https://github.com/aces/Loris-MRI/blob/minor/docs/05-PipelineLaunchOptions.md ) >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> I am not sure if the front-end allows for it >>>>>>>>>>>>>>>>>>>>>>>>>>>>> but if you use batch_uploads_imageuploader, the insertion scripts could >>>>>>>>>>>>>>>>>>>>>>>>>>>>> create the visit label for you. However, it does need to be included in the >>>>>>>>>>>>>>>>>>>>>>>>>>>>> patient name in order for the script to know which label it should use. >>>>>>>>>>>>>>>>>>>>>>>>>>>>> For example: you upload V02 for MTL0123 >>>>>>>>>>>>>>>>>>>>>>>>>>>>> (DCCID: 456789) but V02 was not yet created for MTL0123; the insertion >>>>>>>>>>>>>>>>>>>>>>>>>>>>> scripts will create a V02 visit for MTL0123 if the PatientName field for >>>>>>>>>>>>>>>>>>>>>>>>>>>>> the dataset is MTL0123_456789_V02 with Stage marked as "Not Started". >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> However, *note that for the script to create >>>>>>>>>>>>>>>>>>>>>>>>>>>>> the visit for the candidate, you have to make sure that all the visit label >>>>>>>>>>>>>>>>>>>>>>>>>>>>> of your projects were inserted in the Visit_Windows table* >>>>>>>>>>>>>>>>>>>>>>>>>>>>> (otherwise, the visit will never be created as they were not specified as >>>>>>>>>>>>>>>>>>>>>>>>>>>>> being part of the list of visit label to expect). So in the example above, >>>>>>>>>>>>>>>>>>>>>>>>>>>>> you should have one row in Visit_Windows with Visit_label="V02" set. >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 3) Section 4.3 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/minor/docs/04-Scripts.md >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> What do we do when the folder contains multiple mnc files? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> This is a case by case. Most of the time, the >>>>>>>>>>>>>>>>>>>>>>>>>>>>> MINC files that failed insertion into the imaging browser end up in the MRI >>>>>>>>>>>>>>>>>>>>>>>>>>>>> violation module where you can see what went wrong with the acquisitions >>>>>>>>>>>>>>>>>>>>>>>>>>>>> not inserted. If you notice that the MINC file should be inserted as a >>>>>>>>>>>>>>>>>>>>>>>>>>>>> specific protocol, you can force the insertion as explained in section 4.3. >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> In your case, I have a feeling that you want >>>>>>>>>>>>>>>>>>>>>>>>>>>>> to be able to insert MINC files that did not go through the whole pipeline >>>>>>>>>>>>>>>>>>>>>>>>>>>>> insertion (DICOM archival, then dcm2mnc, then protocol identification, then >>>>>>>>>>>>>>>>>>>>>>>>>>>>> insertion...). In theory, you could call >>>>>>>>>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl on any MINC file, provided >>>>>>>>>>>>>>>>>>>>>>>>>>>>> you have at least the following information: >>>>>>>>>>>>>>>>>>>>>>>>>>>>> - path to the MINC file >>>>>>>>>>>>>>>>>>>>>>>>>>>>> - uploadID associated with the MINC files or >>>>>>>>>>>>>>>>>>>>>>>>>>>>> DICOM archive path from which those MINC files were created from >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Then the minc_insertion.pl script will do the >>>>>>>>>>>>>>>>>>>>>>>>>>>>> subject information and protocol validation etc... >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> If all the MINC files come from the same >>>>>>>>>>>>>>>>>>>>>>>>>>>>> uploadID or TarchiveID, then you could run a loop in bash calling the >>>>>>>>>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl script like this for files >>>>>>>>>>>>>>>>>>>>>>>>>>>>> deriving from uploadID=1: >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> ls /path/to/mnc/folder/* | while read f; do >>>>>>>>>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl -profile prod -uploadID 1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>> -mincPath $f; done >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helped! >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> -- >>>>>>>>>> >>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>> Montreal Neurological Institute >>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>> >>>>>>>>> >>>>>>>> >>>>>>>> -- >>>>>>>> >>>>>>>> christine.rogers at mcgill.ca >>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>> Montreal Neurological Institute >>>>>>>> McGill University | Montreal | Canada >>>>>>>> >>>>>>> _______________________________________________ >>>>>> Loris-dev mailing list >>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>> >>>>> >>>>> >>>>> -- >>>>> >>>>> christine.rogers at mcgill.ca >>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>> Montreal Neurological Institute >>>>> McGill University | Montreal | Canada >>>>> >>>> _______________________________________________ >>>> Loris-dev mailing list >>>> Loris-dev at bic.mni.mcgill.ca >>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>> >>> >>> >>> -- >>> >>> christine.rogers at mcgill.ca >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>> Montreal Neurological Institute >>> McGill University | Montreal | Canada >>> _______________________________________________ >>> Loris-dev mailing list >>> Loris-dev at bic.mni.mcgill.ca >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>> >> >> >> -- >> >> christine.rogers at mcgill.ca >> McGill Centre for Integrative Neuroscience | MCIN.ca >> Montreal Neurological Institute >> McGill University | Montreal | Canada >> _______________________________________________ >> Loris-dev mailing list >> Loris-dev at bic.mni.mcgill.ca >> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >> > > > -- > > christine.rogers at mcgill.ca > McGill Centre for Integrative Neuroscience | MCIN.ca > Montreal Neurological Institute > McGill University | Montreal | Canada > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: loris_access.log Type: text/x-log Size: 58809 bytes Desc: not available URL: From christine.rogers at mcgill.ca Wed Aug 7 10:41:21 2019 From: christine.rogers at mcgill.ca (Christine Rogers, Ms.) Date: Wed, 7 Aug 2019 14:41:21 +0000 Subject: [Loris-dev] Upgrading to Loris 21 - new make file In-Reply-To: References: Message-ID: Hi Sotirios, Thanks, have you tried all of these steps? - clear your browser cache (and refresh a few times) - delete any files in your smarty/templates_c directory (this will clear the template cache - do Not touch smarty/templates/) - run `make` (per the 21 release notes, this replaces the composer commands used in previous releases to update your dependencies) - restart apache (doesn't hurt) Let us know how it goes -- let us know what difference you see after, with your logs. A lso please send us your Config path settings (see these Troubleshooting Queries) if you're still seeing front-end issues. Thanks, Christine On Wed, Aug 7, 2019 at 8:02 AM Sotirios Nikoloutsopoulos > wrote: Hi, lorisadmin at hbp:/var/www/loris$ sudo cat /var/log/apache2/error.log [Wed Aug 07 07:35:02.422501 2019] [mpm_prefork:notice] [pid 1267] AH00163: Apache/2.4.18 (Ubuntu) OpenSSL/1.0.2g configured -- resuming normal operations [Wed Aug 07 07:35:02.422514 2019] [core:notice] [pid 1267] AH00094: Command line: '/usr/sbin/apache2' And as for the access.log the content are empty lorisadmin at hbp:/var/www/loris$ sudo ls -l /var/log/apache2/access.log lorisadmin at hbp:/var/www/loris$ sudo ls -l /var/log/apache2/access.log -rw-r----- 1 root adm 0 ???? 28 14:09 /var/log/apache2/access.log Also i noticed a loris_access.log. The only non-blank pages are: mri_violations, dataquery does not exist at all, statistics, data_team_helper, genomic_browser, configuration and server_processes_manager/ prints "Required configuration settings for Server Processes Manager are missing. Cannot continue." Thanks, Sotirios ???? ???, 6 ??? 2019 ???? 10:13 ?.?., ?/? Christine Rogers, Ms. > ??????: Hi Sotirios and LORIS community -- When upgrading to brand-new release 21 -- just a reminder to follow the release notes and run the new make file to update your dependencies (instead of using composer commands). We've also updated the Wiki page to clarify that the release notes for each version will tell you what to run. If your current version is not the last release (20.3), it's still important to upgrade to each minor release increment (e.g. 20.2, 20.3) before making the leap to 21.0. If you're getting blank pages, post-upgrade -- Try clearing your cache. Got questions or feedback e.g. on the Release Notes? please don't hesitate to let us know. Thanks, Christine The LORIS team On Tue, Aug 6, 2019 at 10:09 AM Christine Rogers, Ms. > wrote: Hi Sotirios, Could you also let us know -- on which pages is content visible, and on which pages/modules is content not visible for you? Thanks, Christine On Tue, Aug 6, 2019 at 9:54 AM Christine Rogers, Ms. > wrote: Thanks Sotirios, That's good to know. It sounds like you've checked that your /var/www/loris/project/config.xml file get populated properly. Please send us the last few errors you're seeing in your apache error log file, and your config paths and we can see what's happening with your front end -- Run these Troubleshooting Queries to get your config path settings, given your front end is not displaying fully. The Loris-MRI repo 21 install/upgrade would then be your next steps. Best, Christine On Tue, Aug 6, 2019 at 7:53 AM Sotirios Nikoloutsopoulos > wrote: I am using a VM. What i did was: 1) Download the files from https://github.com/aces/Loris and replace them to my existing /vaw/www/loris folder. 2) Execute the composer install --no-dev and then composer dump-autoload as mentioned here https://github.com/aces/Loris/wiki/Updating-your-LORIS. 3) Execute install.sh from /var/www/loris/tools and because LORIS already existed i moved a .config file, then re-executed the install.sh successfully 4 ) As for the database, i dropped the schema and i executed the installdb.php ???? ???, 5 ??? 2019 ???? 5:22 ?.?., ?/? Christine Rogers, Ms. > ??????: Hi Sotorios, Thanks - when you re-installed did you start on a fresh root path / VM or might some of your old system setting still apply? (And if you did any steps similar to an upgrade, did you follow the Upgrade steps in the Release Notes, from both repos?) About the TR_range column - it was recently split (MRI pr339) split into TR_min and _max columns. Given the code was trying to query TR_range which does not exist in your mri_protocol table, double-check which version of the Loris repo (tables) and the Loris-MRI repo (code) you have installed to ensure they match. Christine On Mon, Aug 5, 2019 at 9:06 AM Sotirios Nikoloutsopoulos > wrote: I reinstalled LORIS to 21 version and now the content is not visible at all at most pages. [image.png] ???? ???, 5 ??? 2019 ???? 3:19 ?.?., ?/? Sotirios Nikoloutsopoulos > ??????: Hi, Is it easy to upgrade to Loris 21? Also the following fails because the line 1985 of NeuroDB/MRIProcessingUtility.pm query mri_protocol which doesn't have TR_range https://github.com/aces/Loris/blob/21.0-release/SQL/0000-00-00-schema.sql#L556 [image.png] lorisadmin at hbp:/data/loris/bin/mri$ ./batch_uploads_imageuploader -profile prod < ~/Desktop/input.txt > log.txt Use of uninitialized value $_ in pattern match (m//) at ./batch_uploads_imageuploader line 147. base is DCC0000_258024_V1 path is /data/incoming/ type is .tar.gz fullpath is /data/incoming/DCC0000_258024_V1.tar.gz DBD::mysql::st execute failed: Unknown column 'TR_range' in 'where clause' at /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line 1985. DBD::mysql::st fetchrow_array failed: fetch() without execute() at /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line 1986. Use of uninitialized value $count_mri_protocol in numeric gt (>) at /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line 1995. DBD::mysql::st execute failed: Unknown column 'TR_range' in 'field list' at /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 562. Can't exec "mail": No such file or directory at /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 721. print() on closed filehandle MAIL at /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 722. print() on closed filehandle MAIL at /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 723. print() on closed filehandle MAIL at /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 724. print() on closed filehandle MAIL at /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 725. No Mincs inserted Thanks, Sotirios ???? ???, 3 ??? 2019 ???? 1:08 ?.?., ?/? Christine Rogers, Ms. > ??????: Hi Sotirios, First, just a note: we've released LORIS 21 this week with some major new features and cleanup -- especially if you are early in your setup phase, check out the Release notes for both the LORIS and Loris-MRI repos. Thanks for your screenshots -- your empty mri_protocol table should be at the root of these issues : The mri_protocol table must be populated in order for your scans to be registered in LORIS -- it serves as a whitelist for the insertion pipeline which filters out scans that aren't identified or matched to scan types in this table. By default, this table is populated with entries for t1, t2, fMRI and DTI (Insert statements for 21 release branch are here) Feel free to restore our default records and broaden their parameters to match all your scan types. re Defaced, native, selected -- these filter the scans displayed as you move to the next page (View Session), instead of viewing "all types" of scans from a given session : * "defaced" means that a defacing script has masked the subject's face in the volume (for patient privacy) * "native" means that no pre-processing has been performed on the scan (it's raw data), * "selected" will show only volumes that have been QC'd and "selected" as the best of their type -- used to display only the best quality T1 image instead of all T1s acquired in a session, e.g. re QC Comments -- Once you have successfully loaded scans (matched to the mri_protocol table), you'll be able to use the Imaging Browser's View Session subpage to enter/view QC comments on each volume, or for each visit. These are stored directly in the database, and linked to each scan. (Table name: feedback_mri_comments) (Visit-level QC comments are linked to the session.) For a walkthrough of the Imaging setup - please see the Imaging Setup guide - An old LORIS walkthrough video can also walk you through some of the Imaging front-end features, starting at 8:00 LORIS' imaging modules have been updated many times since this video, but the functionality and workflow is similar. Let us know how it goes once you have entries in your mri_protocol table - Best, Christine On Fri, Aug 2, 2019 at 7:58 AM Sotirios Nikoloutsopoulos > wrote: Hi Christine, In the candidate_list page i can see this patient [image.png] If i press the link under PSCID i get to see [image.png] and if i press the link under Scan Done it redirects me to imaging_browser [image.png] At the mri_violations page i also see No results ( neither on resolved / not resolved ). At the imaging_uploader i can see the record that failed. [image.png] If i click on the tarchive info i get to see the Protocol Name which i think is the acquisition we wanted? [image.png] Also my mri_protocol table is empty. Furthermore i would like to ask about the defaced, native, selected. What exactly is native and selected? And where are the qc comments stored? [image.png] Finally a walkthrough would be helpful. Thanks, Sotirios ???? ???, 30 ???? 2019 ???? 8:29 ?.?., ?/? Christine Rogers, Ms. > ??????: Hi Sotirios, Glad to hear you're making progress with the visit labels. To follow up on your last few emails: a- The Wiki's Setup Guide contains Sample insert statements for the Visit Windows table. As Cecile mentioned, the consistency of visit label format is important: V01, v01, V1, 01 -- whichever you select to use is fine; we use V01 by default across all documentation. b- For Password reset, there is a script in the tools/ directory so that a back-end administrator can reset any front-end user password, including Admin. (See info on setting up / resetting User passwords in the Wiki's Setup Guide) c- The minc file not being registered -- due to AcquisitionProtocol unknown. This means the SeriesDescription (Acquisition Protocol) in you Dicom header was not matched to any scan listed in the mri_protocol database table. (In the online Loris-MRI Troubleshooting Guide, this is Table 3, 2nd-last item "no MINCs inserted"). The MRI Violations module (Readme here) will show you the details of this mismatch -- Go to the module (under the Imaging menu), find your scan and click the link "Could not identify scan type" -- in the next subpage you can compare the scan's actual parameters against the mri_protocol table. To resolve this, adjust your mri_protocol table values or perhaps ensure your DICOMs are labelled consistently. Let us know if this works for you -- we can also walk you through an example of non-identified scans on Demo.loris.ca (MRI Violations module). Best, Christine The LORIS team On Tue, Jul 30, 2019 at 10:47 AM Sotirios Nikoloutsopoulos > wrote: I hope this is sufficient as the error for the visit label disappeared. [image.png] Please see the attached file. Also something i found. lorisadmin at hbp:/data/loris/bin/mri$ cat /data/loris/data//logs/TarLoad-17-39-xubBdv.log ==> Loading file from disk /tmp/TarLoad-17-39-UyQcG2/dcc0000_258024_v1_20121205_102108_501e1_mri.mnc --> mapping DICOM parameter for /tmp/TarLoad-17-39-UyQcG2/dcc0000_258024_v1_20121205_102108_501e1_mri.mnc ==> computing md5 hash for MINC body. --> md5: 6b1202fd63e29de4c9be1cd9925888a5 ==> verifying acquisition protocol Acquisition protocol is unknown --> The minc file cannot be registered since the AcquisitionProtocol is unknown ???? ???, 30 ???? 2019 ???? 4:58 ?.?., ?/? Sotirios Nikoloutsopoulos > ??????: Ok I fixed the login problem by using a known hash and by deleting the rows from the login_history i was able to login. ???? ???, 30 ???? 2019 ???? 4:50 ?.?., ?/? Sotirios Nikoloutsopoulos > ??????: Hi, there was no visit label 01 in the Visit_Windows table and i don't know how to insert it because the record requires lots of attributes. Also the system for a reason asked me to update my password and now i don't remember it and my account got suspended. Is there a way to reset it or set a simple password? I updated the password hash in the users table by using the hash from another LORIS setup we had and i still couldn't login ( also the attribute password is always NULL and the expiration date is 1999-01-01 for some reason ). Thanks ???? ???, 29 ???? 2019 ???? 5:21 ?.?., ?/? Cecile Madjar > ??????: Hi Sotirios, Can you try adding the visit label v01 to the Visit_Windows table? However, I noticed that in a previous dataset, the label was V1. Does that refer to the same visit? If so, you might want to harmonize the visit labels so they are all the same across datasets for a given timepoint, meaning you will need to relabel scans when the visit label is different but referring to the same visit label (v01 = V1 etc...). Hope this helps, C?cile On Mon, Jul 29, 2019 at 10:15 AM Sotirios Nikoloutsopoulos > wrote: Hi, Could you help me with the "Visit label does not exist"? I had changed $subjectID{'createVisitLabel'} to 1 as you had suggested but it appears that this problem hasn't been resolved yet. lorisadmin at hbp:/data/loris/bin/mri$ cat /data/loris/data//logs/TarLoad-14-58-9Xog7H.log ==> Loading file from disk /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc --> mapping DICOM parameter for /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc --> using user-defined filterParameters for /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc Candidate Mismatch Error is Visit label does not exist -> WARNING: This candidate was invalid. Logging to MRICandidateErrors table with reason Visit label does not exist Thank you, Sotirios ???? ???, 26 ???? 2019 ???? 3:02 ?.?., ?/? Sotirios Nikoloutsopoulos > ??????: Hi Cecile, The Center error was fixed. Still the insertion of mincs fails. Please see the output.txt file i attached. Also is there something else i need to change at the paths configuration? Thank you, Sotirios ???? ???, 25 ???? 2019 ???? 6:55 ?.?., ?/? Cecile Madjar > ??????: Hi Sotirios, We are making progress! I have a feeling this error comes from the fact that your psc table does not have the MRI_alias populated for the DCC site. Running the following query in the mysql database should fix this: UPDATE psc SET MRI_alias="DCC", Alias="DCC" WHERE Name="Data Coordinating Center"; Repeat the same with all your sites (make sure to change the Aliases between sites, they should all be unique). Let me know how it goes! Best, C?cile On Thu, Jul 25, 2019 at 11:43 AM Sotirios Nikoloutsopoulos > wrote: Dear Cecile, You were right about your guesses. I did the modifications you suggested, i still get the "no mincs inserted" error, now i am getting the "No center found this candidate" error ( how do i fix that? from what i see the .dcm files contains a 'Institution Name', is that the center? ), so i guess that's why the validation fails, but i changed the force variable of tarchiveLoader to 1, shouldn't it have inserted the mincs then? Also it is optional to have a mail server, right? ( from what i see the mail error does not affect the $valid_study, so i assume we are okay with that ) Thank you a lot, Sotirios ???? ???, 25 ???? 2019 ???? 5:48 ?.?., ?/? Cecile Madjar > ??????: Hi Sotirios, From what I understand, I believe you just need to update a few config settings from the frontend in the Config module (under the Admin menu). [Screen Shot 2019-07-25 at 10.31.35 AM.png] Then go to the Paths section of the config module and update the "LORIS-MRI code" config setting to /data/loris/bin/mri (my guess is that currently, it is set to /data/LORIS/data) and click on the submit button. [Screen Shot 2019-07-25 at 10.32.50 AM.png] Then, go to Imaging Pipeline section of the Configuration module and update the "Loris-MRI Data Directory" to /data/loris/data/ (my guess is that it is empty at the moment in your database which is why $data_dir is not defined when you run the tarchiveLoader step of the insertion pipeline). [Screen Shot 2019-07-25 at 10.40.52 AM.png] Finally, I took a look at your environment file and it might be a good idea to update your PERL5LIB variable to the following (it has been added to the code a few releases ago as we realized this was needed for the libraries. Not sure which version of LORIS-MRI you are using but it does not hurt to update this variable to what I suggest below): export PERL5LIB=/data/loris/bin/mri/uploadNeuroDB:/data/loris/bin/mri/dicom-archive:$PERL5LIB Hope this helps. Sorry you are experiencing so much trouble setting things up. We probably need to update our WIKI. Best, C?cile On Thu, Jul 25, 2019 at 9:48 AM Sotirios Nikoloutsopoulos > wrote: The "Loris-MRI Data Directory" should be in the environment file? ???? ???, 25 ???? 2019 ???? 12:59 ?.?., ?/? Sotirios Nikoloutsopoulos > ??????: The scripts are located in /data/loris/bin/mri/. Somewhere I might have messed something up but i remember following the instructions in the wiki.For example when i tried to execute the batch_uploads_imageuploader perl script the line my $command = "$bin_dir/uploadNeuroDB/imaging_upload_file.pl " was pointing to an invalid path, for example: it was repeating a pattern and had LORIS instead of loris ( i think the mistake was that in the wiki it suggested to use $PROJECT for the name of the folder and i choosed 'loris' https://github.com/aces/Loris/wiki/Imaging-Database ). See also the in image for the modification i did. Also i didn't find the section to config the $data_dir variable. Thank you, Sotirios ???? ???, 24 ???? 2019 ???? 6:05 ?.?., ?/? Cecile Madjar > ??????: Hi Sotirios, It looks like you have one Config setting not set (based on the first error message you got when running it the first time). You need to set a value for "Loris-MRI Data Directory" in the Config module under the Imaging pipeline section (from what I can see, it would be /data/loris/data/ for your setup). The reason you got that error message the second time is that the pipeline checks if the DICOM study was already inserted in the tarchive table. Since you ran the study once already, the study is inserted into the tarchive, hence the message. However, the pipeline did not complete as the MINC files were not created and inserted into the files/parameter_file table. In order to continue the insertion, you will then need to run the tarchiveLoader command suggested in the terminal during the second run: /data/LORIS/data//uploadNeuroDB/tarchiveLoader -globLocation -profile prod /data/loris/data/tarchive//2012/DCM_2012-12-05_ImagingUpload-17-43-ZUEFjb.tar -verbose Finally, I am a bit confused by your setup. Where are the scripts located? In /data/loris/bin/mri or /data/loris/data? It feels like the Config setting "LORIS-MRI code" in the Paths section was set to "/data/LORIS/data" but it should have been set to the directory where the scripts are located (most probably /data/loris/bin/mri). Hope this helps, C?cile On Wed, Jul 24, 2019 at 10:55 AM Sotirios Nikoloutsopoulos > wrote: Ok first i execute this command: "lorisadmin at hbp:/data/loris/bin/mri$ ./batch_uploads_imageuploader -profile prod < ~/Desktop/input.txt > log.txt Use of uninitialized value $data_dir in concatenation (.) or string at ./batch_uploads_imageuploader line 143. Use of uninitialized value $data_dir in concatenation (.) or string at ./batch_uploads_imageuploader line 143. Use of uninitialized value $_ in pattern match (m//) at ./batch_uploads_imageuploader line 147. base is DCC0000_258024_V01 path is /data/incoming/ type is .tar.gz fullpath is /data/incoming/DCC0000_258024_V01.tar.gz source /tmp/ImagingUpload-17-43-ZUEFjb targetlocation /data/loris/data/tarchive Use of uninitialized value $data_dir in concatenation (.) or string at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 256. Use of uninitialized value $data_dir in concatenation (.) or string at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 284. Use of uninitialized value $data_dir in concatenation (.) or string at /data/loris/bin/mri/uploadNeuroDB/tarchive_validation.pl line 219. Use of uninitialized value $data_dir in concatenation (.) or string at /data/loris/bin/mri/uploadNeuroDB/minc_insertion.pl line 270. Use of uninitialized value $data_dir in concatenation (.) or string at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 711. Can't exec "mail": No such file or directory at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 721. print() on closed filehandle MAIL at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 722. print() on closed filehandle MAIL at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 723. Use of uninitialized value $data_dir in concatenation (.) or string at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 724. print() on closed filehandle MAIL at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 724. print() on closed filehandle MAIL at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 725. Use of uninitialized value $data_dir in concatenation (.) or string at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 735. No Mincs inserted The tarchiveLoader insertion script has failed. Running now the following command: /data/loris/data/uploadNeuroDB/imaging_upload_file.pl -profile prod -upload_id 3 /data/incoming/DCC0000_258024_V01.tar.gz -verbose" I inserted the VisitLabel, but still the Mincs are not inserted and i am getting this error "lorisadmin at hbp:/data/loris/bin/mri$ /data/loris/data/uploadNeuroDB/imaging_upload_file.pl -profile prod -upload_id 3 /data/incoming/DCC0000_258024_V01.tar.gz -verbose find -path \/tmp\/ImagingUpload\-17\-45\-5MsWEd -name '__MACOSX' -delete Spool message is: The Scan for the uploadID 3 has already been run with tarchiveID: 7. To continue with the rest of the insertion pipeline, please run tarchiveLoader from a terminal as follows: /data/LORIS/data//uploadNeuroDB/tarchiveLoader -globLocation -profile prod /data/loris/data/tarchive//2012/DCM_2012-12-05_ImagingUpload-17-43-ZUEFjb.tar -verbose" Which files should i delete? I thought that deleting the files from the tarchive was enough. And i executed the last proposed command to continue to rest of the insertion pipeline ( check the image ). Thank you ???? ???, 24 ???? 2019 ???? 5:05 ?.?., ?/? Cecile Madjar > ??????: Hi Sotirios, Sorry I was not clear before. Every visits of candidates are created in the session table with one entry per CandID/VisitLabel. So if the imaging pipeline created visits in the session table (that are not attached to instruments) and you want to clean your database completely, you can delete entries in that table as well. Regarding your point 2, the imaging pipeline can create the visit in the session table as long as the visit label is present in the Visit_Windows table (which means the visit label stored in the PatientName is a valid visit label). However, in your prod file, if the variable $subjectID{'createVisitLabel'} is set to 1 for candidates, the visit label should be created in the Visit_Windows table I believe. Here is the line of the prod file you would need to change. In general, we prefer populating the Visit_Windows table and set the $subjectID{'createVisitLabel'} to 0 for candidate data to avoid insertion of badly labelled MRI data that are complex to relabel. Finally, regarding the candidate creation, if you execute the following steps, the pipeline should be able to create candidates: - set in the Imaging Pipeline section of the config module the config setting "Upload creation of candidates" to Yes - manually transfer the scans to the LORIS server instead of uploading it via the imaging browser - run batch_imaging_upload.pl as you did until now. Hope this helps! Best, C?cile On Wed, Jul 24, 2019 at 8:47 AM Sotirios Nikoloutsopoulos > wrote: About my second question i replaced the name of the patient in the .dcm files and now i am getting an error that the visit label does not exist. I thought it was supposed to be automatically created. "Done adding archive info into database /data/LORIS/data//uploadNeuroDB/tarchiveLoader -globLocation -profile prod /data/loris/data/tarchive//DCM_2012-12-05_ImagingUpload-15-42-yUwQQV.tar -verbose md5sum /data/loris/data/tarchive/DCM_2012-12-05_ImagingUpload-15-42-yUwQQV.tar PSCID is: DCC0000 CandID id: 258024 visit_label is: V1 PSCID is: DCC0000 CandID id: 258024 visit_label is: V1 candidate id 258024 => No Visit labelVisit label does not exist Set centerID = 1 PSCID is: DCC0000 CandID id: 258024 visit_label is: V1 PSCID is: DCC0000 CandID id: 258024 visit_label is: V1 Number of MINC files that will be considered for inserting into the database: 1 log dir is /logs and log file is /logs/TarLoad-15-42-L6pocU.log PSCID is: DCC0000 CandID id: 258024 visit_label is: V1 PSCID is: DCC0000 CandID id: 258024 visit_label is: V1 candidate id 258024 => No Visit label Cleaning up temp files: rm -rf /tmp/TarLoad-15-42-J2rQms/ImagingUpload-15-42-yUwQQV*" ???? ???, 24 ???? 2019 ???? 3:38 ?.?., ?/? Sotirios Nikoloutsopoulos > ??????: Hi, 1) What are the records in the session table? 2) I tried to upload a non-phantom file like this input_file.txt: /data/incoming/DCC0000_258024_V1.tar.gz N DCC0000_258024_V1 Terminal: ./batch_uploads_imageuploader -profile prod < ~/Desktop/input.txt > log.txt and i get the following error in the log.txt file "Running now the following command: /data/loris/data/uploadNeuroDB/imaging_upload_file.pl -profile prod -upload_id 7 /data/incoming/DCC0000_258024_V1.tar.gz -verbose find -path \/tmp\/ImagingUpload\-14\-56\-FeLCB4 -name '__MACOSX' -delete Spool message is: The PatientName read from the DICOM header does not start with DCC0000_258024_V1 from the mri_upload table " and the spool message is repeated for each .dcm file. Should i preprocess every .dcm file and change the PatientName to "DCC0000_258024_V1"? 3) As far as it concerns the candidate profile i have to create a new one each time before i try to upload a file? Is there already a way to create a candidate profile and get the DCCID and PSCID without the user interface? Thank you, Sotirios ???? ???, 18 ???? 2019 ???? 5:00 ?.?., ?/? Cecile Madjar > ??????: Hi Sotirios, See answers to your questions below. About the 1st case we had a dicom with a blank studyUID, maybe someone accidentally removed it. That is strange. Something must have been done to the DICOM files. I have never seen a study with no StudyUID out of the scanner. Usually, you need to manually erase it with some tool. However, DICOMs never cease to surprise me... Some other questions: 1) What are the steps to remove all of my patients and uploads?: because i want to try to reupload all the testing dicoms we had with a clean database. Release 21.0 of LORIS-MRI will offer a script to remove all the entries and files specific to an upload. However, this release is not yet out. Hopefully in the next few weeks. In the meantime, since your case is particular and that you just want to start with a clean database, the following deletes should work (hopefully I won't forget any tables): delete from mri_violations_log; delete from mri_protocol_violated_scans; delete from MRICandidateErrors; delete from parameter_file; delete from files_qcstatus; # (if you played with the QC part of the imaging browser for testing) delete from feedback_mri_comments; # (if you played with the QC part of the imaging browser for testing) delete from tarchive_series; delete from tarchive_files; delete from mri_upload; delete from tarchive; delete from mri_scanner; delete from candidate where PSCID="scanner"; I don't know if you want to also delete entries in the session and candidate table too? 2) We do not need to create the profile of a patient ( are the patients stored in the candidate table? because i can't see the ghosts ), because will it automatically be created when importing a dicom? I am not sure I understand fully this question. All candidates are stored in the candidate table. The phantom scans however are attached to a scanner candidate depending on where the scan happened. It is a bit of a weird concept that we have to redesign eventually but never got a chance to get to it. Hopefully this answered your question, otherwise, don't hesitate to let me know. 3) What is the difference between uploading a dicom as phantom instead of importing as PSCCID_DCCID_VisitLabel? When you upload the scan as PSCID_DCCID_VisitLabel, there is a check that makes sure the candidate IDs and visit label are valid at the time of upload. When you upload a scan as phantom, it expects that the DICOM field PatientName and uploaded filename contains the string "phantom". We enforced this behaviour on the imaging uploader side in recent releases but I can't remember which one. Probably the upcoming 21.0 release. All those verifications might seem cumbersome but they are here to ensure that the files inserted are all valid and labelled properly as it is a bit messy to have to delete files that were wrongly labelled. At least, the delete script present in release 21.0 will make this process easier but it is still good practice to verify those things. Thank you, With pleasure. Hopefully the answers to your questions will be helpful. Best, C?cile PS: loris-dev mailing list: you will find the initial answer I gave Sotirios below. I forgot to cc the loris-dev in my earlier reply... ???? ???, 16 ???? 2019 ???? 12:02 ?.?., ?/? Cecile Madjar > ??????: Dear Sotirios, Thank you for reaching out. Since your email was already organized in points, I will reply directly below your questions below. Best, C?cile 1) What do we do when the StudyUID is blank on the header? https://github.com/aces/Loris-MRI/blob/minor/docs/AppendixA-Troubleshooting_guideline.md There solution provided at the table 3 does not guide us how to find the information ( is possible ). The StudyUID is the field used in our pipeline at the moment to check whether a DICOM study was already inserted into LORIS with that same StudyUID since it is supposed to be unique for every single study. Currently, we do not support insertion of DICOM studies if they do not have a StudyUID associated with them. Is there a specific reason why the StudyUID is blank in the DICOM headers in your DICOM files? Did they go through some processes before upload to LORIS? 2) When i am about to upload a non-phanton case i need a 'Visit Label'. Is there already a script that can create a new visit label for a specific Candidate, so i can provide it as input afterwards to the batch_uploads_imageuploader ( See option 5.1.3 https://github.com/aces/Loris-MRI/blob/minor/docs/05-PipelineLaunchOptions.md ) I am not sure if the front-end allows for it but if you use batch_uploads_imageuploader, the insertion scripts could create the visit label for you. However, it does need to be included in the patient name in order for the script to know which label it should use. For example: you upload V02 for MTL0123 (DCCID: 456789) but V02 was not yet created for MTL0123; the insertion scripts will create a V02 visit for MTL0123 if the PatientName field for the dataset is MTL0123_456789_V02 with Stage marked as "Not Started". However, note that for the script to create the visit for the candidate, you have to make sure that all the visit label of your projects were inserted in the Visit_Windows table (otherwise, the visit will never be created as they were not specified as being part of the list of visit label to expect). So in the example above, you should have one row in Visit_Windows with Visit_label="V02" set. 3) Section 4.3 https://github.com/aces/Loris-MRI/blob/minor/docs/04-Scripts.md What do we do when the folder contains multiple mnc files? This is a case by case. Most of the time, the MINC files that failed insertion into the imaging browser end up in the MRI violation module where you can see what went wrong with the acquisitions not inserted. If you notice that the MINC file should be inserted as a specific protocol, you can force the insertion as explained in section 4.3. In your case, I have a feeling that you want to be able to insert MINC files that did not go through the whole pipeline insertion (DICOM archival, then dcm2mnc, then protocol identification, then insertion...). In theory, you could call minc_insertion.pl on any MINC file, provided you have at least the following information: - path to the MINC file - uploadID associated with the MINC files or DICOM archive path from which those MINC files were created from Then the minc_insertion.pl script will do the subject information and protocol validation etc... If all the MINC files come from the same uploadID or TarchiveID, then you could run a loop in bash calling the minc_insertion.pl script like this for files deriving from uploadID=1: ls /path/to/mnc/folder/* | while read f; do minc_insertion.pl -profile prod -uploadID 1 -mincPath $f; done Thank you, Hope this helped! _______________________________________________ Loris-dev mailing list Loris-dev at bic.mni.mcgill.ca https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev -- christine.rogers at mcgill.ca McGill Centre for Integrative Neuroscience | MCIN.ca Montreal Neurological Institute McGill University | Montreal | Canada -- christine.rogers at mcgill.ca McGill Centre for Integrative Neuroscience | MCIN.ca Montreal Neurological Institute McGill University | Montreal | Canada _______________________________________________ Loris-dev mailing list Loris-dev at bic.mni.mcgill.ca https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev -- christine.rogers at mcgill.ca McGill Centre for Integrative Neuroscience | MCIN.ca Montreal Neurological Institute McGill University | Montreal | Canada _______________________________________________ Loris-dev mailing list Loris-dev at bic.mni.mcgill.ca https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev -- christine.rogers at mcgill.ca McGill Centre for Integrative Neuroscience | MCIN.ca Montreal Neurological Institute McGill University | Montreal | Canada _______________________________________________ Loris-dev mailing list Loris-dev at bic.mni.mcgill.ca https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev -- christine.rogers at mcgill.ca McGill Centre for Integrative Neuroscience | MCIN.ca Montreal Neurological Institute McGill University | Montreal | Canada _______________________________________________ Loris-dev mailing list Loris-dev at bic.mni.mcgill.ca https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev -- christine.rogers at mcgill.ca McGill Centre for Integrative Neuroscience | MCIN.ca Montreal Neurological Institute McGill University | Montreal | Canada _______________________________________________ Loris-dev mailing list Loris-dev at bic.mni.mcgill.ca https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev -- christine.rogers at mcgill.ca McGill Centre for Integrative Neuroscience | MCIN.ca Montreal Neurological Institute McGill University | Montreal | Canada -------------- next part -------------- An HTML attachment was scrubbed... URL: From sotirisnik at gmail.com Thu Aug 8 08:36:56 2019 From: sotirisnik at gmail.com (Sotirios Nikoloutsopoulos) Date: Thu, 8 Aug 2019 15:36:56 +0300 Subject: [Loris-dev] Upgrading to Loris 21 - new make file In-Reply-To: References: Message-ID: Hi, I runned make and also included the file it reports at the end. lorisadmin at hbp:/var/www/loris$ make npm install npm WARN optional Skipping failed optional dependency /chokidar/fsevents: npm WARN notsup Not compatible with your operating system or architecture: fsevents at 1.2.9 npm WARN optional Skipping failed optional dependency /watchpack/chokidar/fsevents: npm WARN notsup Not compatible with your operating system or architecture: fsevents at 1.2.9 npm run compile > loris at 1.0.0 compile /var/www/loris > webpack /var/www/loris/node_modules/webpack/bin/webpack.js:86 let notify = ^^^ SyntaxError: Block-scoped declarations (let, const, function, class) not yet supported outside strict mode at exports.runInThisContext (vm.js:53:16) at Module._compile (module.js:374:25) at Object.Module._extensions..js (module.js:417:10) at Module.load (module.js:344:32) at Function.Module._load (module.js:301:12) at Function.Module.runMain (module.js:442:10) at startup (node.js:136:18) at node.js:966:3 npm ERR! Linux 4.15.0-55-generic npm ERR! argv "/usr/bin/nodejs" "/usr/bin/npm" "run" "compile" npm ERR! node v4.2.6 npm ERR! npm v3.5.2 npm ERR! code ELIFECYCLE npm ERR! loris at 1.0.0 compile: `webpack` npm ERR! Exit status 1 npm ERR! npm ERR! Failed at the loris at 1.0.0 compile script 'webpack'. npm ERR! Make sure you have the latest version of node.js and npm installed. npm ERR! If you do, this is most likely a problem with the loris package, npm ERR! not with npm itself. npm ERR! Tell the author that this fails on your system: npm ERR! webpack npm ERR! You can get information on how to open an issue for this project with: npm ERR! npm bugs loris npm ERR! Or if that isn't available, you can get their info via: npm ERR! npm owner ls loris npm ERR! There is likely additional logging output above. npm ERR! Please include the following file with any support request: npm ERR! /var/www/loris/npm-debug.log Makefile:14: recipe for target 'javascript' failed make: *** [javascript] Error 1 Thanks, Sotirios ???? ???, 7 ??? 2019 ???? 5:41 ?.?., ?/? Christine Rogers, Ms. < christine.rogers at mcgill.ca> ??????: > Hi Sotirios, > > Thanks, have you tried all of these steps? > - clear your browser cache (and refresh a few times) > - delete any files in your smarty/templates_c directory (this will clear > the template cache - do Not touch smarty/templates/) > - run `make` (per the 21 release notes, this replaces the composer > commands used in previous releases to update your dependencies) > - restart apache (doesn't hurt) > > Let us know how it goes -- let us know what difference you see after, with > your logs. A > lso please send us your Config path settings (see these Troubleshooting > Queries > ) > if you're still seeing front-end issues. > > Thanks, > Christine > > On Wed, Aug 7, 2019 at 8:02 AM Sotirios Nikoloutsopoulos < > sotirisnik at gmail.com> wrote: > >> Hi, >> >> lorisadmin at hbp:/var/www/loris$ sudo cat /var/log/apache2/error.log >> [Wed Aug 07 07:35:02.422501 2019] [mpm_prefork:notice] [pid 1267] >> AH00163: Apache/2.4.18 (Ubuntu) OpenSSL/1.0.2g configured -- resuming >> normal operations >> [Wed Aug 07 07:35:02.422514 2019] [core:notice] [pid 1267] AH00094: >> Command line: '/usr/sbin/apache2' >> >> And as for the access.log the content are empty >> lorisadmin at hbp:/var/www/loris$ sudo ls -l /var/log/apache2/access.log >> lorisadmin at hbp:/var/www/loris$ sudo ls -l /var/log/apache2/access.log >> -rw-r----- 1 root adm 0 ???? 28 14:09 /var/log/apache2/access.log >> >> Also i noticed a loris_access.log. >> >> The only non-blank pages are: >> mri_violations, dataquery does not exist at all, statistics, >> data_team_helper, genomic_browser, configuration and >> server_processes_manager/ prints "Required configuration settings for >> Server Processes Manager are missing. Cannot continue." >> >> Thanks, >> Sotirios >> >> ???? ???, 6 ??? 2019 ???? 10:13 ?.?., ?/? Christine Rogers, Ms. < >> christine.rogers at mcgill.ca> ??????: >> >>> Hi Sotirios and LORIS community -- >>> >>> When upgrading to brand-new release 21 -- just a reminder to follow the >>> release notes and run the new *make* file to update your dependencies >>> (instead of using *composer* commands). >>> We've also updated the Wiki page >>> to clarify >>> that the release notes for each version will tell you what to run. >>> >>> If your current version is not the last release (20.3), it's still >>> important to upgrade to each minor release increment (e.g. 20.2, 20.3) >>> before making the leap to 21.0. >>> >>> If you're getting blank pages, post-upgrade -- Try clearing your cache. >>> >>> Got questions or feedback e.g. on the Release Notes? please don't >>> hesitate to let us know. >>> Thanks, >>> Christine >>> The LORIS team >>> >>> >>> >>> On Tue, Aug 6, 2019 at 10:09 AM Christine Rogers, Ms. < >>> christine.rogers at mcgill.ca> wrote: >>> >>>> Hi Sotirios, >>>> Could you also let us know -- on which pages is content visible, and on >>>> which pages/modules is content not visible for you? >>>> Thanks, >>>> Christine >>>> >>>> On Tue, Aug 6, 2019 at 9:54 AM Christine Rogers, Ms. < >>>> christine.rogers at mcgill.ca> wrote: >>>> >>>>> Thanks Sotirios, >>>>> That's good to know. It sounds like you've checked that your >>>>> /var/www/loris/project/config.xml file get populated properly. >>>>> >>>>> Please send us the last few errors you're seeing in your apache error >>>>> log file, and your config paths and we can see what's happening with your >>>>> front end -- >>>>> Run these Troubleshooting Queries >>>>> >>>>> to get your config path settings, given your front end is not displaying >>>>> fully. >>>>> >>>>> The Loris-MRI repo >>>>> 21 >>>>> install/upgrade would then be your next steps. >>>>> Best, >>>>> Christine >>>>> >>>>> On Tue, Aug 6, 2019 at 7:53 AM Sotirios Nikoloutsopoulos < >>>>> sotirisnik at gmail.com> wrote: >>>>> >>>>>> I am using a VM. What i did was: >>>>>> 1) Download the files from https://github.com/aces/Loris and replace >>>>>> them to my existing /vaw/www/loris folder. >>>>>> 2) Execute the composer install --no-dev and then composer >>>>>> dump-autoload as mentioned here >>>>>> https://github.com/aces/Loris/wiki/Updating-your-LORIS. >>>>>> 3) Execute install.sh from /var/www/loris/tools and because LORIS >>>>>> already existed i moved a .config file, then re-executed the install.sh >>>>>> successfully >>>>>> 4 ) As for the database, i dropped the schema and i executed the >>>>>> installdb.php >>>>>> >>>>>> ???? ???, 5 ??? 2019 ???? 5:22 ?.?., ?/? Christine Rogers, Ms. < >>>>>> christine.rogers at mcgill.ca> ??????: >>>>>> >>>>>>> Hi Sotorios, >>>>>>> >>>>>>> Thanks - when you re-installed did you start on a fresh root path / >>>>>>> VM or might some of your old system setting still apply? >>>>>>> (And if you did any steps similar to an upgrade, did you follow the >>>>>>> Upgrade steps in the Release Notes, from both repos?) >>>>>>> >>>>>>> About the TR_range column - it was recently split (MRI pr339 >>>>>>> ) split into TR_min and >>>>>>> _max columns. Given the code was trying to query TR_range which does not >>>>>>> exist in your mri_protocol table, double-check which version of the Loris >>>>>>> repo (tables) and the Loris-MRI repo (code) you have installed to ensure >>>>>>> they match. >>>>>>> >>>>>>> Christine >>>>>>> >>>>>>> >>>>>>> On Mon, Aug 5, 2019 at 9:06 AM Sotirios Nikoloutsopoulos < >>>>>>> sotirisnik at gmail.com> wrote: >>>>>>> >>>>>>>> I reinstalled LORIS to 21 version and now the content is not >>>>>>>> visible at all at most pages. >>>>>>>> >>>>>>>> [image: image.png] >>>>>>>> >>>>>>>> ???? ???, 5 ??? 2019 ???? 3:19 ?.?., ?/? Sotirios Nikoloutsopoulos < >>>>>>>> sotirisnik at gmail.com> ??????: >>>>>>>> >>>>>>>>> Hi, >>>>>>>>> >>>>>>>>> Is it easy to upgrade to Loris 21? Also the following fails >>>>>>>>> because the line 1985 of NeuroDB/MRIProcessingUtility.pm query mri_protocol >>>>>>>>> which doesn't have TR_range >>>>>>>>> https://github.com/aces/Loris/blob/21.0-release/SQL/0000-00-00-schema.sql#L556 >>>>>>>>> >>>>>>>>> [image: image.png] >>>>>>>>> >>>>>>>>> lorisadmin at hbp:/data/loris/bin/mri$ ./batch_uploads_imageuploader >>>>>>>>> -profile prod < ~/Desktop/input.txt > log.txt >>>>>>>>> Use of uninitialized value $_ in pattern match (m//) at >>>>>>>>> ./batch_uploads_imageuploader line 147. >>>>>>>>> base is DCC0000_258024_V1 >>>>>>>>> path is /data/incoming/ >>>>>>>>> type is .tar.gz >>>>>>>>> fullpath is /data/incoming/DCC0000_258024_V1.tar.gz >>>>>>>>> DBD::mysql::st execute failed: Unknown column 'TR_range' in 'where >>>>>>>>> clause' at >>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line 1985. >>>>>>>>> DBD::mysql::st fetchrow_array failed: fetch() without execute() at >>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line 1986. >>>>>>>>> Use of uninitialized value $count_mri_protocol in numeric gt (>) >>>>>>>>> at /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line >>>>>>>>> 1995. >>>>>>>>> DBD::mysql::st execute failed: Unknown column 'TR_range' in 'field >>>>>>>>> list' at /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 562. >>>>>>>>> Can't exec "mail": No such file or directory at >>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 721. >>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 722. >>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 723. >>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 724. >>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 725. >>>>>>>>> >>>>>>>>> No Mincs inserted >>>>>>>>> >>>>>>>>> Thanks, >>>>>>>>> >>>>>>>>> Sotirios >>>>>>>>> >>>>>>>>> ???? ???, 3 ??? 2019 ???? 1:08 ?.?., ?/? Christine Rogers, Ms. < >>>>>>>>> christine.rogers at mcgill.ca> ??????: >>>>>>>>> >>>>>>>>>> Hi Sotirios, >>>>>>>>>> >>>>>>>>>> First, just a note: we've released LORIS 21 this week with some >>>>>>>>>> major new features and cleanup -- especially if you are early in your setup >>>>>>>>>> phase, check out the Release notes for both the LORIS >>>>>>>>>> and >>>>>>>>>> Loris-MRI >>>>>>>>>> repos. >>>>>>>>>> >>>>>>>>>> Thanks for your screenshots -- your empty mri_protocol table >>>>>>>>>> should be at the root of these issues : >>>>>>>>>> >>>>>>>>>> The mri_protocol table must be populated >>>>>>>>>> >>>>>>>>>> in order for your scans to be registered in LORIS -- it serves as a >>>>>>>>>> whitelist for the insertion pipeline which filters out scans that aren't >>>>>>>>>> identified or matched to scan types in this table. >>>>>>>>>> >>>>>>>>>> By default, this table is populated with entries for t1, t2, fMRI >>>>>>>>>> and DTI (Insert statements for 21 release branch are here >>>>>>>>>> >>>>>>>>>> ) >>>>>>>>>> Feel free to restore our default records and broaden their >>>>>>>>>> parameters to match all your scan types. >>>>>>>>>> >>>>>>>>>> re Defaced, native, selected -- these filter the scans displayed >>>>>>>>>> as you move to the next page (View Session), instead of viewing "all types" >>>>>>>>>> of scans from a given session : >>>>>>>>>> >>>>>>>>>> - "defaced" means that a defacing script >>>>>>>>>> >>>>>>>>>> has masked the subject's face in the volume (for patient privacy) >>>>>>>>>> - "native" means that no pre-processing has been performed on >>>>>>>>>> the scan (it's raw data), >>>>>>>>>> - "selected" will show only volumes that have been QC'd and >>>>>>>>>> "selected" as the best of their type -- used to display only the best >>>>>>>>>> quality T1 image instead of all T1s acquired in a session, e.g. >>>>>>>>>> >>>>>>>>>> re QC Comments -- >>>>>>>>>> Once you have successfully loaded scans (matched to the >>>>>>>>>> mri_protocol table), you'll be able to use the Imaging Browser's View >>>>>>>>>> Session subpage to enter/view QC comments on each volume, or for each >>>>>>>>>> visit. >>>>>>>>>> These are stored directly in the database, and linked to each >>>>>>>>>> scan. (Table name: feedback_mri_comments) >>>>>>>>>> (Visit-level QC comments are linked to the session.) >>>>>>>>>> >>>>>>>>>> For a walkthrough of the Imaging setup - please see the Imaging >>>>>>>>>> Setup guide >>>>>>>>>> >>>>>>>>>> - >>>>>>>>>> >>>>>>>>>> An old LORIS walkthrough video >>>>>>>>>> can also walk you >>>>>>>>>> through some of the Imaging front-end features, starting at 8:00 >>>>>>>>>> LORIS' imaging modules have been updated many times since this >>>>>>>>>> video, but the functionality and workflow is similar. >>>>>>>>>> >>>>>>>>>> Let us know how it goes once you have entries in your >>>>>>>>>> mri_protocol table - >>>>>>>>>> Best, >>>>>>>>>> Christine >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> On Fri, Aug 2, 2019 at 7:58 AM Sotirios Nikoloutsopoulos < >>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>> >>>>>>>>>>> Hi Christine, >>>>>>>>>>> >>>>>>>>>>> In the candidate_list page i can see this patient >>>>>>>>>>> >>>>>>>>>>> [image: image.png] >>>>>>>>>>> >>>>>>>>>>> If i press the link under PSCID i get to see >>>>>>>>>>> [image: image.png] >>>>>>>>>>> >>>>>>>>>>> and if i press the link under Scan Done it redirects me to >>>>>>>>>>> imaging_browser >>>>>>>>>>> >>>>>>>>>>> [image: image.png] >>>>>>>>>>> >>>>>>>>>>> At the mri_violations page i also see No results ( neither on >>>>>>>>>>> resolved / not resolved ). >>>>>>>>>>> >>>>>>>>>>> At the imaging_uploader i can see the record that failed. >>>>>>>>>>> >>>>>>>>>>> [image: image.png] >>>>>>>>>>> >>>>>>>>>>> If i click on the tarchive info i get to see the Protocol Name >>>>>>>>>>> which i think is the acquisition we wanted? >>>>>>>>>>> [image: image.png] >>>>>>>>>>> >>>>>>>>>>> Also my mri_protocol table is empty. >>>>>>>>>>> >>>>>>>>>>> Furthermore i would like to ask about the defaced, native, >>>>>>>>>>> selected. What exactly is native and selected? And where are the qc >>>>>>>>>>> comments stored? >>>>>>>>>>> >>>>>>>>>>> [image: image.png] >>>>>>>>>>> >>>>>>>>>>> Finally a walkthrough would be helpful. >>>>>>>>>>> >>>>>>>>>>> Thanks, >>>>>>>>>>> >>>>>>>>>>> Sotirios >>>>>>>>>>> >>>>>>>>>>> ???? ???, 30 ???? 2019 ???? 8:29 ?.?., ?/? Christine Rogers, Ms. >>>>>>>>>>> ??????: >>>>>>>>>>> >>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>> Glad to hear you're making progress with the visit labels. To >>>>>>>>>>>> follow up on your last few emails: >>>>>>>>>>>> >>>>>>>>>>>> a- The Wiki's Setup Guide contains Sample insert statements >>>>>>>>>>>> for the Visit Windows table >>>>>>>>>>>> >>>>>>>>>>>> . >>>>>>>>>>>> >>>>>>>>>>>> As Cecile mentioned, the consistency of visit label format is >>>>>>>>>>>> important: V01, v01, V1, 01 -- whichever you select to use is fine; we use >>>>>>>>>>>> V01 by default across all documentation. >>>>>>>>>>>> >>>>>>>>>>>> b- For Password reset, there is a script in the tools/ >>>>>>>>>>>> directory so that a back-end administrator can reset any front-end user >>>>>>>>>>>> password, including Admin. (See info on setting up / resetting User >>>>>>>>>>>> passwords in the Wiki's Setup Guide >>>>>>>>>>>> >>>>>>>>>>>> ) >>>>>>>>>>>> >>>>>>>>>>>> c- The minc file not being registered -- due to >>>>>>>>>>>> AcquisitionProtocol unknown. >>>>>>>>>>>> This means the SeriesDescription (Acquisition Protocol) in you >>>>>>>>>>>> Dicom header was not matched to any scan listed in the mri_protocol >>>>>>>>>>>> database table. >>>>>>>>>>>> (In the online Loris-MRI Troubleshooting Guide, >>>>>>>>>>>> this >>>>>>>>>>>> is Table 3, 2nd-last item "no MINCs inserted"). >>>>>>>>>>>> >>>>>>>>>>>> The MRI Violations module (Readme here) >>>>>>>>>>>> will show >>>>>>>>>>>> you the details of this mismatch -- >>>>>>>>>>>> Go to the module (under the Imaging menu), find your scan and >>>>>>>>>>>> click the link "Could not identify scan type" -- in the next subpage you >>>>>>>>>>>> can compare the scan's actual parameters against the mri_protocol table. >>>>>>>>>>>> >>>>>>>>>>>> To resolve this, adjust your mri_protocol table values or >>>>>>>>>>>> perhaps ensure your DICOMs are labelled consistently. >>>>>>>>>>>> >>>>>>>>>>>> Let us know if this works for you -- we can also walk you >>>>>>>>>>>> through an example of non-identified scans on Demo.loris.ca >>>>>>>>>>>> (MRI Violations module). >>>>>>>>>>>> >>>>>>>>>>>> Best, >>>>>>>>>>>> Christine >>>>>>>>>>>> >>>>>>>>>>>> The LORIS team >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> On Tue, Jul 30, 2019 at 10:47 AM Sotirios Nikoloutsopoulos < >>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>> >>>>>>>>>>>>> I hope this is sufficient as the error for the visit label >>>>>>>>>>>>> disappeared. >>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>> >>>>>>>>>>>>> Please see the attached file. Also something i found. >>>>>>>>>>>>> >>>>>>>>>>>>> lorisadmin at hbp:/data/loris/bin/mri$ cat >>>>>>>>>>>>> /data/loris/data//logs/TarLoad-17-39-xubBdv.log >>>>>>>>>>>>> >>>>>>>>>>>>> ==> Loading file from disk >>>>>>>>>>>>> /tmp/TarLoad-17-39-UyQcG2/dcc0000_258024_v1_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>> >>>>>>>>>>>>> --> mapping DICOM parameter for >>>>>>>>>>>>> /tmp/TarLoad-17-39-UyQcG2/dcc0000_258024_v1_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>> >>>>>>>>>>>>> ==> computing md5 hash for MINC body. >>>>>>>>>>>>> >>>>>>>>>>>>> --> md5: 6b1202fd63e29de4c9be1cd9925888a5 >>>>>>>>>>>>> >>>>>>>>>>>>> ==> verifying acquisition protocol >>>>>>>>>>>>> >>>>>>>>>>>>> Acquisition protocol is unknown >>>>>>>>>>>>> >>>>>>>>>>>>> --> The minc file cannot be registered since the >>>>>>>>>>>>> AcquisitionProtocol is unknown >>>>>>>>>>>>> >>>>>>>>>>>>> ???? ???, 30 ???? 2019 ???? 4:58 ?.?., ?/? Sotirios >>>>>>>>>>>>> Nikoloutsopoulos ??????: >>>>>>>>>>>>> >>>>>>>>>>>>>> Ok I fixed the login problem by using a known hash and by >>>>>>>>>>>>>> deleting the rows from the login_history i was able to login. >>>>>>>>>>>>>> >>>>>>>>>>>>>> ???? ???, 30 ???? 2019 ???? 4:50 ?.?., ?/? Sotirios >>>>>>>>>>>>>> Nikoloutsopoulos ??????: >>>>>>>>>>>>>> >>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> there was no visit label 01 in the Visit_Windows table and i >>>>>>>>>>>>>>> don't know how to insert it because the record requires lots of attributes. >>>>>>>>>>>>>>> Also the system for a reason asked me to update my password and now i don't >>>>>>>>>>>>>>> remember it and my account got suspended. Is there a way to reset it or set >>>>>>>>>>>>>>> a simple password? I updated the password hash in the users table by using >>>>>>>>>>>>>>> the hash from another LORIS setup we had and i still couldn't login ( also >>>>>>>>>>>>>>> the attribute password is always NULL and the expiration date is 1999-01-01 >>>>>>>>>>>>>>> for some reason ). >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> Thanks >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> ???? ???, 29 ???? 2019 ???? 5:21 ?.?., ?/? Cecile Madjar < >>>>>>>>>>>>>>> cecile.madjar at mcin.ca> ??????: >>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Can you try adding the visit label v01 to the Visit_Windows >>>>>>>>>>>>>>>> table? >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> However, I noticed that in a previous dataset, the label >>>>>>>>>>>>>>>> was V1. Does that refer to the same visit? If so, you might want to >>>>>>>>>>>>>>>> harmonize the visit labels so they are all the same across datasets for a >>>>>>>>>>>>>>>> given timepoint, meaning you will need to relabel scans when the visit >>>>>>>>>>>>>>>> label is different but referring to the same visit label (v01 = V1 etc...). >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Hope this helps, >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> On Mon, Jul 29, 2019 at 10:15 AM Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Could you help me with the "Visit label does not exist"? I >>>>>>>>>>>>>>>>> had changed $subjectID{'createVisitLabel'} to 1 as you had suggested but >>>>>>>>>>>>>>>>> it appears that this problem hasn't been resolved yet. >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> lorisadmin at hbp:/data/loris/bin/mri$ cat >>>>>>>>>>>>>>>>> /data/loris/data//logs/TarLoad-14-58-9Xog7H.log >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> ==> Loading file from disk >>>>>>>>>>>>>>>>> /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> --> mapping DICOM parameter for >>>>>>>>>>>>>>>>> /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> --> using user-defined filterParameters for >>>>>>>>>>>>>>>>> /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Candidate Mismatch Error is Visit label does not exist >>>>>>>>>>>>>>>>> -> WARNING: This candidate was invalid. Logging to >>>>>>>>>>>>>>>>> MRICandidateErrors table with reason Visit >>>>>>>>>>>>>>>>> label does not exist >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> ???? ???, 26 ???? 2019 ???? 3:02 ?.?., ?/? Sotirios >>>>>>>>>>>>>>>>> Nikoloutsopoulos ??????: >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Hi Cecile, >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> The Center error was fixed. Still the insertion of mincs >>>>>>>>>>>>>>>>>> fails. Please see the output.txt file i attached. Also is there something >>>>>>>>>>>>>>>>>> else i need to change at the paths configuration? >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> ???? ???, 25 ???? 2019 ???? 6:55 ?.?., ?/? Cecile Madjar < >>>>>>>>>>>>>>>>>> cecile.madjar at mcin.ca> ??????: >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> We are making progress! >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> I have a feeling this error comes from the fact that >>>>>>>>>>>>>>>>>>> your psc table does not have the MRI_alias populated for the DCC site. >>>>>>>>>>>>>>>>>>> Running the following query in the mysql database should fix this: >>>>>>>>>>>>>>>>>>> UPDATE psc SET MRI_alias="DCC", Alias="DCC" WHERE >>>>>>>>>>>>>>>>>>> Name="Data Coordinating Center"; >>>>>>>>>>>>>>>>>>> Repeat the same with all your sites (make sure to change >>>>>>>>>>>>>>>>>>> the Aliases between sites, they should all be unique). >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Let me know how it goes! >>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> On Thu, Jul 25, 2019 at 11:43 AM Sotirios >>>>>>>>>>>>>>>>>>> Nikoloutsopoulos wrote: >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Dear Cecile, >>>>>>>>>>>>>>>>>>>> You were right about your guesses. I did the >>>>>>>>>>>>>>>>>>>> modifications you suggested, i still get the "no mincs inserted" error, now >>>>>>>>>>>>>>>>>>>> i am getting the "No center found this candidate" error ( how do i fix >>>>>>>>>>>>>>>>>>>> that? from what i see the .dcm files contains a 'Institution Name', is that >>>>>>>>>>>>>>>>>>>> the center? ), so i guess that's why the validation fails, but i changed >>>>>>>>>>>>>>>>>>>> the force variable of tarchiveLoader to 1, shouldn't it have inserted the >>>>>>>>>>>>>>>>>>>> mincs then? Also it is optional to have a mail server, right? ( from what i >>>>>>>>>>>>>>>>>>>> see the mail error does not affect the $valid_study, so i assume we are >>>>>>>>>>>>>>>>>>>> okay with that ) >>>>>>>>>>>>>>>>>>>> Thank you a lot, >>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> ???? ???, 25 ???? 2019 ???? 5:48 ?.?., ?/? Cecile >>>>>>>>>>>>>>>>>>>> Madjar ??????: >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> From what I understand, I believe you just need to >>>>>>>>>>>>>>>>>>>>> update a few config settings from the frontend in the Config module (under >>>>>>>>>>>>>>>>>>>>> the Admin menu). >>>>>>>>>>>>>>>>>>>>> [image: Screen Shot 2019-07-25 at 10.31.35 AM.png] >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> Then go to the Paths section of the config module and >>>>>>>>>>>>>>>>>>>>> update the "LORIS-MRI code" config setting to /data/loris/bin/mri (my guess >>>>>>>>>>>>>>>>>>>>> is that currently, it is set to /data/LORIS/data) and click on the submit >>>>>>>>>>>>>>>>>>>>> button. >>>>>>>>>>>>>>>>>>>>> [image: Screen Shot 2019-07-25 at 10.32.50 AM.png] >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> Then, go to Imaging Pipeline section of the >>>>>>>>>>>>>>>>>>>>> Configuration module and update the "Loris-MRI Data Directory" to >>>>>>>>>>>>>>>>>>>>> /data/loris/data/ (my guess is that it is empty at the moment in your >>>>>>>>>>>>>>>>>>>>> database which is why $data_dir is not defined when you run the >>>>>>>>>>>>>>>>>>>>> tarchiveLoader step of the insertion pipeline). >>>>>>>>>>>>>>>>>>>>> [image: Screen Shot 2019-07-25 at 10.40.52 AM.png] >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> Finally, I took a look at your environment file and it >>>>>>>>>>>>>>>>>>>>> might be a good idea to update your PERL5LIB variable to the following (it >>>>>>>>>>>>>>>>>>>>> has been added to the code a few releases ago as we realized this was >>>>>>>>>>>>>>>>>>>>> needed for the libraries. Not sure which version of LORIS-MRI you are using >>>>>>>>>>>>>>>>>>>>> but it does not hurt to update this variable to what I suggest below): >>>>>>>>>>>>>>>>>>>>> export >>>>>>>>>>>>>>>>>>>>> PERL5LIB=/data/loris/bin/mri/uploadNeuroDB:/data/loris/bin/mri/dicom-archive:$PERL5LIB >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> Hope this helps. Sorry you are experiencing so much >>>>>>>>>>>>>>>>>>>>> trouble setting things up. We probably need to update our WIKI. >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> On Thu, Jul 25, 2019 at 9:48 AM Sotirios >>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos wrote: >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> The "Loris-MRI Data Directory" should be in the >>>>>>>>>>>>>>>>>>>>>> environment file? >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> ???? ???, 25 ???? 2019 ???? 12:59 ?.?., ?/? Sotirios >>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos ??????: >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> The scripts are located in /data/loris/bin/mri/. >>>>>>>>>>>>>>>>>>>>>>> Somewhere I might have messed something up but i remember following the >>>>>>>>>>>>>>>>>>>>>>> instructions in the wiki.For example when i tried to execute the >>>>>>>>>>>>>>>>>>>>>>> batch_uploads_imageuploader perl script the line >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> my $command = "$bin_dir/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl " >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> was pointing to an invalid path, for example: it was >>>>>>>>>>>>>>>>>>>>>>> repeating a pattern and had LORIS instead of loris ( i think the mistake >>>>>>>>>>>>>>>>>>>>>>> was that in the wiki it suggested to use $PROJECT for the name of the >>>>>>>>>>>>>>>>>>>>>>> folder and i choosed 'loris' >>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris/wiki/Imaging-Database >>>>>>>>>>>>>>>>>>>>>>> ). See also the in image for the modification i did. Also i didn't find the >>>>>>>>>>>>>>>>>>>>>>> section to config the $data_dir variable. >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> ???? ???, 24 ???? 2019 ???? 6:05 ?.?., ?/? Cecile >>>>>>>>>>>>>>>>>>>>>>> Madjar ??????: >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> It looks like you have one Config setting not set >>>>>>>>>>>>>>>>>>>>>>>> (based on the first error message you got when running it the first time). >>>>>>>>>>>>>>>>>>>>>>>> You need to set a value for "Loris-MRI Data Directory" in the Config module >>>>>>>>>>>>>>>>>>>>>>>> under the Imaging pipeline section (from what I can see, it would be >>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/ for your setup). >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> The reason you got that error message the second >>>>>>>>>>>>>>>>>>>>>>>> time is that the pipeline checks if the DICOM study was already inserted in >>>>>>>>>>>>>>>>>>>>>>>> the tarchive table. Since you ran the study once already, the study is >>>>>>>>>>>>>>>>>>>>>>>> inserted into the tarchive, hence the message. However, the pipeline did >>>>>>>>>>>>>>>>>>>>>>>> not complete as the MINC files were not created and inserted into the >>>>>>>>>>>>>>>>>>>>>>>> files/parameter_file table. In order to continue the insertion, you will >>>>>>>>>>>>>>>>>>>>>>>> then need to run the tarchiveLoader command suggested in the terminal >>>>>>>>>>>>>>>>>>>>>>>> during the second run: >>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader >>>>>>>>>>>>>>>>>>>>>>>> -globLocation -profile prod >>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive//2012/DCM_2012-12-05_ImagingUpload-17-43-ZUEFjb.tar >>>>>>>>>>>>>>>>>>>>>>>> -verbose >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> Finally, I am a bit confused by your setup. Where >>>>>>>>>>>>>>>>>>>>>>>> are the scripts located? In /data/loris/bin/mri or /data/loris/data? It >>>>>>>>>>>>>>>>>>>>>>>> feels like the Config setting "LORIS-MRI code" in the Paths section was set >>>>>>>>>>>>>>>>>>>>>>>> to "/data/LORIS/data" but it should have been set to the directory where >>>>>>>>>>>>>>>>>>>>>>>> the scripts are located (most probably /data/loris/bin/mri). >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> Hope this helps, >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> On Wed, Jul 24, 2019 at 10:55 AM Sotirios >>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos wrote: >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> Ok first i execute this command: >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> "lorisadmin at hbp:/data/loris/bin/mri$ >>>>>>>>>>>>>>>>>>>>>>>>> ./batch_uploads_imageuploader -profile prod < ~/Desktop/input.txt > log.txt >>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at ./batch_uploads_imageuploader line 143. >>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at ./batch_uploads_imageuploader line 143. >>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $_ in pattern match >>>>>>>>>>>>>>>>>>>>>>>>> (m//) at ./batch_uploads_imageuploader line 147. >>>>>>>>>>>>>>>>>>>>>>>>> base is DCC0000_258024_V01 >>>>>>>>>>>>>>>>>>>>>>>>> path is /data/incoming/ >>>>>>>>>>>>>>>>>>>>>>>>> type is .tar.gz >>>>>>>>>>>>>>>>>>>>>>>>> fullpath is >>>>>>>>>>>>>>>>>>>>>>>>> /data/incoming/DCC0000_258024_V01.tar.gz >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> source /tmp/ImagingUpload-17-43-ZUEFjb >>>>>>>>>>>>>>>>>>>>>>>>> targetlocation /data/loris/data/tarchive >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 256. >>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 284. >>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at /data/loris/bin/mri/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>> tarchive_validation.pl line 219. >>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at /data/loris/bin/mri/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl line 270. >>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 711. >>>>>>>>>>>>>>>>>>>>>>>>> Can't exec "mail": No such file or directory at >>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 721. >>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 722. >>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 723. >>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 724. >>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 724. >>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 725. >>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 735. >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> No Mincs inserted >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> The tarchiveLoader insertion script has failed. >>>>>>>>>>>>>>>>>>>>>>>>> Running now the following command: >>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl -profile prod -upload_id 3 >>>>>>>>>>>>>>>>>>>>>>>>> /data/incoming/DCC0000_258024_V01.tar.gz -verbose" >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> I inserted the VisitLabel, but still the Mincs are >>>>>>>>>>>>>>>>>>>>>>>>> not inserted and i am getting this error >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> "lorisadmin at hbp:/data/loris/bin/mri$ >>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl -profile prod -upload_id 3 >>>>>>>>>>>>>>>>>>>>>>>>> /data/incoming/DCC0000_258024_V01.tar.gz -verbose >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> find -path \/tmp\/ImagingUpload\-17\-45\-5MsWEd >>>>>>>>>>>>>>>>>>>>>>>>> -name '__MACOSX' -delete >>>>>>>>>>>>>>>>>>>>>>>>> Spool message is: >>>>>>>>>>>>>>>>>>>>>>>>> The Scan for the uploadID 3 has already been run >>>>>>>>>>>>>>>>>>>>>>>>> with tarchiveID: 7. >>>>>>>>>>>>>>>>>>>>>>>>> To continue with the rest of the insertion >>>>>>>>>>>>>>>>>>>>>>>>> pipeline, please run tarchiveLoader from a terminal as follows: >>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader -globLocation -profile prod >>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive//2012/DCM_2012-12-05_ImagingUpload-17-43-ZUEFjb.tar >>>>>>>>>>>>>>>>>>>>>>>>> -verbose" >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> Which files should i delete? I thought that >>>>>>>>>>>>>>>>>>>>>>>>> deleting the files from the tarchive was enough. And i executed the last >>>>>>>>>>>>>>>>>>>>>>>>> proposed command to continue to rest of the insertion pipeline ( check the >>>>>>>>>>>>>>>>>>>>>>>>> image ). >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> Thank you >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 24 ???? 2019 ???? 5:05 ?.?., ?/? Cecile >>>>>>>>>>>>>>>>>>>>>>>>> Madjar ??????: >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> Sorry I was not clear before. Every visits of >>>>>>>>>>>>>>>>>>>>>>>>>> candidates are created in the session table with one entry per >>>>>>>>>>>>>>>>>>>>>>>>>> CandID/VisitLabel. So if the imaging pipeline created visits in the session >>>>>>>>>>>>>>>>>>>>>>>>>> table (that are not attached to instruments) and you want to clean your >>>>>>>>>>>>>>>>>>>>>>>>>> database completely, you can delete entries in that table as well. >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> Regarding your point 2, the imaging pipeline can >>>>>>>>>>>>>>>>>>>>>>>>>> create the visit in the session table as long as the visit label is present >>>>>>>>>>>>>>>>>>>>>>>>>> in the Visit_Windows table (which means the visit label stored in the >>>>>>>>>>>>>>>>>>>>>>>>>> PatientName is a valid visit label). >>>>>>>>>>>>>>>>>>>>>>>>>> However, in your prod file, if the >>>>>>>>>>>>>>>>>>>>>>>>>> variable $subjectID{'createVisitLabel'} is set to 1 for candidates, the >>>>>>>>>>>>>>>>>>>>>>>>>> visit label should be created in the Visit_Windows table I believe. Here >>>>>>>>>>>>>>>>>>>>>>>>>> is the line of the prod file you would need to change >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> . >>>>>>>>>>>>>>>>>>>>>>>>>> In general, we prefer populating the >>>>>>>>>>>>>>>>>>>>>>>>>> Visit_Windows table and set the $subjectID{'createVisitLabel'} to 0 for >>>>>>>>>>>>>>>>>>>>>>>>>> candidate data to avoid insertion of badly labelled MRI data that are >>>>>>>>>>>>>>>>>>>>>>>>>> complex to relabel. >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> Finally, regarding the candidate creation, if you >>>>>>>>>>>>>>>>>>>>>>>>>> execute the following steps, the pipeline should be able to create >>>>>>>>>>>>>>>>>>>>>>>>>> candidates: >>>>>>>>>>>>>>>>>>>>>>>>>> - set in the Imaging Pipeline section of the >>>>>>>>>>>>>>>>>>>>>>>>>> config module the config setting "Upload creation of candidates" to Yes >>>>>>>>>>>>>>>>>>>>>>>>>> - manually transfer the scans to the LORIS server >>>>>>>>>>>>>>>>>>>>>>>>>> instead of uploading it via the imaging browser >>>>>>>>>>>>>>>>>>>>>>>>>> - run batch_imaging_upload.pl as you did until >>>>>>>>>>>>>>>>>>>>>>>>>> now. >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helps! >>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> On Wed, Jul 24, 2019 at 8:47 AM Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos wrote: >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> About my second question i replaced the name of >>>>>>>>>>>>>>>>>>>>>>>>>>> the patient in the .dcm files and now i am getting an error that the visit >>>>>>>>>>>>>>>>>>>>>>>>>>> label does not exist. >>>>>>>>>>>>>>>>>>>>>>>>>>> I thought it was supposed to be automatically >>>>>>>>>>>>>>>>>>>>>>>>>>> created. >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> "Done adding archive info into database >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader >>>>>>>>>>>>>>>>>>>>>>>>>>> -globLocation -profile prod >>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive//DCM_2012-12-05_ImagingUpload-15-42-yUwQQV.tar >>>>>>>>>>>>>>>>>>>>>>>>>>> -verbose >>>>>>>>>>>>>>>>>>>>>>>>>>> md5sum >>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive/DCM_2012-12-05_ImagingUpload-15-42-yUwQQV.tar >>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>> candidate id 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> => No Visit labelVisit label does not exist >>>>>>>>>>>>>>>>>>>>>>>>>>> Set centerID = 1 >>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> Number of MINC files that will be considered for >>>>>>>>>>>>>>>>>>>>>>>>>>> inserting into the database: 1 >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> log dir is /logs and log file is >>>>>>>>>>>>>>>>>>>>>>>>>>> /logs/TarLoad-15-42-L6pocU.log >>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>> candidate id 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> => No Visit label >>>>>>>>>>>>>>>>>>>>>>>>>>> Cleaning up temp files: rm -rf >>>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-15-42-J2rQms/ImagingUpload-15-42-yUwQQV*" >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 24 ???? 2019 ???? 3:38 ?.?., ?/? >>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos >>>>>>>>>>>>>>>>>>>>>>>>>>> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> 1) What are the records in the session table? >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> 2) I tried to upload a non-phantom file like >>>>>>>>>>>>>>>>>>>>>>>>>>>> this >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> input_file.txt: >>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/incoming/DCC0000_258024_V1.tar.gz N >>>>>>>>>>>>>>>>>>>>>>>>>>>> DCC0000_258024_V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> Terminal: >>>>>>>>>>>>>>>>>>>>>>>>>>>> ./batch_uploads_imageuploader -profile prod < >>>>>>>>>>>>>>>>>>>>>>>>>>>> ~/Desktop/input.txt > log.txt >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> and i get the following error in the log.txt >>>>>>>>>>>>>>>>>>>>>>>>>>>> file >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> "Running now the following command: >>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl -profile prod >>>>>>>>>>>>>>>>>>>>>>>>>>>> -upload_id 7 /data/incoming/DCC0000_258024_V1.tar.gz -verbose >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> find -path >>>>>>>>>>>>>>>>>>>>>>>>>>>> \/tmp\/ImagingUpload\-14\-56\-FeLCB4 -name '__MACOSX' -delete >>>>>>>>>>>>>>>>>>>>>>>>>>>> Spool message is: >>>>>>>>>>>>>>>>>>>>>>>>>>>> The PatientName read from the DICOM header does >>>>>>>>>>>>>>>>>>>>>>>>>>>> not start with DCC0000_258024_V1 from the mri_upload table >>>>>>>>>>>>>>>>>>>>>>>>>>>> " >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> and the spool message is repeated for each .dcm >>>>>>>>>>>>>>>>>>>>>>>>>>>> file. Should i preprocess every .dcm file and change the PatientName to >>>>>>>>>>>>>>>>>>>>>>>>>>>> "DCC0000_258024_V1"? >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> 3) As far as it concerns the candidate profile >>>>>>>>>>>>>>>>>>>>>>>>>>>> i have to create a new one each time before i try to upload a file? Is >>>>>>>>>>>>>>>>>>>>>>>>>>>> there already a way to create a candidate profile and get the DCCID and >>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID without the user interface? >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 18 ???? 2019 ???? 5:00 ?.?., ?/? >>>>>>>>>>>>>>>>>>>>>>>>>>>> Cecile Madjar ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> See answers to your questions below. >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> About the 1st case we had a dicom with a blank >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> studyUID, maybe someone accidentally removed it. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> That is strange. Something must have been done >>>>>>>>>>>>>>>>>>>>>>>>>>>>> to the DICOM files. I have never seen a study with no StudyUID out of the >>>>>>>>>>>>>>>>>>>>>>>>>>>>> scanner. Usually, you need to manually erase it with some tool. However, >>>>>>>>>>>>>>>>>>>>>>>>>>>>> DICOMs never cease to surprise me... >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Some other questions: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 1) What are the steps to remove all of my >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> patients and uploads?: because i want to try to reupload all the testing >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> dicoms we had with a clean database. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Release 21.0 of LORIS-MRI will offer a script >>>>>>>>>>>>>>>>>>>>>>>>>>>>> to remove all the entries and files specific to an upload. However, this >>>>>>>>>>>>>>>>>>>>>>>>>>>>> release is not yet out. Hopefully in the next few weeks. >>>>>>>>>>>>>>>>>>>>>>>>>>>>> In the meantime, since your case is particular >>>>>>>>>>>>>>>>>>>>>>>>>>>>> and that you just want to start with a clean database, the following >>>>>>>>>>>>>>>>>>>>>>>>>>>>> deletes should work (hopefully I won't forget any tables): >>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from mri_violations_log; >>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from mri_protocol_violated_scans; >>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from MRICandidateErrors; >>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from parameter_file; >>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from files_qcstatus; # (if you played >>>>>>>>>>>>>>>>>>>>>>>>>>>>> with the QC part of the imaging browser for testing) >>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from feedback_mri_comments; # (if you >>>>>>>>>>>>>>>>>>>>>>>>>>>>> played with the QC part of the imaging browser for testing) >>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from tarchive_series; >>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from tarchive_files; >>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from mri_upload; >>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from tarchive; >>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from mri_scanner; >>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from candidate where PSCID="scanner"; >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> I don't know if you want to also delete >>>>>>>>>>>>>>>>>>>>>>>>>>>>> entries in the session and candidate table too? >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> 2) We do not need to create the profile of a >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> patient ( are the patients stored in the candidate table? because i can't >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> see the ghosts ), because will it automatically be created when importing a >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> dicom? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> I am not sure I understand fully this >>>>>>>>>>>>>>>>>>>>>>>>>>>>> question. All candidates are stored in the candidate table. The phantom >>>>>>>>>>>>>>>>>>>>>>>>>>>>> scans however are attached to a scanner candidate depending on where the >>>>>>>>>>>>>>>>>>>>>>>>>>>>> scan happened. It is a bit of a weird concept that we have to redesign >>>>>>>>>>>>>>>>>>>>>>>>>>>>> eventually but never got a chance to get to it. >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hopefully this answered your question, >>>>>>>>>>>>>>>>>>>>>>>>>>>>> otherwise, don't hesitate to let me know. >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> 3) What is the difference between uploading a >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> dicom as phantom instead of importing as PSCCID_DCCID_VisitLabel? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> When you upload the scan as >>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID_DCCID_VisitLabel, there is a check that makes sure the candidate IDs >>>>>>>>>>>>>>>>>>>>>>>>>>>>> and visit label are valid at the time of upload. >>>>>>>>>>>>>>>>>>>>>>>>>>>>> When you upload a scan as phantom, it expects >>>>>>>>>>>>>>>>>>>>>>>>>>>>> that the DICOM field PatientName and uploaded filename contains the string >>>>>>>>>>>>>>>>>>>>>>>>>>>>> "phantom". We enforced this behaviour on the imaging uploader side in >>>>>>>>>>>>>>>>>>>>>>>>>>>>> recent releases but I can't remember which one. Probably the upcoming 21.0 >>>>>>>>>>>>>>>>>>>>>>>>>>>>> release. >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> All those verifications might seem cumbersome >>>>>>>>>>>>>>>>>>>>>>>>>>>>> but they are here to ensure that the files inserted are all valid and >>>>>>>>>>>>>>>>>>>>>>>>>>>>> labelled properly as it is a bit messy to have to delete files that were >>>>>>>>>>>>>>>>>>>>>>>>>>>>> wrongly labelled. At least, the delete script present in release 21.0 will >>>>>>>>>>>>>>>>>>>>>>>>>>>>> make this process easier but it is still good practice to verify those >>>>>>>>>>>>>>>>>>>>>>>>>>>>> things. >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> With pleasure. Hopefully the answers to your >>>>>>>>>>>>>>>>>>>>>>>>>>>>> questions will be helpful. >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> PS: loris-dev mailing list: you will find the >>>>>>>>>>>>>>>>>>>>>>>>>>>>> initial answer I gave Sotirios below. I forgot to cc the loris-dev in my >>>>>>>>>>>>>>>>>>>>>>>>>>>>> earlier reply... >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 16 ???? 2019 ???? 12:02 ?.?., ?/? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Cecile Madjar ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Dear Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you for reaching out. Since your email >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> was already organized in points, I will reply directly below your questions >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> below. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 1) What do we do when the StudyUID is blank >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> on the header? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/minor/docs/AppendixA-Troubleshooting_guideline.md >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> There solution provided at the table 3 does not guide us how to find the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> information ( is possible ). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The StudyUID is the field used in our >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> pipeline at the moment to check whether a DICOM study was already inserted >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> into LORIS with that same StudyUID since it is supposed to be unique for >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> every single study. Currently, we do not support insertion of DICOM studies >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> if they do not have a StudyUID associated with them. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Is there a specific reason why the StudyUID >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> is blank in the DICOM headers in your DICOM files? Did they go through some >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> processes before upload to LORIS? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 2) When i am about to upload a non-phanton >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> case i need a 'Visit Label'. Is there already a script that can create a >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> new visit label for a specific Candidate, so i can provide it as input >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> afterwards to the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> batch_uploads_imageuploader ( See option 5.1.3 https://github.com/aces/Loris-MRI/blob/minor/docs/05-PipelineLaunchOptions.md ) >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I am not sure if the front-end allows for it >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> but if you use batch_uploads_imageuploader, the insertion scripts could >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> create the visit label for you. However, it does need to be included in the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> patient name in order for the script to know which label it should use. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> For example: you upload V02 for MTL0123 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> (DCCID: 456789) but V02 was not yet created for MTL0123; the insertion >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> scripts will create a V02 visit for MTL0123 if the PatientName field for >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the dataset is MTL0123_456789_V02 with Stage marked as "Not Started". >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> However, *note that for the script to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> create the visit for the candidate, you have to make sure that all the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit label of your projects were inserted in the Visit_Windows table* >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> (otherwise, the visit will never be created as they were not specified as >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> being part of the list of visit label to expect). So in the example above, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> you should have one row in Visit_Windows with Visit_label="V02" set. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 3) Section 4.3 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/minor/docs/04-Scripts.md >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> What do we do when the folder contains multiple mnc files? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> This is a case by case. Most of the time, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the MINC files that failed insertion into the imaging browser end up in the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> MRI violation module where you can see what went wrong with the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> acquisitions not inserted. If you notice that the MINC file should be >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> inserted as a specific protocol, you can force the insertion as explained >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in section 4.3. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> In your case, I have a feeling that you want >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> to be able to insert MINC files that did not go through the whole pipeline >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> insertion (DICOM archival, then dcm2mnc, then protocol identification, then >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> insertion...). In theory, you could call >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl on any MINC file, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> provided you have at least the following information: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - path to the MINC file >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - uploadID associated with the MINC files or >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DICOM archive path from which those MINC files were created from >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Then the minc_insertion.pl script will do >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the subject information and protocol validation etc... >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> If all the MINC files come from the same >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> uploadID or TarchiveID, then you could run a loop in bash calling the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl script like this for >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> files deriving from uploadID=1: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ls /path/to/mnc/folder/* | while read f; do >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl -profile prod -uploadID 1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -mincPath $f; done >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helped! >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> -- >>>>>>>>>>>> >>>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>> >>>>>>>>>> -- >>>>>>>>>> >>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>> Montreal Neurological Institute >>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>> >>>>>>>>> _______________________________________________ >>>>>>>> Loris-dev mailing list >>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>> >>>>>>> >>>>>>> >>>>>>> -- >>>>>>> >>>>>>> christine.rogers at mcgill.ca >>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>> Montreal Neurological Institute >>>>>>> McGill University | Montreal | Canada >>>>>>> >>>>>> _______________________________________________ >>>>>> Loris-dev mailing list >>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>> >>>>> >>>>> >>>>> -- >>>>> >>>>> christine.rogers at mcgill.ca >>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>> Montreal Neurological Institute >>>>> McGill University | Montreal | Canada >>>>> _______________________________________________ >>>>> Loris-dev mailing list >>>>> Loris-dev at bic.mni.mcgill.ca >>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>> >>>> >>>> >>>> -- >>>> >>>> christine.rogers at mcgill.ca >>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>> Montreal Neurological Institute >>>> McGill University | Montreal | Canada >>>> _______________________________________________ >>>> Loris-dev mailing list >>>> Loris-dev at bic.mni.mcgill.ca >>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>> >>> >>> >>> -- >>> >>> christine.rogers at mcgill.ca >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>> Montreal Neurological Institute >>> McGill University | Montreal | Canada >>> >> _______________________________________________ >> Loris-dev mailing list >> Loris-dev at bic.mni.mcgill.ca >> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >> > > > -- > > christine.rogers at mcgill.ca > McGill Centre for Integrative Neuroscience | MCIN.ca > Montreal Neurological Institute > McGill University | Montreal | Canada > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: npm-debug.log Type: text/x-log Size: 2585 bytes Desc: not available URL: From dave.macfarlane at mcin.ca Thu Aug 8 09:31:49 2019 From: dave.macfarlane at mcin.ca (Dave MacFarlane) Date: Thu, 8 Aug 2019 09:31:49 -0400 Subject: [Loris-dev] Upgrading to Loris 21 - new make file In-Reply-To: References: Message-ID: It looks like the javascript snippet shown in the error message when trying to compile the js is truncated. Have you run out of disk space? On Thu, Aug 8, 2019 at 8:37 AM Sotirios Nikoloutsopoulos < sotirisnik at gmail.com> wrote: > Hi, > > I runned make and also included the file it reports at the end. > > lorisadmin at hbp:/var/www/loris$ make > npm install > npm WARN optional Skipping failed optional dependency /chokidar/fsevents: > npm WARN notsup Not compatible with your operating system or architecture: > fsevents at 1.2.9 > npm WARN optional Skipping failed optional dependency > /watchpack/chokidar/fsevents: > npm WARN notsup Not compatible with your operating system or architecture: > fsevents at 1.2.9 > npm run compile > > > loris at 1.0.0 compile /var/www/loris > > webpack > > /var/www/loris/node_modules/webpack/bin/webpack.js:86 > let notify = > ^^^ > > SyntaxError: Block-scoped declarations (let, const, function, class) not > yet supported outside strict mode > at exports.runInThisContext (vm.js:53:16) > at Module._compile (module.js:374:25) > at Object.Module._extensions..js (module.js:417:10) > at Module.load (module.js:344:32) > at Function.Module._load (module.js:301:12) > at Function.Module.runMain (module.js:442:10) > at startup (node.js:136:18) > at node.js:966:3 > > npm ERR! Linux 4.15.0-55-generic > npm ERR! argv "/usr/bin/nodejs" "/usr/bin/npm" "run" "compile" > npm ERR! node v4.2.6 > npm ERR! npm v3.5.2 > npm ERR! code ELIFECYCLE > npm ERR! loris at 1.0.0 compile: `webpack` > npm ERR! Exit status 1 > npm ERR! > npm ERR! Failed at the loris at 1.0.0 compile script 'webpack'. > npm ERR! Make sure you have the latest version of node.js and npm > installed. > npm ERR! If you do, this is most likely a problem with the loris package, > npm ERR! not with npm itself. > npm ERR! Tell the author that this fails on your system: > npm ERR! webpack > npm ERR! You can get information on how to open an issue for this project > with: > npm ERR! npm bugs loris > npm ERR! Or if that isn't available, you can get their info via: > npm ERR! npm owner ls loris > npm ERR! There is likely additional logging output above. > > npm ERR! Please include the following file with any support request: > npm ERR! /var/www/loris/npm-debug.log > Makefile:14: recipe for target 'javascript' failed > make: *** [javascript] Error 1 > > Thanks, > > Sotirios > > ???? ???, 7 ??? 2019 ???? 5:41 ?.?., ?/? Christine Rogers, Ms. < > christine.rogers at mcgill.ca> ??????: > >> Hi Sotirios, >> >> Thanks, have you tried all of these steps? >> - clear your browser cache (and refresh a few times) >> - delete any files in your smarty/templates_c directory (this will clear >> the template cache - do Not touch smarty/templates/) >> - run `make` (per the 21 release notes, this replaces the composer >> commands used in previous releases to update your dependencies) >> - restart apache (doesn't hurt) >> >> Let us know how it goes -- let us know what difference you see after, >> with your logs. A >> lso please send us your Config path settings (see these Troubleshooting >> Queries >> ) >> if you're still seeing front-end issues. >> >> Thanks, >> Christine >> >> On Wed, Aug 7, 2019 at 8:02 AM Sotirios Nikoloutsopoulos < >> sotirisnik at gmail.com> wrote: >> >>> Hi, >>> >>> lorisadmin at hbp:/var/www/loris$ sudo cat /var/log/apache2/error.log >>> [Wed Aug 07 07:35:02.422501 2019] [mpm_prefork:notice] [pid 1267] >>> AH00163: Apache/2.4.18 (Ubuntu) OpenSSL/1.0.2g configured -- resuming >>> normal operations >>> [Wed Aug 07 07:35:02.422514 2019] [core:notice] [pid 1267] AH00094: >>> Command line: '/usr/sbin/apache2' >>> >>> And as for the access.log the content are empty >>> lorisadmin at hbp:/var/www/loris$ sudo ls -l /var/log/apache2/access.log >>> lorisadmin at hbp:/var/www/loris$ sudo ls -l /var/log/apache2/access.log >>> -rw-r----- 1 root adm 0 ???? 28 14:09 /var/log/apache2/access.log >>> >>> Also i noticed a loris_access.log. >>> >>> The only non-blank pages are: >>> mri_violations, dataquery does not exist at all, statistics, >>> data_team_helper, genomic_browser, configuration and >>> server_processes_manager/ prints "Required configuration settings for >>> Server Processes Manager are missing. Cannot continue." >>> >>> Thanks, >>> Sotirios >>> >>> ???? ???, 6 ??? 2019 ???? 10:13 ?.?., ?/? Christine Rogers, Ms. < >>> christine.rogers at mcgill.ca> ??????: >>> >>>> Hi Sotirios and LORIS community -- >>>> >>>> When upgrading to brand-new release 21 -- just a reminder to follow >>>> the release notes and run the new *make* file to update your >>>> dependencies (instead of using *composer* commands). >>>> We've also updated the Wiki page >>>> to clarify >>>> that the release notes for each version will tell you what to run. >>>> >>>> If your current version is not the last release (20.3), it's still >>>> important to upgrade to each minor release increment (e.g. 20.2, 20.3) >>>> before making the leap to 21.0. >>>> >>>> If you're getting blank pages, post-upgrade -- Try clearing your cache. >>>> >>>> Got questions or feedback e.g. on the Release Notes? please don't >>>> hesitate to let us know. >>>> Thanks, >>>> Christine >>>> The LORIS team >>>> >>>> >>>> >>>> On Tue, Aug 6, 2019 at 10:09 AM Christine Rogers, Ms. < >>>> christine.rogers at mcgill.ca> wrote: >>>> >>>>> Hi Sotirios, >>>>> Could you also let us know -- on which pages is content visible, and >>>>> on which pages/modules is content not visible for you? >>>>> Thanks, >>>>> Christine >>>>> >>>>> On Tue, Aug 6, 2019 at 9:54 AM Christine Rogers, Ms. < >>>>> christine.rogers at mcgill.ca> wrote: >>>>> >>>>>> Thanks Sotirios, >>>>>> That's good to know. It sounds like you've checked that your >>>>>> /var/www/loris/project/config.xml file get populated properly. >>>>>> >>>>>> Please send us the last few errors you're seeing in your apache error >>>>>> log file, and your config paths and we can see what's happening with your >>>>>> front end -- >>>>>> Run these Troubleshooting Queries >>>>>> >>>>>> to get your config path settings, given your front end is not displaying >>>>>> fully. >>>>>> >>>>>> The Loris-MRI repo >>>>>> 21 >>>>>> install/upgrade would then be your next steps. >>>>>> Best, >>>>>> Christine >>>>>> >>>>>> On Tue, Aug 6, 2019 at 7:53 AM Sotirios Nikoloutsopoulos < >>>>>> sotirisnik at gmail.com> wrote: >>>>>> >>>>>>> I am using a VM. What i did was: >>>>>>> 1) Download the files from https://github.com/aces/Loris and >>>>>>> replace them to my existing /vaw/www/loris folder. >>>>>>> 2) Execute the composer install --no-dev and then composer >>>>>>> dump-autoload as mentioned here >>>>>>> https://github.com/aces/Loris/wiki/Updating-your-LORIS. >>>>>>> 3) Execute install.sh from /var/www/loris/tools and because LORIS >>>>>>> already existed i moved a .config file, then re-executed the install.sh >>>>>>> successfully >>>>>>> 4 ) As for the database, i dropped the schema and i executed the >>>>>>> installdb.php >>>>>>> >>>>>>> ???? ???, 5 ??? 2019 ???? 5:22 ?.?., ?/? Christine Rogers, Ms. < >>>>>>> christine.rogers at mcgill.ca> ??????: >>>>>>> >>>>>>>> Hi Sotorios, >>>>>>>> >>>>>>>> Thanks - when you re-installed did you start on a fresh root path / >>>>>>>> VM or might some of your old system setting still apply? >>>>>>>> (And if you did any steps similar to an upgrade, did you follow the >>>>>>>> Upgrade steps in the Release Notes, from both repos?) >>>>>>>> >>>>>>>> About the TR_range column - it was recently split (MRI pr339 >>>>>>>> ) split into TR_min >>>>>>>> and _max columns. Given the code was trying to query TR_range which does >>>>>>>> not exist in your mri_protocol table, double-check which version of the >>>>>>>> Loris repo (tables) and the Loris-MRI repo (code) you have installed to >>>>>>>> ensure they match. >>>>>>>> >>>>>>>> Christine >>>>>>>> >>>>>>>> >>>>>>>> On Mon, Aug 5, 2019 at 9:06 AM Sotirios Nikoloutsopoulos < >>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>> >>>>>>>>> I reinstalled LORIS to 21 version and now the content is not >>>>>>>>> visible at all at most pages. >>>>>>>>> >>>>>>>>> [image: image.png] >>>>>>>>> >>>>>>>>> ???? ???, 5 ??? 2019 ???? 3:19 ?.?., ?/? Sotirios Nikoloutsopoulos >>>>>>>>> ??????: >>>>>>>>> >>>>>>>>>> Hi, >>>>>>>>>> >>>>>>>>>> Is it easy to upgrade to Loris 21? Also the following fails >>>>>>>>>> because the line 1985 of NeuroDB/MRIProcessingUtility.pm query mri_protocol >>>>>>>>>> which doesn't have TR_range >>>>>>>>>> https://github.com/aces/Loris/blob/21.0-release/SQL/0000-00-00-schema.sql#L556 >>>>>>>>>> >>>>>>>>>> [image: image.png] >>>>>>>>>> >>>>>>>>>> lorisadmin at hbp:/data/loris/bin/mri$ >>>>>>>>>> ./batch_uploads_imageuploader -profile prod < ~/Desktop/input.txt > log.txt >>>>>>>>>> Use of uninitialized value $_ in pattern match (m//) at >>>>>>>>>> ./batch_uploads_imageuploader line 147. >>>>>>>>>> base is DCC0000_258024_V1 >>>>>>>>>> path is /data/incoming/ >>>>>>>>>> type is .tar.gz >>>>>>>>>> fullpath is /data/incoming/DCC0000_258024_V1.tar.gz >>>>>>>>>> DBD::mysql::st execute failed: Unknown column 'TR_range' in >>>>>>>>>> 'where clause' at >>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line 1985. >>>>>>>>>> DBD::mysql::st fetchrow_array failed: fetch() without execute() >>>>>>>>>> at /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line >>>>>>>>>> 1986. >>>>>>>>>> Use of uninitialized value $count_mri_protocol in numeric gt (>) >>>>>>>>>> at /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line >>>>>>>>>> 1995. >>>>>>>>>> DBD::mysql::st execute failed: Unknown column 'TR_range' in >>>>>>>>>> 'field list' at /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 562. >>>>>>>>>> Can't exec "mail": No such file or directory at >>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 721. >>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 722. >>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 723. >>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 724. >>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 725. >>>>>>>>>> >>>>>>>>>> No Mincs inserted >>>>>>>>>> >>>>>>>>>> Thanks, >>>>>>>>>> >>>>>>>>>> Sotirios >>>>>>>>>> >>>>>>>>>> ???? ???, 3 ??? 2019 ???? 1:08 ?.?., ?/? Christine Rogers, Ms. < >>>>>>>>>> christine.rogers at mcgill.ca> ??????: >>>>>>>>>> >>>>>>>>>>> Hi Sotirios, >>>>>>>>>>> >>>>>>>>>>> First, just a note: we've released LORIS 21 this week with some >>>>>>>>>>> major new features and cleanup -- especially if you are early in your setup >>>>>>>>>>> phase, check out the Release notes for both the LORIS >>>>>>>>>>> and >>>>>>>>>>> Loris-MRI >>>>>>>>>>> repos. >>>>>>>>>>> >>>>>>>>>>> Thanks for your screenshots -- your empty mri_protocol table >>>>>>>>>>> should be at the root of these issues : >>>>>>>>>>> >>>>>>>>>>> The mri_protocol table must be populated >>>>>>>>>>> >>>>>>>>>>> in order for your scans to be registered in LORIS -- it serves as a >>>>>>>>>>> whitelist for the insertion pipeline which filters out scans that aren't >>>>>>>>>>> identified or matched to scan types in this table. >>>>>>>>>>> >>>>>>>>>>> By default, this table is populated with entries for t1, t2, >>>>>>>>>>> fMRI and DTI (Insert statements for 21 release branch are here >>>>>>>>>>> >>>>>>>>>>> ) >>>>>>>>>>> Feel free to restore our default records and broaden their >>>>>>>>>>> parameters to match all your scan types. >>>>>>>>>>> >>>>>>>>>>> re Defaced, native, selected -- these filter the scans displayed >>>>>>>>>>> as you move to the next page (View Session), instead of viewing "all types" >>>>>>>>>>> of scans from a given session : >>>>>>>>>>> >>>>>>>>>>> - "defaced" means that a defacing script >>>>>>>>>>> >>>>>>>>>>> has masked the subject's face in the volume (for patient privacy) >>>>>>>>>>> - "native" means that no pre-processing has been performed >>>>>>>>>>> on the scan (it's raw data), >>>>>>>>>>> - "selected" will show only volumes that have been QC'd and >>>>>>>>>>> "selected" as the best of their type -- used to display only the best >>>>>>>>>>> quality T1 image instead of all T1s acquired in a session, e.g. >>>>>>>>>>> >>>>>>>>>>> re QC Comments -- >>>>>>>>>>> Once you have successfully loaded scans (matched to the >>>>>>>>>>> mri_protocol table), you'll be able to use the Imaging Browser's View >>>>>>>>>>> Session subpage to enter/view QC comments on each volume, or for each >>>>>>>>>>> visit. >>>>>>>>>>> These are stored directly in the database, and linked to each >>>>>>>>>>> scan. (Table name: feedback_mri_comments) >>>>>>>>>>> (Visit-level QC comments are linked to the session.) >>>>>>>>>>> >>>>>>>>>>> For a walkthrough of the Imaging setup - please see the Imaging >>>>>>>>>>> Setup guide >>>>>>>>>>> >>>>>>>>>>> - >>>>>>>>>>> >>>>>>>>>>> An old LORIS walkthrough video >>>>>>>>>>> can also walk you >>>>>>>>>>> through some of the Imaging front-end features, starting at 8:00 >>>>>>>>>>> LORIS' imaging modules have been updated many times since this >>>>>>>>>>> video, but the functionality and workflow is similar. >>>>>>>>>>> >>>>>>>>>>> Let us know how it goes once you have entries in your >>>>>>>>>>> mri_protocol table - >>>>>>>>>>> Best, >>>>>>>>>>> Christine >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> On Fri, Aug 2, 2019 at 7:58 AM Sotirios Nikoloutsopoulos < >>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>> >>>>>>>>>>>> Hi Christine, >>>>>>>>>>>> >>>>>>>>>>>> In the candidate_list page i can see this patient >>>>>>>>>>>> >>>>>>>>>>>> [image: image.png] >>>>>>>>>>>> >>>>>>>>>>>> If i press the link under PSCID i get to see >>>>>>>>>>>> [image: image.png] >>>>>>>>>>>> >>>>>>>>>>>> and if i press the link under Scan Done it redirects me to >>>>>>>>>>>> imaging_browser >>>>>>>>>>>> >>>>>>>>>>>> [image: image.png] >>>>>>>>>>>> >>>>>>>>>>>> At the mri_violations page i also see No results ( neither on >>>>>>>>>>>> resolved / not resolved ). >>>>>>>>>>>> >>>>>>>>>>>> At the imaging_uploader i can see the record that failed. >>>>>>>>>>>> >>>>>>>>>>>> [image: image.png] >>>>>>>>>>>> >>>>>>>>>>>> If i click on the tarchive info i get to see the Protocol Name >>>>>>>>>>>> which i think is the acquisition we wanted? >>>>>>>>>>>> [image: image.png] >>>>>>>>>>>> >>>>>>>>>>>> Also my mri_protocol table is empty. >>>>>>>>>>>> >>>>>>>>>>>> Furthermore i would like to ask about the defaced, native, >>>>>>>>>>>> selected. What exactly is native and selected? And where are the qc >>>>>>>>>>>> comments stored? >>>>>>>>>>>> >>>>>>>>>>>> [image: image.png] >>>>>>>>>>>> >>>>>>>>>>>> Finally a walkthrough would be helpful. >>>>>>>>>>>> >>>>>>>>>>>> Thanks, >>>>>>>>>>>> >>>>>>>>>>>> Sotirios >>>>>>>>>>>> >>>>>>>>>>>> ???? ???, 30 ???? 2019 ???? 8:29 ?.?., ?/? Christine Rogers, >>>>>>>>>>>> Ms. ??????: >>>>>>>>>>>> >>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>> Glad to hear you're making progress with the visit labels. To >>>>>>>>>>>>> follow up on your last few emails: >>>>>>>>>>>>> >>>>>>>>>>>>> a- The Wiki's Setup Guide contains Sample insert statements >>>>>>>>>>>>> for the Visit Windows table >>>>>>>>>>>>> >>>>>>>>>>>>> . >>>>>>>>>>>>> >>>>>>>>>>>>> As Cecile mentioned, the consistency of visit label format is >>>>>>>>>>>>> important: V01, v01, V1, 01 -- whichever you select to use is fine; we use >>>>>>>>>>>>> V01 by default across all documentation. >>>>>>>>>>>>> >>>>>>>>>>>>> b- For Password reset, there is a script in the tools/ >>>>>>>>>>>>> directory so that a back-end administrator can reset any front-end user >>>>>>>>>>>>> password, including Admin. (See info on setting up / resetting User >>>>>>>>>>>>> passwords in the Wiki's Setup Guide >>>>>>>>>>>>> >>>>>>>>>>>>> ) >>>>>>>>>>>>> >>>>>>>>>>>>> c- The minc file not being registered -- due to >>>>>>>>>>>>> AcquisitionProtocol unknown. >>>>>>>>>>>>> This means the SeriesDescription (Acquisition Protocol) in you >>>>>>>>>>>>> Dicom header was not matched to any scan listed in the mri_protocol >>>>>>>>>>>>> database table. >>>>>>>>>>>>> (In the online Loris-MRI Troubleshooting Guide, >>>>>>>>>>>>> this >>>>>>>>>>>>> is Table 3, 2nd-last item "no MINCs inserted"). >>>>>>>>>>>>> >>>>>>>>>>>>> The MRI Violations module (Readme here) >>>>>>>>>>>>> will show >>>>>>>>>>>>> you the details of this mismatch -- >>>>>>>>>>>>> Go to the module (under the Imaging menu), find your scan and >>>>>>>>>>>>> click the link "Could not identify scan type" -- in the next subpage you >>>>>>>>>>>>> can compare the scan's actual parameters against the mri_protocol table. >>>>>>>>>>>>> >>>>>>>>>>>>> To resolve this, adjust your mri_protocol table values or >>>>>>>>>>>>> perhaps ensure your DICOMs are labelled consistently. >>>>>>>>>>>>> >>>>>>>>>>>>> Let us know if this works for you -- we can also walk you >>>>>>>>>>>>> through an example of non-identified scans on Demo.loris.ca >>>>>>>>>>>>> (MRI Violations module). >>>>>>>>>>>>> >>>>>>>>>>>>> Best, >>>>>>>>>>>>> Christine >>>>>>>>>>>>> >>>>>>>>>>>>> The LORIS team >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> On Tue, Jul 30, 2019 at 10:47 AM Sotirios Nikoloutsopoulos < >>>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>> >>>>>>>>>>>>>> I hope this is sufficient as the error for the visit label >>>>>>>>>>>>>> disappeared. >>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>> >>>>>>>>>>>>>> Please see the attached file. Also something i found. >>>>>>>>>>>>>> >>>>>>>>>>>>>> lorisadmin at hbp:/data/loris/bin/mri$ cat >>>>>>>>>>>>>> /data/loris/data//logs/TarLoad-17-39-xubBdv.log >>>>>>>>>>>>>> >>>>>>>>>>>>>> ==> Loading file from disk >>>>>>>>>>>>>> /tmp/TarLoad-17-39-UyQcG2/dcc0000_258024_v1_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>> >>>>>>>>>>>>>> --> mapping DICOM parameter for >>>>>>>>>>>>>> /tmp/TarLoad-17-39-UyQcG2/dcc0000_258024_v1_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>> >>>>>>>>>>>>>> ==> computing md5 hash for MINC body. >>>>>>>>>>>>>> >>>>>>>>>>>>>> --> md5: 6b1202fd63e29de4c9be1cd9925888a5 >>>>>>>>>>>>>> >>>>>>>>>>>>>> ==> verifying acquisition protocol >>>>>>>>>>>>>> >>>>>>>>>>>>>> Acquisition protocol is unknown >>>>>>>>>>>>>> >>>>>>>>>>>>>> --> The minc file cannot be registered since the >>>>>>>>>>>>>> AcquisitionProtocol is unknown >>>>>>>>>>>>>> >>>>>>>>>>>>>> ???? ???, 30 ???? 2019 ???? 4:58 ?.?., ?/? Sotirios >>>>>>>>>>>>>> Nikoloutsopoulos ??????: >>>>>>>>>>>>>> >>>>>>>>>>>>>>> Ok I fixed the login problem by using a known hash and by >>>>>>>>>>>>>>> deleting the rows from the login_history i was able to login. >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> ???? ???, 30 ???? 2019 ???? 4:50 ?.?., ?/? Sotirios >>>>>>>>>>>>>>> Nikoloutsopoulos ??????: >>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> there was no visit label 01 in the Visit_Windows table and >>>>>>>>>>>>>>>> i don't know how to insert it because the record requires lots of >>>>>>>>>>>>>>>> attributes. Also the system for a reason asked me to update my password and >>>>>>>>>>>>>>>> now i don't remember it and my account got suspended. Is there a way to >>>>>>>>>>>>>>>> reset it or set a simple password? I updated the password hash in the >>>>>>>>>>>>>>>> users table by using the hash from another LORIS setup we had and i still >>>>>>>>>>>>>>>> couldn't login ( also the attribute password is always NULL and the >>>>>>>>>>>>>>>> expiration date is 1999-01-01 for some reason ). >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Thanks >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> ???? ???, 29 ???? 2019 ???? 5:21 ?.?., ?/? Cecile Madjar < >>>>>>>>>>>>>>>> cecile.madjar at mcin.ca> ??????: >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Can you try adding the visit label v01 to the >>>>>>>>>>>>>>>>> Visit_Windows table? >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> However, I noticed that in a previous dataset, the label >>>>>>>>>>>>>>>>> was V1. Does that refer to the same visit? If so, you might want to >>>>>>>>>>>>>>>>> harmonize the visit labels so they are all the same across datasets for a >>>>>>>>>>>>>>>>> given timepoint, meaning you will need to relabel scans when the visit >>>>>>>>>>>>>>>>> label is different but referring to the same visit label (v01 = V1 etc...). >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Hope this helps, >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> On Mon, Jul 29, 2019 at 10:15 AM Sotirios Nikoloutsopoulos >>>>>>>>>>>>>>>>> wrote: >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Could you help me with the "Visit label does not exist"? >>>>>>>>>>>>>>>>>> I had changed $subjectID{'createVisitLabel'} to 1 as you had suggested but >>>>>>>>>>>>>>>>>> it appears that this problem hasn't been resolved yet. >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> lorisadmin at hbp:/data/loris/bin/mri$ cat >>>>>>>>>>>>>>>>>> /data/loris/data//logs/TarLoad-14-58-9Xog7H.log >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> ==> Loading file from disk >>>>>>>>>>>>>>>>>> /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> --> mapping DICOM parameter for >>>>>>>>>>>>>>>>>> /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> --> using user-defined filterParameters for >>>>>>>>>>>>>>>>>> /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Candidate Mismatch Error is Visit label does not exist >>>>>>>>>>>>>>>>>> -> WARNING: This candidate was invalid. Logging to >>>>>>>>>>>>>>>>>> MRICandidateErrors table with reason Visit >>>>>>>>>>>>>>>>>> label does not exist >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> ???? ???, 26 ???? 2019 ???? 3:02 ?.?., ?/? Sotirios >>>>>>>>>>>>>>>>>> Nikoloutsopoulos ??????: >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Hi Cecile, >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> The Center error was fixed. Still the insertion of mincs >>>>>>>>>>>>>>>>>>> fails. Please see the output.txt file i attached. Also is there something >>>>>>>>>>>>>>>>>>> else i need to change at the paths configuration? >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> ???? ???, 25 ???? 2019 ???? 6:55 ?.?., ?/? Cecile Madjar >>>>>>>>>>>>>>>>>>> ??????: >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> We are making progress! >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> I have a feeling this error comes from the fact that >>>>>>>>>>>>>>>>>>>> your psc table does not have the MRI_alias populated for the DCC site. >>>>>>>>>>>>>>>>>>>> Running the following query in the mysql database should fix this: >>>>>>>>>>>>>>>>>>>> UPDATE psc SET MRI_alias="DCC", Alias="DCC" WHERE >>>>>>>>>>>>>>>>>>>> Name="Data Coordinating Center"; >>>>>>>>>>>>>>>>>>>> Repeat the same with all your sites (make sure to >>>>>>>>>>>>>>>>>>>> change the Aliases between sites, they should all be unique). >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Let me know how it goes! >>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> On Thu, Jul 25, 2019 at 11:43 AM Sotirios >>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos wrote: >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> Dear Cecile, >>>>>>>>>>>>>>>>>>>>> You were right about your guesses. I did the >>>>>>>>>>>>>>>>>>>>> modifications you suggested, i still get the "no mincs inserted" error, now >>>>>>>>>>>>>>>>>>>>> i am getting the "No center found this candidate" error ( how do i fix >>>>>>>>>>>>>>>>>>>>> that? from what i see the .dcm files contains a 'Institution Name', is that >>>>>>>>>>>>>>>>>>>>> the center? ), so i guess that's why the validation fails, but i changed >>>>>>>>>>>>>>>>>>>>> the force variable of tarchiveLoader to 1, shouldn't it have inserted the >>>>>>>>>>>>>>>>>>>>> mincs then? Also it is optional to have a mail server, right? ( from what i >>>>>>>>>>>>>>>>>>>>> see the mail error does not affect the $valid_study, so i assume we are >>>>>>>>>>>>>>>>>>>>> okay with that ) >>>>>>>>>>>>>>>>>>>>> Thank you a lot, >>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> ???? ???, 25 ???? 2019 ???? 5:48 ?.?., ?/? Cecile >>>>>>>>>>>>>>>>>>>>> Madjar ??????: >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> From what I understand, I believe you just need to >>>>>>>>>>>>>>>>>>>>>> update a few config settings from the frontend in the Config module (under >>>>>>>>>>>>>>>>>>>>>> the Admin menu). >>>>>>>>>>>>>>>>>>>>>> [image: Screen Shot 2019-07-25 at 10.31.35 AM.png] >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> Then go to the Paths section of the config module and >>>>>>>>>>>>>>>>>>>>>> update the "LORIS-MRI code" config setting to /data/loris/bin/mri (my guess >>>>>>>>>>>>>>>>>>>>>> is that currently, it is set to /data/LORIS/data) and click on the submit >>>>>>>>>>>>>>>>>>>>>> button. >>>>>>>>>>>>>>>>>>>>>> [image: Screen Shot 2019-07-25 at 10.32.50 AM.png] >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> Then, go to Imaging Pipeline section of the >>>>>>>>>>>>>>>>>>>>>> Configuration module and update the "Loris-MRI Data Directory" to >>>>>>>>>>>>>>>>>>>>>> /data/loris/data/ (my guess is that it is empty at the moment in your >>>>>>>>>>>>>>>>>>>>>> database which is why $data_dir is not defined when you run the >>>>>>>>>>>>>>>>>>>>>> tarchiveLoader step of the insertion pipeline). >>>>>>>>>>>>>>>>>>>>>> [image: Screen Shot 2019-07-25 at 10.40.52 AM.png] >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> Finally, I took a look at your environment file and >>>>>>>>>>>>>>>>>>>>>> it might be a good idea to update your PERL5LIB variable to the following >>>>>>>>>>>>>>>>>>>>>> (it has been added to the code a few releases ago as we realized this was >>>>>>>>>>>>>>>>>>>>>> needed for the libraries. Not sure which version of LORIS-MRI you are using >>>>>>>>>>>>>>>>>>>>>> but it does not hurt to update this variable to what I suggest below): >>>>>>>>>>>>>>>>>>>>>> export >>>>>>>>>>>>>>>>>>>>>> PERL5LIB=/data/loris/bin/mri/uploadNeuroDB:/data/loris/bin/mri/dicom-archive:$PERL5LIB >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> Hope this helps. Sorry you are experiencing so much >>>>>>>>>>>>>>>>>>>>>> trouble setting things up. We probably need to update our WIKI. >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> On Thu, Jul 25, 2019 at 9:48 AM Sotirios >>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos wrote: >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> The "Loris-MRI Data Directory" should be in the >>>>>>>>>>>>>>>>>>>>>>> environment file? >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> ???? ???, 25 ???? 2019 ???? 12:59 ?.?., ?/? Sotirios >>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos ??????: >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> The scripts are located in /data/loris/bin/mri/. >>>>>>>>>>>>>>>>>>>>>>>> Somewhere I might have messed something up but i remember following the >>>>>>>>>>>>>>>>>>>>>>>> instructions in the wiki.For example when i tried to execute the >>>>>>>>>>>>>>>>>>>>>>>> batch_uploads_imageuploader perl script the line >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> my $command = "$bin_dir/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl " >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> was pointing to an invalid path, for example: it >>>>>>>>>>>>>>>>>>>>>>>> was repeating a pattern and had LORIS instead of loris ( i think the >>>>>>>>>>>>>>>>>>>>>>>> mistake was that in the wiki it suggested to use $PROJECT for the name of >>>>>>>>>>>>>>>>>>>>>>>> the folder and i choosed 'loris' >>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris/wiki/Imaging-Database >>>>>>>>>>>>>>>>>>>>>>>> ). See also the in image for the modification i did. Also i didn't find the >>>>>>>>>>>>>>>>>>>>>>>> section to config the $data_dir variable. >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 24 ???? 2019 ???? 6:05 ?.?., ?/? Cecile >>>>>>>>>>>>>>>>>>>>>>>> Madjar ??????: >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> It looks like you have one Config setting not set >>>>>>>>>>>>>>>>>>>>>>>>> (based on the first error message you got when running it the first time). >>>>>>>>>>>>>>>>>>>>>>>>> You need to set a value for "Loris-MRI Data Directory" in the Config module >>>>>>>>>>>>>>>>>>>>>>>>> under the Imaging pipeline section (from what I can see, it would be >>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/ for your setup). >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> The reason you got that error message the second >>>>>>>>>>>>>>>>>>>>>>>>> time is that the pipeline checks if the DICOM study was already inserted in >>>>>>>>>>>>>>>>>>>>>>>>> the tarchive table. Since you ran the study once already, the study is >>>>>>>>>>>>>>>>>>>>>>>>> inserted into the tarchive, hence the message. However, the pipeline did >>>>>>>>>>>>>>>>>>>>>>>>> not complete as the MINC files were not created and inserted into the >>>>>>>>>>>>>>>>>>>>>>>>> files/parameter_file table. In order to continue the insertion, you will >>>>>>>>>>>>>>>>>>>>>>>>> then need to run the tarchiveLoader command suggested in the terminal >>>>>>>>>>>>>>>>>>>>>>>>> during the second run: >>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader >>>>>>>>>>>>>>>>>>>>>>>>> -globLocation -profile prod >>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive//2012/DCM_2012-12-05_ImagingUpload-17-43-ZUEFjb.tar >>>>>>>>>>>>>>>>>>>>>>>>> -verbose >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> Finally, I am a bit confused by your setup. Where >>>>>>>>>>>>>>>>>>>>>>>>> are the scripts located? In /data/loris/bin/mri or /data/loris/data? It >>>>>>>>>>>>>>>>>>>>>>>>> feels like the Config setting "LORIS-MRI code" in the Paths section was set >>>>>>>>>>>>>>>>>>>>>>>>> to "/data/LORIS/data" but it should have been set to the directory where >>>>>>>>>>>>>>>>>>>>>>>>> the scripts are located (most probably /data/loris/bin/mri). >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> Hope this helps, >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> On Wed, Jul 24, 2019 at 10:55 AM Sotirios >>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos wrote: >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> Ok first i execute this command: >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> "lorisadmin at hbp:/data/loris/bin/mri$ >>>>>>>>>>>>>>>>>>>>>>>>>> ./batch_uploads_imageuploader -profile prod < ~/Desktop/input.txt > log.txt >>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at ./batch_uploads_imageuploader line 143. >>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at ./batch_uploads_imageuploader line 143. >>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $_ in pattern match >>>>>>>>>>>>>>>>>>>>>>>>>> (m//) at ./batch_uploads_imageuploader line 147. >>>>>>>>>>>>>>>>>>>>>>>>>> base is DCC0000_258024_V01 >>>>>>>>>>>>>>>>>>>>>>>>>> path is /data/incoming/ >>>>>>>>>>>>>>>>>>>>>>>>>> type is .tar.gz >>>>>>>>>>>>>>>>>>>>>>>>>> fullpath is >>>>>>>>>>>>>>>>>>>>>>>>>> /data/incoming/DCC0000_258024_V01.tar.gz >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> source /tmp/ImagingUpload-17-43-ZUEFjb >>>>>>>>>>>>>>>>>>>>>>>>>> targetlocation /data/loris/data/tarchive >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 256. >>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 284. >>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at /data/loris/bin/mri/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>> tarchive_validation.pl line 219. >>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at /data/loris/bin/mri/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl line 270. >>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 711. >>>>>>>>>>>>>>>>>>>>>>>>>> Can't exec "mail": No such file or directory at >>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 721. >>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 722. >>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 723. >>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 724. >>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 724. >>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 725. >>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 735. >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> No Mincs inserted >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> The tarchiveLoader insertion script has failed. >>>>>>>>>>>>>>>>>>>>>>>>>> Running now the following command: >>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl -profile prod -upload_id >>>>>>>>>>>>>>>>>>>>>>>>>> 3 /data/incoming/DCC0000_258024_V01.tar.gz -verbose" >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> I inserted the VisitLabel, but still the Mincs >>>>>>>>>>>>>>>>>>>>>>>>>> are not inserted and i am getting this error >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> "lorisadmin at hbp:/data/loris/bin/mri$ >>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl -profile prod -upload_id >>>>>>>>>>>>>>>>>>>>>>>>>> 3 /data/incoming/DCC0000_258024_V01.tar.gz -verbose >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> find -path \/tmp\/ImagingUpload\-17\-45\-5MsWEd >>>>>>>>>>>>>>>>>>>>>>>>>> -name '__MACOSX' -delete >>>>>>>>>>>>>>>>>>>>>>>>>> Spool message is: >>>>>>>>>>>>>>>>>>>>>>>>>> The Scan for the uploadID 3 has already been run >>>>>>>>>>>>>>>>>>>>>>>>>> with tarchiveID: 7. >>>>>>>>>>>>>>>>>>>>>>>>>> To continue with the rest of the insertion >>>>>>>>>>>>>>>>>>>>>>>>>> pipeline, please run tarchiveLoader from a terminal as follows: >>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader -globLocation -profile prod >>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive//2012/DCM_2012-12-05_ImagingUpload-17-43-ZUEFjb.tar >>>>>>>>>>>>>>>>>>>>>>>>>> -verbose" >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> Which files should i delete? I thought that >>>>>>>>>>>>>>>>>>>>>>>>>> deleting the files from the tarchive was enough. And i executed the last >>>>>>>>>>>>>>>>>>>>>>>>>> proposed command to continue to rest of the insertion pipeline ( check the >>>>>>>>>>>>>>>>>>>>>>>>>> image ). >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> Thank you >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 24 ???? 2019 ???? 5:05 ?.?., ?/? Cecile >>>>>>>>>>>>>>>>>>>>>>>>>> Madjar ??????: >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> Sorry I was not clear before. Every visits of >>>>>>>>>>>>>>>>>>>>>>>>>>> candidates are created in the session table with one entry per >>>>>>>>>>>>>>>>>>>>>>>>>>> CandID/VisitLabel. So if the imaging pipeline created visits in the session >>>>>>>>>>>>>>>>>>>>>>>>>>> table (that are not attached to instruments) and you want to clean your >>>>>>>>>>>>>>>>>>>>>>>>>>> database completely, you can delete entries in that table as well. >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> Regarding your point 2, the imaging pipeline can >>>>>>>>>>>>>>>>>>>>>>>>>>> create the visit in the session table as long as the visit label is present >>>>>>>>>>>>>>>>>>>>>>>>>>> in the Visit_Windows table (which means the visit label stored in the >>>>>>>>>>>>>>>>>>>>>>>>>>> PatientName is a valid visit label). >>>>>>>>>>>>>>>>>>>>>>>>>>> However, in your prod file, if the >>>>>>>>>>>>>>>>>>>>>>>>>>> variable $subjectID{'createVisitLabel'} is set to 1 for candidates, the >>>>>>>>>>>>>>>>>>>>>>>>>>> visit label should be created in the Visit_Windows table I believe. Here >>>>>>>>>>>>>>>>>>>>>>>>>>> is the line of the prod file you would need to change >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> . >>>>>>>>>>>>>>>>>>>>>>>>>>> In general, we prefer populating the >>>>>>>>>>>>>>>>>>>>>>>>>>> Visit_Windows table and set the $subjectID{'createVisitLabel'} to 0 for >>>>>>>>>>>>>>>>>>>>>>>>>>> candidate data to avoid insertion of badly labelled MRI data that are >>>>>>>>>>>>>>>>>>>>>>>>>>> complex to relabel. >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> Finally, regarding the candidate creation, if >>>>>>>>>>>>>>>>>>>>>>>>>>> you execute the following steps, the pipeline should be able to create >>>>>>>>>>>>>>>>>>>>>>>>>>> candidates: >>>>>>>>>>>>>>>>>>>>>>>>>>> - set in the Imaging Pipeline section of the >>>>>>>>>>>>>>>>>>>>>>>>>>> config module the config setting "Upload creation of candidates" to Yes >>>>>>>>>>>>>>>>>>>>>>>>>>> - manually transfer the scans to the LORIS >>>>>>>>>>>>>>>>>>>>>>>>>>> server instead of uploading it via the imaging browser >>>>>>>>>>>>>>>>>>>>>>>>>>> - run batch_imaging_upload.pl as you did until >>>>>>>>>>>>>>>>>>>>>>>>>>> now. >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helps! >>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> On Wed, Jul 24, 2019 at 8:47 AM Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos wrote: >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> About my second question i replaced the name of >>>>>>>>>>>>>>>>>>>>>>>>>>>> the patient in the .dcm files and now i am getting an error that the visit >>>>>>>>>>>>>>>>>>>>>>>>>>>> label does not exist. >>>>>>>>>>>>>>>>>>>>>>>>>>>> I thought it was supposed to be automatically >>>>>>>>>>>>>>>>>>>>>>>>>>>> created. >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> "Done adding archive info into database >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader >>>>>>>>>>>>>>>>>>>>>>>>>>>> -globLocation -profile prod >>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive//DCM_2012-12-05_ImagingUpload-15-42-yUwQQV.tar >>>>>>>>>>>>>>>>>>>>>>>>>>>> -verbose >>>>>>>>>>>>>>>>>>>>>>>>>>>> md5sum >>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive/DCM_2012-12-05_ImagingUpload-15-42-yUwQQV.tar >>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>> candidate id 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> => No Visit labelVisit label does not exist >>>>>>>>>>>>>>>>>>>>>>>>>>>> Set centerID = 1 >>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> Number of MINC files that will be considered >>>>>>>>>>>>>>>>>>>>>>>>>>>> for inserting into the database: 1 >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> log dir is /logs and log file is >>>>>>>>>>>>>>>>>>>>>>>>>>>> /logs/TarLoad-15-42-L6pocU.log >>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>> candidate id 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> => No Visit label >>>>>>>>>>>>>>>>>>>>>>>>>>>> Cleaning up temp files: rm -rf >>>>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-15-42-J2rQms/ImagingUpload-15-42-yUwQQV*" >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 24 ???? 2019 ???? 3:38 ?.?., ?/? >>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos >>>>>>>>>>>>>>>>>>>>>>>>>>>> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> 1) What are the records in the session table? >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> 2) I tried to upload a non-phantom file like >>>>>>>>>>>>>>>>>>>>>>>>>>>>> this >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> input_file.txt: >>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/incoming/DCC0000_258024_V1.tar.gz N >>>>>>>>>>>>>>>>>>>>>>>>>>>>> DCC0000_258024_V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Terminal: >>>>>>>>>>>>>>>>>>>>>>>>>>>>> ./batch_uploads_imageuploader -profile prod < >>>>>>>>>>>>>>>>>>>>>>>>>>>>> ~/Desktop/input.txt > log.txt >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> and i get the following error in the log.txt >>>>>>>>>>>>>>>>>>>>>>>>>>>>> file >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> "Running now the following command: >>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl -profile prod >>>>>>>>>>>>>>>>>>>>>>>>>>>>> -upload_id 7 /data/incoming/DCC0000_258024_V1.tar.gz -verbose >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> find -path >>>>>>>>>>>>>>>>>>>>>>>>>>>>> \/tmp\/ImagingUpload\-14\-56\-FeLCB4 -name '__MACOSX' -delete >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Spool message is: >>>>>>>>>>>>>>>>>>>>>>>>>>>>> The PatientName read from the DICOM header >>>>>>>>>>>>>>>>>>>>>>>>>>>>> does not start with DCC0000_258024_V1 from the mri_upload table >>>>>>>>>>>>>>>>>>>>>>>>>>>>> " >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> and the spool message is repeated for each >>>>>>>>>>>>>>>>>>>>>>>>>>>>> .dcm file. Should i preprocess every .dcm file and change the PatientName >>>>>>>>>>>>>>>>>>>>>>>>>>>>> to "DCC0000_258024_V1"? >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> 3) As far as it concerns the candidate profile >>>>>>>>>>>>>>>>>>>>>>>>>>>>> i have to create a new one each time before i try to upload a file? Is >>>>>>>>>>>>>>>>>>>>>>>>>>>>> there already a way to create a candidate profile and get the DCCID and >>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID without the user interface? >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 18 ???? 2019 ???? 5:00 ?.?., ?/? >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Cecile Madjar ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> See answers to your questions below. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> About the 1st case we had a dicom with a >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> blank studyUID, maybe someone accidentally removed it. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> That is strange. Something must have been >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> done to the DICOM files. I have never seen a study with no StudyUID out of >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the scanner. Usually, you need to manually erase it with some tool. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> However, DICOMs never cease to surprise me... >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Some other questions: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 1) What are the steps to remove all of my >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> patients and uploads?: because i want to try to reupload all the testing >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> dicoms we had with a clean database. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Release 21.0 of LORIS-MRI will offer a script >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> to remove all the entries and files specific to an upload. However, this >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> release is not yet out. Hopefully in the next few weeks. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> In the meantime, since your case is >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> particular and that you just want to start with a clean database, the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> following deletes should work (hopefully I won't forget any tables): >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from mri_violations_log; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from mri_protocol_violated_scans; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from MRICandidateErrors; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from parameter_file; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from files_qcstatus; # (if you played >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> with the QC part of the imaging browser for testing) >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from feedback_mri_comments; # (if you >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> played with the QC part of the imaging browser for testing) >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from tarchive_series; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from tarchive_files; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from mri_upload; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from tarchive; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from mri_scanner; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from candidate where PSCID="scanner"; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I don't know if you want to also delete >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> entries in the session and candidate table too? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 2) We do not need to create the profile of a >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> patient ( are the patients stored in the candidate table? because i can't >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> see the ghosts ), because will it automatically be created when importing a >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> dicom? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I am not sure I understand fully this >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> question. All candidates are stored in the candidate table. The phantom >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> scans however are attached to a scanner candidate depending on where the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> scan happened. It is a bit of a weird concept that we have to redesign >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> eventually but never got a chance to get to it. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hopefully this answered your question, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> otherwise, don't hesitate to let me know. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 3) What is the difference between uploading a >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> dicom as phantom instead of importing as PSCCID_DCCID_VisitLabel? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> When you upload the scan as >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID_DCCID_VisitLabel, there is a check that makes sure the candidate IDs >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and visit label are valid at the time of upload. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> When you upload a scan as phantom, it expects >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> that the DICOM field PatientName and uploaded filename contains the string >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> "phantom". We enforced this behaviour on the imaging uploader side in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> recent releases but I can't remember which one. Probably the upcoming 21.0 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> release. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> All those verifications might seem cumbersome >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> but they are here to ensure that the files inserted are all valid and >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> labelled properly as it is a bit messy to have to delete files that were >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> wrongly labelled. At least, the delete script present in release 21.0 will >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> make this process easier but it is still good practice to verify those >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> things. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> With pleasure. Hopefully the answers to your >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> questions will be helpful. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PS: loris-dev mailing list: you will find the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> initial answer I gave Sotirios below. I forgot to cc the loris-dev in my >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> earlier reply... >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 16 ???? 2019 ???? 12:02 ?.?., ?/? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Cecile Madjar >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Dear Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you for reaching out. Since your >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> email was already organized in points, I will reply directly below your >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> questions below. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 1) What do we do when the StudyUID is blank >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> on the header? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/minor/docs/AppendixA-Troubleshooting_guideline.md >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> There solution provided at the table 3 does not guide us how to find the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> information ( is possible ). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The StudyUID is the field used in our >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> pipeline at the moment to check whether a DICOM study was already inserted >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> into LORIS with that same StudyUID since it is supposed to be unique for >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> every single study. Currently, we do not support insertion of DICOM studies >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> if they do not have a StudyUID associated with them. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Is there a specific reason why the StudyUID >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> is blank in the DICOM headers in your DICOM files? Did they go through some >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> processes before upload to LORIS? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 2) When i am about to upload a non-phanton >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> case i need a 'Visit Label'. Is there already a script that can create a >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> new visit label for a specific Candidate, so i can provide it as input >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> afterwards to the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> batch_uploads_imageuploader ( See option 5.1.3 https://github.com/aces/Loris-MRI/blob/minor/docs/05-PipelineLaunchOptions.md ) >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I am not sure if the front-end allows for >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> it but if you use batch_uploads_imageuploader, the insertion scripts could >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> create the visit label for you. However, it does need to be included in the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> patient name in order for the script to know which label it should use. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> For example: you upload V02 for MTL0123 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> (DCCID: 456789) but V02 was not yet created for MTL0123; the insertion >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> scripts will create a V02 visit for MTL0123 if the PatientName field for >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the dataset is MTL0123_456789_V02 with Stage marked as "Not Started". >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> However, *note that for the script to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> create the visit for the candidate, you have to make sure that all the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit label of your projects were inserted in the Visit_Windows table* >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> (otherwise, the visit will never be created as they were not specified as >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> being part of the list of visit label to expect). So in the example above, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> you should have one row in Visit_Windows with Visit_label="V02" set. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 3) Section 4.3 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/minor/docs/04-Scripts.md >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> What do we do when the folder contains multiple mnc files? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> This is a case by case. Most of the time, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the MINC files that failed insertion into the imaging browser end up in the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> MRI violation module where you can see what went wrong with the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> acquisitions not inserted. If you notice that the MINC file should be >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> inserted as a specific protocol, you can force the insertion as explained >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in section 4.3. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> In your case, I have a feeling that you >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> want to be able to insert MINC files that did not go through the whole >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> pipeline insertion (DICOM archival, then dcm2mnc, then protocol >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> identification, then insertion...). In theory, you could call >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl on any MINC file, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> provided you have at least the following information: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - path to the MINC file >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - uploadID associated with the MINC files >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> or DICOM archive path from which those MINC files were created from >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Then the minc_insertion.pl script will do >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the subject information and protocol validation etc... >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> If all the MINC files come from the same >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> uploadID or TarchiveID, then you could run a loop in bash calling the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl script like this for >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> files deriving from uploadID=1: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ls /path/to/mnc/folder/* | while read f; do >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl -profile prod -uploadID >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 1 -mincPath $f; done >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helped! >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> -- >>>>>>>>>>>>> >>>>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> -- >>>>>>>>>>> >>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>> >>>>>>>>>> _______________________________________________ >>>>>>>>> Loris-dev mailing list >>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> -- >>>>>>>> >>>>>>>> christine.rogers at mcgill.ca >>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>> Montreal Neurological Institute >>>>>>>> McGill University | Montreal | Canada >>>>>>>> >>>>>>> _______________________________________________ >>>>>>> Loris-dev mailing list >>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>> >>>>>> >>>>>> >>>>>> -- >>>>>> >>>>>> christine.rogers at mcgill.ca >>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>> Montreal Neurological Institute >>>>>> McGill University | Montreal | Canada >>>>>> _______________________________________________ >>>>>> Loris-dev mailing list >>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>> >>>>> >>>>> >>>>> -- >>>>> >>>>> christine.rogers at mcgill.ca >>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>> Montreal Neurological Institute >>>>> McGill University | Montreal | Canada >>>>> _______________________________________________ >>>>> Loris-dev mailing list >>>>> Loris-dev at bic.mni.mcgill.ca >>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>> >>>> >>>> >>>> -- >>>> >>>> christine.rogers at mcgill.ca >>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>> Montreal Neurological Institute >>>> McGill University | Montreal | Canada >>>> >>> _______________________________________________ >>> Loris-dev mailing list >>> Loris-dev at bic.mni.mcgill.ca >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>> >> >> >> -- >> >> christine.rogers at mcgill.ca >> McGill Centre for Integrative Neuroscience | MCIN.ca >> Montreal Neurological Institute >> McGill University | Montreal | Canada >> > _______________________________________________ > Loris-dev mailing list > Loris-dev at bic.mni.mcgill.ca > https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > -------------- next part -------------- An HTML attachment was scrubbed... URL: From sotirisnik at gmail.com Thu Aug 8 14:37:56 2019 From: sotirisnik at gmail.com (Sotirios Nikoloutsopoulos) Date: Thu, 8 Aug 2019 21:37:56 +0300 Subject: [Loris-dev] Upgrading to Loris 21 - new make file In-Reply-To: References: Message-ID: It's not a disk space issue, as you can see below i have still 74GB available. lorisadmin at hbp:/var/www/loris$ df -h Filesystem Size Used Avail Use% Mounted on udev 2,9G 0 2,9G 0% /dev tmpfs 597M 8,6M 588M 2% /run /dev/sda1 98G 19G 74G 21% / Maybe we have to pass a flag to get into strict mode? as stated "SyntaxError: Block-scoped declarations (let, const, function, class) not yet supported outside strict mode" Thanks, Sotirios ???? ???, 8 ??? 2019 ???? 4:32 ?.?., ?/? Dave MacFarlane < dave.macfarlane at mcin.ca> ??????: > It looks like the javascript snippet shown in the error message when > trying to compile the js is truncated. Have you run out of disk space? > > On Thu, Aug 8, 2019 at 8:37 AM Sotirios Nikoloutsopoulos < > sotirisnik at gmail.com> wrote: > >> Hi, >> >> I runned make and also included the file it reports at the end. >> >> lorisadmin at hbp:/var/www/loris$ make >> npm install >> npm WARN optional Skipping failed optional dependency /chokidar/fsevents: >> npm WARN notsup Not compatible with your operating system or >> architecture: fsevents at 1.2.9 >> npm WARN optional Skipping failed optional dependency >> /watchpack/chokidar/fsevents: >> npm WARN notsup Not compatible with your operating system or >> architecture: fsevents at 1.2.9 >> npm run compile >> >> > loris at 1.0.0 compile /var/www/loris >> > webpack >> >> /var/www/loris/node_modules/webpack/bin/webpack.js:86 >> let notify = >> ^^^ >> >> SyntaxError: Block-scoped declarations (let, const, function, class) not >> yet supported outside strict mode >> at exports.runInThisContext (vm.js:53:16) >> at Module._compile (module.js:374:25) >> at Object.Module._extensions..js (module.js:417:10) >> at Module.load (module.js:344:32) >> at Function.Module._load (module.js:301:12) >> at Function.Module.runMain (module.js:442:10) >> at startup (node.js:136:18) >> at node.js:966:3 >> >> npm ERR! Linux 4.15.0-55-generic >> npm ERR! argv "/usr/bin/nodejs" "/usr/bin/npm" "run" "compile" >> npm ERR! node v4.2.6 >> npm ERR! npm v3.5.2 >> npm ERR! code ELIFECYCLE >> npm ERR! loris at 1.0.0 compile: `webpack` >> npm ERR! Exit status 1 >> npm ERR! >> npm ERR! Failed at the loris at 1.0.0 compile script 'webpack'. >> npm ERR! Make sure you have the latest version of node.js and npm >> installed. >> npm ERR! If you do, this is most likely a problem with the loris package, >> npm ERR! not with npm itself. >> npm ERR! Tell the author that this fails on your system: >> npm ERR! webpack >> npm ERR! You can get information on how to open an issue for this project >> with: >> npm ERR! npm bugs loris >> npm ERR! Or if that isn't available, you can get their info via: >> npm ERR! npm owner ls loris >> npm ERR! There is likely additional logging output above. >> >> npm ERR! Please include the following file with any support request: >> npm ERR! /var/www/loris/npm-debug.log >> Makefile:14: recipe for target 'javascript' failed >> make: *** [javascript] Error 1 >> >> Thanks, >> >> Sotirios >> >> ???? ???, 7 ??? 2019 ???? 5:41 ?.?., ?/? Christine Rogers, Ms. < >> christine.rogers at mcgill.ca> ??????: >> >>> Hi Sotirios, >>> >>> Thanks, have you tried all of these steps? >>> - clear your browser cache (and refresh a few times) >>> - delete any files in your smarty/templates_c directory (this will clear >>> the template cache - do Not touch smarty/templates/) >>> - run `make` (per the 21 release notes, this replaces the composer >>> commands used in previous releases to update your dependencies) >>> - restart apache (doesn't hurt) >>> >>> Let us know how it goes -- let us know what difference you see after, >>> with your logs. A >>> lso please send us your Config path settings (see these Troubleshooting >>> Queries >>> ) >>> if you're still seeing front-end issues. >>> >>> Thanks, >>> Christine >>> >>> On Wed, Aug 7, 2019 at 8:02 AM Sotirios Nikoloutsopoulos < >>> sotirisnik at gmail.com> wrote: >>> >>>> Hi, >>>> >>>> lorisadmin at hbp:/var/www/loris$ sudo cat /var/log/apache2/error.log >>>> [Wed Aug 07 07:35:02.422501 2019] [mpm_prefork:notice] [pid 1267] >>>> AH00163: Apache/2.4.18 (Ubuntu) OpenSSL/1.0.2g configured -- resuming >>>> normal operations >>>> [Wed Aug 07 07:35:02.422514 2019] [core:notice] [pid 1267] AH00094: >>>> Command line: '/usr/sbin/apache2' >>>> >>>> And as for the access.log the content are empty >>>> lorisadmin at hbp:/var/www/loris$ sudo ls -l /var/log/apache2/access.log >>>> lorisadmin at hbp:/var/www/loris$ sudo ls -l /var/log/apache2/access.log >>>> -rw-r----- 1 root adm 0 ???? 28 14:09 /var/log/apache2/access.log >>>> >>>> Also i noticed a loris_access.log. >>>> >>>> The only non-blank pages are: >>>> mri_violations, dataquery does not exist at all, statistics, >>>> data_team_helper, genomic_browser, configuration and >>>> server_processes_manager/ prints "Required configuration settings for >>>> Server Processes Manager are missing. Cannot continue." >>>> >>>> Thanks, >>>> Sotirios >>>> >>>> ???? ???, 6 ??? 2019 ???? 10:13 ?.?., ?/? Christine Rogers, Ms. < >>>> christine.rogers at mcgill.ca> ??????: >>>> >>>>> Hi Sotirios and LORIS community -- >>>>> >>>>> When upgrading to brand-new release 21 -- just a reminder to follow >>>>> the release notes and run the new *make* file to update your >>>>> dependencies (instead of using *composer* commands). >>>>> We've also updated the Wiki page >>>>> to clarify >>>>> that the release notes for each version will tell you what to run. >>>>> >>>>> If your current version is not the last release (20.3), it's still >>>>> important to upgrade to each minor release increment (e.g. 20.2, 20.3) >>>>> before making the leap to 21.0. >>>>> >>>>> If you're getting blank pages, post-upgrade -- Try clearing your >>>>> cache. >>>>> >>>>> Got questions or feedback e.g. on the Release Notes? please don't >>>>> hesitate to let us know. >>>>> Thanks, >>>>> Christine >>>>> The LORIS team >>>>> >>>>> >>>>> >>>>> On Tue, Aug 6, 2019 at 10:09 AM Christine Rogers, Ms. < >>>>> christine.rogers at mcgill.ca> wrote: >>>>> >>>>>> Hi Sotirios, >>>>>> Could you also let us know -- on which pages is content visible, and >>>>>> on which pages/modules is content not visible for you? >>>>>> Thanks, >>>>>> Christine >>>>>> >>>>>> On Tue, Aug 6, 2019 at 9:54 AM Christine Rogers, Ms. < >>>>>> christine.rogers at mcgill.ca> wrote: >>>>>> >>>>>>> Thanks Sotirios, >>>>>>> That's good to know. It sounds like you've checked that your >>>>>>> /var/www/loris/project/config.xml file get populated properly. >>>>>>> >>>>>>> Please send us the last few errors you're seeing in your apache >>>>>>> error log file, and your config paths and we can see what's happening with >>>>>>> your front end -- >>>>>>> Run these Troubleshooting Queries >>>>>>> >>>>>>> to get your config path settings, given your front end is not displaying >>>>>>> fully. >>>>>>> >>>>>>> The Loris-MRI repo >>>>>>> 21 >>>>>>> install/upgrade would then be your next steps. >>>>>>> Best, >>>>>>> Christine >>>>>>> >>>>>>> On Tue, Aug 6, 2019 at 7:53 AM Sotirios Nikoloutsopoulos < >>>>>>> sotirisnik at gmail.com> wrote: >>>>>>> >>>>>>>> I am using a VM. What i did was: >>>>>>>> 1) Download the files from https://github.com/aces/Loris and >>>>>>>> replace them to my existing /vaw/www/loris folder. >>>>>>>> 2) Execute the composer install --no-dev and then composer >>>>>>>> dump-autoload as mentioned here >>>>>>>> https://github.com/aces/Loris/wiki/Updating-your-LORIS. >>>>>>>> 3) Execute install.sh from /var/www/loris/tools and because LORIS >>>>>>>> already existed i moved a .config file, then re-executed the install.sh >>>>>>>> successfully >>>>>>>> 4 ) As for the database, i dropped the schema and i executed the >>>>>>>> installdb.php >>>>>>>> >>>>>>>> ???? ???, 5 ??? 2019 ???? 5:22 ?.?., ?/? Christine Rogers, Ms. < >>>>>>>> christine.rogers at mcgill.ca> ??????: >>>>>>>> >>>>>>>>> Hi Sotorios, >>>>>>>>> >>>>>>>>> Thanks - when you re-installed did you start on a fresh root path >>>>>>>>> / VM or might some of your old system setting still apply? >>>>>>>>> (And if you did any steps similar to an upgrade, did you follow >>>>>>>>> the Upgrade steps in the Release Notes, from both repos?) >>>>>>>>> >>>>>>>>> About the TR_range column - it was recently split (MRI pr339 >>>>>>>>> ) split into TR_min >>>>>>>>> and _max columns. Given the code was trying to query TR_range which does >>>>>>>>> not exist in your mri_protocol table, double-check which version of the >>>>>>>>> Loris repo (tables) and the Loris-MRI repo (code) you have installed to >>>>>>>>> ensure they match. >>>>>>>>> >>>>>>>>> Christine >>>>>>>>> >>>>>>>>> >>>>>>>>> On Mon, Aug 5, 2019 at 9:06 AM Sotirios Nikoloutsopoulos < >>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>> >>>>>>>>>> I reinstalled LORIS to 21 version and now the content is not >>>>>>>>>> visible at all at most pages. >>>>>>>>>> >>>>>>>>>> [image: image.png] >>>>>>>>>> >>>>>>>>>> ???? ???, 5 ??? 2019 ???? 3:19 ?.?., ?/? Sotirios >>>>>>>>>> Nikoloutsopoulos ??????: >>>>>>>>>> >>>>>>>>>>> Hi, >>>>>>>>>>> >>>>>>>>>>> Is it easy to upgrade to Loris 21? Also the following fails >>>>>>>>>>> because the line 1985 of NeuroDB/MRIProcessingUtility.pm query mri_protocol >>>>>>>>>>> which doesn't have TR_range >>>>>>>>>>> https://github.com/aces/Loris/blob/21.0-release/SQL/0000-00-00-schema.sql#L556 >>>>>>>>>>> >>>>>>>>>>> [image: image.png] >>>>>>>>>>> >>>>>>>>>>> lorisadmin at hbp:/data/loris/bin/mri$ >>>>>>>>>>> ./batch_uploads_imageuploader -profile prod < ~/Desktop/input.txt > log.txt >>>>>>>>>>> Use of uninitialized value $_ in pattern match (m//) at >>>>>>>>>>> ./batch_uploads_imageuploader line 147. >>>>>>>>>>> base is DCC0000_258024_V1 >>>>>>>>>>> path is /data/incoming/ >>>>>>>>>>> type is .tar.gz >>>>>>>>>>> fullpath is /data/incoming/DCC0000_258024_V1.tar.gz >>>>>>>>>>> DBD::mysql::st execute failed: Unknown column 'TR_range' in >>>>>>>>>>> 'where clause' at >>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line 1985. >>>>>>>>>>> DBD::mysql::st fetchrow_array failed: fetch() without execute() >>>>>>>>>>> at /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line >>>>>>>>>>> 1986. >>>>>>>>>>> Use of uninitialized value $count_mri_protocol in numeric gt (>) >>>>>>>>>>> at /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line >>>>>>>>>>> 1995. >>>>>>>>>>> DBD::mysql::st execute failed: Unknown column 'TR_range' in >>>>>>>>>>> 'field list' at /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 562. >>>>>>>>>>> Can't exec "mail": No such file or directory at >>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 721. >>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 722. >>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 723. >>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 724. >>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 725. >>>>>>>>>>> >>>>>>>>>>> No Mincs inserted >>>>>>>>>>> >>>>>>>>>>> Thanks, >>>>>>>>>>> >>>>>>>>>>> Sotirios >>>>>>>>>>> >>>>>>>>>>> ???? ???, 3 ??? 2019 ???? 1:08 ?.?., ?/? Christine Rogers, Ms. < >>>>>>>>>>> christine.rogers at mcgill.ca> ??????: >>>>>>>>>>> >>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>> >>>>>>>>>>>> First, just a note: we've released LORIS 21 this week with >>>>>>>>>>>> some major new features and cleanup -- especially if you are early in your >>>>>>>>>>>> setup phase, check out the Release notes for both the LORIS >>>>>>>>>>>> and >>>>>>>>>>>> Loris-MRI >>>>>>>>>>>> >>>>>>>>>>>> repos. >>>>>>>>>>>> >>>>>>>>>>>> Thanks for your screenshots -- your empty mri_protocol table >>>>>>>>>>>> should be at the root of these issues : >>>>>>>>>>>> >>>>>>>>>>>> The mri_protocol table must be populated >>>>>>>>>>>> >>>>>>>>>>>> in order for your scans to be registered in LORIS -- it serves as a >>>>>>>>>>>> whitelist for the insertion pipeline which filters out scans that aren't >>>>>>>>>>>> identified or matched to scan types in this table. >>>>>>>>>>>> >>>>>>>>>>>> By default, this table is populated with entries for t1, t2, >>>>>>>>>>>> fMRI and DTI (Insert statements for 21 release branch are here >>>>>>>>>>>> >>>>>>>>>>>> ) >>>>>>>>>>>> Feel free to restore our default records and broaden their >>>>>>>>>>>> parameters to match all your scan types. >>>>>>>>>>>> >>>>>>>>>>>> re Defaced, native, selected -- these filter the scans >>>>>>>>>>>> displayed as you move to the next page (View Session), instead of viewing >>>>>>>>>>>> "all types" of scans from a given session : >>>>>>>>>>>> >>>>>>>>>>>> - "defaced" means that a defacing script >>>>>>>>>>>> >>>>>>>>>>>> has masked the subject's face in the volume (for patient privacy) >>>>>>>>>>>> - "native" means that no pre-processing has been performed >>>>>>>>>>>> on the scan (it's raw data), >>>>>>>>>>>> - "selected" will show only volumes that have been QC'd >>>>>>>>>>>> and "selected" as the best of their type -- used to display only the best >>>>>>>>>>>> quality T1 image instead of all T1s acquired in a session, e.g. >>>>>>>>>>>> >>>>>>>>>>>> re QC Comments -- >>>>>>>>>>>> Once you have successfully loaded scans (matched to the >>>>>>>>>>>> mri_protocol table), you'll be able to use the Imaging Browser's View >>>>>>>>>>>> Session subpage to enter/view QC comments on each volume, or for each >>>>>>>>>>>> visit. >>>>>>>>>>>> These are stored directly in the database, and linked to each >>>>>>>>>>>> scan. (Table name: feedback_mri_comments) >>>>>>>>>>>> (Visit-level QC comments are linked to the session.) >>>>>>>>>>>> >>>>>>>>>>>> For a walkthrough of the Imaging setup - please see the Imaging >>>>>>>>>>>> Setup guide >>>>>>>>>>>> >>>>>>>>>>>> - >>>>>>>>>>>> >>>>>>>>>>>> An old LORIS walkthrough video >>>>>>>>>>>> can also walk >>>>>>>>>>>> you through some of the Imaging front-end features, starting at 8:00 >>>>>>>>>>>> LORIS' imaging modules have been updated many times since this >>>>>>>>>>>> video, but the functionality and workflow is similar. >>>>>>>>>>>> >>>>>>>>>>>> Let us know how it goes once you have entries in your >>>>>>>>>>>> mri_protocol table - >>>>>>>>>>>> Best, >>>>>>>>>>>> Christine >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> On Fri, Aug 2, 2019 at 7:58 AM Sotirios Nikoloutsopoulos < >>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>> >>>>>>>>>>>>> Hi Christine, >>>>>>>>>>>>> >>>>>>>>>>>>> In the candidate_list page i can see this patient >>>>>>>>>>>>> >>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>> >>>>>>>>>>>>> If i press the link under PSCID i get to see >>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>> >>>>>>>>>>>>> and if i press the link under Scan Done it redirects me to >>>>>>>>>>>>> imaging_browser >>>>>>>>>>>>> >>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>> >>>>>>>>>>>>> At the mri_violations page i also see No results ( neither on >>>>>>>>>>>>> resolved / not resolved ). >>>>>>>>>>>>> >>>>>>>>>>>>> At the imaging_uploader i can see the record that failed. >>>>>>>>>>>>> >>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>> >>>>>>>>>>>>> If i click on the tarchive info i get to see the Protocol Name >>>>>>>>>>>>> which i think is the acquisition we wanted? >>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>> >>>>>>>>>>>>> Also my mri_protocol table is empty. >>>>>>>>>>>>> >>>>>>>>>>>>> Furthermore i would like to ask about the defaced, native, >>>>>>>>>>>>> selected. What exactly is native and selected? And where are the qc >>>>>>>>>>>>> comments stored? >>>>>>>>>>>>> >>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>> >>>>>>>>>>>>> Finally a walkthrough would be helpful. >>>>>>>>>>>>> >>>>>>>>>>>>> Thanks, >>>>>>>>>>>>> >>>>>>>>>>>>> Sotirios >>>>>>>>>>>>> >>>>>>>>>>>>> ???? ???, 30 ???? 2019 ???? 8:29 ?.?., ?/? Christine Rogers, >>>>>>>>>>>>> Ms. ??????: >>>>>>>>>>>>> >>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>> Glad to hear you're making progress with the visit labels. >>>>>>>>>>>>>> To follow up on your last few emails: >>>>>>>>>>>>>> >>>>>>>>>>>>>> a- The Wiki's Setup Guide contains Sample insert statements >>>>>>>>>>>>>> for the Visit Windows table >>>>>>>>>>>>>> >>>>>>>>>>>>>> . >>>>>>>>>>>>>> >>>>>>>>>>>>>> As Cecile mentioned, the consistency of visit label format is >>>>>>>>>>>>>> important: V01, v01, V1, 01 -- whichever you select to use is fine; we use >>>>>>>>>>>>>> V01 by default across all documentation. >>>>>>>>>>>>>> >>>>>>>>>>>>>> b- For Password reset, there is a script in the tools/ >>>>>>>>>>>>>> directory so that a back-end administrator can reset any front-end user >>>>>>>>>>>>>> password, including Admin. (See info on setting up / resetting User >>>>>>>>>>>>>> passwords in the Wiki's Setup Guide >>>>>>>>>>>>>> >>>>>>>>>>>>>> ) >>>>>>>>>>>>>> >>>>>>>>>>>>>> c- The minc file not being registered -- due to >>>>>>>>>>>>>> AcquisitionProtocol unknown. >>>>>>>>>>>>>> This means the SeriesDescription (Acquisition Protocol) in >>>>>>>>>>>>>> you Dicom header was not matched to any scan listed in the mri_protocol >>>>>>>>>>>>>> database table. >>>>>>>>>>>>>> (In the online Loris-MRI Troubleshooting Guide, >>>>>>>>>>>>>> this >>>>>>>>>>>>>> is Table 3, 2nd-last item "no MINCs inserted"). >>>>>>>>>>>>>> >>>>>>>>>>>>>> The MRI Violations module (Readme here) >>>>>>>>>>>>>> will show >>>>>>>>>>>>>> you the details of this mismatch -- >>>>>>>>>>>>>> Go to the module (under the Imaging menu), find your scan and >>>>>>>>>>>>>> click the link "Could not identify scan type" -- in the next subpage you >>>>>>>>>>>>>> can compare the scan's actual parameters against the mri_protocol table. >>>>>>>>>>>>>> >>>>>>>>>>>>>> To resolve this, adjust your mri_protocol table values or >>>>>>>>>>>>>> perhaps ensure your DICOMs are labelled consistently. >>>>>>>>>>>>>> >>>>>>>>>>>>>> Let us know if this works for you -- we can also walk you >>>>>>>>>>>>>> through an example of non-identified scans on Demo.loris.ca >>>>>>>>>>>>>> (MRI Violations module). >>>>>>>>>>>>>> >>>>>>>>>>>>>> Best, >>>>>>>>>>>>>> Christine >>>>>>>>>>>>>> >>>>>>>>>>>>>> The LORIS team >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> On Tue, Jul 30, 2019 at 10:47 AM Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>> >>>>>>>>>>>>>>> I hope this is sufficient as the error for the visit label >>>>>>>>>>>>>>> disappeared. >>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> Please see the attached file. Also something i found. >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> lorisadmin at hbp:/data/loris/bin/mri$ cat >>>>>>>>>>>>>>> /data/loris/data//logs/TarLoad-17-39-xubBdv.log >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> ==> Loading file from disk >>>>>>>>>>>>>>> /tmp/TarLoad-17-39-UyQcG2/dcc0000_258024_v1_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> --> mapping DICOM parameter for >>>>>>>>>>>>>>> /tmp/TarLoad-17-39-UyQcG2/dcc0000_258024_v1_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> ==> computing md5 hash for MINC body. >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> --> md5: 6b1202fd63e29de4c9be1cd9925888a5 >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> ==> verifying acquisition protocol >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> Acquisition protocol is unknown >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> --> The minc file cannot be registered since the >>>>>>>>>>>>>>> AcquisitionProtocol is unknown >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> ???? ???, 30 ???? 2019 ???? 4:58 ?.?., ?/? Sotirios >>>>>>>>>>>>>>> Nikoloutsopoulos ??????: >>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Ok I fixed the login problem by using a known hash and by >>>>>>>>>>>>>>>> deleting the rows from the login_history i was able to login. >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> ???? ???, 30 ???? 2019 ???? 4:50 ?.?., ?/? Sotirios >>>>>>>>>>>>>>>> Nikoloutsopoulos ??????: >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> there was no visit label 01 in the Visit_Windows table and >>>>>>>>>>>>>>>>> i don't know how to insert it because the record requires lots of >>>>>>>>>>>>>>>>> attributes. Also the system for a reason asked me to update my password and >>>>>>>>>>>>>>>>> now i don't remember it and my account got suspended. Is there a way to >>>>>>>>>>>>>>>>> reset it or set a simple password? I updated the password hash in the >>>>>>>>>>>>>>>>> users table by using the hash from another LORIS setup we had and i still >>>>>>>>>>>>>>>>> couldn't login ( also the attribute password is always NULL and the >>>>>>>>>>>>>>>>> expiration date is 1999-01-01 for some reason ). >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Thanks >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> ???? ???, 29 ???? 2019 ???? 5:21 ?.?., ?/? Cecile Madjar < >>>>>>>>>>>>>>>>> cecile.madjar at mcin.ca> ??????: >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Can you try adding the visit label v01 to the >>>>>>>>>>>>>>>>>> Visit_Windows table? >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> However, I noticed that in a previous dataset, the label >>>>>>>>>>>>>>>>>> was V1. Does that refer to the same visit? If so, you might want to >>>>>>>>>>>>>>>>>> harmonize the visit labels so they are all the same across datasets for a >>>>>>>>>>>>>>>>>> given timepoint, meaning you will need to relabel scans when the visit >>>>>>>>>>>>>>>>>> label is different but referring to the same visit label (v01 = V1 etc...). >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Hope this helps, >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> On Mon, Jul 29, 2019 at 10:15 AM Sotirios >>>>>>>>>>>>>>>>>> Nikoloutsopoulos wrote: >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Could you help me with the "Visit label does not exist"? >>>>>>>>>>>>>>>>>>> I had changed $subjectID{'createVisitLabel'} to 1 as you had suggested but >>>>>>>>>>>>>>>>>>> it appears that this problem hasn't been resolved yet. >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> lorisadmin at hbp:/data/loris/bin/mri$ cat >>>>>>>>>>>>>>>>>>> /data/loris/data//logs/TarLoad-14-58-9Xog7H.log >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> ==> Loading file from disk >>>>>>>>>>>>>>>>>>> /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> --> mapping DICOM parameter for >>>>>>>>>>>>>>>>>>> /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> --> using user-defined filterParameters for >>>>>>>>>>>>>>>>>>> /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Candidate Mismatch Error is Visit label does not exist >>>>>>>>>>>>>>>>>>> -> WARNING: This candidate was invalid. Logging to >>>>>>>>>>>>>>>>>>> MRICandidateErrors table with reason Visit >>>>>>>>>>>>>>>>>>> label does not exist >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> ???? ???, 26 ???? 2019 ???? 3:02 ?.?., ?/? Sotirios >>>>>>>>>>>>>>>>>>> Nikoloutsopoulos ??????: >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Hi Cecile, >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> The Center error was fixed. Still the insertion of >>>>>>>>>>>>>>>>>>>> mincs fails. Please see the output.txt file i attached. Also is there >>>>>>>>>>>>>>>>>>>> something else i need to change at the paths configuration? >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> ???? ???, 25 ???? 2019 ???? 6:55 ?.?., ?/? Cecile >>>>>>>>>>>>>>>>>>>> Madjar ??????: >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> We are making progress! >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> I have a feeling this error comes from the fact that >>>>>>>>>>>>>>>>>>>>> your psc table does not have the MRI_alias populated for the DCC site. >>>>>>>>>>>>>>>>>>>>> Running the following query in the mysql database should fix this: >>>>>>>>>>>>>>>>>>>>> UPDATE psc SET MRI_alias="DCC", Alias="DCC" WHERE >>>>>>>>>>>>>>>>>>>>> Name="Data Coordinating Center"; >>>>>>>>>>>>>>>>>>>>> Repeat the same with all your sites (make sure to >>>>>>>>>>>>>>>>>>>>> change the Aliases between sites, they should all be unique). >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> Let me know how it goes! >>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> On Thu, Jul 25, 2019 at 11:43 AM Sotirios >>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos wrote: >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> Dear Cecile, >>>>>>>>>>>>>>>>>>>>>> You were right about your guesses. I did the >>>>>>>>>>>>>>>>>>>>>> modifications you suggested, i still get the "no mincs inserted" error, now >>>>>>>>>>>>>>>>>>>>>> i am getting the "No center found this candidate" error ( how do i fix >>>>>>>>>>>>>>>>>>>>>> that? from what i see the .dcm files contains a 'Institution Name', is that >>>>>>>>>>>>>>>>>>>>>> the center? ), so i guess that's why the validation fails, but i changed >>>>>>>>>>>>>>>>>>>>>> the force variable of tarchiveLoader to 1, shouldn't it have inserted the >>>>>>>>>>>>>>>>>>>>>> mincs then? Also it is optional to have a mail server, right? ( from what i >>>>>>>>>>>>>>>>>>>>>> see the mail error does not affect the $valid_study, so i assume we are >>>>>>>>>>>>>>>>>>>>>> okay with that ) >>>>>>>>>>>>>>>>>>>>>> Thank you a lot, >>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> ???? ???, 25 ???? 2019 ???? 5:48 ?.?., ?/? Cecile >>>>>>>>>>>>>>>>>>>>>> Madjar ??????: >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> From what I understand, I believe you just need to >>>>>>>>>>>>>>>>>>>>>>> update a few config settings from the frontend in the Config module (under >>>>>>>>>>>>>>>>>>>>>>> the Admin menu). >>>>>>>>>>>>>>>>>>>>>>> [image: Screen Shot 2019-07-25 at 10.31.35 AM.png] >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> Then go to the Paths section of the config module >>>>>>>>>>>>>>>>>>>>>>> and update the "LORIS-MRI code" config setting to /data/loris/bin/mri (my >>>>>>>>>>>>>>>>>>>>>>> guess is that currently, it is set to /data/LORIS/data) and click on the >>>>>>>>>>>>>>>>>>>>>>> submit button. >>>>>>>>>>>>>>>>>>>>>>> [image: Screen Shot 2019-07-25 at 10.32.50 AM.png] >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> Then, go to Imaging Pipeline section of the >>>>>>>>>>>>>>>>>>>>>>> Configuration module and update the "Loris-MRI Data Directory" to >>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/ (my guess is that it is empty at the moment in your >>>>>>>>>>>>>>>>>>>>>>> database which is why $data_dir is not defined when you run the >>>>>>>>>>>>>>>>>>>>>>> tarchiveLoader step of the insertion pipeline). >>>>>>>>>>>>>>>>>>>>>>> [image: Screen Shot 2019-07-25 at 10.40.52 AM.png] >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> Finally, I took a look at your environment file and >>>>>>>>>>>>>>>>>>>>>>> it might be a good idea to update your PERL5LIB variable to the following >>>>>>>>>>>>>>>>>>>>>>> (it has been added to the code a few releases ago as we realized this was >>>>>>>>>>>>>>>>>>>>>>> needed for the libraries. Not sure which version of LORIS-MRI you are using >>>>>>>>>>>>>>>>>>>>>>> but it does not hurt to update this variable to what I suggest below): >>>>>>>>>>>>>>>>>>>>>>> export >>>>>>>>>>>>>>>>>>>>>>> PERL5LIB=/data/loris/bin/mri/uploadNeuroDB:/data/loris/bin/mri/dicom-archive:$PERL5LIB >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> Hope this helps. Sorry you are experiencing so much >>>>>>>>>>>>>>>>>>>>>>> trouble setting things up. We probably need to update our WIKI. >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> On Thu, Jul 25, 2019 at 9:48 AM Sotirios >>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos wrote: >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> The "Loris-MRI Data Directory" should be in the >>>>>>>>>>>>>>>>>>>>>>>> environment file? >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 25 ???? 2019 ???? 12:59 ?.?., ?/? >>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos >>>>>>>>>>>>>>>>>>>>>>>> ??????: >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> The scripts are located in /data/loris/bin/mri/. >>>>>>>>>>>>>>>>>>>>>>>>> Somewhere I might have messed something up but i remember following the >>>>>>>>>>>>>>>>>>>>>>>>> instructions in the wiki.For example when i tried to execute the >>>>>>>>>>>>>>>>>>>>>>>>> batch_uploads_imageuploader perl script the line >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> my $command = "$bin_dir/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl " >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> was pointing to an invalid path, for example: it >>>>>>>>>>>>>>>>>>>>>>>>> was repeating a pattern and had LORIS instead of loris ( i think the >>>>>>>>>>>>>>>>>>>>>>>>> mistake was that in the wiki it suggested to use $PROJECT for the name of >>>>>>>>>>>>>>>>>>>>>>>>> the folder and i choosed 'loris' >>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris/wiki/Imaging-Database >>>>>>>>>>>>>>>>>>>>>>>>> ). See also the in image for the modification i did. Also i didn't find the >>>>>>>>>>>>>>>>>>>>>>>>> section to config the $data_dir variable. >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 24 ???? 2019 ???? 6:05 ?.?., ?/? Cecile >>>>>>>>>>>>>>>>>>>>>>>>> Madjar ??????: >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> It looks like you have one Config setting not set >>>>>>>>>>>>>>>>>>>>>>>>>> (based on the first error message you got when running it the first time). >>>>>>>>>>>>>>>>>>>>>>>>>> You need to set a value for "Loris-MRI Data Directory" in the Config module >>>>>>>>>>>>>>>>>>>>>>>>>> under the Imaging pipeline section (from what I can see, it would be >>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/ for your setup). >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> The reason you got that error message the second >>>>>>>>>>>>>>>>>>>>>>>>>> time is that the pipeline checks if the DICOM study was already inserted in >>>>>>>>>>>>>>>>>>>>>>>>>> the tarchive table. Since you ran the study once already, the study is >>>>>>>>>>>>>>>>>>>>>>>>>> inserted into the tarchive, hence the message. However, the pipeline did >>>>>>>>>>>>>>>>>>>>>>>>>> not complete as the MINC files were not created and inserted into the >>>>>>>>>>>>>>>>>>>>>>>>>> files/parameter_file table. In order to continue the insertion, you will >>>>>>>>>>>>>>>>>>>>>>>>>> then need to run the tarchiveLoader command suggested in the terminal >>>>>>>>>>>>>>>>>>>>>>>>>> during the second run: >>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader >>>>>>>>>>>>>>>>>>>>>>>>>> -globLocation -profile prod >>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive//2012/DCM_2012-12-05_ImagingUpload-17-43-ZUEFjb.tar >>>>>>>>>>>>>>>>>>>>>>>>>> -verbose >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> Finally, I am a bit confused by your setup. Where >>>>>>>>>>>>>>>>>>>>>>>>>> are the scripts located? In /data/loris/bin/mri or /data/loris/data? It >>>>>>>>>>>>>>>>>>>>>>>>>> feels like the Config setting "LORIS-MRI code" in the Paths section was set >>>>>>>>>>>>>>>>>>>>>>>>>> to "/data/LORIS/data" but it should have been set to the directory where >>>>>>>>>>>>>>>>>>>>>>>>>> the scripts are located (most probably /data/loris/bin/mri). >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helps, >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> On Wed, Jul 24, 2019 at 10:55 AM Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos wrote: >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> Ok first i execute this command: >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> "lorisadmin at hbp:/data/loris/bin/mri$ >>>>>>>>>>>>>>>>>>>>>>>>>>> ./batch_uploads_imageuploader -profile prod < ~/Desktop/input.txt > log.txt >>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at ./batch_uploads_imageuploader line 143. >>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at ./batch_uploads_imageuploader line 143. >>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $_ in pattern match >>>>>>>>>>>>>>>>>>>>>>>>>>> (m//) at ./batch_uploads_imageuploader line 147. >>>>>>>>>>>>>>>>>>>>>>>>>>> base is DCC0000_258024_V01 >>>>>>>>>>>>>>>>>>>>>>>>>>> path is /data/incoming/ >>>>>>>>>>>>>>>>>>>>>>>>>>> type is .tar.gz >>>>>>>>>>>>>>>>>>>>>>>>>>> fullpath is >>>>>>>>>>>>>>>>>>>>>>>>>>> /data/incoming/DCC0000_258024_V01.tar.gz >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> source /tmp/ImagingUpload-17-43-ZUEFjb >>>>>>>>>>>>>>>>>>>>>>>>>>> targetlocation /data/loris/data/tarchive >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 256. >>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 284. >>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at /data/loris/bin/mri/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>> tarchive_validation.pl line 219. >>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at /data/loris/bin/mri/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl line 270. >>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 711. >>>>>>>>>>>>>>>>>>>>>>>>>>> Can't exec "mail": No such file or directory at >>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 721. >>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 722. >>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 723. >>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 724. >>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 724. >>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 725. >>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 735. >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> No Mincs inserted >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> The tarchiveLoader insertion script has failed. >>>>>>>>>>>>>>>>>>>>>>>>>>> Running now the following command: >>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl -profile prod -upload_id >>>>>>>>>>>>>>>>>>>>>>>>>>> 3 /data/incoming/DCC0000_258024_V01.tar.gz -verbose" >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> I inserted the VisitLabel, but still the Mincs >>>>>>>>>>>>>>>>>>>>>>>>>>> are not inserted and i am getting this error >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> "lorisadmin at hbp:/data/loris/bin/mri$ >>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl -profile prod -upload_id >>>>>>>>>>>>>>>>>>>>>>>>>>> 3 /data/incoming/DCC0000_258024_V01.tar.gz -verbose >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> find -path \/tmp\/ImagingUpload\-17\-45\-5MsWEd >>>>>>>>>>>>>>>>>>>>>>>>>>> -name '__MACOSX' -delete >>>>>>>>>>>>>>>>>>>>>>>>>>> Spool message is: >>>>>>>>>>>>>>>>>>>>>>>>>>> The Scan for the uploadID 3 has already been run >>>>>>>>>>>>>>>>>>>>>>>>>>> with tarchiveID: 7. >>>>>>>>>>>>>>>>>>>>>>>>>>> To continue with the rest of the insertion >>>>>>>>>>>>>>>>>>>>>>>>>>> pipeline, please run tarchiveLoader from a terminal as follows: >>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader -globLocation -profile prod >>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive//2012/DCM_2012-12-05_ImagingUpload-17-43-ZUEFjb.tar >>>>>>>>>>>>>>>>>>>>>>>>>>> -verbose" >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> Which files should i delete? I thought that >>>>>>>>>>>>>>>>>>>>>>>>>>> deleting the files from the tarchive was enough. And i executed the last >>>>>>>>>>>>>>>>>>>>>>>>>>> proposed command to continue to rest of the insertion pipeline ( check the >>>>>>>>>>>>>>>>>>>>>>>>>>> image ). >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 24 ???? 2019 ???? 5:05 ?.?., ?/? >>>>>>>>>>>>>>>>>>>>>>>>>>> Cecile Madjar ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> Sorry I was not clear before. Every visits of >>>>>>>>>>>>>>>>>>>>>>>>>>>> candidates are created in the session table with one entry per >>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID/VisitLabel. So if the imaging pipeline created visits in the session >>>>>>>>>>>>>>>>>>>>>>>>>>>> table (that are not attached to instruments) and you want to clean your >>>>>>>>>>>>>>>>>>>>>>>>>>>> database completely, you can delete entries in that table as well. >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> Regarding your point 2, the imaging pipeline >>>>>>>>>>>>>>>>>>>>>>>>>>>> can create the visit in the session table as long as the visit label is >>>>>>>>>>>>>>>>>>>>>>>>>>>> present in the Visit_Windows table (which means the visit label stored in >>>>>>>>>>>>>>>>>>>>>>>>>>>> the PatientName is a valid visit label). >>>>>>>>>>>>>>>>>>>>>>>>>>>> However, in your prod file, if the >>>>>>>>>>>>>>>>>>>>>>>>>>>> variable $subjectID{'createVisitLabel'} is set to 1 for candidates, the >>>>>>>>>>>>>>>>>>>>>>>>>>>> visit label should be created in the Visit_Windows table I believe. Here >>>>>>>>>>>>>>>>>>>>>>>>>>>> is the line of the prod file you would need to change >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> . >>>>>>>>>>>>>>>>>>>>>>>>>>>> In general, we prefer populating the >>>>>>>>>>>>>>>>>>>>>>>>>>>> Visit_Windows table and set the $subjectID{'createVisitLabel'} to 0 for >>>>>>>>>>>>>>>>>>>>>>>>>>>> candidate data to avoid insertion of badly labelled MRI data that are >>>>>>>>>>>>>>>>>>>>>>>>>>>> complex to relabel. >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> Finally, regarding the candidate creation, if >>>>>>>>>>>>>>>>>>>>>>>>>>>> you execute the following steps, the pipeline should be able to create >>>>>>>>>>>>>>>>>>>>>>>>>>>> candidates: >>>>>>>>>>>>>>>>>>>>>>>>>>>> - set in the Imaging Pipeline section of the >>>>>>>>>>>>>>>>>>>>>>>>>>>> config module the config setting "Upload creation of candidates" to Yes >>>>>>>>>>>>>>>>>>>>>>>>>>>> - manually transfer the scans to the LORIS >>>>>>>>>>>>>>>>>>>>>>>>>>>> server instead of uploading it via the imaging browser >>>>>>>>>>>>>>>>>>>>>>>>>>>> - run batch_imaging_upload.pl as you did until >>>>>>>>>>>>>>>>>>>>>>>>>>>> now. >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helps! >>>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> On Wed, Jul 24, 2019 at 8:47 AM Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos wrote: >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> About my second question i replaced the name >>>>>>>>>>>>>>>>>>>>>>>>>>>>> of the patient in the .dcm files and now i am getting an error that the >>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit label does not exist. >>>>>>>>>>>>>>>>>>>>>>>>>>>>> I thought it was supposed to be automatically >>>>>>>>>>>>>>>>>>>>>>>>>>>>> created. >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> "Done adding archive info into database >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader >>>>>>>>>>>>>>>>>>>>>>>>>>>>> -globLocation -profile prod >>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive//DCM_2012-12-05_ImagingUpload-15-42-yUwQQV.tar >>>>>>>>>>>>>>>>>>>>>>>>>>>>> -verbose >>>>>>>>>>>>>>>>>>>>>>>>>>>>> md5sum >>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive/DCM_2012-12-05_ImagingUpload-15-42-yUwQQV.tar >>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>> candidate id 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> => No Visit labelVisit label does not exist >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Set centerID = 1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Number of MINC files that will be considered >>>>>>>>>>>>>>>>>>>>>>>>>>>>> for inserting into the database: 1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> log dir is /logs and log file is >>>>>>>>>>>>>>>>>>>>>>>>>>>>> /logs/TarLoad-15-42-L6pocU.log >>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>> candidate id 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> => No Visit label >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Cleaning up temp files: rm -rf >>>>>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-15-42-J2rQms/ImagingUpload-15-42-yUwQQV*" >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 24 ???? 2019 ???? 3:38 ?.?., ?/? >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 1) What are the records in the session table? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 2) I tried to upload a non-phantom file like >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> this >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> input_file.txt: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/incoming/DCC0000_258024_V1.tar.gz N >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DCC0000_258024_V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Terminal: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ./batch_uploads_imageuploader -profile prod >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> < ~/Desktop/input.txt > log.txt >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and i get the following error in the log.txt >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> file >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> "Running now the following command: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl -profile prod >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -upload_id 7 /data/incoming/DCC0000_258024_V1.tar.gz -verbose >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> find -path >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> \/tmp\/ImagingUpload\-14\-56\-FeLCB4 -name '__MACOSX' -delete >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Spool message is: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The PatientName read from the DICOM header >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> does not start with DCC0000_258024_V1 from the mri_upload table >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> " >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and the spool message is repeated for each >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> .dcm file. Should i preprocess every .dcm file and change the PatientName >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> to "DCC0000_258024_V1"? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 3) As far as it concerns the candidate >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> profile i have to create a new one each time before i try to upload a file? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Is there already a way to create a candidate profile and get the DCCID and >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID without the user interface? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 18 ???? 2019 ???? 5:00 ?.?., ?/? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Cecile Madjar ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> See answers to your questions below. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> About the 1st case we had a dicom with a >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> blank studyUID, maybe someone accidentally removed it. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> That is strange. Something must have been >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> done to the DICOM files. I have never seen a study with no StudyUID out of >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the scanner. Usually, you need to manually erase it with some tool. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> However, DICOMs never cease to surprise me... >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Some other questions: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 1) What are the steps to remove all of my >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> patients and uploads?: because i want to try to reupload all the testing >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> dicoms we had with a clean database. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Release 21.0 of LORIS-MRI will offer a >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> script to remove all the entries and files specific to an upload. However, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> this release is not yet out. Hopefully in the next few weeks. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> In the meantime, since your case is >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> particular and that you just want to start with a clean database, the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> following deletes should work (hopefully I won't forget any tables): >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from mri_violations_log; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from mri_protocol_violated_scans; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from MRICandidateErrors; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from parameter_file; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from files_qcstatus; # (if you played >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> with the QC part of the imaging browser for testing) >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from feedback_mri_comments; # (if you >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> played with the QC part of the imaging browser for testing) >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from tarchive_series; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from tarchive_files; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from mri_upload; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from tarchive; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from mri_scanner; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from candidate where PSCID="scanner"; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I don't know if you want to also delete >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> entries in the session and candidate table too? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 2) We do not need to create the profile of a >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> patient ( are the patients stored in the candidate table? because i can't >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> see the ghosts ), because will it automatically be created when importing a >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> dicom? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I am not sure I understand fully this >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> question. All candidates are stored in the candidate table. The phantom >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> scans however are attached to a scanner candidate depending on where the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> scan happened. It is a bit of a weird concept that we have to redesign >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> eventually but never got a chance to get to it. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hopefully this answered your question, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> otherwise, don't hesitate to let me know. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 3) What is the difference between uploading >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> a dicom as phantom instead of importing as PSCCID_DCCID_VisitLabel? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> When you upload the scan as >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID_DCCID_VisitLabel, there is a check that makes sure the candidate IDs >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and visit label are valid at the time of upload. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> When you upload a scan as phantom, it >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> expects that the DICOM field PatientName and uploaded filename contains the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> string "phantom". We enforced this behaviour on the imaging uploader side >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in recent releases but I can't remember which one. Probably the upcoming >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 21.0 release. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> All those verifications might seem >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> cumbersome but they are here to ensure that the files inserted are all >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> valid and labelled properly as it is a bit messy to have to delete files >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> that were wrongly labelled. At least, the delete script present in release >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 21.0 will make this process easier but it is still good practice to verify >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> those things. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> With pleasure. Hopefully the answers to your >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> questions will be helpful. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PS: loris-dev mailing list: you will find >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the initial answer I gave Sotirios below. I forgot to cc the loris-dev in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> my earlier reply... >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 16 ???? 2019 ???? 12:02 ?.?., ?/? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Cecile Madjar >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Dear Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you for reaching out. Since your >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> email was already organized in points, I will reply directly below your >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> questions below. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 1) What do we do when the StudyUID is >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> blank on the header? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/minor/docs/AppendixA-Troubleshooting_guideline.md >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> There solution provided at the table 3 does not guide us how to find the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> information ( is possible ). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The StudyUID is the field used in our >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> pipeline at the moment to check whether a DICOM study was already inserted >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> into LORIS with that same StudyUID since it is supposed to be unique for >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> every single study. Currently, we do not support insertion of DICOM studies >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> if they do not have a StudyUID associated with them. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Is there a specific reason why the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> StudyUID is blank in the DICOM headers in your DICOM files? Did they go >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> through some processes before upload to LORIS? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 2) When i am about to upload a non-phanton >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> case i need a 'Visit Label'. Is there already a script that can create a >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> new visit label for a specific Candidate, so i can provide it as input >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> afterwards to the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> batch_uploads_imageuploader ( See option 5.1.3 https://github.com/aces/Loris-MRI/blob/minor/docs/05-PipelineLaunchOptions.md ) >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I am not sure if the front-end allows for >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> it but if you use batch_uploads_imageuploader, the insertion scripts could >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> create the visit label for you. However, it does need to be included in the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> patient name in order for the script to know which label it should use. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> For example: you upload V02 for MTL0123 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> (DCCID: 456789) but V02 was not yet created for MTL0123; the insertion >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> scripts will create a V02 visit for MTL0123 if the PatientName field for >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the dataset is MTL0123_456789_V02 with Stage marked as "Not Started". >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> However, *note that for the script to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> create the visit for the candidate, you have to make sure that all the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit label of your projects were inserted in the Visit_Windows table* >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> (otherwise, the visit will never be created as they were not specified as >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> being part of the list of visit label to expect). So in the example above, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> you should have one row in Visit_Windows with Visit_label="V02" set. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 3) Section 4.3 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/minor/docs/04-Scripts.md >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> What do we do when the folder contains multiple mnc files? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> This is a case by case. Most of the time, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the MINC files that failed insertion into the imaging browser end up in the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> MRI violation module where you can see what went wrong with the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> acquisitions not inserted. If you notice that the MINC file should be >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> inserted as a specific protocol, you can force the insertion as explained >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in section 4.3. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> In your case, I have a feeling that you >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> want to be able to insert MINC files that did not go through the whole >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> pipeline insertion (DICOM archival, then dcm2mnc, then protocol >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> identification, then insertion...). In theory, you could call >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl on any MINC file, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> provided you have at least the following information: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - path to the MINC file >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - uploadID associated with the MINC files >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> or DICOM archive path from which those MINC files were created from >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Then the minc_insertion.pl script will do >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the subject information and protocol validation etc... >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> If all the MINC files come from the same >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> uploadID or TarchiveID, then you could run a loop in bash calling the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl script like this for >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> files deriving from uploadID=1: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ls /path/to/mnc/folder/* | while read f; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> do minc_insertion.pl -profile prod >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -uploadID 1 -mincPath $f; done >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helped! >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> -- >>>>>>>>>>>>>> >>>>>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> -- >>>>>>>>>>>> >>>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>>> >>>>>>>>>>> _______________________________________________ >>>>>>>>>> Loris-dev mailing list >>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> -- >>>>>>>>> >>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>> Montreal Neurological Institute >>>>>>>>> McGill University | Montreal | Canada >>>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> Loris-dev mailing list >>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>> >>>>>>> >>>>>>> >>>>>>> -- >>>>>>> >>>>>>> christine.rogers at mcgill.ca >>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>> Montreal Neurological Institute >>>>>>> McGill University | Montreal | Canada >>>>>>> _______________________________________________ >>>>>>> Loris-dev mailing list >>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>> >>>>>> >>>>>> >>>>>> -- >>>>>> >>>>>> christine.rogers at mcgill.ca >>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>> Montreal Neurological Institute >>>>>> McGill University | Montreal | Canada >>>>>> _______________________________________________ >>>>>> Loris-dev mailing list >>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>> >>>>> >>>>> >>>>> -- >>>>> >>>>> christine.rogers at mcgill.ca >>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>> Montreal Neurological Institute >>>>> McGill University | Montreal | Canada >>>>> >>>> _______________________________________________ >>>> Loris-dev mailing list >>>> Loris-dev at bic.mni.mcgill.ca >>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>> >>> >>> >>> -- >>> >>> christine.rogers at mcgill.ca >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>> Montreal Neurological Institute >>> McGill University | Montreal | Canada >>> >> _______________________________________________ >> Loris-dev mailing list >> Loris-dev at bic.mni.mcgill.ca >> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From christine.rogers at mcgill.ca Mon Aug 12 15:19:49 2019 From: christine.rogers at mcgill.ca (Christine Rogers, Ms.) Date: Mon, 12 Aug 2019 19:19:49 +0000 Subject: [Loris-dev] Upgrading to Loris 21 - new make file In-Reply-To: References: Message-ID: Hi Sotirios, We've seen some users installing LORIS 21 or upgrading to 21 whose version of node doesn't work well with webpack, due to updated packages they're missing. If so, update your node : curl -sL https://deb.nodesource.com/setup_8.x | sudo -E bash - sudo apt-get install -y nodejs Let us know how that goes -- please send us output from the same log if any issues. Best, Christine On Thu, Aug 8, 2019 at 2:38 PM Sotirios Nikoloutsopoulos > wrote: It's not a disk space issue, as you can see below i have still 74GB available. lorisadmin at hbp:/var/www/loris$ df -h Filesystem Size Used Avail Use% Mounted on udev 2,9G 0 2,9G 0% /dev tmpfs 597M 8,6M 588M 2% /run /dev/sda1 98G 19G 74G 21% / Maybe we have to pass a flag to get into strict mode? as stated "SyntaxError: Block-scoped declarations (let, const, function, class) not yet supported outside strict mode" Thanks, Sotirios ???? ???, 8 ??? 2019 ???? 4:32 ?.?., ?/? Dave MacFarlane > ??????: It looks like the javascript snippet shown in the error message when trying to compile the js is truncated. Have you run out of disk space? On Thu, Aug 8, 2019 at 8:37 AM Sotirios Nikoloutsopoulos > wrote: Hi, I runned make and also included the file it reports at the end. lorisadmin at hbp:/var/www/loris$ make npm install npm WARN optional Skipping failed optional dependency /chokidar/fsevents: npm WARN notsup Not compatible with your operating system or architecture: fsevents at 1.2.9 npm WARN optional Skipping failed optional dependency /watchpack/chokidar/fsevents: npm WARN notsup Not compatible with your operating system or architecture: fsevents at 1.2.9 npm run compile > loris at 1.0.0 compile /var/www/loris > webpack /var/www/loris/node_modules/webpack/bin/webpack.js:86 let notify = ^^^ SyntaxError: Block-scoped declarations (let, const, function, class) not yet supported outside strict mode at exports.runInThisContext (vm.js:53:16) at Module._compile (module.js:374:25) at Object.Module._extensions..js (module.js:417:10) at Module.load (module.js:344:32) at Function.Module._load (module.js:301:12) at Function.Module.runMain (module.js:442:10) at startup (node.js:136:18) at node.js:966:3 npm ERR! Linux 4.15.0-55-generic npm ERR! argv "/usr/bin/nodejs" "/usr/bin/npm" "run" "compile" npm ERR! node v4.2.6 npm ERR! npm v3.5.2 npm ERR! code ELIFECYCLE npm ERR! loris at 1.0.0 compile: `webpack` npm ERR! Exit status 1 npm ERR! npm ERR! Failed at the loris at 1.0.0 compile script 'webpack'. npm ERR! Make sure you have the latest version of node.js and npm installed. npm ERR! If you do, this is most likely a problem with the loris package, npm ERR! not with npm itself. npm ERR! Tell the author that this fails on your system: npm ERR! webpack npm ERR! You can get information on how to open an issue for this project with: npm ERR! npm bugs loris npm ERR! Or if that isn't available, you can get their info via: npm ERR! npm owner ls loris npm ERR! There is likely additional logging output above. npm ERR! Please include the following file with any support request: npm ERR! /var/www/loris/npm-debug.log Makefile:14: recipe for target 'javascript' failed make: *** [javascript] Error 1 Thanks, Sotirios ???? ???, 7 ??? 2019 ???? 5:41 ?.?., ?/? Christine Rogers, Ms. > ??????: Hi Sotirios, Thanks, have you tried all of these steps? - clear your browser cache (and refresh a few times) - delete any files in your smarty/templates_c directory (this will clear the template cache - do Not touch smarty/templates/) - run `make` (per the 21 release notes, this replaces the composer commands used in previous releases to update your dependencies) - restart apache (doesn't hurt) Let us know how it goes -- let us know what difference you see after, with your logs. A lso please send us your Config path settings (see these Troubleshooting Queries) if you're still seeing front-end issues. Thanks, Christine On Wed, Aug 7, 2019 at 8:02 AM Sotirios Nikoloutsopoulos > wrote: Hi, lorisadmin at hbp:/var/www/loris$ sudo cat /var/log/apache2/error.log [Wed Aug 07 07:35:02.422501 2019] [mpm_prefork:notice] [pid 1267] AH00163: Apache/2.4.18 (Ubuntu) OpenSSL/1.0.2g configured -- resuming normal operations [Wed Aug 07 07:35:02.422514 2019] [core:notice] [pid 1267] AH00094: Command line: '/usr/sbin/apache2' And as for the access.log the content are empty lorisadmin at hbp:/var/www/loris$ sudo ls -l /var/log/apache2/access.log lorisadmin at hbp:/var/www/loris$ sudo ls -l /var/log/apache2/access.log -rw-r----- 1 root adm 0 ???? 28 14:09 /var/log/apache2/access.log Also i noticed a loris_access.log. The only non-blank pages are: mri_violations, dataquery does not exist at all, statistics, data_team_helper, genomic_browser, configuration and server_processes_manager/ prints "Required configuration settings for Server Processes Manager are missing. Cannot continue." Thanks, Sotirios ???? ???, 6 ??? 2019 ???? 10:13 ?.?., ?/? Christine Rogers, Ms. > ??????: Hi Sotirios and LORIS community -- When upgrading to brand-new release 21 -- just a reminder to follow the release notes and run the new make file to update your dependencies (instead of using composer commands). We've also updated the Wiki page to clarify that the release notes for each version will tell you what to run. If your current version is not the last release (20.3), it's still important to upgrade to each minor release increment (e.g. 20.2, 20.3) before making the leap to 21.0. If you're getting blank pages, post-upgrade -- Try clearing your cache. Got questions or feedback e.g. on the Release Notes? please don't hesitate to let us know. Thanks, Christine The LORIS team On Tue, Aug 6, 2019 at 10:09 AM Christine Rogers, Ms. > wrote: Hi Sotirios, Could you also let us know -- on which pages is content visible, and on which pages/modules is content not visible for you? Thanks, Christine On Tue, Aug 6, 2019 at 9:54 AM Christine Rogers, Ms. > wrote: Thanks Sotirios, That's good to know. It sounds like you've checked that your /var/www/loris/project/config.xml file get populated properly. Please send us the last few errors you're seeing in your apache error log file, and your config paths and we can see what's happening with your front end -- Run these Troubleshooting Queries to get your config path settings, given your front end is not displaying fully. The Loris-MRI repo 21 install/upgrade would then be your next steps. Best, Christine On Tue, Aug 6, 2019 at 7:53 AM Sotirios Nikoloutsopoulos > wrote: I am using a VM. What i did was: 1) Download the files from https://github.com/aces/Loris and replace them to my existing /vaw/www/loris folder. 2) Execute the composer install --no-dev and then composer dump-autoload as mentioned here https://github.com/aces/Loris/wiki/Updating-your-LORIS. 3) Execute install.sh from /var/www/loris/tools and because LORIS already existed i moved a .config file, then re-executed the install.sh successfully 4 ) As for the database, i dropped the schema and i executed the installdb.php ???? ???, 5 ??? 2019 ???? 5:22 ?.?., ?/? Christine Rogers, Ms. > ??????: Hi Sotorios, Thanks - when you re-installed did you start on a fresh root path / VM or might some of your old system setting still apply? (And if you did any steps similar to an upgrade, did you follow the Upgrade steps in the Release Notes, from both repos?) About the TR_range column - it was recently split (MRI pr339) split into TR_min and _max columns. Given the code was trying to query TR_range which does not exist in your mri_protocol table, double-check which version of the Loris repo (tables) and the Loris-MRI repo (code) you have installed to ensure they match. Christine On Mon, Aug 5, 2019 at 9:06 AM Sotirios Nikoloutsopoulos > wrote: I reinstalled LORIS to 21 version and now the content is not visible at all at most pages. [image.png] ???? ???, 5 ??? 2019 ???? 3:19 ?.?., ?/? Sotirios Nikoloutsopoulos > ??????: Hi, Is it easy to upgrade to Loris 21? Also the following fails because the line 1985 of NeuroDB/MRIProcessingUtility.pm query mri_protocol which doesn't have TR_range https://github.com/aces/Loris/blob/21.0-release/SQL/0000-00-00-schema.sql#L556 [image.png] lorisadmin at hbp:/data/loris/bin/mri$ ./batch_uploads_imageuploader -profile prod < ~/Desktop/input.txt > log.txt Use of uninitialized value $_ in pattern match (m//) at ./batch_uploads_imageuploader line 147. base is DCC0000_258024_V1 path is /data/incoming/ type is .tar.gz fullpath is /data/incoming/DCC0000_258024_V1.tar.gz DBD::mysql::st execute failed: Unknown column 'TR_range' in 'where clause' at /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line 1985. DBD::mysql::st fetchrow_array failed: fetch() without execute() at /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line 1986. Use of uninitialized value $count_mri_protocol in numeric gt (>) at /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line 1995. DBD::mysql::st execute failed: Unknown column 'TR_range' in 'field list' at /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 562. Can't exec "mail": No such file or directory at /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 721. print() on closed filehandle MAIL at /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 722. print() on closed filehandle MAIL at /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 723. print() on closed filehandle MAIL at /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 724. print() on closed filehandle MAIL at /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 725. No Mincs inserted Thanks, Sotirios ???? ???, 3 ??? 2019 ???? 1:08 ?.?., ?/? Christine Rogers, Ms. > ??????: Hi Sotirios, First, just a note: we've released LORIS 21 this week with some major new features and cleanup -- especially if you are early in your setup phase, check out the Release notes for both the LORIS and Loris-MRI repos. Thanks for your screenshots -- your empty mri_protocol table should be at the root of these issues : The mri_protocol table must be populated in order for your scans to be registered in LORIS -- it serves as a whitelist for the insertion pipeline which filters out scans that aren't identified or matched to scan types in this table. By default, this table is populated with entries for t1, t2, fMRI and DTI (Insert statements for 21 release branch are here) Feel free to restore our default records and broaden their parameters to match all your scan types. re Defaced, native, selected -- these filter the scans displayed as you move to the next page (View Session), instead of viewing "all types" of scans from a given session : * "defaced" means that a defacing script has masked the subject's face in the volume (for patient privacy) * "native" means that no pre-processing has been performed on the scan (it's raw data), * "selected" will show only volumes that have been QC'd and "selected" as the best of their type -- used to display only the best quality T1 image instead of all T1s acquired in a session, e.g. re QC Comments -- Once you have successfully loaded scans (matched to the mri_protocol table), you'll be able to use the Imaging Browser's View Session subpage to enter/view QC comments on each volume, or for each visit. These are stored directly in the database, and linked to each scan. (Table name: feedback_mri_comments) (Visit-level QC comments are linked to the session.) For a walkthrough of the Imaging setup - please see the Imaging Setup guide - An old LORIS walkthrough video can also walk you through some of the Imaging front-end features, starting at 8:00 LORIS' imaging modules have been updated many times since this video, but the functionality and workflow is similar. Let us know how it goes once you have entries in your mri_protocol table - Best, Christine On Fri, Aug 2, 2019 at 7:58 AM Sotirios Nikoloutsopoulos > wrote: Hi Christine, In the candidate_list page i can see this patient [image.png] If i press the link under PSCID i get to see [image.png] and if i press the link under Scan Done it redirects me to imaging_browser [image.png] At the mri_violations page i also see No results ( neither on resolved / not resolved ). At the imaging_uploader i can see the record that failed. [image.png] If i click on the tarchive info i get to see the Protocol Name which i think is the acquisition we wanted? [image.png] Also my mri_protocol table is empty. Furthermore i would like to ask about the defaced, native, selected. What exactly is native and selected? And where are the qc comments stored? [image.png] Finally a walkthrough would be helpful. Thanks, Sotirios ???? ???, 30 ???? 2019 ???? 8:29 ?.?., ?/? Christine Rogers, Ms. > ??????: Hi Sotirios, Glad to hear you're making progress with the visit labels. To follow up on your last few emails: a- The Wiki's Setup Guide contains Sample insert statements for the Visit Windows table. As Cecile mentioned, the consistency of visit label format is important: V01, v01, V1, 01 -- whichever you select to use is fine; we use V01 by default across all documentation. b- For Password reset, there is a script in the tools/ directory so that a back-end administrator can reset any front-end user password, including Admin. (See info on setting up / resetting User passwords in the Wiki's Setup Guide) c- The minc file not being registered -- due to AcquisitionProtocol unknown. This means the SeriesDescription (Acquisition Protocol) in you Dicom header was not matched to any scan listed in the mri_protocol database table. (In the online Loris-MRI Troubleshooting Guide, this is Table 3, 2nd-last item "no MINCs inserted"). The MRI Violations module (Readme here) will show you the details of this mismatch -- Go to the module (under the Imaging menu), find your scan and click the link "Could not identify scan type" -- in the next subpage you can compare the scan's actual parameters against the mri_protocol table. To resolve this, adjust your mri_protocol table values or perhaps ensure your DICOMs are labelled consistently. Let us know if this works for you -- we can also walk you through an example of non-identified scans on Demo.loris.ca (MRI Violations module). Best, Christine The LORIS team On Tue, Jul 30, 2019 at 10:47 AM Sotirios Nikoloutsopoulos > wrote: I hope this is sufficient as the error for the visit label disappeared. [image.png] Please see the attached file. Also something i found. lorisadmin at hbp:/data/loris/bin/mri$ cat /data/loris/data//logs/TarLoad-17-39-xubBdv.log ==> Loading file from disk /tmp/TarLoad-17-39-UyQcG2/dcc0000_258024_v1_20121205_102108_501e1_mri.mnc --> mapping DICOM parameter for /tmp/TarLoad-17-39-UyQcG2/dcc0000_258024_v1_20121205_102108_501e1_mri.mnc ==> computing md5 hash for MINC body. --> md5: 6b1202fd63e29de4c9be1cd9925888a5 ==> verifying acquisition protocol Acquisition protocol is unknown --> The minc file cannot be registered since the AcquisitionProtocol is unknown ???? ???, 30 ???? 2019 ???? 4:58 ?.?., ?/? Sotirios Nikoloutsopoulos > ??????: Ok I fixed the login problem by using a known hash and by deleting the rows from the login_history i was able to login. ???? ???, 30 ???? 2019 ???? 4:50 ?.?., ?/? Sotirios Nikoloutsopoulos > ??????: Hi, there was no visit label 01 in the Visit_Windows table and i don't know how to insert it because the record requires lots of attributes. Also the system for a reason asked me to update my password and now i don't remember it and my account got suspended. Is there a way to reset it or set a simple password? I updated the password hash in the users table by using the hash from another LORIS setup we had and i still couldn't login ( also the attribute password is always NULL and the expiration date is 1999-01-01 for some reason ). Thanks ???? ???, 29 ???? 2019 ???? 5:21 ?.?., ?/? Cecile Madjar > ??????: Hi Sotirios, Can you try adding the visit label v01 to the Visit_Windows table? However, I noticed that in a previous dataset, the label was V1. Does that refer to the same visit? If so, you might want to harmonize the visit labels so they are all the same across datasets for a given timepoint, meaning you will need to relabel scans when the visit label is different but referring to the same visit label (v01 = V1 etc...). Hope this helps, C?cile On Mon, Jul 29, 2019 at 10:15 AM Sotirios Nikoloutsopoulos > wrote: Hi, Could you help me with the "Visit label does not exist"? I had changed $subjectID{'createVisitLabel'} to 1 as you had suggested but it appears that this problem hasn't been resolved yet. lorisadmin at hbp:/data/loris/bin/mri$ cat /data/loris/data//logs/TarLoad-14-58-9Xog7H.log ==> Loading file from disk /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc --> mapping DICOM parameter for /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc --> using user-defined filterParameters for /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc Candidate Mismatch Error is Visit label does not exist -> WARNING: This candidate was invalid. Logging to MRICandidateErrors table with reason Visit label does not exist Thank you, Sotirios ???? ???, 26 ???? 2019 ???? 3:02 ?.?., ?/? Sotirios Nikoloutsopoulos > ??????: Hi Cecile, The Center error was fixed. Still the insertion of mincs fails. Please see the output.txt file i attached. Also is there something else i need to change at the paths configuration? Thank you, Sotirios ???? ???, 25 ???? 2019 ???? 6:55 ?.?., ?/? Cecile Madjar > ??????: Hi Sotirios, We are making progress! I have a feeling this error comes from the fact that your psc table does not have the MRI_alias populated for the DCC site. Running the following query in the mysql database should fix this: UPDATE psc SET MRI_alias="DCC", Alias="DCC" WHERE Name="Data Coordinating Center"; Repeat the same with all your sites (make sure to change the Aliases between sites, they should all be unique). Let me know how it goes! Best, C?cile On Thu, Jul 25, 2019 at 11:43 AM Sotirios Nikoloutsopoulos > wrote: Dear Cecile, You were right about your guesses. I did the modifications you suggested, i still get the "no mincs inserted" error, now i am getting the "No center found this candidate" error ( how do i fix that? from what i see the .dcm files contains a 'Institution Name', is that the center? ), so i guess that's why the validation fails, but i changed the force variable of tarchiveLoader to 1, shouldn't it have inserted the mincs then? Also it is optional to have a mail server, right? ( from what i see the mail error does not affect the $valid_study, so i assume we are okay with that ) Thank you a lot, Sotirios ???? ???, 25 ???? 2019 ???? 5:48 ?.?., ?/? Cecile Madjar > ??????: Hi Sotirios, From what I understand, I believe you just need to update a few config settings from the frontend in the Config module (under the Admin menu). [Screen Shot 2019-07-25 at 10.31.35 AM.png] Then go to the Paths section of the config module and update the "LORIS-MRI code" config setting to /data/loris/bin/mri (my guess is that currently, it is set to /data/LORIS/data) and click on the submit button. [Screen Shot 2019-07-25 at 10.32.50 AM.png] Then, go to Imaging Pipeline section of the Configuration module and update the "Loris-MRI Data Directory" to /data/loris/data/ (my guess is that it is empty at the moment in your database which is why $data_dir is not defined when you run the tarchiveLoader step of the insertion pipeline). [Screen Shot 2019-07-25 at 10.40.52 AM.png] Finally, I took a look at your environment file and it might be a good idea to update your PERL5LIB variable to the following (it has been added to the code a few releases ago as we realized this was needed for the libraries. Not sure which version of LORIS-MRI you are using but it does not hurt to update this variable to what I suggest below): export PERL5LIB=/data/loris/bin/mri/uploadNeuroDB:/data/loris/bin/mri/dicom-archive:$PERL5LIB Hope this helps. Sorry you are experiencing so much trouble setting things up. We probably need to update our WIKI. Best, C?cile On Thu, Jul 25, 2019 at 9:48 AM Sotirios Nikoloutsopoulos > wrote: The "Loris-MRI Data Directory" should be in the environment file? ???? ???, 25 ???? 2019 ???? 12:59 ?.?., ?/? Sotirios Nikoloutsopoulos > ??????: The scripts are located in /data/loris/bin/mri/. Somewhere I might have messed something up but i remember following the instructions in the wiki.For example when i tried to execute the batch_uploads_imageuploader perl script the line my $command = "$bin_dir/uploadNeuroDB/imaging_upload_file.pl " was pointing to an invalid path, for example: it was repeating a pattern and had LORIS instead of loris ( i think the mistake was that in the wiki it suggested to use $PROJECT for the name of the folder and i choosed 'loris' https://github.com/aces/Loris/wiki/Imaging-Database ). See also the in image for the modification i did. Also i didn't find the section to config the $data_dir variable. Thank you, Sotirios ???? ???, 24 ???? 2019 ???? 6:05 ?.?., ?/? Cecile Madjar > ??????: Hi Sotirios, It looks like you have one Config setting not set (based on the first error message you got when running it the first time). You need to set a value for "Loris-MRI Data Directory" in the Config module under the Imaging pipeline section (from what I can see, it would be /data/loris/data/ for your setup). The reason you got that error message the second time is that the pipeline checks if the DICOM study was already inserted in the tarchive table. Since you ran the study once already, the study is inserted into the tarchive, hence the message. However, the pipeline did not complete as the MINC files were not created and inserted into the files/parameter_file table. In order to continue the insertion, you will then need to run the tarchiveLoader command suggested in the terminal during the second run: /data/LORIS/data//uploadNeuroDB/tarchiveLoader -globLocation -profile prod /data/loris/data/tarchive//2012/DCM_2012-12-05_ImagingUpload-17-43-ZUEFjb.tar -verbose Finally, I am a bit confused by your setup. Where are the scripts located? In /data/loris/bin/mri or /data/loris/data? It feels like the Config setting "LORIS-MRI code" in the Paths section was set to "/data/LORIS/data" but it should have been set to the directory where the scripts are located (most probably /data/loris/bin/mri). Hope this helps, C?cile On Wed, Jul 24, 2019 at 10:55 AM Sotirios Nikoloutsopoulos > wrote: Ok first i execute this command: "lorisadmin at hbp:/data/loris/bin/mri$ ./batch_uploads_imageuploader -profile prod < ~/Desktop/input.txt > log.txt Use of uninitialized value $data_dir in concatenation (.) or string at ./batch_uploads_imageuploader line 143. Use of uninitialized value $data_dir in concatenation (.) or string at ./batch_uploads_imageuploader line 143. Use of uninitialized value $_ in pattern match (m//) at ./batch_uploads_imageuploader line 147. base is DCC0000_258024_V01 path is /data/incoming/ type is .tar.gz fullpath is /data/incoming/DCC0000_258024_V01.tar.gz source /tmp/ImagingUpload-17-43-ZUEFjb targetlocation /data/loris/data/tarchive Use of uninitialized value $data_dir in concatenation (.) or string at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 256. Use of uninitialized value $data_dir in concatenation (.) or string at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 284. Use of uninitialized value $data_dir in concatenation (.) or string at /data/loris/bin/mri/uploadNeuroDB/tarchive_validation.pl line 219. Use of uninitialized value $data_dir in concatenation (.) or string at /data/loris/bin/mri/uploadNeuroDB/minc_insertion.pl line 270. Use of uninitialized value $data_dir in concatenation (.) or string at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 711. Can't exec "mail": No such file or directory at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 721. print() on closed filehandle MAIL at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 722. print() on closed filehandle MAIL at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 723. Use of uninitialized value $data_dir in concatenation (.) or string at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 724. print() on closed filehandle MAIL at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 724. print() on closed filehandle MAIL at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 725. Use of uninitialized value $data_dir in concatenation (.) or string at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 735. No Mincs inserted The tarchiveLoader insertion script has failed. Running now the following command: /data/loris/data/uploadNeuroDB/imaging_upload_file.pl -profile prod -upload_id 3 /data/incoming/DCC0000_258024_V01.tar.gz -verbose" I inserted the VisitLabel, but still the Mincs are not inserted and i am getting this error "lorisadmin at hbp:/data/loris/bin/mri$ /data/loris/data/uploadNeuroDB/imaging_upload_file.pl -profile prod -upload_id 3 /data/incoming/DCC0000_258024_V01.tar.gz -verbose find -path \/tmp\/ImagingUpload\-17\-45\-5MsWEd -name '__MACOSX' -delete Spool message is: The Scan for the uploadID 3 has already been run with tarchiveID: 7. To continue with the rest of the insertion pipeline, please run tarchiveLoader from a terminal as follows: /data/LORIS/data//uploadNeuroDB/tarchiveLoader -globLocation -profile prod /data/loris/data/tarchive//2012/DCM_2012-12-05_ImagingUpload-17-43-ZUEFjb.tar -verbose" Which files should i delete? I thought that deleting the files from the tarchive was enough. And i executed the last proposed command to continue to rest of the insertion pipeline ( check the image ). Thank you ???? ???, 24 ???? 2019 ???? 5:05 ?.?., ?/? Cecile Madjar > ??????: Hi Sotirios, Sorry I was not clear before. Every visits of candidates are created in the session table with one entry per CandID/VisitLabel. So if the imaging pipeline created visits in the session table (that are not attached to instruments) and you want to clean your database completely, you can delete entries in that table as well. Regarding your point 2, the imaging pipeline can create the visit in the session table as long as the visit label is present in the Visit_Windows table (which means the visit label stored in the PatientName is a valid visit label). However, in your prod file, if the variable $subjectID{'createVisitLabel'} is set to 1 for candidates, the visit label should be created in the Visit_Windows table I believe. Here is the line of the prod file you would need to change. In general, we prefer populating the Visit_Windows table and set the $subjectID{'createVisitLabel'} to 0 for candidate data to avoid insertion of badly labelled MRI data that are complex to relabel. Finally, regarding the candidate creation, if you execute the following steps, the pipeline should be able to create candidates: - set in the Imaging Pipeline section of the config module the config setting "Upload creation of candidates" to Yes - manually transfer the scans to the LORIS server instead of uploading it via the imaging browser - run batch_imaging_upload.pl as you did until now. Hope this helps! Best, C?cile On Wed, Jul 24, 2019 at 8:47 AM Sotirios Nikoloutsopoulos > wrote: About my second question i replaced the name of the patient in the .dcm files and now i am getting an error that the visit label does not exist. I thought it was supposed to be automatically created. "Done adding archive info into database /data/LORIS/data//uploadNeuroDB/tarchiveLoader -globLocation -profile prod /data/loris/data/tarchive//DCM_2012-12-05_ImagingUpload-15-42-yUwQQV.tar -verbose md5sum /data/loris/data/tarchive/DCM_2012-12-05_ImagingUpload-15-42-yUwQQV.tar PSCID is: DCC0000 CandID id: 258024 visit_label is: V1 PSCID is: DCC0000 CandID id: 258024 visit_label is: V1 candidate id 258024 => No Visit labelVisit label does not exist Set centerID = 1 PSCID is: DCC0000 CandID id: 258024 visit_label is: V1 PSCID is: DCC0000 CandID id: 258024 visit_label is: V1 Number of MINC files that will be considered for inserting into the database: 1 log dir is /logs and log file is /logs/TarLoad-15-42-L6pocU.log PSCID is: DCC0000 CandID id: 258024 visit_label is: V1 PSCID is: DCC0000 CandID id: 258024 visit_label is: V1 candidate id 258024 => No Visit label Cleaning up temp files: rm -rf /tmp/TarLoad-15-42-J2rQms/ImagingUpload-15-42-yUwQQV*" ???? ???, 24 ???? 2019 ???? 3:38 ?.?., ?/? Sotirios Nikoloutsopoulos > ??????: Hi, 1) What are the records in the session table? 2) I tried to upload a non-phantom file like this input_file.txt: /data/incoming/DCC0000_258024_V1.tar.gz N DCC0000_258024_V1 Terminal: ./batch_uploads_imageuploader -profile prod < ~/Desktop/input.txt > log.txt and i get the following error in the log.txt file "Running now the following command: /data/loris/data/uploadNeuroDB/imaging_upload_file.pl -profile prod -upload_id 7 /data/incoming/DCC0000_258024_V1.tar.gz -verbose find -path \/tmp\/ImagingUpload\-14\-56\-FeLCB4 -name '__MACOSX' -delete Spool message is: The PatientName read from the DICOM header does not start with DCC0000_258024_V1 from the mri_upload table " and the spool message is repeated for each .dcm file. Should i preprocess every .dcm file and change the PatientName to "DCC0000_258024_V1"? 3) As far as it concerns the candidate profile i have to create a new one each time before i try to upload a file? Is there already a way to create a candidate profile and get the DCCID and PSCID without the user interface? Thank you, Sotirios ???? ???, 18 ???? 2019 ???? 5:00 ?.?., ?/? Cecile Madjar > ??????: Hi Sotirios, See answers to your questions below. About the 1st case we had a dicom with a blank studyUID, maybe someone accidentally removed it. That is strange. Something must have been done to the DICOM files. I have never seen a study with no StudyUID out of the scanner. Usually, you need to manually erase it with some tool. However, DICOMs never cease to surprise me... Some other questions: 1) What are the steps to remove all of my patients and uploads?: because i want to try to reupload all the testing dicoms we had with a clean database. Release 21.0 of LORIS-MRI will offer a script to remove all the entries and files specific to an upload. However, this release is not yet out. Hopefully in the next few weeks. In the meantime, since your case is particular and that you just want to start with a clean database, the following deletes should work (hopefully I won't forget any tables): delete from mri_violations_log; delete from mri_protocol_violated_scans; delete from MRICandidateErrors; delete from parameter_file; delete from files_qcstatus; # (if you played with the QC part of the imaging browser for testing) delete from feedback_mri_comments; # (if you played with the QC part of the imaging browser for testing) delete from tarchive_series; delete from tarchive_files; delete from mri_upload; delete from tarchive; delete from mri_scanner; delete from candidate where PSCID="scanner"; I don't know if you want to also delete entries in the session and candidate table too? 2) We do not need to create the profile of a patient ( are the patients stored in the candidate table? because i can't see the ghosts ), because will it automatically be created when importing a dicom? I am not sure I understand fully this question. All candidates are stored in the candidate table. The phantom scans however are attached to a scanner candidate depending on where the scan happened. It is a bit of a weird concept that we have to redesign eventually but never got a chance to get to it. Hopefully this answered your question, otherwise, don't hesitate to let me know. 3) What is the difference between uploading a dicom as phantom instead of importing as PSCCID_DCCID_VisitLabel? When you upload the scan as PSCID_DCCID_VisitLabel, there is a check that makes sure the candidate IDs and visit label are valid at the time of upload. When you upload a scan as phantom, it expects that the DICOM field PatientName and uploaded filename contains the string "phantom". We enforced this behaviour on the imaging uploader side in recent releases but I can't remember which one. Probably the upcoming 21.0 release. All those verifications might seem cumbersome but they are here to ensure that the files inserted are all valid and labelled properly as it is a bit messy to have to delete files that were wrongly labelled. At least, the delete script present in release 21.0 will make this process easier but it is still good practice to verify those things. Thank you, With pleasure. Hopefully the answers to your questions will be helpful. Best, C?cile PS: loris-dev mailing list: you will find the initial answer I gave Sotirios below. I forgot to cc the loris-dev in my earlier reply... ???? ???, 16 ???? 2019 ???? 12:02 ?.?., ?/? Cecile Madjar > ??????: Dear Sotirios, Thank you for reaching out. Since your email was already organized in points, I will reply directly below your questions below. Best, C?cile 1) What do we do when the StudyUID is blank on the header? https://github.com/aces/Loris-MRI/blob/minor/docs/AppendixA-Troubleshooting_guideline.md There solution provided at the table 3 does not guide us how to find the information ( is possible ). The StudyUID is the field used in our pipeline at the moment to check whether a DICOM study was already inserted into LORIS with that same StudyUID since it is supposed to be unique for every single study. Currently, we do not support insertion of DICOM studies if they do not have a StudyUID associated with them. Is there a specific reason why the StudyUID is blank in the DICOM headers in your DICOM files? Did they go through some processes before upload to LORIS? 2) When i am about to upload a non-phanton case i need a 'Visit Label'. Is there already a script that can create a new visit label for a specific Candidate, so i can provide it as input afterwards to the batch_uploads_imageuploader ( See option 5.1.3 https://github.com/aces/Loris-MRI/blob/minor/docs/05-PipelineLaunchOptions.md ) I am not sure if the front-end allows for it but if you use batch_uploads_imageuploader, the insertion scripts could create the visit label for you. However, it does need to be included in the patient name in order for the script to know which label it should use. For example: you upload V02 for MTL0123 (DCCID: 456789) but V02 was not yet created for MTL0123; the insertion scripts will create a V02 visit for MTL0123 if the PatientName field for the dataset is MTL0123_456789_V02 with Stage marked as "Not Started". However, note that for the script to create the visit for the candidate, you have to make sure that all the visit label of your projects were inserted in the Visit_Windows table (otherwise, the visit will never be created as they were not specified as being part of the list of visit label to expect). So in the example above, you should have one row in Visit_Windows with Visit_label="V02" set. 3) Section 4.3 https://github.com/aces/Loris-MRI/blob/minor/docs/04-Scripts.md What do we do when the folder contains multiple mnc files? This is a case by case. Most of the time, the MINC files that failed insertion into the imaging browser end up in the MRI violation module where you can see what went wrong with the acquisitions not inserted. If you notice that the MINC file should be inserted as a specific protocol, you can force the insertion as explained in section 4.3. In your case, I have a feeling that you want to be able to insert MINC files that did not go through the whole pipeline insertion (DICOM archival, then dcm2mnc, then protocol identification, then insertion...). In theory, you could call minc_insertion.pl on any MINC file, provided you have at least the following information: - path to the MINC file - uploadID associated with the MINC files or DICOM archive path from which those MINC files were created from Then the minc_insertion.pl script will do the subject information and protocol validation etc... If all the MINC files come from the same uploadID or TarchiveID, then you could run a loop in bash calling the minc_insertion.pl script like this for files deriving from uploadID=1: ls /path/to/mnc/folder/* | while read f; do minc_insertion.pl -profile prod -uploadID 1 -mincPath $f; done Thank you, Hope this helped! _______________________________________________ Loris-dev mailing list Loris-dev at bic.mni.mcgill.ca https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev -- christine.rogers at mcgill.ca McGill Centre for Integrative Neuroscience | MCIN.ca Montreal Neurological Institute McGill University | Montreal | Canada -- christine.rogers at mcgill.ca McGill Centre for Integrative Neuroscience | MCIN.ca Montreal Neurological Institute McGill University | Montreal | Canada _______________________________________________ Loris-dev mailing list Loris-dev at bic.mni.mcgill.ca https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev -- christine.rogers at mcgill.ca McGill Centre for Integrative Neuroscience | MCIN.ca Montreal Neurological Institute McGill University | Montreal | Canada _______________________________________________ Loris-dev mailing list Loris-dev at bic.mni.mcgill.ca https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev -- christine.rogers at mcgill.ca McGill Centre for Integrative Neuroscience | MCIN.ca Montreal Neurological Institute McGill University | Montreal | Canada _______________________________________________ Loris-dev mailing list Loris-dev at bic.mni.mcgill.ca https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev -- christine.rogers at mcgill.ca McGill Centre for Integrative Neuroscience | MCIN.ca Montreal Neurological Institute McGill University | Montreal | Canada _______________________________________________ Loris-dev mailing list Loris-dev at bic.mni.mcgill.ca https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev -- christine.rogers at mcgill.ca McGill Centre for Integrative Neuroscience | MCIN.ca Montreal Neurological Institute McGill University | Montreal | Canada _______________________________________________ Loris-dev mailing list Loris-dev at bic.mni.mcgill.ca https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev -- christine.rogers at mcgill.ca McGill Centre for Integrative Neuroscience | MCIN.ca Montreal Neurological Institute McGill University | Montreal | Canada _______________________________________________ Loris-dev mailing list Loris-dev at bic.mni.mcgill.ca https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev _______________________________________________ Loris-dev mailing list Loris-dev at bic.mni.mcgill.ca https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev -- christine.rogers at mcgill.ca McGill Centre for Integrative Neuroscience | MCIN.ca Montreal Neurological Institute McGill University | Montreal | Canada -------------- next part -------------- An HTML attachment was scrubbed... URL: From basilia1123 at gmail.com Mon Aug 12 20:23:32 2019 From: basilia1123 at gmail.com (=?UTF-8?B?7J207Jyg67aA?=) Date: Tue, 13 Aug 2019 09:23:32 +0900 Subject: [Loris-dev] LORIS installation inquiry -- regarding Message-ID: Dear Sir/Madam, We are currently trying to install LORIS on Ubuntu 18.04 platform following the steps from https://github.com/aces/Loris/wiki/Installing-Loris-in-Depth 1. Following the above link, we installed the prerequisites mentioned in https://github.com/aces/Loris/wiki/Installing-Loris-in-Depth#getting-prerequisites, which are all verified to be installed normally. 2. We ensured that mySQL credentials are set up properly (as pasted below) mysql> select host, user, authentication_string from user -> ; +-----------+------------------+-------------------------------------------+ | host | user | authentication_string | +-----------+------------------+-------------------------------------------+ | localhost | root | | | localhost | mysql.session | *THISISNOTAVALIDPASSWORDTHATCANBEUSEDHERE | | localhost | mysql.sys | *THISISNOTAVALIDPASSWORDTHATCANBEUSEDHERE | | localhost | debian-sys-maint | *C9BF7C6E59BFF0FA879E6650D174264C9EE87F25 | +-----------+------------------+-------------------------------------------+ 4 rows in set (0.00 sec) mysql> update user set authentication_string=password('yubu') where user='root'; Query OK, 1 row affected, 1 warning (0.00 sec) Rows matched: 1 Changed: 1 Warnings: 1 mysql> flush privileges; Query OK, 0 rows affected (0.01 sec) mysql> select host, user, authentication_string from user -> ; +-----------+------------------+-------------------------------------------+ | host | user | authentication_string | +-----------+------------------+-------------------------------------------+ | localhost | root | *E311E16EECE7E8900098CFEB4103D5266A343F5F | | localhost | mysql.session | *THISISNOTAVALIDPASSWORDTHATCANBEUSEDHERE | | localhost | mysql.sys | *THISISNOTAVALIDPASSWORDTHATCANBEUSEDHERE | | localhost | debian-sys-maint | *C9BF7C6E59BFF0FA879E6650D174264C9EE87F25 | +-----------+------------------+-------------------------------------------+ 4 rows in set (0.00 sec) 3. We then opened http://localhost/installdb.php and have gotten the login page for LORIS installation and typed the credentials as follows: [image: Screenshot from 2019-08-13 09-14-51.png] 4. Once we submitted the page we obtained error as follows [image: Screenshot from 2019-08-13 09-14-56.png] We really do not know how to proceed further from this point onward. Kindly let us know how to proceed further in order to get the LORIS installed. Thank you. Your Sincerely, ====================================================== Yubu Lee, Ph.D. Research Professor, Center for Neuroscience Imaging Research, Institute for Basic Science #86332, N Center, SungKyunKwan University 2066, Seobu-Ro, Jangan-gu, Suwon, Gyeonggi-do, 16419, Korea E-mail: basilia1123 at gmail.com Tel: +82-31-299-4411 Fax: +82-31-299-4506 ====================================================== -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Screenshot from 2019-08-13 09-14-51.png Type: image/png Size: 283124 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Screenshot from 2019-08-13 09-14-56.png Type: image/png Size: 124916 bytes Desc: not available URL: From basilia1123 at gmail.com Tue Aug 13 03:11:42 2019 From: basilia1123 at gmail.com (=?UTF-8?B?7J207Jyg67aA?=) Date: Tue, 13 Aug 2019 16:11:42 +0900 Subject: [Loris-dev] LORIS installation inquiry -- regarding Message-ID: Dear Sir/Madam, We are currently trying to install LORIS on Ubuntu 18.04 platform following the steps from https://github.com/aces/Loris/wiki/Installing-Loris-in-Depth 1. Following the above link, we installed the prerequisites mentioned in https://github.com/aces/Loris/wiki/Installing-Loris-in-Depth#getting-prerequisites, which are all verified to be installed normally. 2. We ensured that mySQL credentials are set up properly (as pasted below) mysql> select host, user, authentication_string from user -> ; +-----------+------------------+-------------------------------------------+ | host | user | authentication_string | +-----------+------------------+-------------------------------------------+ | localhost | root | | | localhost | mysql.session | *THISISNOTAVALIDPASSWORDTHATCANBEUSEDHERE | | localhost | mysql.sys | *THISISNOTAVALIDPASSWORDTHATCANBEUSEDHERE | | localhost | debian-sys-maint | *C9BF7C6E59BFF0FA879E6650D174264C9EE87F25 | +-----------+------------------+-------------------------------------------+ 4 rows in set (0.00 sec) mysql> update user set authentication_string=password('yubu') where user='root'; Query OK, 1 row affected, 1 warning (0.00 sec) Rows matched: 1 Changed: 1 Warnings: 1 mysql> flush privileges; Query OK, 0 rows affected (0.01 sec) mysql> select host, user, authentication_string from user -> ; +-----------+------------------+-------------------------------------------+ | host | user | authentication_string | +-----------+------------------+-------------------------------------------+ | localhost | root | *E311E16EECE7E8900098CFEB4103D5266A343F5F | | localhost | mysql.session | *THISISNOTAVALIDPASSWORDTHATCANBEUSEDHERE | | localhost | mysql.sys | *THISISNOTAVALIDPASSWORDTHATCANBEUSEDHERE | | localhost | debian-sys-maint | *C9BF7C6E59BFF0FA879E6650D174264C9EE87F25 | +-----------+------------------+-------------------------------------------+ 4 rows in set (0.00 sec) 3. We then opened http://localhost/installdb.php and have gotten the login page for LORIS installation and typed the credentials as follows: [image: Screenshot from 2019-08-13 09-14-51.png] 4. Once we submitted the page we obtained error as follows [image: Screenshot from 2019-08-13 09-14-56.png] We really do not know how to proceed further from this point onward. Kindly let us know how to proceed further in order to get the LORIS installed. Thank you. Your Sincerely, ====================================================== Yubu Lee, Ph.D. Research Professor, Center for Neuroscience Imaging Research, Institute for Basic Science #86332, N Center, SungKyunKwan University 2066, Seobu-Ro, Jangan-gu, Suwon, Gyeonggi-do, 16419, Korea E-mail: basilia1123 at gmail.com Tel: +82-31-299-4411 Fax: +82-31-299-4506 ====================================================== -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Screenshot from 2019-08-13 09-14-56.png Type: image/png Size: 124916 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Screenshot from 2019-08-13 09-14-51.png Type: image/png Size: 283124 bytes Desc: not available URL: From wangshen.mcin at gmail.com Tue Aug 13 09:20:53 2019 From: wangshen.mcin at gmail.com (Shen Wang) Date: Tue, 13 Aug 2019 09:20:53 -0400 Subject: [Loris-dev] LORIS installation inquiry -- regarding In-Reply-To: References: Message-ID: Hi Yubu, We need more information to debug this issue. 1 Which version of Loris are you using? 2 Mysql version? 3 [sudo tail -f /var/log/apache2/loris-error.log] Please running this in the backend, then try loading the installdb.php again, with a different database name. Please send us the error message. Your Sincerely, Shen On Mon, 12 Aug 2019 at 22:27, ??? wrote: > Dear Sir/Madam, > > We are currently trying to install LORIS on Ubuntu 18.04 platform > following the steps from > https://github.com/aces/Loris/wiki/Installing-Loris-in-Depth > > 1. Following the above link, we installed the prerequisites mentioned in > https://github.com/aces/Loris/wiki/Installing-Loris-in-Depth#getting-prerequisites, > which are all verified to be installed normally. > > 2. We ensured that mySQL credentials are set up properly (as pasted below) > mysql> select host, user, authentication_string from user > -> ; > > +-----------+------------------+-------------------------------------------+ > | host | user | authentication_string > | > > +-----------+------------------+-------------------------------------------+ > | localhost | root | > | > | localhost | mysql.session | *THISISNOTAVALIDPASSWORDTHATCANBEUSEDHERE > | > | localhost | mysql.sys | *THISISNOTAVALIDPASSWORDTHATCANBEUSEDHERE > | > | localhost | debian-sys-maint | *C9BF7C6E59BFF0FA879E6650D174264C9EE87F25 > | > > +-----------+------------------+-------------------------------------------+ > 4 rows in set (0.00 sec) > > mysql> update user set authentication_string=password('yubu') where > user='root'; > Query OK, 1 row affected, 1 warning (0.00 sec) > Rows matched: 1 Changed: 1 Warnings: 1 > > mysql> flush privileges; > Query OK, 0 rows affected (0.01 sec) > > mysql> select host, user, authentication_string from user > -> ; > > +-----------+------------------+-------------------------------------------+ > | host | user | authentication_string > | > > +-----------+------------------+-------------------------------------------+ > | localhost | root | *E311E16EECE7E8900098CFEB4103D5266A343F5F > | > | localhost | mysql.session | *THISISNOTAVALIDPASSWORDTHATCANBEUSEDHERE > | > | localhost | mysql.sys | *THISISNOTAVALIDPASSWORDTHATCANBEUSEDHERE > | > | localhost | debian-sys-maint | *C9BF7C6E59BFF0FA879E6650D174264C9EE87F25 > | > > +-----------+------------------+-------------------------------------------+ > 4 rows in set (0.00 sec) > > 3. We then opened http://localhost/installdb.php and have gotten the > login page for LORIS installation and typed the credentials as follows: > [image: Screenshot from 2019-08-13 09-14-51.png] > 4. Once we submitted the page we obtained error as follows > > [image: Screenshot from 2019-08-13 09-14-56.png] > > > > We really do not know how to proceed further from this point onward. > Kindly let us know how to proceed further in order to get the LORIS > installed. > > Thank you. > > Your Sincerely, > > ====================================================== > > Yubu Lee, Ph.D. > > Research Professor, > > Center for Neuroscience Imaging Research, Institute for Basic Science > > > #86332, N Center, SungKyunKwan University > 2066, Seobu-Ro, Jangan-gu, Suwon, Gyeonggi-do, 16419, Korea > > E-mail: basilia1123 at gmail.com > > Tel: +82-31-299-4411 > > Fax: +82-31-299-4506 > > ====================================================== > _______________________________________________ > Loris-dev mailing list > Loris-dev at bic.mni.mcgill.ca > https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > -- Shen Wang Loris Developer Montreal Neurological Institute McGill University -------------- next part -------------- An HTML attachment was scrubbed... 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Name: Screenshot from 2019-08-13 09-14-56.png Type: image/png Size: 124916 bytes Desc: not available URL: From sotirisnik at gmail.com Tue Aug 13 14:21:12 2019 From: sotirisnik at gmail.com (Sotirios Nikoloutsopoulos) Date: Tue, 13 Aug 2019 21:21:12 +0300 Subject: [Loris-dev] Upgrading to Loris 21 - new make file In-Reply-To: References: Message-ID: Hi, I executed the commands for the node and now i am get the followings: lorisadmin at hbp:/var/www/loris$ make > ~/make_output npm WARN The package prop-types is included as both a dev and production dependency. npm WARN optional SKIPPING OPTIONAL DEPENDENCY: fsevents at 1.2.4 (node_modules/fsevents): npm WARN notsup SKIPPING OPTIONAL DEPENDENCY: Unsupported platform for fsevents at 1.2.4: wanted {"os":"darwin","arch":"any"} (current: {"os":"linux","arch":"x64"}) npm ERR! code ELIFECYCLE npm ERR! errno 2 npm ERR! loris at 1.0.0 compile: `webpack` npm ERR! Exit status 2 npm ERR! npm ERR! Failed at the loris at 1.0.0 compile script. npm ERR! This is probably not a problem with npm. There is likely additional logging output above. npm ERR! A complete log of this run can be found in: npm ERR! /home/lorisadmin/.npm/_logs/2019-08-13T18_12_05_378Z-debug.log make: *** [javascript] Error 2 Thanks, Sotirios ???? ???, 12 ??? 2019 ???? 10:19 ?.?., ?/? Christine Rogers, Ms. < christine.rogers at mcgill.ca> ??????: > Hi Sotirios, > > We've seen some users installing LORIS 21 or upgrading to 21 whose version > of node doesn't work well with webpack, due to updated packages they're > missing. > If so, update your node : > > curl -sL https://deb.nodesource.com/setup_8.x | sudo -E bash - > sudo apt-get install -y nodejs > > Let us know how that goes -- please send us output from the same log if > any issues. > Best, > Christine > > > On Thu, Aug 8, 2019 at 2:38 PM Sotirios Nikoloutsopoulos < > sotirisnik at gmail.com> wrote: > >> It's not a disk space issue, as you can see below i have still 74GB >> available. >> >> lorisadmin at hbp:/var/www/loris$ df -h >> Filesystem Size Used Avail Use% Mounted on >> udev 2,9G 0 2,9G 0% /dev >> tmpfs 597M 8,6M 588M 2% /run >> /dev/sda1 98G 19G 74G 21% / >> >> Maybe we have to pass a flag to get into strict mode? as stated >> "SyntaxError: Block-scoped declarations (let, const, function, class) not >> yet supported outside strict mode" >> >> Thanks, >> Sotirios >> >> ???? ???, 8 ??? 2019 ???? 4:32 ?.?., ?/? Dave MacFarlane < >> dave.macfarlane at mcin.ca> ??????: >> >>> It looks like the javascript snippet shown in the error message when >>> trying to compile the js is truncated. Have you run out of disk space? >>> >>> On Thu, Aug 8, 2019 at 8:37 AM Sotirios Nikoloutsopoulos < >>> sotirisnik at gmail.com> wrote: >>> >>>> Hi, >>>> >>>> I runned make and also included the file it reports at the end. >>>> >>>> lorisadmin at hbp:/var/www/loris$ make >>>> npm install >>>> npm WARN optional Skipping failed optional dependency >>>> /chokidar/fsevents: >>>> npm WARN notsup Not compatible with your operating system or >>>> architecture: fsevents at 1.2.9 >>>> npm WARN optional Skipping failed optional dependency >>>> /watchpack/chokidar/fsevents: >>>> npm WARN notsup Not compatible with your operating system or >>>> architecture: fsevents at 1.2.9 >>>> npm run compile >>>> >>>> > loris at 1.0.0 compile /var/www/loris >>>> > webpack >>>> >>>> /var/www/loris/node_modules/webpack/bin/webpack.js:86 >>>> let notify = >>>> ^^^ >>>> >>>> SyntaxError: Block-scoped declarations (let, const, function, class) >>>> not yet supported outside strict mode >>>> at exports.runInThisContext (vm.js:53:16) >>>> at Module._compile (module.js:374:25) >>>> at Object.Module._extensions..js (module.js:417:10) >>>> at Module.load (module.js:344:32) >>>> at Function.Module._load (module.js:301:12) >>>> at Function.Module.runMain (module.js:442:10) >>>> at startup (node.js:136:18) >>>> at node.js:966:3 >>>> >>>> npm ERR! Linux 4.15.0-55-generic >>>> npm ERR! argv "/usr/bin/nodejs" "/usr/bin/npm" "run" "compile" >>>> npm ERR! node v4.2.6 >>>> npm ERR! npm v3.5.2 >>>> npm ERR! code ELIFECYCLE >>>> npm ERR! loris at 1.0.0 compile: `webpack` >>>> npm ERR! Exit status 1 >>>> npm ERR! >>>> npm ERR! Failed at the loris at 1.0.0 compile script 'webpack'. >>>> npm ERR! Make sure you have the latest version of node.js and npm >>>> installed. >>>> npm ERR! If you do, this is most likely a problem with the loris >>>> package, >>>> npm ERR! not with npm itself. >>>> npm ERR! Tell the author that this fails on your system: >>>> npm ERR! webpack >>>> npm ERR! You can get information on how to open an issue for this >>>> project with: >>>> npm ERR! npm bugs loris >>>> npm ERR! Or if that isn't available, you can get their info via: >>>> npm ERR! npm owner ls loris >>>> npm ERR! There is likely additional logging output above. >>>> >>>> npm ERR! Please include the following file with any support request: >>>> npm ERR! /var/www/loris/npm-debug.log >>>> Makefile:14: recipe for target 'javascript' failed >>>> make: *** [javascript] Error 1 >>>> >>>> Thanks, >>>> >>>> Sotirios >>>> >>>> ???? ???, 7 ??? 2019 ???? 5:41 ?.?., ?/? Christine Rogers, Ms. < >>>> christine.rogers at mcgill.ca> ??????: >>>> >>>>> Hi Sotirios, >>>>> >>>>> Thanks, have you tried all of these steps? >>>>> - clear your browser cache (and refresh a few times) >>>>> - delete any files in your smarty/templates_c directory (this will >>>>> clear the template cache - do Not touch smarty/templates/) >>>>> - run `make` (per the 21 release notes, this replaces the composer >>>>> commands used in previous releases to update your dependencies) >>>>> - restart apache (doesn't hurt) >>>>> >>>>> Let us know how it goes -- let us know what difference you see after, >>>>> with your logs. A >>>>> lso please send us your Config path settings (see these >>>>> Troubleshooting Queries >>>>> ) >>>>> if you're still seeing front-end issues. >>>>> >>>>> Thanks, >>>>> Christine >>>>> >>>>> On Wed, Aug 7, 2019 at 8:02 AM Sotirios Nikoloutsopoulos < >>>>> sotirisnik at gmail.com> wrote: >>>>> >>>>>> Hi, >>>>>> >>>>>> lorisadmin at hbp:/var/www/loris$ sudo cat /var/log/apache2/error.log >>>>>> [Wed Aug 07 07:35:02.422501 2019] [mpm_prefork:notice] [pid 1267] >>>>>> AH00163: Apache/2.4.18 (Ubuntu) OpenSSL/1.0.2g configured -- resuming >>>>>> normal operations >>>>>> [Wed Aug 07 07:35:02.422514 2019] [core:notice] [pid 1267] AH00094: >>>>>> Command line: '/usr/sbin/apache2' >>>>>> >>>>>> And as for the access.log the content are empty >>>>>> lorisadmin at hbp:/var/www/loris$ sudo ls -l /var/log/apache2/access.log >>>>>> lorisadmin at hbp:/var/www/loris$ sudo ls -l /var/log/apache2/access.log >>>>>> -rw-r----- 1 root adm 0 ???? 28 14:09 /var/log/apache2/access.log >>>>>> >>>>>> Also i noticed a loris_access.log. >>>>>> >>>>>> The only non-blank pages are: >>>>>> mri_violations, dataquery does not exist at all, statistics, >>>>>> data_team_helper, genomic_browser, configuration and >>>>>> server_processes_manager/ prints "Required configuration settings for >>>>>> Server Processes Manager are missing. Cannot continue." >>>>>> >>>>>> Thanks, >>>>>> Sotirios >>>>>> >>>>>> ???? ???, 6 ??? 2019 ???? 10:13 ?.?., ?/? Christine Rogers, Ms. < >>>>>> christine.rogers at mcgill.ca> ??????: >>>>>> >>>>>>> Hi Sotirios and LORIS community -- >>>>>>> >>>>>>> When upgrading to brand-new release 21 -- just a reminder to follow >>>>>>> the release notes and run the new *make* file to update your >>>>>>> dependencies (instead of using *composer* commands). >>>>>>> We've also updated the Wiki page >>>>>>> to clarify >>>>>>> that the release notes for each version will tell you what to run. >>>>>>> >>>>>>> If your current version is not the last release (20.3), it's still >>>>>>> important to upgrade to each minor release increment (e.g. 20.2, 20.3) >>>>>>> before making the leap to 21.0. >>>>>>> >>>>>>> If you're getting blank pages, post-upgrade -- Try clearing your >>>>>>> cache. >>>>>>> >>>>>>> Got questions or feedback e.g. on the Release Notes? please don't >>>>>>> hesitate to let us know. >>>>>>> Thanks, >>>>>>> Christine >>>>>>> The LORIS team >>>>>>> >>>>>>> >>>>>>> >>>>>>> On Tue, Aug 6, 2019 at 10:09 AM Christine Rogers, Ms. < >>>>>>> christine.rogers at mcgill.ca> wrote: >>>>>>> >>>>>>>> Hi Sotirios, >>>>>>>> Could you also let us know -- on which pages is content visible, >>>>>>>> and on which pages/modules is content not visible for you? >>>>>>>> Thanks, >>>>>>>> Christine >>>>>>>> >>>>>>>> On Tue, Aug 6, 2019 at 9:54 AM Christine Rogers, Ms. < >>>>>>>> christine.rogers at mcgill.ca> wrote: >>>>>>>> >>>>>>>>> Thanks Sotirios, >>>>>>>>> That's good to know. It sounds like you've checked that your >>>>>>>>> /var/www/loris/project/config.xml file get populated properly. >>>>>>>>> >>>>>>>>> Please send us the last few errors you're seeing in your apache >>>>>>>>> error log file, and your config paths and we can see what's happening with >>>>>>>>> your front end -- >>>>>>>>> Run these Troubleshooting Queries >>>>>>>>> >>>>>>>>> to get your config path settings, given your front end is not displaying >>>>>>>>> fully. >>>>>>>>> >>>>>>>>> The Loris-MRI repo >>>>>>>>> 21 >>>>>>>>> install/upgrade would then be your next steps. >>>>>>>>> Best, >>>>>>>>> Christine >>>>>>>>> >>>>>>>>> On Tue, Aug 6, 2019 at 7:53 AM Sotirios Nikoloutsopoulos < >>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>> >>>>>>>>>> I am using a VM. What i did was: >>>>>>>>>> 1) Download the files from https://github.com/aces/Loris and >>>>>>>>>> replace them to my existing /vaw/www/loris folder. >>>>>>>>>> 2) Execute the composer install --no-dev and then composer >>>>>>>>>> dump-autoload as mentioned here >>>>>>>>>> https://github.com/aces/Loris/wiki/Updating-your-LORIS. >>>>>>>>>> 3) Execute install.sh from /var/www/loris/tools and because >>>>>>>>>> LORIS already existed i moved a .config file, then re-executed the >>>>>>>>>> install.sh successfully >>>>>>>>>> 4 ) As for the database, i dropped the schema and i executed the >>>>>>>>>> installdb.php >>>>>>>>>> >>>>>>>>>> ???? ???, 5 ??? 2019 ???? 5:22 ?.?., ?/? Christine Rogers, Ms. < >>>>>>>>>> christine.rogers at mcgill.ca> ??????: >>>>>>>>>> >>>>>>>>>>> Hi Sotorios, >>>>>>>>>>> >>>>>>>>>>> Thanks - when you re-installed did you start on a fresh root >>>>>>>>>>> path / VM or might some of your old system setting still apply? >>>>>>>>>>> (And if you did any steps similar to an upgrade, did you follow >>>>>>>>>>> the Upgrade steps in the Release Notes, from both repos?) >>>>>>>>>>> >>>>>>>>>>> About the TR_range column - it was recently split (MRI pr339 >>>>>>>>>>> ) split into TR_min >>>>>>>>>>> and _max columns. Given the code was trying to query TR_range which does >>>>>>>>>>> not exist in your mri_protocol table, double-check which version of the >>>>>>>>>>> Loris repo (tables) and the Loris-MRI repo (code) you have installed to >>>>>>>>>>> ensure they match. >>>>>>>>>>> >>>>>>>>>>> Christine >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> On Mon, Aug 5, 2019 at 9:06 AM Sotirios Nikoloutsopoulos < >>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>> >>>>>>>>>>>> I reinstalled LORIS to 21 version and now the content is not >>>>>>>>>>>> visible at all at most pages. >>>>>>>>>>>> >>>>>>>>>>>> [image: image.png] >>>>>>>>>>>> >>>>>>>>>>>> ???? ???, 5 ??? 2019 ???? 3:19 ?.?., ?/? Sotirios >>>>>>>>>>>> Nikoloutsopoulos ??????: >>>>>>>>>>>> >>>>>>>>>>>>> Hi, >>>>>>>>>>>>> >>>>>>>>>>>>> Is it easy to upgrade to Loris 21? Also the following fails >>>>>>>>>>>>> because the line 1985 of NeuroDB/MRIProcessingUtility.pm query mri_protocol >>>>>>>>>>>>> which doesn't have TR_range >>>>>>>>>>>>> https://github.com/aces/Loris/blob/21.0-release/SQL/0000-00-00-schema.sql#L556 >>>>>>>>>>>>> >>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>> >>>>>>>>>>>>> lorisadmin at hbp:/data/loris/bin/mri$ >>>>>>>>>>>>> ./batch_uploads_imageuploader -profile prod < ~/Desktop/input.txt > log.txt >>>>>>>>>>>>> Use of uninitialized value $_ in pattern match (m//) at >>>>>>>>>>>>> ./batch_uploads_imageuploader line 147. >>>>>>>>>>>>> base is DCC0000_258024_V1 >>>>>>>>>>>>> path is /data/incoming/ >>>>>>>>>>>>> type is .tar.gz >>>>>>>>>>>>> fullpath is /data/incoming/DCC0000_258024_V1.tar.gz >>>>>>>>>>>>> DBD::mysql::st execute failed: Unknown column 'TR_range' in >>>>>>>>>>>>> 'where clause' at >>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line 1985. >>>>>>>>>>>>> DBD::mysql::st fetchrow_array failed: fetch() without >>>>>>>>>>>>> execute() at >>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line 1986. >>>>>>>>>>>>> Use of uninitialized value $count_mri_protocol in numeric gt >>>>>>>>>>>>> (>) at /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm >>>>>>>>>>>>> line 1995. >>>>>>>>>>>>> DBD::mysql::st execute failed: Unknown column 'TR_range' in >>>>>>>>>>>>> 'field list' at /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 562. >>>>>>>>>>>>> Can't exec "mail": No such file or directory at >>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 721. >>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 722. >>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 723. >>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 724. >>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 725. >>>>>>>>>>>>> >>>>>>>>>>>>> No Mincs inserted >>>>>>>>>>>>> >>>>>>>>>>>>> Thanks, >>>>>>>>>>>>> >>>>>>>>>>>>> Sotirios >>>>>>>>>>>>> >>>>>>>>>>>>> ???? ???, 3 ??? 2019 ???? 1:08 ?.?., ?/? Christine Rogers, Ms. >>>>>>>>>>>>> ??????: >>>>>>>>>>>>> >>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>> >>>>>>>>>>>>>> First, just a note: we've released LORIS 21 this week with >>>>>>>>>>>>>> some major new features and cleanup -- especially if you are early in your >>>>>>>>>>>>>> setup phase, check out the Release notes for both the LORIS >>>>>>>>>>>>>> and >>>>>>>>>>>>>> Loris-MRI >>>>>>>>>>>>>> >>>>>>>>>>>>>> repos. >>>>>>>>>>>>>> >>>>>>>>>>>>>> Thanks for your screenshots -- your empty mri_protocol table >>>>>>>>>>>>>> should be at the root of these issues : >>>>>>>>>>>>>> >>>>>>>>>>>>>> The mri_protocol table must be populated >>>>>>>>>>>>>> >>>>>>>>>>>>>> in order for your scans to be registered in LORIS -- it serves as a >>>>>>>>>>>>>> whitelist for the insertion pipeline which filters out scans that aren't >>>>>>>>>>>>>> identified or matched to scan types in this table. >>>>>>>>>>>>>> >>>>>>>>>>>>>> By default, this table is populated with entries for t1, t2, >>>>>>>>>>>>>> fMRI and DTI (Insert statements for 21 release branch are >>>>>>>>>>>>>> here >>>>>>>>>>>>>> >>>>>>>>>>>>>> ) >>>>>>>>>>>>>> Feel free to restore our default records and broaden their >>>>>>>>>>>>>> parameters to match all your scan types. >>>>>>>>>>>>>> >>>>>>>>>>>>>> re Defaced, native, selected -- these filter the scans >>>>>>>>>>>>>> displayed as you move to the next page (View Session), instead of viewing >>>>>>>>>>>>>> "all types" of scans from a given session : >>>>>>>>>>>>>> >>>>>>>>>>>>>> - "defaced" means that a defacing script >>>>>>>>>>>>>> >>>>>>>>>>>>>> has masked the subject's face in the volume (for patient privacy) >>>>>>>>>>>>>> - "native" means that no pre-processing has been >>>>>>>>>>>>>> performed on the scan (it's raw data), >>>>>>>>>>>>>> - "selected" will show only volumes that have been QC'd >>>>>>>>>>>>>> and "selected" as the best of their type -- used to display only the best >>>>>>>>>>>>>> quality T1 image instead of all T1s acquired in a session, e.g. >>>>>>>>>>>>>> >>>>>>>>>>>>>> re QC Comments -- >>>>>>>>>>>>>> Once you have successfully loaded scans (matched to the >>>>>>>>>>>>>> mri_protocol table), you'll be able to use the Imaging Browser's View >>>>>>>>>>>>>> Session subpage to enter/view QC comments on each volume, or for each >>>>>>>>>>>>>> visit. >>>>>>>>>>>>>> These are stored directly in the database, and linked to each >>>>>>>>>>>>>> scan. (Table name: feedback_mri_comments) >>>>>>>>>>>>>> (Visit-level QC comments are linked to the session.) >>>>>>>>>>>>>> >>>>>>>>>>>>>> For a walkthrough of the Imaging setup - please see the Imaging >>>>>>>>>>>>>> Setup guide >>>>>>>>>>>>>> >>>>>>>>>>>>>> - >>>>>>>>>>>>>> >>>>>>>>>>>>>> An old LORIS walkthrough video >>>>>>>>>>>>>> can also walk >>>>>>>>>>>>>> you through some of the Imaging front-end features, starting at 8:00 >>>>>>>>>>>>>> LORIS' imaging modules have been updated many times since >>>>>>>>>>>>>> this video, but the functionality and workflow is similar. >>>>>>>>>>>>>> >>>>>>>>>>>>>> Let us know how it goes once you have entries in your >>>>>>>>>>>>>> mri_protocol table - >>>>>>>>>>>>>> Best, >>>>>>>>>>>>>> Christine >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> On Fri, Aug 2, 2019 at 7:58 AM Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>> >>>>>>>>>>>>>>> Hi Christine, >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> In the candidate_list page i can see this patient >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> If i press the link under PSCID i get to see >>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> and if i press the link under Scan Done it redirects me to >>>>>>>>>>>>>>> imaging_browser >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> At the mri_violations page i also see No results ( neither >>>>>>>>>>>>>>> on resolved / not resolved ). >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> At the imaging_uploader i can see the record that failed. >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> If i click on the tarchive info i get to see the Protocol >>>>>>>>>>>>>>> Name which i think is the acquisition we wanted? >>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> Also my mri_protocol table is empty. >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> Furthermore i would like to ask about the defaced, native, >>>>>>>>>>>>>>> selected. What exactly is native and selected? And where are the qc >>>>>>>>>>>>>>> comments stored? >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> Finally a walkthrough would be helpful. >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> Thanks, >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> ???? ???, 30 ???? 2019 ???? 8:29 ?.?., ?/? Christine Rogers, >>>>>>>>>>>>>>> Ms. ??????: >>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>> Glad to hear you're making progress with the visit labels. >>>>>>>>>>>>>>>> To follow up on your last few emails: >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> a- The Wiki's Setup Guide contains Sample insert >>>>>>>>>>>>>>>> statements for the Visit Windows table >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> . >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> As Cecile mentioned, the consistency of visit label format >>>>>>>>>>>>>>>> is important: V01, v01, V1, 01 -- whichever you select to use is fine; we >>>>>>>>>>>>>>>> use V01 by default across all documentation. >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> b- For Password reset, there is a script in the tools/ >>>>>>>>>>>>>>>> directory so that a back-end administrator can reset any front-end user >>>>>>>>>>>>>>>> password, including Admin. (See info on setting up / resetting User >>>>>>>>>>>>>>>> passwords in the Wiki's Setup Guide >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> ) >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> c- The minc file not being registered -- due to >>>>>>>>>>>>>>>> AcquisitionProtocol unknown. >>>>>>>>>>>>>>>> This means the SeriesDescription (Acquisition Protocol) in >>>>>>>>>>>>>>>> you Dicom header was not matched to any scan listed in the mri_protocol >>>>>>>>>>>>>>>> database table. >>>>>>>>>>>>>>>> (In the online Loris-MRI Troubleshooting Guide, >>>>>>>>>>>>>>>> this >>>>>>>>>>>>>>>> is Table 3, 2nd-last item "no MINCs inserted"). >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> The MRI Violations module (Readme here) >>>>>>>>>>>>>>>> will show >>>>>>>>>>>>>>>> you the details of this mismatch -- >>>>>>>>>>>>>>>> Go to the module (under the Imaging menu), find your scan >>>>>>>>>>>>>>>> and click the link "Could not identify scan type" -- in the next subpage >>>>>>>>>>>>>>>> you can compare the scan's actual parameters against the mri_protocol >>>>>>>>>>>>>>>> table. >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> To resolve this, adjust your mri_protocol table values or >>>>>>>>>>>>>>>> perhaps ensure your DICOMs are labelled consistently. >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Let us know if this works for you -- we can also walk you >>>>>>>>>>>>>>>> through an example of non-identified scans on Demo.loris.ca >>>>>>>>>>>>>>>> (MRI Violations module). >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>> Christine >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> The LORIS team >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> On Tue, Jul 30, 2019 at 10:47 AM Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> I hope this is sufficient as the error for the visit label >>>>>>>>>>>>>>>>> disappeared. >>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Please see the attached file. Also something i found. >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> lorisadmin at hbp:/data/loris/bin/mri$ cat >>>>>>>>>>>>>>>>> /data/loris/data//logs/TarLoad-17-39-xubBdv.log >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> ==> Loading file from disk >>>>>>>>>>>>>>>>> /tmp/TarLoad-17-39-UyQcG2/dcc0000_258024_v1_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> --> mapping DICOM parameter for >>>>>>>>>>>>>>>>> /tmp/TarLoad-17-39-UyQcG2/dcc0000_258024_v1_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> ==> computing md5 hash for MINC body. >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> --> md5: 6b1202fd63e29de4c9be1cd9925888a5 >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> ==> verifying acquisition protocol >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Acquisition protocol is unknown >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> --> The minc file cannot be registered since the >>>>>>>>>>>>>>>>> AcquisitionProtocol is unknown >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> ???? ???, 30 ???? 2019 ???? 4:58 ?.?., ?/? Sotirios >>>>>>>>>>>>>>>>> Nikoloutsopoulos ??????: >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Ok I fixed the login problem by using a known hash and by >>>>>>>>>>>>>>>>>> deleting the rows from the login_history i was able to login. >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> ???? ???, 30 ???? 2019 ???? 4:50 ?.?., ?/? Sotirios >>>>>>>>>>>>>>>>>> Nikoloutsopoulos ??????: >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> there was no visit label 01 in the Visit_Windows table >>>>>>>>>>>>>>>>>>> and i don't know how to insert it because the record requires lots of >>>>>>>>>>>>>>>>>>> attributes. Also the system for a reason asked me to update my password and >>>>>>>>>>>>>>>>>>> now i don't remember it and my account got suspended. Is there a way to >>>>>>>>>>>>>>>>>>> reset it or set a simple password? I updated the password hash in the >>>>>>>>>>>>>>>>>>> users table by using the hash from another LORIS setup we had and i still >>>>>>>>>>>>>>>>>>> couldn't login ( also the attribute password is always NULL and the >>>>>>>>>>>>>>>>>>> expiration date is 1999-01-01 for some reason ). >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Thanks >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> ???? ???, 29 ???? 2019 ???? 5:21 ?.?., ?/? Cecile Madjar >>>>>>>>>>>>>>>>>>> ??????: >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Can you try adding the visit label v01 to the >>>>>>>>>>>>>>>>>>>> Visit_Windows table? >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> However, I noticed that in a previous dataset, the >>>>>>>>>>>>>>>>>>>> label was V1. Does that refer to the same visit? If so, you might want to >>>>>>>>>>>>>>>>>>>> harmonize the visit labels so they are all the same across datasets for a >>>>>>>>>>>>>>>>>>>> given timepoint, meaning you will need to relabel scans when the visit >>>>>>>>>>>>>>>>>>>> label is different but referring to the same visit label (v01 = V1 etc...). >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Hope this helps, >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> On Mon, Jul 29, 2019 at 10:15 AM Sotirios >>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos wrote: >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> Could you help me with the "Visit label does not >>>>>>>>>>>>>>>>>>>>> exist"? I had changed $subjectID{'createVisitLabel'} to 1 as you had >>>>>>>>>>>>>>>>>>>>> suggested but it appears that this problem hasn't been resolved yet. >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> lorisadmin at hbp:/data/loris/bin/mri$ cat >>>>>>>>>>>>>>>>>>>>> /data/loris/data//logs/TarLoad-14-58-9Xog7H.log >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> ==> Loading file from disk >>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> --> mapping DICOM parameter for >>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> --> using user-defined filterParameters for >>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> Candidate Mismatch Error is Visit label does not exist >>>>>>>>>>>>>>>>>>>>> -> WARNING: This candidate was invalid. Logging to >>>>>>>>>>>>>>>>>>>>> MRICandidateErrors table with reason >>>>>>>>>>>>>>>>>>>>> Visit label does not exist >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> ???? ???, 26 ???? 2019 ???? 3:02 ?.?., ?/? Sotirios >>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos ??????: >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> Hi Cecile, >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> The Center error was fixed. Still the insertion of >>>>>>>>>>>>>>>>>>>>>> mincs fails. Please see the output.txt file i attached. Also is there >>>>>>>>>>>>>>>>>>>>>> something else i need to change at the paths configuration? >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> ???? ???, 25 ???? 2019 ???? 6:55 ?.?., ?/? Cecile >>>>>>>>>>>>>>>>>>>>>> Madjar ??????: >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> We are making progress! >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> I have a feeling this error comes from the fact that >>>>>>>>>>>>>>>>>>>>>>> your psc table does not have the MRI_alias populated for the DCC site. >>>>>>>>>>>>>>>>>>>>>>> Running the following query in the mysql database should fix this: >>>>>>>>>>>>>>>>>>>>>>> UPDATE psc SET MRI_alias="DCC", Alias="DCC" WHERE >>>>>>>>>>>>>>>>>>>>>>> Name="Data Coordinating Center"; >>>>>>>>>>>>>>>>>>>>>>> Repeat the same with all your sites (make sure to >>>>>>>>>>>>>>>>>>>>>>> change the Aliases between sites, they should all be unique). >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> Let me know how it goes! >>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> On Thu, Jul 25, 2019 at 11:43 AM Sotirios >>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos wrote: >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> Dear Cecile, >>>>>>>>>>>>>>>>>>>>>>>> You were right about your guesses. I did the >>>>>>>>>>>>>>>>>>>>>>>> modifications you suggested, i still get the "no mincs inserted" error, now >>>>>>>>>>>>>>>>>>>>>>>> i am getting the "No center found this candidate" error ( how do i fix >>>>>>>>>>>>>>>>>>>>>>>> that? from what i see the .dcm files contains a 'Institution Name', is that >>>>>>>>>>>>>>>>>>>>>>>> the center? ), so i guess that's why the validation fails, but i changed >>>>>>>>>>>>>>>>>>>>>>>> the force variable of tarchiveLoader to 1, shouldn't it have inserted the >>>>>>>>>>>>>>>>>>>>>>>> mincs then? Also it is optional to have a mail server, right? ( from what i >>>>>>>>>>>>>>>>>>>>>>>> see the mail error does not affect the $valid_study, so i assume we are >>>>>>>>>>>>>>>>>>>>>>>> okay with that ) >>>>>>>>>>>>>>>>>>>>>>>> Thank you a lot, >>>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 25 ???? 2019 ???? 5:48 ?.?., ?/? Cecile >>>>>>>>>>>>>>>>>>>>>>>> Madjar ??????: >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> From what I understand, I believe you just need to >>>>>>>>>>>>>>>>>>>>>>>>> update a few config settings from the frontend in the Config module (under >>>>>>>>>>>>>>>>>>>>>>>>> the Admin menu). >>>>>>>>>>>>>>>>>>>>>>>>> [image: Screen Shot 2019-07-25 at 10.31.35 AM.png] >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> Then go to the Paths section of the config module >>>>>>>>>>>>>>>>>>>>>>>>> and update the "LORIS-MRI code" config setting to /data/loris/bin/mri (my >>>>>>>>>>>>>>>>>>>>>>>>> guess is that currently, it is set to /data/LORIS/data) and click on the >>>>>>>>>>>>>>>>>>>>>>>>> submit button. >>>>>>>>>>>>>>>>>>>>>>>>> [image: Screen Shot 2019-07-25 at 10.32.50 AM.png] >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> Then, go to Imaging Pipeline section of the >>>>>>>>>>>>>>>>>>>>>>>>> Configuration module and update the "Loris-MRI Data Directory" to >>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/ (my guess is that it is empty at the moment in your >>>>>>>>>>>>>>>>>>>>>>>>> database which is why $data_dir is not defined when you run the >>>>>>>>>>>>>>>>>>>>>>>>> tarchiveLoader step of the insertion pipeline). >>>>>>>>>>>>>>>>>>>>>>>>> [image: Screen Shot 2019-07-25 at 10.40.52 AM.png] >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> Finally, I took a look at your environment file >>>>>>>>>>>>>>>>>>>>>>>>> and it might be a good idea to update your PERL5LIB variable to the >>>>>>>>>>>>>>>>>>>>>>>>> following (it has been added to the code a few releases ago as we realized >>>>>>>>>>>>>>>>>>>>>>>>> this was needed for the libraries. Not sure which version of LORIS-MRI you >>>>>>>>>>>>>>>>>>>>>>>>> are using but it does not hurt to update this variable to what I suggest >>>>>>>>>>>>>>>>>>>>>>>>> below): >>>>>>>>>>>>>>>>>>>>>>>>> export >>>>>>>>>>>>>>>>>>>>>>>>> PERL5LIB=/data/loris/bin/mri/uploadNeuroDB:/data/loris/bin/mri/dicom-archive:$PERL5LIB >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> Hope this helps. Sorry you are experiencing so >>>>>>>>>>>>>>>>>>>>>>>>> much trouble setting things up. We probably need to update our WIKI. >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> On Thu, Jul 25, 2019 at 9:48 AM Sotirios >>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos wrote: >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> The "Loris-MRI Data Directory" should be in the >>>>>>>>>>>>>>>>>>>>>>>>>> environment file? >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 25 ???? 2019 ???? 12:59 ?.?., ?/? >>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos >>>>>>>>>>>>>>>>>>>>>>>>>> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> The scripts are located in >>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/. Somewhere I might have messed something up but i >>>>>>>>>>>>>>>>>>>>>>>>>>> remember following the instructions in the wiki.For example when i tried to >>>>>>>>>>>>>>>>>>>>>>>>>>> execute the batch_uploads_imageuploader perl script the line >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> my $command = "$bin_dir/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl " >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> was pointing to an invalid path, for example: it >>>>>>>>>>>>>>>>>>>>>>>>>>> was repeating a pattern and had LORIS instead of loris ( i think the >>>>>>>>>>>>>>>>>>>>>>>>>>> mistake was that in the wiki it suggested to use $PROJECT for the name of >>>>>>>>>>>>>>>>>>>>>>>>>>> the folder and i choosed 'loris' >>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris/wiki/Imaging-Database >>>>>>>>>>>>>>>>>>>>>>>>>>> ). See also the in image for the modification i did. Also i didn't find the >>>>>>>>>>>>>>>>>>>>>>>>>>> section to config the $data_dir variable. >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 24 ???? 2019 ???? 6:05 ?.?., ?/? >>>>>>>>>>>>>>>>>>>>>>>>>>> Cecile Madjar ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> It looks like you have one Config setting not >>>>>>>>>>>>>>>>>>>>>>>>>>>> set (based on the first error message you got when running it the first >>>>>>>>>>>>>>>>>>>>>>>>>>>> time). You need to set a value for "Loris-MRI Data Directory" in the Config >>>>>>>>>>>>>>>>>>>>>>>>>>>> module under the Imaging pipeline section (from what I can see, it would be >>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/ for your setup). >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> The reason you got that error message the >>>>>>>>>>>>>>>>>>>>>>>>>>>> second time is that the pipeline checks if the DICOM study was already >>>>>>>>>>>>>>>>>>>>>>>>>>>> inserted in the tarchive table. Since you ran the study once already, the >>>>>>>>>>>>>>>>>>>>>>>>>>>> study is inserted into the tarchive, hence the message. However, the >>>>>>>>>>>>>>>>>>>>>>>>>>>> pipeline did not complete as the MINC files were not created and inserted >>>>>>>>>>>>>>>>>>>>>>>>>>>> into the files/parameter_file table. In order to continue the insertion, >>>>>>>>>>>>>>>>>>>>>>>>>>>> you will then need to run the tarchiveLoader command suggested in the >>>>>>>>>>>>>>>>>>>>>>>>>>>> terminal during the second run: >>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader >>>>>>>>>>>>>>>>>>>>>>>>>>>> -globLocation -profile prod >>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive//2012/DCM_2012-12-05_ImagingUpload-17-43-ZUEFjb.tar >>>>>>>>>>>>>>>>>>>>>>>>>>>> -verbose >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> Finally, I am a bit confused by your setup. >>>>>>>>>>>>>>>>>>>>>>>>>>>> Where are the scripts located? In /data/loris/bin/mri or /data/loris/data? >>>>>>>>>>>>>>>>>>>>>>>>>>>> It feels like the Config setting "LORIS-MRI code" in the Paths section was >>>>>>>>>>>>>>>>>>>>>>>>>>>> set to "/data/LORIS/data" but it should have been set to the directory >>>>>>>>>>>>>>>>>>>>>>>>>>>> where the scripts are located (most probably /data/loris/bin/mri). >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helps, >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> On Wed, Jul 24, 2019 at 10:55 AM Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos wrote: >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Ok first i execute this command: >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> "lorisadmin at hbp:/data/loris/bin/mri$ >>>>>>>>>>>>>>>>>>>>>>>>>>>>> ./batch_uploads_imageuploader -profile prod < ~/Desktop/input.txt > log.txt >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at ./batch_uploads_imageuploader line 143. >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at ./batch_uploads_imageuploader line 143. >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $_ in pattern match >>>>>>>>>>>>>>>>>>>>>>>>>>>>> (m//) at ./batch_uploads_imageuploader line 147. >>>>>>>>>>>>>>>>>>>>>>>>>>>>> base is DCC0000_258024_V01 >>>>>>>>>>>>>>>>>>>>>>>>>>>>> path is /data/incoming/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>> type is .tar.gz >>>>>>>>>>>>>>>>>>>>>>>>>>>>> fullpath is >>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/incoming/DCC0000_258024_V01.tar.gz >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> source /tmp/ImagingUpload-17-43-ZUEFjb >>>>>>>>>>>>>>>>>>>>>>>>>>>>> targetlocation /data/loris/data/tarchive >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 256. >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 284. >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at /data/loris/bin/mri/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>> tarchive_validation.pl line 219. >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at /data/loris/bin/mri/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl line 270. >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 711. >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Can't exec "mail": No such file or directory >>>>>>>>>>>>>>>>>>>>>>>>>>>>> at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 721. >>>>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 722. >>>>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 723. >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 724. >>>>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 724. >>>>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 725. >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 735. >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> No Mincs inserted >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> The tarchiveLoader insertion script has failed. >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Running now the following command: >>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl -profile prod >>>>>>>>>>>>>>>>>>>>>>>>>>>>> -upload_id 3 /data/incoming/DCC0000_258024_V01.tar.gz -verbose" >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> I inserted the VisitLabel, but still the Mincs >>>>>>>>>>>>>>>>>>>>>>>>>>>>> are not inserted and i am getting this error >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> "lorisadmin at hbp:/data/loris/bin/mri$ >>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl -profile prod >>>>>>>>>>>>>>>>>>>>>>>>>>>>> -upload_id 3 /data/incoming/DCC0000_258024_V01.tar.gz -verbose >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> find -path >>>>>>>>>>>>>>>>>>>>>>>>>>>>> \/tmp\/ImagingUpload\-17\-45\-5MsWEd -name '__MACOSX' -delete >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Spool message is: >>>>>>>>>>>>>>>>>>>>>>>>>>>>> The Scan for the uploadID 3 has already been >>>>>>>>>>>>>>>>>>>>>>>>>>>>> run with tarchiveID: 7. >>>>>>>>>>>>>>>>>>>>>>>>>>>>> To continue with the rest of the insertion >>>>>>>>>>>>>>>>>>>>>>>>>>>>> pipeline, please run tarchiveLoader from a terminal as follows: >>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader -globLocation -profile prod >>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive//2012/DCM_2012-12-05_ImagingUpload-17-43-ZUEFjb.tar >>>>>>>>>>>>>>>>>>>>>>>>>>>>> -verbose" >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Which files should i delete? I thought that >>>>>>>>>>>>>>>>>>>>>>>>>>>>> deleting the files from the tarchive was enough. And i executed the last >>>>>>>>>>>>>>>>>>>>>>>>>>>>> proposed command to continue to rest of the insertion pipeline ( check the >>>>>>>>>>>>>>>>>>>>>>>>>>>>> image ). >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 24 ???? 2019 ???? 5:05 ?.?., ?/? >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Cecile Madjar ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sorry I was not clear before. Every visits of >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> candidates are created in the session table with one entry per >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID/VisitLabel. So if the imaging pipeline created visits in the session >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> table (that are not attached to instruments) and you want to clean your >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> database completely, you can delete entries in that table as well. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Regarding your point 2, the imaging pipeline >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> can create the visit in the session table as long as the visit label is >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> present in the Visit_Windows table (which means the visit label stored in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the PatientName is a valid visit label). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> However, in your prod file, if the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> variable $subjectID{'createVisitLabel'} is set to 1 for candidates, the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit label should be created in the Visit_Windows table I believe. Here >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> is the line of the prod file you would need to change >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> . >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> In general, we prefer populating the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Visit_Windows table and set the $subjectID{'createVisitLabel'} to 0 for >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> candidate data to avoid insertion of badly labelled MRI data that are >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> complex to relabel. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Finally, regarding the candidate creation, if >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> you execute the following steps, the pipeline should be able to create >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> candidates: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - set in the Imaging Pipeline section of the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> config module the config setting "Upload creation of candidates" to Yes >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - manually transfer the scans to the LORIS >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> server instead of uploading it via the imaging browser >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - run batch_imaging_upload.pl as you did >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> until now. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helps! >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> On Wed, Jul 24, 2019 at 8:47 AM Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> wrote: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> About my second question i replaced the name >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> of the patient in the .dcm files and now i am getting an error that the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit label does not exist. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I thought it was supposed to be >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> automatically created. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> "Done adding archive info into database >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -globLocation -profile prod >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive//DCM_2012-12-05_ImagingUpload-15-42-yUwQQV.tar >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -verbose >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> md5sum >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive/DCM_2012-12-05_ImagingUpload-15-42-yUwQQV.tar >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> candidate id 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> => No Visit labelVisit label does not exist >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Set centerID = 1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Number of MINC files that will be considered >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> for inserting into the database: 1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> log dir is /logs and log file is >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /logs/TarLoad-15-42-L6pocU.log >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> candidate id 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> => No Visit label >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Cleaning up temp files: rm -rf >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-15-42-J2rQms/ImagingUpload-15-42-yUwQQV*" >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 24 ???? 2019 ???? 3:38 ?.?., ?/? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 1) What are the records in the session >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> table? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 2) I tried to upload a non-phantom file >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> like this >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> input_file.txt: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/incoming/DCC0000_258024_V1.tar.gz N >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DCC0000_258024_V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Terminal: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ./batch_uploads_imageuploader -profile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> prod < ~/Desktop/input.txt > log.txt >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and i get the following error in the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> log.txt file >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> "Running now the following command: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl -profile prod >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -upload_id 7 /data/incoming/DCC0000_258024_V1.tar.gz -verbose >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> find -path >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> \/tmp\/ImagingUpload\-14\-56\-FeLCB4 -name '__MACOSX' -delete >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Spool message is: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The PatientName read from the DICOM header >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> does not start with DCC0000_258024_V1 from the mri_upload table >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> " >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and the spool message is repeated for each >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> .dcm file. Should i preprocess every .dcm file and change the PatientName >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> to "DCC0000_258024_V1"? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 3) As far as it concerns the candidate >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> profile i have to create a new one each time before i try to upload a file? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Is there already a way to create a candidate profile and get the DCCID and >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID without the user interface? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 18 ???? 2019 ???? 5:00 ?.?., ?/? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Cecile Madjar >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> See answers to your questions below. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> About the 1st case we had a dicom with a >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> blank studyUID, maybe someone accidentally removed it. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> That is strange. Something must have been >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> done to the DICOM files. I have never seen a study with no StudyUID out of >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the scanner. Usually, you need to manually erase it with some tool. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> However, DICOMs never cease to surprise me... >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Some other questions: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 1) What are the steps to remove all of my >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> patients and uploads?: because i want to try to reupload all the testing >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> dicoms we had with a clean database. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Release 21.0 of LORIS-MRI will offer a >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> script to remove all the entries and files specific to an upload. However, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> this release is not yet out. Hopefully in the next few weeks. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> In the meantime, since your case is >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> particular and that you just want to start with a clean database, the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> following deletes should work (hopefully I won't forget any tables): >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from mri_violations_log; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from mri_protocol_violated_scans; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from MRICandidateErrors; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from parameter_file; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from files_qcstatus; # (if you >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> played with the QC part of the imaging browser for testing) >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from feedback_mri_comments; # (if >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> you played with the QC part of the imaging browser for testing) >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from tarchive_series; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from tarchive_files; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from mri_upload; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from tarchive; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from mri_scanner; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from candidate where >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID="scanner"; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I don't know if you want to also delete >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> entries in the session and candidate table too? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 2) We do not need to create the profile of >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> a patient ( are the patients stored in the candidate table? because i can't >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> see the ghosts ), because will it automatically be created when importing a >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> dicom? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I am not sure I understand fully this >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> question. All candidates are stored in the candidate table. The phantom >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> scans however are attached to a scanner candidate depending on where the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> scan happened. It is a bit of a weird concept that we have to redesign >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> eventually but never got a chance to get to it. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hopefully this answered your question, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> otherwise, don't hesitate to let me know. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 3) What is the difference between >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> uploading a dicom as phantom instead of importing as >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCCID_DCCID_VisitLabel? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> When you upload the scan as >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID_DCCID_VisitLabel, there is a check that makes sure the candidate IDs >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and visit label are valid at the time of upload. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> When you upload a scan as phantom, it >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> expects that the DICOM field PatientName and uploaded filename contains the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> string "phantom". We enforced this behaviour on the imaging uploader side >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in recent releases but I can't remember which one. Probably the upcoming >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 21.0 release. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> All those verifications might seem >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> cumbersome but they are here to ensure that the files inserted are all >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> valid and labelled properly as it is a bit messy to have to delete files >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> that were wrongly labelled. At least, the delete script present in release >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 21.0 will make this process easier but it is still good practice to verify >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> those things. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> With pleasure. Hopefully the answers to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> your questions will be helpful. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PS: loris-dev mailing list: you will find >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the initial answer I gave Sotirios below. I forgot to cc the loris-dev in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> my earlier reply... >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 16 ???? 2019 ???? 12:02 ?.?., >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ?/? Cecile Madjar >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Dear Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you for reaching out. Since your >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> email was already organized in points, I will reply directly below your >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> questions below. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 1) What do we do when the StudyUID is >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> blank on the header? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/minor/docs/AppendixA-Troubleshooting_guideline.md >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> There solution provided at the table 3 does not guide us how to find the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> information ( is possible ). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The StudyUID is the field used in our >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> pipeline at the moment to check whether a DICOM study was already inserted >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> into LORIS with that same StudyUID since it is supposed to be unique for >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> every single study. Currently, we do not support insertion of DICOM studies >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> if they do not have a StudyUID associated with them. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Is there a specific reason why the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> StudyUID is blank in the DICOM headers in your DICOM files? Did they go >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> through some processes before upload to LORIS? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 2) When i am about to upload a >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> non-phanton case i need a 'Visit Label'. Is there already a script that can >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> create a new visit label for a specific Candidate, so i can provide it as >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> input afterwards to the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> batch_uploads_imageuploader ( See option 5.1.3 https://github.com/aces/Loris-MRI/blob/minor/docs/05-PipelineLaunchOptions.md ) >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I am not sure if the front-end allows >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> for it but if you use batch_uploads_imageuploader, the insertion scripts >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> could create the visit label for you. However, it does need to be included >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in the patient name in order for the script to know which label it should >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> use. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> For example: you upload V02 for MTL0123 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> (DCCID: 456789) but V02 was not yet created for MTL0123; the insertion >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> scripts will create a V02 visit for MTL0123 if the PatientName field for >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the dataset is MTL0123_456789_V02 with Stage marked as "Not Started". >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> However, *note that for the script to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> create the visit for the candidate, you have to make sure that all the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit label of your projects were inserted in the Visit_Windows table* >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> (otherwise, the visit will never be created as they were not specified as >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> being part of the list of visit label to expect). So in the example above, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> you should have one row in Visit_Windows with Visit_label="V02" set. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 3) Section 4.3 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/minor/docs/04-Scripts.md >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> What do we do when the folder contains multiple mnc files? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> This is a case by case. Most of the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> time, the MINC files that failed insertion into the imaging browser end up >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in the MRI violation module where you can see what went wrong with the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> acquisitions not inserted. If you notice that the MINC file should be >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> inserted as a specific protocol, you can force the insertion as explained >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in section 4.3. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> In your case, I have a feeling that you >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> want to be able to insert MINC files that did not go through the whole >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> pipeline insertion (DICOM archival, then dcm2mnc, then protocol >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> identification, then insertion...). In theory, you could call >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl on any MINC file, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> provided you have at least the following information: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - path to the MINC file >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - uploadID associated with the MINC >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> files or DICOM archive path from which those MINC files were created from >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Then the minc_insertion.pl script will >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> do the subject information and protocol validation etc... >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> If all the MINC files come from the same >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> uploadID or TarchiveID, then you could run a loop in bash calling the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl script like this for >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> files deriving from uploadID=1: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ls /path/to/mnc/folder/* | while read f; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> do minc_insertion.pl -profile prod >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -uploadID 1 -mincPath $f; done >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helped! >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> -- >>>>>>>>>>>>>> >>>>>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>>>>> >>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> -- >>>>>>>>>>> >>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>> >>>>>>>>>> _______________________________________________ >>>>>>>>>> Loris-dev mailing list >>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> -- >>>>>>>>> >>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>> Montreal Neurological Institute >>>>>>>>> McGill University | Montreal | Canada >>>>>>>>> _______________________________________________ >>>>>>>>> Loris-dev mailing list >>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> -- >>>>>>>> >>>>>>>> christine.rogers at mcgill.ca >>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>> Montreal Neurological Institute >>>>>>>> McGill University | Montreal | Canada >>>>>>>> _______________________________________________ >>>>>>>> Loris-dev mailing list >>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>> >>>>>>> >>>>>>> >>>>>>> -- >>>>>>> >>>>>>> christine.rogers at mcgill.ca >>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>> Montreal Neurological Institute >>>>>>> McGill University | Montreal | Canada >>>>>>> >>>>>> _______________________________________________ >>>>>> Loris-dev mailing list >>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>> >>>>> >>>>> >>>>> -- >>>>> >>>>> christine.rogers at mcgill.ca >>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>> Montreal Neurological Institute >>>>> McGill University | Montreal | Canada >>>>> >>>> _______________________________________________ >>>> Loris-dev mailing list >>>> Loris-dev at bic.mni.mcgill.ca >>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>> >>> _______________________________________________ >> Loris-dev mailing list >> Loris-dev at bic.mni.mcgill.ca >> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >> > > > -- > > christine.rogers at mcgill.ca > McGill Centre for Integrative Neuroscience | MCIN.ca > Montreal Neurological Institute > McGill University | Montreal | Canada > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- lorisadmin at hbp:/var/www/loris$ cat /home/lorisadmin/.npm/_logs/2019-08-13T18_12_05_378Z-debug.log 0 info it worked if it ends with ok 1 verbose cli [ '/usr/bin/node', '/usr/bin/npm', 'run', 'compile' ] 2 info using npm at 6.4.1 3 info using node at v8.16.0 4 verbose run-script [ 'precompile', 'compile', 'postcompile' ] 5 info lifecycle loris at 1.0.0~precompile: loris at 1.0.0 6 info lifecycle loris at 1.0.0~compile: loris at 1.0.0 7 verbose lifecycle loris at 1.0.0~compile: unsafe-perm in lifecycle true 8 verbose lifecycle loris at 1.0.0~compile: PATH: /usr/lib/node_modules/npm/node_modules/npm-lifecycle/node-gyp-bin:/var/www/loris/node_modules/.bin:/opt/minc/1.9.16/bin:/opt/minc/1.9.16/pipeline:/opt/minc/bin:/data/loris/bin/mri:/data/loris/bin/mri/uploadNeuroDB:/data/loris/bin/mri/uploadNeuroDB/bin:/data/loris/bin/mri/dicom-archive:/home/lorisadmin/bin:/home/lorisadmin/.local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin 9 verbose lifecycle loris at 1.0.0~compile: CWD: /var/www/loris 10 silly lifecycle loris at 1.0.0~compile: Args: [ '-c', 'webpack' ] 11 silly lifecycle loris at 1.0.0~compile: Returned: code: 2 signal: null 12 info lifecycle loris at 1.0.0~compile: Failed to exec compile script 13 verbose stack Error: loris at 1.0.0 compile: `webpack` 13 verbose stack Exit status 2 13 verbose stack at EventEmitter. (/usr/lib/node_modules/npm/node_modules/npm-lifecycle/index.js:301:16) 13 verbose stack at emitTwo (events.js:126:13) 13 verbose stack at EventEmitter.emit (events.js:214:7) 13 verbose stack at ChildProcess. (/usr/lib/node_modules/npm/node_modules/npm-lifecycle/lib/spawn.js:55:14) 13 verbose stack at emitTwo (events.js:126:13) 13 verbose stack at ChildProcess.emit (events.js:214:7) 13 verbose stack at maybeClose (internal/child_process.js:915:16) 13 verbose stack at Process.ChildProcess._handle.onexit (internal/child_process.js:209:5) 14 verbose pkgid loris at 1.0.0 15 verbose cwd /var/www/loris 16 verbose Linux 4.15.0-55-generic 17 verbose argv "/usr/bin/node" "/usr/bin/npm" "run" "compile" 18 verbose node v8.16.0 19 verbose npm v6.4.1 20 error code ELIFECYCLE 21 error errno 2 22 error loris at 1.0.0 compile: `webpack` 22 error Exit status 2 23 error Failed at the loris at 1.0.0 compile script. 23 error This is probably not a problem with npm. 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Set 'mode' option to 'development' or 'production' to enable defaults for each environment. You can also set it to 'none' to disable any default behavior. Learn more: https://webpack.js.org/concepts/mode/ ERROR in ./modules/dataquery/jsx/react.tabs.js Module build failed (from ./node_modules/eslint-loader/index.js): Error: No ESLint configuration found. at Config.getLocalConfigHierarchy (/var/www/loris/node_modules/eslint/lib/config.js:255:39) at Config.getConfigHierarchy (/var/www/loris/node_modules/eslint/lib/config.js:179:43) at Config.getConfigVector (/var/www/loris/node_modules/eslint/lib/config.js:286:21) at Config.getConfig (/var/www/loris/node_modules/eslint/lib/config.js:329:29) at processText (/var/www/loris/node_modules/eslint/lib/cli-engine.js:162:33) at CLIEngine.executeOnText (/var/www/loris/node_modules/eslint/lib/cli-engine.js:596:17) at lint (/var/www/loris/node_modules/eslint-loader/index.js:237:17) at Object.module.exports (/var/www/loris/node_modules/eslint-loader/index.js:232:21) ERROR in ./jsx/DynamicDataTable.js Module build failed (from ./node_modules/eslint-loader/index.js): Error: No ESLint configuration found. at Config.getLocalConfigHierarchy (/var/www/loris/node_modules/eslint/lib/config.js:255:39) at Config.getConfigHierarchy (/var/www/loris/node_modules/eslint/lib/config.js:179:43) at Config.getConfigVector (/var/www/loris/node_modules/eslint/lib/config.js:286:21) at Config.getConfig (/var/www/loris/node_modules/eslint/lib/config.js:329:29) at processText (/var/www/loris/node_modules/eslint/lib/cli-engine.js:162:33) at CLIEngine.executeOnText (/var/www/loris/node_modules/eslint/lib/cli-engine.js:596:17) at lint (/var/www/loris/node_modules/eslint-loader/index.js:237:17) at Object.module.exports (/var/www/loris/node_modules/eslint-loader/index.js:232:21) ERROR in ./jsx/StaticDataTable.js Module build failed (from ./node_modules/eslint-loader/index.js): Error: No ESLint configuration found. at Config.getLocalConfigHierarchy (/var/www/loris/node_modules/eslint/lib/config.js:255:39) at Config.getConfigHierarchy (/var/www/loris/node_modules/eslint/lib/config.js:179:43) at Config.getConfigVector (/var/www/loris/node_modules/eslint/lib/config.js:286:21) at Config.getConfig (/var/www/loris/node_modules/eslint/lib/config.js:329:29) at processText (/var/www/loris/node_modules/eslint/lib/cli-engine.js:162:33) at CLIEngine.executeOnText (/var/www/loris/node_modules/eslint/lib/cli-engine.js:596:17) at lint (/var/www/loris/node_modules/eslint-loader/index.js:237:17) at Object.module.exports (/var/www/loris/node_modules/eslint-loader/index.js:232:21) ERROR in ./jsx/MultiSelectDropdown.js Module build failed (from ./node_modules/eslint-loader/index.js): Error: No ESLint configuration found. at Config.getLocalConfigHierarchy (/var/www/loris/node_modules/eslint/lib/config.js:255:39) at Config.getConfigHierarchy (/var/www/loris/node_modules/eslint/lib/config.js:179:43) at Config.getConfigVector (/var/www/loris/node_modules/eslint/lib/config.js:286:21) at Config.getConfig (/var/www/loris/node_modules/eslint/lib/config.js:329:29) at processText (/var/www/loris/node_modules/eslint/lib/cli-engine.js:162:33) at CLIEngine.executeOnText (/var/www/loris/node_modules/eslint/lib/cli-engine.js:596:17) at lint (/var/www/loris/node_modules/eslint-loader/index.js:237:17) at Object.module.exports (/var/www/loris/node_modules/eslint-loader/index.js:232:21) ERROR in ./jsx/Breadcrumbs.js Module build failed (from ./node_modules/eslint-loader/index.js): Error: No ESLint configuration found. at Config.getLocalConfigHierarchy (/var/www/loris/node_modules/eslint/lib/config.js:255:39) at Config.getConfigHierarchy (/var/www/loris/node_modules/eslint/lib/config.js:179:43) at Config.getConfigVector (/var/www/loris/node_modules/eslint/lib/config.js:286:21) at Config.getConfig (/var/www/loris/node_modules/eslint/lib/config.js:329:29) at processText (/var/www/loris/node_modules/eslint/lib/cli-engine.js:162:33) at CLIEngine.executeOnText (/var/www/loris/node_modules/eslint/lib/cli-engine.js:596:17) at lint (/var/www/loris/node_modules/eslint-loader/index.js:237:17) at Object.module.exports (/var/www/loris/node_modules/eslint-loader/index.js:232:21) ERROR in ./jsx/Form.js Module build failed (from ./node_modules/eslint-loader/index.js): Error: No ESLint configuration found. at Config.getLocalConfigHierarchy (/var/www/loris/node_modules/eslint/lib/config.js:255:39) at Config.getConfigHierarchy (/var/www/loris/node_modules/eslint/lib/config.js:179:43) at Config.getConfigVector (/var/www/loris/node_modules/eslint/lib/config.js:286:21) at Config.getConfig (/var/www/loris/node_modules/eslint/lib/config.js:329:29) at processText (/var/www/loris/node_modules/eslint/lib/cli-engine.js:162:33) at CLIEngine.executeOnText (/var/www/loris/node_modules/eslint/lib/cli-engine.js:596:17) at lint (/var/www/loris/node_modules/eslint-loader/index.js:237:17) at Object.module.exports (/var/www/loris/node_modules/eslint-loader/index.js:232:21) ERROR in ./jsx/Markdown.js Module build failed (from ./node_modules/eslint-loader/index.js): Error: No ESLint configuration found. at Config.getLocalConfigHierarchy (/var/www/loris/node_modules/eslint/lib/config.js:255:39) at Config.getConfigHierarchy (/var/www/loris/node_modules/eslint/lib/config.js:179:43) at Config.getConfigVector (/var/www/loris/node_modules/eslint/lib/config.js:286:21) at Config.getConfig (/var/www/loris/node_modules/eslint/lib/config.js:329:29) at processText (/var/www/loris/node_modules/eslint/lib/cli-engine.js:162:33) at CLIEngine.executeOnText (/var/www/loris/node_modules/eslint/lib/cli-engine.js:596:17) at lint (/var/www/loris/node_modules/eslint-loader/index.js:237:17) at Object.module.exports (/var/www/loris/node_modules/eslint-loader/index.js:232:21) ERROR in ./modules/media/jsx/mediaIndex.js Module build failed (from ./node_modules/eslint-loader/index.js): Error: No ESLint configuration found. at Config.getLocalConfigHierarchy (/var/www/loris/node_modules/eslint/lib/config.js:255:39) at Config.getConfigHierarchy (/var/www/loris/node_modules/eslint/lib/config.js:179:43) at Config.getConfigVector (/var/www/loris/node_modules/eslint/lib/config.js:286:21) at Config.getConfig (/var/www/loris/node_modules/eslint/lib/config.js:329:29) at processText (/var/www/loris/node_modules/eslint/lib/cli-engine.js:162:33) at CLIEngine.executeOnText (/var/www/loris/node_modules/eslint/lib/cli-engine.js:596:17) at lint (/var/www/loris/node_modules/eslint-loader/index.js:237:17) at Object.module.exports (/var/www/loris/node_modules/eslint-loader/index.js:232:21) ERROR in ./modules/issue_tracker/jsx/issueTrackerIndex.js Module build failed (from ./node_modules/eslint-loader/index.js): Error: No ESLint configuration found. at Config.getLocalConfigHierarchy (/var/www/loris/node_modules/eslint/lib/config.js:255:39) at Config.getConfigHierarchy (/var/www/loris/node_modules/eslint/lib/config.js:179:43) at Config.getConfigVector (/var/www/loris/node_modules/eslint/lib/config.js:286:21) at Config.getConfig (/var/www/loris/node_modules/eslint/lib/config.js:329:29) at processText (/var/www/loris/node_modules/eslint/lib/cli-engine.js:162:33) at CLIEngine.executeOnText (/var/www/loris/node_modules/eslint/lib/cli-engine.js:596:17) at lint (/var/www/loris/node_modules/eslint-loader/index.js:237:17) at Object.module.exports (/var/www/loris/node_modules/eslint-loader/index.js:232:21) ERROR in ./modules/issue_tracker/jsx/index.js Module build failed (from ./node_modules/eslint-loader/index.js): Error: No ESLint configuration found. at Config.getLocalConfigHierarchy (/var/www/loris/node_modules/eslint/lib/config.js:255:39) at Config.getConfigHierarchy (/var/www/loris/node_modules/eslint/lib/config.js:179:43) at Config.getConfigVector (/var/www/loris/node_modules/eslint/lib/config.js:286:21) at Config.getConfig (/var/www/loris/node_modules/eslint/lib/config.js:329:29) at processText (/var/www/loris/node_modules/eslint/lib/cli-engine.js:162:33) at CLIEngine.executeOnText (/var/www/loris/node_modules/eslint/lib/cli-engine.js:596:17) at lint (/var/www/loris/node_modules/eslint-loader/index.js:237:17) at Object.module.exports (/var/www/loris/node_modules/eslint-loader/index.js:232:21) ERROR in ./modules/candidate_parameters/jsx/CandidateParameters.js Module build failed (from ./node_modules/eslint-loader/index.js): Error: No ESLint configuration found. at Config.getLocalConfigHierarchy (/var/www/loris/node_modules/eslint/lib/config.js:255:39) at Config.getConfigHierarchy (/var/www/loris/node_modules/eslint/lib/config.js:179:43) at Config.getConfigVector (/var/www/loris/node_modules/eslint/lib/config.js:286:21) at Config.getConfig (/var/www/loris/node_modules/eslint/lib/config.js:329:29) at processText (/var/www/loris/node_modules/eslint/lib/cli-engine.js:162:33) at CLIEngine.executeOnText (/var/www/loris/node_modules/eslint/lib/cli-engine.js:596:17) at lint (/var/www/loris/node_modules/eslint-loader/index.js:237:17) at Object.module.exports (/var/www/loris/node_modules/eslint-loader/index.js:232:21) ERROR in ./modules/configuration/jsx/SubprojectRelations.js Module build failed (from ./node_modules/eslint-loader/index.js): Error: No ESLint configuration found. at Config.getLocalConfigHierarchy (/var/www/loris/node_modules/eslint/lib/config.js:255:39) at Config.getConfigHierarchy (/var/www/loris/node_modules/eslint/lib/config.js:179:43) at Config.getConfigVector (/var/www/loris/node_modules/eslint/lib/config.js:286:21) at Config.getConfig (/var/www/loris/node_modules/eslint/lib/config.js:329:29) at processText (/var/www/loris/node_modules/eslint/lib/cli-engine.js:162:33) at CLIEngine.executeOnText (/var/www/loris/node_modules/eslint/lib/cli-engine.js:596:17) at lint (/var/www/loris/node_modules/eslint-loader/index.js:237:17) at Object.module.exports (/var/www/loris/node_modules/eslint-loader/index.js:232:21) ERROR in ./modules/conflict_resolver/jsx/conflictResolverIndex.js Module build failed (from ./node_modules/eslint-loader/index.js): Error: No ESLint configuration found. at Config.getLocalConfigHierarchy (/var/www/loris/node_modules/eslint/lib/config.js:255:39) at Config.getConfigHierarchy (/var/www/loris/node_modules/eslint/lib/config.js:179:43) at Config.getConfigVector (/var/www/loris/node_modules/eslint/lib/config.js:286:21) at Config.getConfig (/var/www/loris/node_modules/eslint/lib/config.js:329:29) at processText (/var/www/loris/node_modules/eslint/lib/cli-engine.js:162:33) at CLIEngine.executeOnText (/var/www/loris/node_modules/eslint/lib/cli-engine.js:596:17) at lint (/var/www/loris/node_modules/eslint-loader/index.js:237:17) at Object.module.exports (/var/www/loris/node_modules/eslint-loader/index.js:232:21) ERROR in ./modules/conflict_resolver/jsx/resolvedConflictsIndex.js Module build failed (from ./node_modules/eslint-loader/index.js): Error: No ESLint configuration found. at Config.getLocalConfigHierarchy (/var/www/loris/node_modules/eslint/lib/config.js:255:39) at Config.getConfigHierarchy (/var/www/loris/node_modules/eslint/lib/config.js:179:43) at Config.getConfigVector (/var/www/loris/node_modules/eslint/lib/config.js:286:21) at Config.getConfig (/var/www/loris/node_modules/eslint/lib/config.js:329:29) at processText (/var/www/loris/node_modules/eslint/lib/cli-engine.js:162:33) at CLIEngine.executeOnText (/var/www/loris/node_modules/eslint/lib/cli-engine.js:596:17) at lint (/var/www/loris/node_modules/eslint-loader/index.js:237:17) at Object.module.exports (/var/www/loris/node_modules/eslint-loader/index.js:232:21) ERROR in ./modules/bvl_feedback/jsx/react.behavioural_feedback_panel.js Module build failed (from ./node_modules/eslint-loader/index.js): Error: No ESLint configuration found. at Config.getLocalConfigHierarchy (/var/www/loris/node_modules/eslint/lib/config.js:255:39) at Config.getConfigHierarchy (/var/www/loris/node_modules/eslint/lib/config.js:179:43) at Config.getConfigVector (/var/www/loris/node_modules/eslint/lib/config.js:286:21) at Config.getConfig (/var/www/loris/node_modules/eslint/lib/config.js:329:29) at processText (/var/www/loris/node_modules/eslint/lib/cli-engine.js:162:33) at CLIEngine.executeOnText (/var/www/loris/node_modules/eslint/lib/cli-engine.js:596:17) at lint (/var/www/loris/node_modules/eslint-loader/index.js:237:17) at Object.module.exports (/var/www/loris/node_modules/eslint-loader/index.js:232:21) ERROR in ./modules/data_team_helper/jsx/behavioural_qc_module.js Module build failed (from ./node_modules/eslint-loader/index.js): Error: No ESLint configuration found. at Config.getLocalConfigHierarchy (/var/www/loris/node_modules/eslint/lib/config.js:255:39) at Config.getConfigHierarchy (/var/www/loris/node_modules/eslint/lib/config.js:179:43) at Config.getConfigVector (/var/www/loris/node_modules/eslint/lib/config.js:286:21) at Config.getConfig (/var/www/loris/node_modules/eslint/lib/config.js:329:29) at processText (/var/www/loris/node_modules/eslint/lib/cli-engine.js:162:33) at CLIEngine.executeOnText (/var/www/loris/node_modules/eslint/lib/cli-engine.js:596:17) at lint (/var/www/loris/node_modules/eslint-loader/index.js:237:17) at Object.module.exports (/var/www/loris/node_modules/eslint-loader/index.js:232:21) ERROR in ./modules/candidate_list/jsx/openProfileForm.js Module build failed (from ./node_modules/eslint-loader/index.js): Error: No ESLint configuration found. at Config.getLocalConfigHierarchy (/var/www/loris/node_modules/eslint/lib/config.js:255:39) at Config.getConfigHierarchy (/var/www/loris/node_modules/eslint/lib/config.js:179:43) at Config.getConfigVector (/var/www/loris/node_modules/eslint/lib/config.js:286:21) at Config.getConfig (/var/www/loris/node_modules/eslint/lib/config.js:329:29) at processText (/var/www/loris/node_modules/eslint/lib/cli-engine.js:162:33) at CLIEngine.executeOnText (/var/www/loris/node_modules/eslint/lib/cli-engine.js:596:17) at lint (/var/www/loris/node_modules/eslint-loader/index.js:237:17) at Object.module.exports (/var/www/loris/node_modules/eslint-loader/index.js:232:21) ERROR in ./modules/candidate_list/jsx/onLoad.js Module build failed (from ./node_modules/eslint-loader/index.js): Error: No ESLint configuration found. at Config.getLocalConfigHierarchy (/var/www/loris/node_modules/eslint/lib/config.js:255:39) at Config.getConfigHierarchy (/var/www/loris/node_modules/eslint/lib/config.js:179:43) at Config.getConfigVector (/var/www/loris/node_modules/eslint/lib/config.js:286:21) at Config.getConfig (/var/www/loris/node_modules/eslint/lib/config.js:329:29) at processText (/var/www/loris/node_modules/eslint/lib/cli-engine.js:162:33) at CLIEngine.executeOnText (/var/www/loris/node_modules/eslint/lib/cli-engine.js:596:17) at lint (/var/www/loris/node_modules/eslint-loader/index.js:237:17) at Object.module.exports (/var/www/loris/node_modules/eslint-loader/index.js:232:21) ERROR in ./modules/candidate_list/jsx/candidateListIndex.js Module build failed (from ./node_modules/eslint-loader/index.js): Error: No ESLint configuration found. at Config.getLocalConfigHierarchy (/var/www/loris/node_modules/eslint/lib/config.js:255:39) at Config.getConfigHierarchy (/var/www/loris/node_modules/eslint/lib/config.js:179:43) at Config.getConfigVector (/var/www/loris/node_modules/eslint/lib/config.js:286:21) at Config.getConfig (/var/www/loris/node_modules/eslint/lib/config.js:329:29) at processText (/var/www/loris/node_modules/eslint/lib/cli-engine.js:162:33) at CLIEngine.executeOnText (/var/www/loris/node_modules/eslint/lib/cli-engine.js:596:17) at lint (/var/www/loris/node_modules/eslint-loader/index.js:237:17) at Object.module.exports (/var/www/loris/node_modules/eslint-loader/index.js:232:21) ERROR in ./modules/datadict/jsx/dataDictIndex.js Module build failed (from ./node_modules/eslint-loader/index.js): Error: No ESLint configuration found. at Config.getLocalConfigHierarchy (/var/www/loris/node_modules/eslint/lib/config.js:255:39) at Config.getConfigHierarchy (/var/www/loris/node_modules/eslint/lib/config.js:179:43) at Config.getConfigVector (/var/www/loris/node_modules/eslint/lib/config.js:286:21) at Config.getConfig (/var/www/loris/node_modules/eslint/lib/config.js:329:29) at processText (/var/www/loris/node_modules/eslint/lib/cli-engine.js:162:33) at CLIEngine.executeOnText (/var/www/loris/node_modules/eslint/lib/cli-engine.js:596:17) at lint (/var/www/loris/node_modules/eslint-loader/index.js:237:17) at Object.module.exports (/var/www/loris/node_modules/eslint-loader/index.js:232:21) ERROR in ./modules/data_integrity_flag/jsx/dataIntegrityFlagIndex.js Module build failed (from ./node_modules/eslint-loader/index.js): Error: No ESLint configuration found. at Config.getLocalConfigHierarchy (/var/www/loris/node_modules/eslint/lib/config.js:255:39) at Config.getConfigHierarchy (/var/www/loris/node_modules/eslint/lib/config.js:179:43) at Config.getConfigVector (/var/www/loris/node_modules/eslint/lib/config.js:286:21) at Config.getConfig (/var/www/loris/node_modules/eslint/lib/config.js:329:29) at processText (/var/www/loris/node_modules/eslint/lib/cli-engine.js:162:33) at CLIEngine.executeOnText (/var/www/loris/node_modules/eslint/lib/cli-engine.js:596:17) at lint (/var/www/loris/node_modules/eslint-loader/index.js:237:17) at Object.module.exports (/var/www/loris/node_modules/eslint-loader/index.js:232:21) ERROR in ./modules/dataquery/jsx/react.app.js Module build failed (from ./node_modules/eslint-loader/index.js): Error: No ESLint configuration found. at Config.getLocalConfigHierarchy (/var/www/loris/node_modules/eslint/lib/config.js:255:39) at Config.getConfigHierarchy (/var/www/loris/node_modules/eslint/lib/config.js:179:43) at Config.getConfigVector (/var/www/loris/node_modules/eslint/lib/config.js:286:21) at Config.getConfig (/var/www/loris/node_modules/eslint/lib/config.js:329:29) at processText (/var/www/loris/node_modules/eslint/lib/cli-engine.js:162:33) at CLIEngine.executeOnText (/var/www/loris/node_modules/eslint/lib/cli-engine.js:596:17) at lint (/var/www/loris/node_modules/eslint-loader/index.js:237:17) at Object.module.exports (/var/www/loris/node_modules/eslint-loader/index.js:232:21) ERROR in ./modules/dataquery/jsx/react.fieldselector.js Module build failed (from ./node_modules/eslint-loader/index.js): Error: No ESLint configuration found. at Config.getLocalConfigHierarchy (/var/www/loris/node_modules/eslint/lib/config.js:255:39) at Config.getConfigHierarchy (/var/www/loris/node_modules/eslint/lib/config.js:179:43) at Config.getConfigVector (/var/www/loris/node_modules/eslint/lib/config.js:286:21) at Config.getConfig (/var/www/loris/node_modules/eslint/lib/config.js:329:29) at processText (/var/www/loris/node_modules/eslint/lib/cli-engine.js:162:33) at CLIEngine.executeOnText (/var/www/loris/node_modules/eslint/lib/cli-engine.js:596:17) at lint (/var/www/loris/node_modules/eslint-loader/index.js:237:17) at Object.module.exports (/var/www/loris/node_modules/eslint-loader/index.js:232:21) ERROR in ./modules/dataquery/jsx/react.filterBuilder.js Module build failed (from ./node_modules/eslint-loader/index.js): Error: No ESLint configuration found. at Config.getLocalConfigHierarchy (/var/www/loris/node_modules/eslint/lib/config.js:255:39) at Config.getConfigHierarchy (/var/www/loris/node_modules/eslint/lib/config.js:179:43) at Config.getConfigVector (/var/www/loris/node_modules/eslint/lib/config.js:286:21) at Config.getConfig (/var/www/loris/node_modules/eslint/lib/config.js:329:29) at processText (/var/www/loris/node_modules/eslint/lib/cli-engine.js:162:33) at CLIEngine.executeOnText (/var/www/loris/node_modules/eslint/lib/cli-engine.js:596:17) at lint (/var/www/loris/node_modules/eslint-loader/index.js:237:17) at Object.module.exports (/var/www/loris/node_modules/eslint-loader/index.js:232:21) ERROR in ./modules/dataquery/jsx/react.paginator.js Module build failed (from ./node_modules/eslint-loader/index.js): Error: No ESLint configuration found. at Config.getLocalConfigHierarchy (/var/www/loris/node_modules/eslint/lib/config.js:255:39) at Config.getConfigHierarchy (/var/www/loris/node_modules/eslint/lib/config.js:179:43) at Config.getConfigVector (/var/www/loris/node_modules/eslint/lib/config.js:286:21) at Config.getConfig (/var/www/loris/node_modules/eslint/lib/config.js:329:29) at processText (/var/www/loris/node_modules/eslint/lib/cli-engine.js:162:33) at CLIEngine.executeOnText (/var/www/loris/node_modules/eslint/lib/cli-engine.js:596:17) at lint (/var/www/loris/node_modules/eslint-loader/index.js:237:17) at Object.module.exports (/var/www/loris/node_modules/eslint-loader/index.js:232:21) ERROR in ./modules/dataquery/jsx/react.sidebar.js Module build failed (from ./node_modules/eslint-loader/index.js): Error: No ESLint configuration found. at Config.getLocalConfigHierarchy (/var/www/loris/node_modules/eslint/lib/config.js:255:39) at Config.getConfigHierarchy (/var/www/loris/node_modules/eslint/lib/config.js:179:43) at Config.getConfigVector (/var/www/loris/node_modules/eslint/lib/config.js:286:21) at Config.getConfig (/var/www/loris/node_modules/eslint/lib/config.js:329:29) at processText (/var/www/loris/node_modules/eslint/lib/cli-engine.js:162:33) at CLIEngine.executeOnText (/var/www/loris/node_modules/eslint/lib/cli-engine.js:596:17) at lint (/var/www/loris/node_modules/eslint-loader/index.js:237:17) at Object.module.exports (/var/www/loris/node_modules/eslint-loader/index.js:232:21) ERROR in ./jsx/PaginationLinks.js Module build failed (from ./node_modules/eslint-loader/index.js): Error: No ESLint configuration found. at Config.getLocalConfigHierarchy (/var/www/loris/node_modules/eslint/lib/config.js:255:39) at Config.getConfigHierarchy (/var/www/loris/node_modules/eslint/lib/config.js:179:43) at Config.getConfigVector (/var/www/loris/node_modules/eslint/lib/config.js:286:21) at Config.getConfig (/var/www/loris/node_modules/eslint/lib/config.js:329:29) at processText (/var/www/loris/node_modules/eslint/lib/cli-engine.js:162:33) at CLIEngine.executeOnText (/var/www/loris/node_modules/eslint/lib/cli-engine.js:596:17) at lint (/var/www/loris/node_modules/eslint-loader/index.js:237:17) at Object.module.exports (/var/www/loris/node_modules/eslint-loader/index.js:232:21) ERROR in ./modules/dicom_archive/jsx/dicom_archive.js Module build failed (from ./node_modules/eslint-loader/index.js): Error: No ESLint configuration found. at Config.getLocalConfigHierarchy (/var/www/loris/node_modules/eslint/lib/config.js:255:39) at Config.getConfigHierarchy (/var/www/loris/node_modules/eslint/lib/config.js:179:43) at Config.getConfigVector (/var/www/loris/node_modules/eslint/lib/config.js:286:21) at Config.getConfig (/var/www/loris/node_modules/eslint/lib/config.js:329:29) at processText (/var/www/loris/node_modules/eslint/lib/cli-engine.js:162:33) at CLIEngine.executeOnText (/var/www/loris/node_modules/eslint/lib/cli-engine.js:596:17) at lint (/var/www/loris/node_modules/eslint-loader/index.js:237:17) at Object.module.exports (/var/www/loris/node_modules/eslint-loader/index.js:232:21) ERROR in ./modules/genomic_browser/jsx/FileUploadModal.js Module build failed (from ./node_modules/eslint-loader/index.js): Error: No ESLint configuration found. at Config.getLocalConfigHierarchy (/var/www/loris/node_modules/eslint/lib/config.js:255:39) at Config.getConfigHierarchy (/var/www/loris/node_modules/eslint/lib/config.js:179:43) at Config.getConfigVector (/var/www/loris/node_modules/eslint/lib/config.js:286:21) at Config.getConfig (/var/www/loris/node_modules/eslint/lib/config.js:329:29) at processText (/var/www/loris/node_modules/eslint/lib/cli-engine.js:162:33) at CLIEngine.executeOnText (/var/www/loris/node_modules/eslint/lib/cli-engine.js:596:17) at lint (/var/www/loris/node_modules/eslint-loader/index.js:237:17) at Object.module.exports (/var/www/loris/node_modules/eslint-loader/index.js:232:21) ERROR in ./modules/genomic_browser/jsx/profileColumnFormatter.js Module build failed (from ./node_modules/eslint-loader/index.js): Error: No ESLint configuration found. at Config.getLocalConfigHierarchy (/var/www/loris/node_modules/eslint/lib/config.js:255:39) at Config.getConfigHierarchy (/var/www/loris/node_modules/eslint/lib/config.js:179:43) at Config.getConfigVector (/var/www/loris/node_modules/eslint/lib/config.js:286:21) at Config.getConfig (/var/www/loris/node_modules/eslint/lib/config.js:329:29) at processText (/var/www/loris/node_modules/eslint/lib/cli-engine.js:162:33) at CLIEngine.executeOnText (/var/www/loris/node_modules/eslint/lib/cli-engine.js:596:17) at lint (/var/www/loris/node_modules/eslint-loader/index.js:237:17) at Object.module.exports (/var/www/loris/node_modules/eslint-loader/index.js:232:21) ERROR in ./modules/imaging_browser/jsx/ImagePanel.js Module build failed (from ./node_modules/eslint-loader/index.js): Error: No ESLint configuration found. at Config.getLocalConfigHierarchy (/var/www/loris/node_modules/eslint/lib/config.js:255:39) at Config.getConfigHierarchy (/var/www/loris/node_modules/eslint/lib/config.js:179:43) at Config.getConfigVector (/var/www/loris/node_modules/eslint/lib/config.js:286:21) at Config.getConfig (/var/www/loris/node_modules/eslint/lib/config.js:329:29) at processText (/var/www/loris/node_modules/eslint/lib/cli-engine.js:162:33) at CLIEngine.executeOnText (/var/www/loris/node_modules/eslint/lib/cli-engine.js:596:17) at lint (/var/www/loris/node_modules/eslint-loader/index.js:237:17) at Object.module.exports (/var/www/loris/node_modules/eslint-loader/index.js:232:21) ERROR in ./modules/imaging_browser/jsx/imagingBrowserIndex.js Module build failed (from ./node_modules/eslint-loader/index.js): Error: No ESLint configuration found. at Config.getLocalConfigHierarchy (/var/www/loris/node_modules/eslint/lib/config.js:255:39) at Config.getConfigHierarchy (/var/www/loris/node_modules/eslint/lib/config.js:179:43) at Config.getConfigVector (/var/www/loris/node_modules/eslint/lib/config.js:286:21) at Config.getConfig (/var/www/loris/node_modules/eslint/lib/config.js:329:29) at processText (/var/www/loris/node_modules/eslint/lib/cli-engine.js:162:33) at CLIEngine.executeOnText (/var/www/loris/node_modules/eslint/lib/cli-engine.js:596:17) at lint (/var/www/loris/node_modules/eslint-loader/index.js:237:17) at Object.module.exports (/var/www/loris/node_modules/eslint-loader/index.js:232:21) ERROR in ./modules/instrument_builder/jsx/react.instrument_builder.js Module build failed (from ./node_modules/eslint-loader/index.js): Error: No ESLint configuration found. at Config.getLocalConfigHierarchy (/var/www/loris/node_modules/eslint/lib/config.js:255:39) at Config.getConfigHierarchy (/var/www/loris/node_modules/eslint/lib/config.js:179:43) at Config.getConfigVector (/var/www/loris/node_modules/eslint/lib/config.js:286:21) at Config.getConfig (/var/www/loris/node_modules/eslint/lib/config.js:329:29) at processText (/var/www/loris/node_modules/eslint/lib/cli-engine.js:162:33) at CLIEngine.executeOnText (/var/www/loris/node_modules/eslint/lib/cli-engine.js:596:17) at lint (/var/www/loris/node_modules/eslint-loader/index.js:237:17) at Object.module.exports (/var/www/loris/node_modules/eslint-loader/index.js:232:21) ERROR in ./modules/instrument_builder/jsx/react.questions.js Module build failed (from ./node_modules/eslint-loader/index.js): Error: No ESLint configuration found. at Config.getLocalConfigHierarchy (/var/www/loris/node_modules/eslint/lib/config.js:255:39) at Config.getConfigHierarchy (/var/www/loris/node_modules/eslint/lib/config.js:179:43) at Config.getConfigVector (/var/www/loris/node_modules/eslint/lib/config.js:286:21) at Config.getConfig (/var/www/loris/node_modules/eslint/lib/config.js:329:29) at processText (/var/www/loris/node_modules/eslint/lib/cli-engine.js:162:33) at CLIEngine.executeOnText (/var/www/loris/node_modules/eslint/lib/cli-engine.js:596:17) at lint (/var/www/loris/node_modules/eslint-loader/index.js:237:17) at Object.module.exports (/var/www/loris/node_modules/eslint-loader/index.js:232:21) ERROR in ./modules/instrument_manager/jsx/instrumentManagerIndex.js Module build failed (from ./node_modules/eslint-loader/index.js): Error: No ESLint configuration found. at Config.getLocalConfigHierarchy (/var/www/loris/node_modules/eslint/lib/config.js:255:39) at Config.getConfigHierarchy (/var/www/loris/node_modules/eslint/lib/config.js:179:43) at Config.getConfigVector (/var/www/loris/node_modules/eslint/lib/config.js:286:21) at Config.getConfig (/var/www/loris/node_modules/eslint/lib/config.js:329:29) at processText (/var/www/loris/node_modules/eslint/lib/cli-engine.js:162:33) at CLIEngine.executeOnText (/var/www/loris/node_modules/eslint/lib/cli-engine.js:596:17) at lint (/var/www/loris/node_modules/eslint-loader/index.js:237:17) at Object.module.exports (/var/www/loris/node_modules/eslint-loader/index.js:232:21) ERROR in ./modules/survey_accounts/jsx/surveyAccountsIndex.js Module build failed (from ./node_modules/eslint-loader/index.js): Error: No ESLint configuration found. at Config.getLocalConfigHierarchy (/var/www/loris/node_modules/eslint/lib/config.js:255:39) at Config.getConfigHierarchy (/var/www/loris/node_modules/eslint/lib/config.js:179:43) at Config.getConfigVector (/var/www/loris/node_modules/eslint/lib/config.js:286:21) at Config.getConfig (/var/www/loris/node_modules/eslint/lib/config.js:329:29) at processText (/var/www/loris/node_modules/eslint/lib/cli-engine.js:162:33) at CLIEngine.executeOnText (/var/www/loris/node_modules/eslint/lib/cli-engine.js:596:17) at lint (/var/www/loris/node_modules/eslint-loader/index.js:237:17) at Object.module.exports (/var/www/loris/node_modules/eslint-loader/index.js:232:21) ERROR in ./modules/mri_violations/jsx/mri_protocol_check_violations_columnFormatter.js Module build failed (from ./node_modules/eslint-loader/index.js): Error: No ESLint configuration found. at Config.getLocalConfigHierarchy (/var/www/loris/node_modules/eslint/lib/config.js:255:39) at Config.getConfigHierarchy (/var/www/loris/node_modules/eslint/lib/config.js:179:43) at Config.getConfigVector (/var/www/loris/node_modules/eslint/lib/config.js:286:21) at Config.getConfig (/var/www/loris/node_modules/eslint/lib/config.js:329:29) at processText (/var/www/loris/node_modules/eslint/lib/cli-engine.js:162:33) at CLIEngine.executeOnText (/var/www/loris/node_modules/eslint/lib/cli-engine.js:596:17) at lint (/var/www/loris/node_modules/eslint-loader/index.js:237:17) at Object.module.exports (/var/www/loris/node_modules/eslint-loader/index.js:232:21) ERROR in ./modules/mri_violations/jsx/columnFormatter.js Module build failed (from ./node_modules/eslint-loader/index.js): Error: No ESLint configuration found. at Config.getLocalConfigHierarchy (/var/www/loris/node_modules/eslint/lib/config.js:255:39) at Config.getConfigHierarchy (/var/www/loris/node_modules/eslint/lib/config.js:179:43) at Config.getConfigVector (/var/www/loris/node_modules/eslint/lib/config.js:286:21) at Config.getConfig (/var/www/loris/node_modules/eslint/lib/config.js:329:29) at processText (/var/www/loris/node_modules/eslint/lib/cli-engine.js:162:33) at CLIEngine.executeOnText (/var/www/loris/node_modules/eslint/lib/cli-engine.js:596:17) at lint (/var/www/loris/node_modules/eslint-loader/index.js:237:17) at Object.module.exports (/var/www/loris/node_modules/eslint-loader/index.js:232:21) ERROR in ./modules/mri_violations/jsx/columnFormatterUnresolved.js Module build failed (from ./node_modules/eslint-loader/index.js): Error: No ESLint configuration found. at Config.getLocalConfigHierarchy (/var/www/loris/node_modules/eslint/lib/config.js:255:39) at Config.getConfigHierarchy (/var/www/loris/node_modules/eslint/lib/config.js:179:43) at Config.getConfigVector (/var/www/loris/node_modules/eslint/lib/config.js:286:21) at Config.getConfig (/var/www/loris/node_modules/eslint/lib/config.js:329:29) at processText (/var/www/loris/node_modules/eslint/lib/cli-engine.js:162:33) at CLIEngine.executeOnText (/var/www/loris/node_modules/eslint/lib/cli-engine.js:596:17) at lint (/var/www/loris/node_modules/eslint-loader/index.js:237:17) at Object.module.exports (/var/www/loris/node_modules/eslint-loader/index.js:232:21) ERROR in ./modules/mri_violations/jsx/mri_protocol_violations_columnFormatter.js Module build failed (from ./node_modules/eslint-loader/index.js): Error: No ESLint configuration found. at Config.getLocalConfigHierarchy (/var/www/loris/node_modules/eslint/lib/config.js:255:39) at Config.getConfigHierarchy (/var/www/loris/node_modules/eslint/lib/config.js:179:43) at Config.getConfigVector (/var/www/loris/node_modules/eslint/lib/config.js:286:21) at Config.getConfig (/var/www/loris/node_modules/eslint/lib/config.js:329:29) at processText (/var/www/loris/node_modules/eslint/lib/cli-engine.js:162:33) at CLIEngine.executeOnText (/var/www/loris/node_modules/eslint/lib/cli-engine.js:596:17) at lint (/var/www/loris/node_modules/eslint-loader/index.js:237:17) at Object.module.exports (/var/www/loris/node_modules/eslint-loader/index.js:232:21) ERROR in ./modules/user_accounts/jsx/userAccountsIndex.js Module build failed (from ./node_modules/eslint-loader/index.js): Error: No ESLint configuration found. at Config.getLocalConfigHierarchy (/var/www/loris/node_modules/eslint/lib/config.js:255:39) at Config.getConfigHierarchy (/var/www/loris/node_modules/eslint/lib/config.js:179:43) at Config.getConfigVector (/var/www/loris/node_modules/eslint/lib/config.js:286:21) at Config.getConfig (/var/www/loris/node_modules/eslint/lib/config.js:329:29) at processText (/var/www/loris/node_modules/eslint/lib/cli-engine.js:162:33) at CLIEngine.executeOnText (/var/www/loris/node_modules/eslint/lib/cli-engine.js:596:17) at lint (/var/www/loris/node_modules/eslint-loader/index.js:237:17) at Object.module.exports (/var/www/loris/node_modules/eslint-loader/index.js:232:21) ERROR in ./modules/examiner/jsx/examinerIndex.js Module build failed (from ./node_modules/eslint-loader/index.js): Error: No ESLint configuration found. at Config.getLocalConfigHierarchy (/var/www/loris/node_modules/eslint/lib/config.js:255:39) at Config.getConfigHierarchy (/var/www/loris/node_modules/eslint/lib/config.js:179:43) at Config.getConfigVector (/var/www/loris/node_modules/eslint/lib/config.js:286:21) at Config.getConfig (/var/www/loris/node_modules/eslint/lib/config.js:329:29) at processText (/var/www/loris/node_modules/eslint/lib/cli-engine.js:162:33) at CLIEngine.executeOnText (/var/www/loris/node_modules/eslint/lib/cli-engine.js:596:17) at lint (/var/www/loris/node_modules/eslint-loader/index.js:237:17) at Object.module.exports (/var/www/loris/node_modules/eslint-loader/index.js:232:21) ERROR in ./modules/help_editor/jsx/help_editor.js Module build failed (from ./node_modules/eslint-loader/index.js): Error: No ESLint configuration found. at Config.getLocalConfigHierarchy (/var/www/loris/node_modules/eslint/lib/config.js:255:39) at Config.getConfigHierarchy (/var/www/loris/node_modules/eslint/lib/config.js:179:43) at Config.getConfigVector (/var/www/loris/node_modules/eslint/lib/config.js:286:21) at Config.getConfig (/var/www/loris/node_modules/eslint/lib/config.js:329:29) at processText (/var/www/loris/node_modules/eslint/lib/cli-engine.js:162:33) at CLIEngine.executeOnText (/var/www/loris/node_modules/eslint/lib/cli-engine.js:596:17) at lint (/var/www/loris/node_modules/eslint-loader/index.js:237:17) at Object.module.exports (/var/www/loris/node_modules/eslint-loader/index.js:232:21) ERROR in ./modules/brainbrowser/jsx/Brainbrowser.js Module build failed (from ./node_modules/eslint-loader/index.js): Error: No ESLint configuration found. at Config.getLocalConfigHierarchy (/var/www/loris/node_modules/eslint/lib/config.js:255:39) at Config.getConfigHierarchy (/var/www/loris/node_modules/eslint/lib/config.js:179:43) at Config.getConfigVector (/var/www/loris/node_modules/eslint/lib/config.js:286:21) at Config.getConfig (/var/www/loris/node_modules/eslint/lib/config.js:329:29) at processText (/var/www/loris/node_modules/eslint/lib/cli-engine.js:162:33) at CLIEngine.executeOnText (/var/www/loris/node_modules/eslint/lib/cli-engine.js:596:17) at lint (/var/www/loris/node_modules/eslint-loader/index.js:237:17) at Object.module.exports (/var/www/loris/node_modules/eslint-loader/index.js:232:21) ERROR in ./modules/imaging_uploader/jsx/index.js Module build failed (from ./node_modules/eslint-loader/index.js): Error: No ESLint configuration found. at Config.getLocalConfigHierarchy (/var/www/loris/node_modules/eslint/lib/config.js:255:39) at Config.getConfigHierarchy (/var/www/loris/node_modules/eslint/lib/config.js:179:43) at Config.getConfigVector (/var/www/loris/node_modules/eslint/lib/config.js:286:21) at Config.getConfig (/var/www/loris/node_modules/eslint/lib/config.js:329:29) at processText (/var/www/loris/node_modules/eslint/lib/cli-engine.js:162:33) at CLIEngine.executeOnText (/var/www/loris/node_modules/eslint/lib/cli-engine.js:596:17) at lint (/var/www/loris/node_modules/eslint-loader/index.js:237:17) at Object.module.exports (/var/www/loris/node_modules/eslint-loader/index.js:232:21) ERROR in ./modules/acknowledgements/jsx/acknowledgementsIndex.js Module build failed (from ./node_modules/eslint-loader/index.js): Error: No ESLint configuration found. at Config.getLocalConfigHierarchy (/var/www/loris/node_modules/eslint/lib/config.js:255:39) at Config.getConfigHierarchy (/var/www/loris/node_modules/eslint/lib/config.js:179:43) at Config.getConfigVector (/var/www/loris/node_modules/eslint/lib/config.js:286:21) at Config.getConfig (/var/www/loris/node_modules/eslint/lib/config.js:329:29) at processText (/var/www/loris/node_modules/eslint/lib/cli-engine.js:162:33) at CLIEngine.executeOnText (/var/www/loris/node_modules/eslint/lib/cli-engine.js:596:17) at lint (/var/www/loris/node_modules/eslint-loader/index.js:237:17) at Object.module.exports (/var/www/loris/node_modules/eslint-loader/index.js:232:21) ERROR in ./modules/new_profile/jsx/NewProfileIndex.js Module build failed (from ./node_modules/eslint-loader/index.js): Error: No ESLint configuration found. at Config.getLocalConfigHierarchy (/var/www/loris/node_modules/eslint/lib/config.js:255:39) at Config.getConfigHierarchy (/var/www/loris/node_modules/eslint/lib/config.js:179:43) at Config.getConfigVector (/var/www/loris/node_modules/eslint/lib/config.js:286:21) at Config.getConfig (/var/www/loris/node_modules/eslint/lib/config.js:329:29) at processText (/var/www/loris/node_modules/eslint/lib/cli-engine.js:162:33) at CLIEngine.executeOnText (/var/www/loris/node_modules/eslint/lib/cli-engine.js:596:17) at lint (/var/www/loris/node_modules/eslint-loader/index.js:237:17) at Object.module.exports (/var/www/loris/node_modules/eslint-loader/index.js:232:21) ERROR in ./modules/quality_control/jsx/qualityControlIndex.js Module build failed (from ./node_modules/eslint-loader/index.js): Error: No ESLint configuration found. at Config.getLocalConfigHierarchy (/var/www/loris/node_modules/eslint/lib/config.js:255:39) at Config.getConfigHierarchy (/var/www/loris/node_modules/eslint/lib/config.js:179:43) at Config.getConfigVector (/var/www/loris/node_modules/eslint/lib/config.js:286:21) at Config.getConfig (/var/www/loris/node_modules/eslint/lib/config.js:329:29) at processText (/var/www/loris/node_modules/eslint/lib/cli-engine.js:162:33) at CLIEngine.executeOnText (/var/www/loris/node_modules/eslint/lib/cli-engine.js:596:17) at lint (/var/www/loris/node_modules/eslint-loader/index.js:237:17) at Object.module.exports (/var/www/loris/node_modules/eslint-loader/index.js:232:21) ERROR in ./modules/server_processes_manager/jsx/server_processes_managerIndex.js Module build failed (from ./node_modules/eslint-loader/index.js): Error: No ESLint configuration found. at Config.getLocalConfigHierarchy (/var/www/loris/node_modules/eslint/lib/config.js:255:39) at Config.getConfigHierarchy (/var/www/loris/node_modules/eslint/lib/config.js:179:43) at Config.getConfigVector (/var/www/loris/node_modules/eslint/lib/config.js:286:21) at Config.getConfig (/var/www/loris/node_modules/eslint/lib/config.js:329:29) at processText (/var/www/loris/node_modules/eslint/lib/cli-engine.js:162:33) at CLIEngine.executeOnText (/var/www/loris/node_modules/eslint/lib/cli-engine.js:596:17) at lint (/var/www/loris/node_modules/eslint-loader/index.js:237:17) at Object.module.exports (/var/www/loris/node_modules/eslint-loader/index.js:232:21) ERROR in ./modules/document_repository/jsx/docIndex.js Module build failed (from ./node_modules/eslint-loader/index.js): Error: No ESLint configuration found. at Config.getLocalConfigHierarchy (/var/www/loris/node_modules/eslint/lib/config.js:255:39) at Config.getConfigHierarchy (/var/www/loris/node_modules/eslint/lib/config.js:179:43) at Config.getConfigVector (/var/www/loris/node_modules/eslint/lib/config.js:286:21) at Config.getConfig (/var/www/loris/node_modules/eslint/lib/config.js:329:29) at processText (/var/www/loris/node_modules/eslint/lib/cli-engine.js:162:33) at CLIEngine.executeOnText (/var/www/loris/node_modules/eslint/lib/cli-engine.js:596:17) at lint (/var/www/loris/node_modules/eslint-loader/index.js:237:17) at Object.module.exports (/var/www/loris/node_modules/eslint-loader/index.js:232:21) ERROR in ./modules/document_repository/jsx/editFormIndex.js Module build failed (from ./node_modules/eslint-loader/index.js): Error: No ESLint configuration found. at Config.getLocalConfigHierarchy (/var/www/loris/node_modules/eslint/lib/config.js:255:39) at Config.getConfigHierarchy (/var/www/loris/node_modules/eslint/lib/config.js:179:43) at Config.getConfigVector (/var/www/loris/node_modules/eslint/lib/config.js:286:21) at Config.getConfig (/var/www/loris/node_modules/eslint/lib/config.js:329:29) at processText (/var/www/loris/node_modules/eslint/lib/cli-engine.js:162:33) at CLIEngine.executeOnText (/var/www/loris/node_modules/eslint/lib/cli-engine.js:596:17) at lint (/var/www/loris/node_modules/eslint-loader/index.js:237:17) at Object.module.exports (/var/www/loris/node_modules/eslint-loader/index.js:232:21) ERROR in ./modules/publication/jsx/publicationIndex.js Module build failed (from ./node_modules/eslint-loader/index.js): Error: No ESLint configuration found. at Config.getLocalConfigHierarchy (/var/www/loris/node_modules/eslint/lib/config.js:255:39) at Config.getConfigHierarchy (/var/www/loris/node_modules/eslint/lib/config.js:179:43) at Config.getConfigVector (/var/www/loris/node_modules/eslint/lib/config.js:286:21) at Config.getConfig (/var/www/loris/node_modules/eslint/lib/config.js:329:29) at processText (/var/www/loris/node_modules/eslint/lib/cli-engine.js:162:33) at CLIEngine.executeOnText (/var/www/loris/node_modules/eslint/lib/cli-engine.js:596:17) at lint (/var/www/loris/node_modules/eslint-loader/index.js:237:17) at Object.module.exports (/var/www/loris/node_modules/eslint-loader/index.js:232:21) ERROR in ./modules/publication/jsx/viewProjectIndex.js Module build failed (from ./node_modules/eslint-loader/index.js): Error: No ESLint configuration found. at Config.getLocalConfigHierarchy (/var/www/loris/node_modules/eslint/lib/config.js:255:39) at Config.getConfigHierarchy (/var/www/loris/node_modules/eslint/lib/config.js:179:43) at Config.getConfigVector (/var/www/loris/node_modules/eslint/lib/config.js:286:21) at Config.getConfig (/var/www/loris/node_modules/eslint/lib/config.js:329:29) at processText (/var/www/loris/node_modules/eslint/lib/cli-engine.js:162:33) at CLIEngine.executeOnText (/var/www/loris/node_modules/eslint/lib/cli-engine.js:596:17) at lint (/var/www/loris/node_modules/eslint-loader/index.js:237:17) at Object.module.exports (/var/www/loris/node_modules/eslint-loader/index.js:232:21) Makefile:14: recipe for target 'javascript' failed From john.saigle at mcin.ca Tue Aug 13 16:52:10 2019 From: john.saigle at mcin.ca (John Saigle) Date: Tue, 13 Aug 2019 16:52:10 -0400 Subject: [Loris-dev] Upgrading to Loris 21 - new make file In-Reply-To: References: Message-ID: HI Sotirios, The make_output.txt file shows webpack failing because it can't find the ESLint config file. Can you confirm whether the file `.eslintrc.json` exists within your loris root directory (usually `/var/www/loris/`)? When I delete my file I get the same errors as you. If you find that it's missing, you can make a local copy with the contents found here: https://github.com/aces/Loris/blob/e26a6ad49a73fcffef0cd73bb600c4d17b200b62/.eslintrc.json Once you know it exists, try running `make` again. Let us know if that moves you forward. Best, John On Tue, Aug 13, 2019 at 2:21 PM Sotirios Nikoloutsopoulos < sotirisnik at gmail.com> wrote: > Hi, > I executed the commands for the node and now i am get the followings: > > lorisadmin at hbp:/var/www/loris$ make > ~/make_output > npm WARN The package prop-types is included as both a dev and production > dependency. > npm WARN optional SKIPPING OPTIONAL DEPENDENCY: fsevents at 1.2.4 > (node_modules/fsevents): > npm WARN notsup SKIPPING OPTIONAL DEPENDENCY: Unsupported platform for > fsevents at 1.2.4: wanted {"os":"darwin","arch":"any"} (current: > {"os":"linux","arch":"x64"}) > > npm ERR! code ELIFECYCLE > npm ERR! errno 2 > npm ERR! loris at 1.0.0 compile: `webpack` > npm ERR! Exit status 2 > npm ERR! > npm ERR! Failed at the loris at 1.0.0 compile script. > npm ERR! This is probably not a problem with npm. There is likely > additional logging output above. > > npm ERR! A complete log of this run can be found in: > npm ERR! /home/lorisadmin/.npm/_logs/2019-08-13T18_12_05_378Z-debug.log > make: *** [javascript] Error 2 > > Thanks, > Sotirios > > > ???? ???, 12 ??? 2019 ???? 10:19 ?.?., ?/? Christine Rogers, Ms. < > christine.rogers at mcgill.ca> ??????: > >> Hi Sotirios, >> >> We've seen some users installing LORIS 21 or upgrading to 21 whose >> version of node doesn't work well with webpack, due to updated packages >> they're missing. >> If so, update your node : >> >> curl -sL https://deb.nodesource.com/setup_8.x | sudo -E bash - >> sudo apt-get install -y nodejs >> >> Let us know how that goes -- please send us output from the same log if >> any issues. >> Best, >> Christine >> >> >> On Thu, Aug 8, 2019 at 2:38 PM Sotirios Nikoloutsopoulos < >> sotirisnik at gmail.com> wrote: >> >>> It's not a disk space issue, as you can see below i have still 74GB >>> available. >>> >>> lorisadmin at hbp:/var/www/loris$ df -h >>> Filesystem Size Used Avail Use% Mounted on >>> udev 2,9G 0 2,9G 0% /dev >>> tmpfs 597M 8,6M 588M 2% /run >>> /dev/sda1 98G 19G 74G 21% / >>> >>> Maybe we have to pass a flag to get into strict mode? as stated >>> "SyntaxError: Block-scoped declarations (let, const, function, class) not >>> yet supported outside strict mode" >>> >>> Thanks, >>> Sotirios >>> >>> ???? ???, 8 ??? 2019 ???? 4:32 ?.?., ?/? Dave MacFarlane < >>> dave.macfarlane at mcin.ca> ??????: >>> >>>> It looks like the javascript snippet shown in the error message when >>>> trying to compile the js is truncated. Have you run out of disk space? >>>> >>>> On Thu, Aug 8, 2019 at 8:37 AM Sotirios Nikoloutsopoulos < >>>> sotirisnik at gmail.com> wrote: >>>> >>>>> Hi, >>>>> >>>>> I runned make and also included the file it reports at the end. >>>>> >>>>> lorisadmin at hbp:/var/www/loris$ make >>>>> npm install >>>>> npm WARN optional Skipping failed optional dependency >>>>> /chokidar/fsevents: >>>>> npm WARN notsup Not compatible with your operating system or >>>>> architecture: fsevents at 1.2.9 >>>>> npm WARN optional Skipping failed optional dependency >>>>> /watchpack/chokidar/fsevents: >>>>> npm WARN notsup Not compatible with your operating system or >>>>> architecture: fsevents at 1.2.9 >>>>> npm run compile >>>>> >>>>> > loris at 1.0.0 compile /var/www/loris >>>>> > webpack >>>>> >>>>> /var/www/loris/node_modules/webpack/bin/webpack.js:86 >>>>> let notify = >>>>> ^^^ >>>>> >>>>> SyntaxError: Block-scoped declarations (let, const, function, class) >>>>> not yet supported outside strict mode >>>>> at exports.runInThisContext (vm.js:53:16) >>>>> at Module._compile (module.js:374:25) >>>>> at Object.Module._extensions..js (module.js:417:10) >>>>> at Module.load (module.js:344:32) >>>>> at Function.Module._load (module.js:301:12) >>>>> at Function.Module.runMain (module.js:442:10) >>>>> at startup (node.js:136:18) >>>>> at node.js:966:3 >>>>> >>>>> npm ERR! Linux 4.15.0-55-generic >>>>> npm ERR! argv "/usr/bin/nodejs" "/usr/bin/npm" "run" "compile" >>>>> npm ERR! node v4.2.6 >>>>> npm ERR! npm v3.5.2 >>>>> npm ERR! code ELIFECYCLE >>>>> npm ERR! loris at 1.0.0 compile: `webpack` >>>>> npm ERR! Exit status 1 >>>>> npm ERR! >>>>> npm ERR! Failed at the loris at 1.0.0 compile script 'webpack'. >>>>> npm ERR! Make sure you have the latest version of node.js and npm >>>>> installed. >>>>> npm ERR! If you do, this is most likely a problem with the loris >>>>> package, >>>>> npm ERR! not with npm itself. >>>>> npm ERR! Tell the author that this fails on your system: >>>>> npm ERR! webpack >>>>> npm ERR! You can get information on how to open an issue for this >>>>> project with: >>>>> npm ERR! npm bugs loris >>>>> npm ERR! Or if that isn't available, you can get their info via: >>>>> npm ERR! npm owner ls loris >>>>> npm ERR! There is likely additional logging output above. >>>>> >>>>> npm ERR! Please include the following file with any support request: >>>>> npm ERR! /var/www/loris/npm-debug.log >>>>> Makefile:14: recipe for target 'javascript' failed >>>>> make: *** [javascript] Error 1 >>>>> >>>>> Thanks, >>>>> >>>>> Sotirios >>>>> >>>>> ???? ???, 7 ??? 2019 ???? 5:41 ?.?., ?/? Christine Rogers, Ms. < >>>>> christine.rogers at mcgill.ca> ??????: >>>>> >>>>>> Hi Sotirios, >>>>>> >>>>>> Thanks, have you tried all of these steps? >>>>>> - clear your browser cache (and refresh a few times) >>>>>> - delete any files in your smarty/templates_c directory (this will >>>>>> clear the template cache - do Not touch smarty/templates/) >>>>>> - run `make` (per the 21 release notes, this replaces the composer >>>>>> commands used in previous releases to update your dependencies) >>>>>> - restart apache (doesn't hurt) >>>>>> >>>>>> Let us know how it goes -- let us know what difference you see after, >>>>>> with your logs. A >>>>>> lso please send us your Config path settings (see these >>>>>> Troubleshooting Queries >>>>>> ) >>>>>> if you're still seeing front-end issues. >>>>>> >>>>>> Thanks, >>>>>> Christine >>>>>> >>>>>> On Wed, Aug 7, 2019 at 8:02 AM Sotirios Nikoloutsopoulos < >>>>>> sotirisnik at gmail.com> wrote: >>>>>> >>>>>>> Hi, >>>>>>> >>>>>>> lorisadmin at hbp:/var/www/loris$ sudo cat /var/log/apache2/error.log >>>>>>> [Wed Aug 07 07:35:02.422501 2019] [mpm_prefork:notice] [pid 1267] >>>>>>> AH00163: Apache/2.4.18 (Ubuntu) OpenSSL/1.0.2g configured -- resuming >>>>>>> normal operations >>>>>>> [Wed Aug 07 07:35:02.422514 2019] [core:notice] [pid 1267] AH00094: >>>>>>> Command line: '/usr/sbin/apache2' >>>>>>> >>>>>>> And as for the access.log the content are empty >>>>>>> lorisadmin at hbp:/var/www/loris$ sudo ls -l >>>>>>> /var/log/apache2/access.log >>>>>>> lorisadmin at hbp:/var/www/loris$ sudo ls -l >>>>>>> /var/log/apache2/access.log >>>>>>> -rw-r----- 1 root adm 0 ???? 28 14:09 /var/log/apache2/access.log >>>>>>> >>>>>>> Also i noticed a loris_access.log. >>>>>>> >>>>>>> The only non-blank pages are: >>>>>>> mri_violations, dataquery does not exist at all, statistics, >>>>>>> data_team_helper, genomic_browser, configuration and >>>>>>> server_processes_manager/ prints "Required configuration settings for >>>>>>> Server Processes Manager are missing. Cannot continue." >>>>>>> >>>>>>> Thanks, >>>>>>> Sotirios >>>>>>> >>>>>>> ???? ???, 6 ??? 2019 ???? 10:13 ?.?., ?/? Christine Rogers, Ms. < >>>>>>> christine.rogers at mcgill.ca> ??????: >>>>>>> >>>>>>>> Hi Sotirios and LORIS community -- >>>>>>>> >>>>>>>> When upgrading to brand-new release 21 -- just a reminder to >>>>>>>> follow the release notes and run the new *make* file to update >>>>>>>> your dependencies (instead of using *composer* commands). >>>>>>>> We've also updated the Wiki page >>>>>>>> to >>>>>>>> clarify that the release notes for each version will tell you what to run. >>>>>>>> >>>>>>>> If your current version is not the last release (20.3), it's still >>>>>>>> important to upgrade to each minor release increment (e.g. 20.2, 20.3) >>>>>>>> before making the leap to 21.0. >>>>>>>> >>>>>>>> If you're getting blank pages, post-upgrade -- Try clearing your >>>>>>>> cache. >>>>>>>> >>>>>>>> Got questions or feedback e.g. on the Release Notes? please don't >>>>>>>> hesitate to let us know. >>>>>>>> Thanks, >>>>>>>> Christine >>>>>>>> The LORIS team >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> On Tue, Aug 6, 2019 at 10:09 AM Christine Rogers, Ms. < >>>>>>>> christine.rogers at mcgill.ca> wrote: >>>>>>>> >>>>>>>>> Hi Sotirios, >>>>>>>>> Could you also let us know -- on which pages is content visible, >>>>>>>>> and on which pages/modules is content not visible for you? >>>>>>>>> Thanks, >>>>>>>>> Christine >>>>>>>>> >>>>>>>>> On Tue, Aug 6, 2019 at 9:54 AM Christine Rogers, Ms. < >>>>>>>>> christine.rogers at mcgill.ca> wrote: >>>>>>>>> >>>>>>>>>> Thanks Sotirios, >>>>>>>>>> That's good to know. It sounds like you've checked that your >>>>>>>>>> /var/www/loris/project/config.xml file get populated properly. >>>>>>>>>> >>>>>>>>>> Please send us the last few errors you're seeing in your apache >>>>>>>>>> error log file, and your config paths and we can see what's happening with >>>>>>>>>> your front end -- >>>>>>>>>> Run these Troubleshooting Queries >>>>>>>>>> >>>>>>>>>> to get your config path settings, given your front end is not displaying >>>>>>>>>> fully. >>>>>>>>>> >>>>>>>>>> The Loris-MRI repo >>>>>>>>>> 21 >>>>>>>>>> install/upgrade would then be your next steps. >>>>>>>>>> Best, >>>>>>>>>> Christine >>>>>>>>>> >>>>>>>>>> On Tue, Aug 6, 2019 at 7:53 AM Sotirios Nikoloutsopoulos < >>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>> >>>>>>>>>>> I am using a VM. What i did was: >>>>>>>>>>> 1) Download the files from https://github.com/aces/Loris and >>>>>>>>>>> replace them to my existing /vaw/www/loris folder. >>>>>>>>>>> 2) Execute the composer install --no-dev and then composer >>>>>>>>>>> dump-autoload as mentioned here >>>>>>>>>>> https://github.com/aces/Loris/wiki/Updating-your-LORIS. >>>>>>>>>>> 3) Execute install.sh from /var/www/loris/tools and because >>>>>>>>>>> LORIS already existed i moved a .config file, then re-executed the >>>>>>>>>>> install.sh successfully >>>>>>>>>>> 4 ) As for the database, i dropped the schema and i executed the >>>>>>>>>>> installdb.php >>>>>>>>>>> >>>>>>>>>>> ???? ???, 5 ??? 2019 ???? 5:22 ?.?., ?/? Christine Rogers, Ms. < >>>>>>>>>>> christine.rogers at mcgill.ca> ??????: >>>>>>>>>>> >>>>>>>>>>>> Hi Sotorios, >>>>>>>>>>>> >>>>>>>>>>>> Thanks - when you re-installed did you start on a fresh root >>>>>>>>>>>> path / VM or might some of your old system setting still apply? >>>>>>>>>>>> (And if you did any steps similar to an upgrade, did you follow >>>>>>>>>>>> the Upgrade steps in the Release Notes, from both repos?) >>>>>>>>>>>> >>>>>>>>>>>> About the TR_range column - it was recently split (MRI pr339 >>>>>>>>>>>> ) split into >>>>>>>>>>>> TR_min and _max columns. Given the code was trying to query TR_range which >>>>>>>>>>>> does not exist in your mri_protocol table, double-check which version of >>>>>>>>>>>> the Loris repo (tables) and the Loris-MRI repo (code) you have installed to >>>>>>>>>>>> ensure they match. >>>>>>>>>>>> >>>>>>>>>>>> Christine >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> On Mon, Aug 5, 2019 at 9:06 AM Sotirios Nikoloutsopoulos < >>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>> >>>>>>>>>>>>> I reinstalled LORIS to 21 version and now the content is not >>>>>>>>>>>>> visible at all at most pages. >>>>>>>>>>>>> >>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>> >>>>>>>>>>>>> ???? ???, 5 ??? 2019 ???? 3:19 ?.?., ?/? Sotirios >>>>>>>>>>>>> Nikoloutsopoulos ??????: >>>>>>>>>>>>> >>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>> >>>>>>>>>>>>>> Is it easy to upgrade to Loris 21? Also the following fails >>>>>>>>>>>>>> because the line 1985 of NeuroDB/MRIProcessingUtility.pm query mri_protocol >>>>>>>>>>>>>> which doesn't have TR_range >>>>>>>>>>>>>> https://github.com/aces/Loris/blob/21.0-release/SQL/0000-00-00-schema.sql#L556 >>>>>>>>>>>>>> >>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>> >>>>>>>>>>>>>> lorisadmin at hbp:/data/loris/bin/mri$ >>>>>>>>>>>>>> ./batch_uploads_imageuploader -profile prod < ~/Desktop/input.txt > log.txt >>>>>>>>>>>>>> Use of uninitialized value $_ in pattern match (m//) at >>>>>>>>>>>>>> ./batch_uploads_imageuploader line 147. >>>>>>>>>>>>>> base is DCC0000_258024_V1 >>>>>>>>>>>>>> path is /data/incoming/ >>>>>>>>>>>>>> type is .tar.gz >>>>>>>>>>>>>> fullpath is /data/incoming/DCC0000_258024_V1.tar.gz >>>>>>>>>>>>>> DBD::mysql::st execute failed: Unknown column 'TR_range' in >>>>>>>>>>>>>> 'where clause' at >>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line 1985. >>>>>>>>>>>>>> DBD::mysql::st fetchrow_array failed: fetch() without >>>>>>>>>>>>>> execute() at >>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line 1986. >>>>>>>>>>>>>> Use of uninitialized value $count_mri_protocol in numeric gt >>>>>>>>>>>>>> (>) at /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm >>>>>>>>>>>>>> line 1995. >>>>>>>>>>>>>> DBD::mysql::st execute failed: Unknown column 'TR_range' in >>>>>>>>>>>>>> 'field list' at /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 562. >>>>>>>>>>>>>> Can't exec "mail": No such file or directory at >>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 721. >>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 722. >>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 723. >>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 724. >>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 725. >>>>>>>>>>>>>> >>>>>>>>>>>>>> No Mincs inserted >>>>>>>>>>>>>> >>>>>>>>>>>>>> Thanks, >>>>>>>>>>>>>> >>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>> >>>>>>>>>>>>>> ???? ???, 3 ??? 2019 ???? 1:08 ?.?., ?/? Christine Rogers, >>>>>>>>>>>>>> Ms. ??????: >>>>>>>>>>>>>> >>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> First, just a note: we've released LORIS 21 this week with >>>>>>>>>>>>>>> some major new features and cleanup -- especially if you are early in your >>>>>>>>>>>>>>> setup phase, check out the Release notes for both the LORIS >>>>>>>>>>>>>>> and >>>>>>>>>>>>>>> Loris-MRI >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> repos. >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> Thanks for your screenshots -- your empty mri_protocol table >>>>>>>>>>>>>>> should be at the root of these issues : >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> The mri_protocol table must be populated >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> in order for your scans to be registered in LORIS -- it serves as a >>>>>>>>>>>>>>> whitelist for the insertion pipeline which filters out scans that aren't >>>>>>>>>>>>>>> identified or matched to scan types in this table. >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> By default, this table is populated with entries for t1, t2, >>>>>>>>>>>>>>> fMRI and DTI (Insert statements for 21 release branch are >>>>>>>>>>>>>>> here >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> ) >>>>>>>>>>>>>>> Feel free to restore our default records and broaden their >>>>>>>>>>>>>>> parameters to match all your scan types. >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> re Defaced, native, selected -- these filter the scans >>>>>>>>>>>>>>> displayed as you move to the next page (View Session), instead of viewing >>>>>>>>>>>>>>> "all types" of scans from a given session : >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> - "defaced" means that a defacing script >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> has masked the subject's face in the volume (for patient privacy) >>>>>>>>>>>>>>> - "native" means that no pre-processing has been >>>>>>>>>>>>>>> performed on the scan (it's raw data), >>>>>>>>>>>>>>> - "selected" will show only volumes that have been QC'd >>>>>>>>>>>>>>> and "selected" as the best of their type -- used to display only the best >>>>>>>>>>>>>>> quality T1 image instead of all T1s acquired in a session, e.g. >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> re QC Comments -- >>>>>>>>>>>>>>> Once you have successfully loaded scans (matched to the >>>>>>>>>>>>>>> mri_protocol table), you'll be able to use the Imaging Browser's View >>>>>>>>>>>>>>> Session subpage to enter/view QC comments on each volume, or for each >>>>>>>>>>>>>>> visit. >>>>>>>>>>>>>>> These are stored directly in the database, and linked to >>>>>>>>>>>>>>> each scan. (Table name: feedback_mri_comments) >>>>>>>>>>>>>>> (Visit-level QC comments are linked to the session.) >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> For a walkthrough of the Imaging setup - please see the Imaging >>>>>>>>>>>>>>> Setup guide >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> - >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> An old LORIS walkthrough video >>>>>>>>>>>>>>> can also walk >>>>>>>>>>>>>>> you through some of the Imaging front-end features, starting at 8:00 >>>>>>>>>>>>>>> LORIS' imaging modules have been updated many times since >>>>>>>>>>>>>>> this video, but the functionality and workflow is similar. >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> Let us know how it goes once you have entries in your >>>>>>>>>>>>>>> mri_protocol table - >>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>> Christine >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> On Fri, Aug 2, 2019 at 7:58 AM Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Hi Christine, >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> In the candidate_list page i can see this patient >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> If i press the link under PSCID i get to see >>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> and if i press the link under Scan Done it redirects me to >>>>>>>>>>>>>>>> imaging_browser >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> At the mri_violations page i also see No results ( neither >>>>>>>>>>>>>>>> on resolved / not resolved ). >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> At the imaging_uploader i can see the record that failed. >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> If i click on the tarchive info i get to see the Protocol >>>>>>>>>>>>>>>> Name which i think is the acquisition we wanted? >>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Also my mri_protocol table is empty. >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Furthermore i would like to ask about the defaced, native, >>>>>>>>>>>>>>>> selected. What exactly is native and selected? And where are the qc >>>>>>>>>>>>>>>> comments stored? >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Finally a walkthrough would be helpful. >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Thanks, >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> ???? ???, 30 ???? 2019 ???? 8:29 ?.?., ?/? Christine >>>>>>>>>>>>>>>> Rogers, Ms. ??????: >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>> Glad to hear you're making progress with the visit >>>>>>>>>>>>>>>>> labels. To follow up on your last few emails: >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> a- The Wiki's Setup Guide contains Sample insert >>>>>>>>>>>>>>>>> statements for the Visit Windows table >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> . >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> As Cecile mentioned, the consistency of visit label format >>>>>>>>>>>>>>>>> is important: V01, v01, V1, 01 -- whichever you select to use is fine; we >>>>>>>>>>>>>>>>> use V01 by default across all documentation. >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> b- For Password reset, there is a script in the tools/ >>>>>>>>>>>>>>>>> directory so that a back-end administrator can reset any front-end user >>>>>>>>>>>>>>>>> password, including Admin. (See info on setting up / resetting User >>>>>>>>>>>>>>>>> passwords in the Wiki's Setup Guide >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> ) >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> c- The minc file not being registered -- due to >>>>>>>>>>>>>>>>> AcquisitionProtocol unknown. >>>>>>>>>>>>>>>>> This means the SeriesDescription (Acquisition Protocol) in >>>>>>>>>>>>>>>>> you Dicom header was not matched to any scan listed in the mri_protocol >>>>>>>>>>>>>>>>> database table. >>>>>>>>>>>>>>>>> (In the online Loris-MRI Troubleshooting Guide, >>>>>>>>>>>>>>>>> this >>>>>>>>>>>>>>>>> is Table 3, 2nd-last item "no MINCs inserted"). >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> The MRI Violations module (Readme here) >>>>>>>>>>>>>>>>> will show >>>>>>>>>>>>>>>>> you the details of this mismatch -- >>>>>>>>>>>>>>>>> Go to the module (under the Imaging menu), find your scan >>>>>>>>>>>>>>>>> and click the link "Could not identify scan type" -- in the next subpage >>>>>>>>>>>>>>>>> you can compare the scan's actual parameters against the mri_protocol >>>>>>>>>>>>>>>>> table. >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> To resolve this, adjust your mri_protocol table values or >>>>>>>>>>>>>>>>> perhaps ensure your DICOMs are labelled consistently. >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Let us know if this works for you -- we can also walk you >>>>>>>>>>>>>>>>> through an example of non-identified scans on >>>>>>>>>>>>>>>>> Demo.loris.ca (MRI Violations module). >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>> Christine >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> The LORIS team >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> On Tue, Jul 30, 2019 at 10:47 AM Sotirios Nikoloutsopoulos >>>>>>>>>>>>>>>>> wrote: >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> I hope this is sufficient as the error for the visit >>>>>>>>>>>>>>>>>> label disappeared. >>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Please see the attached file. Also something i found. >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> lorisadmin at hbp:/data/loris/bin/mri$ cat >>>>>>>>>>>>>>>>>> /data/loris/data//logs/TarLoad-17-39-xubBdv.log >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> ==> Loading file from disk >>>>>>>>>>>>>>>>>> /tmp/TarLoad-17-39-UyQcG2/dcc0000_258024_v1_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> --> mapping DICOM parameter for >>>>>>>>>>>>>>>>>> /tmp/TarLoad-17-39-UyQcG2/dcc0000_258024_v1_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> ==> computing md5 hash for MINC body. >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> --> md5: 6b1202fd63e29de4c9be1cd9925888a5 >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> ==> verifying acquisition protocol >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Acquisition protocol is unknown >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> --> The minc file cannot be registered since the >>>>>>>>>>>>>>>>>> AcquisitionProtocol is unknown >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> ???? ???, 30 ???? 2019 ???? 4:58 ?.?., ?/? Sotirios >>>>>>>>>>>>>>>>>> Nikoloutsopoulos ??????: >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Ok I fixed the login problem by using a known hash and >>>>>>>>>>>>>>>>>>> by deleting the rows from the login_history i was able to login. >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> ???? ???, 30 ???? 2019 ???? 4:50 ?.?., ?/? Sotirios >>>>>>>>>>>>>>>>>>> Nikoloutsopoulos ??????: >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> there was no visit label 01 in the Visit_Windows table >>>>>>>>>>>>>>>>>>>> and i don't know how to insert it because the record requires lots of >>>>>>>>>>>>>>>>>>>> attributes. Also the system for a reason asked me to update my password and >>>>>>>>>>>>>>>>>>>> now i don't remember it and my account got suspended. Is there a way to >>>>>>>>>>>>>>>>>>>> reset it or set a simple password? I updated the password hash in the >>>>>>>>>>>>>>>>>>>> users table by using the hash from another LORIS setup we had and i still >>>>>>>>>>>>>>>>>>>> couldn't login ( also the attribute password is always NULL and the >>>>>>>>>>>>>>>>>>>> expiration date is 1999-01-01 for some reason ). >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Thanks >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> ???? ???, 29 ???? 2019 ???? 5:21 ?.?., ?/? Cecile >>>>>>>>>>>>>>>>>>>> Madjar ??????: >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> Can you try adding the visit label v01 to the >>>>>>>>>>>>>>>>>>>>> Visit_Windows table? >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> However, I noticed that in a previous dataset, the >>>>>>>>>>>>>>>>>>>>> label was V1. Does that refer to the same visit? If so, you might want to >>>>>>>>>>>>>>>>>>>>> harmonize the visit labels so they are all the same across datasets for a >>>>>>>>>>>>>>>>>>>>> given timepoint, meaning you will need to relabel scans when the visit >>>>>>>>>>>>>>>>>>>>> label is different but referring to the same visit label (v01 = V1 etc...). >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> Hope this helps, >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> On Mon, Jul 29, 2019 at 10:15 AM Sotirios >>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos wrote: >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> Could you help me with the "Visit label does not >>>>>>>>>>>>>>>>>>>>>> exist"? I had changed $subjectID{'createVisitLabel'} to 1 as you had >>>>>>>>>>>>>>>>>>>>>> suggested but it appears that this problem hasn't been resolved yet. >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> lorisadmin at hbp:/data/loris/bin/mri$ cat >>>>>>>>>>>>>>>>>>>>>> /data/loris/data//logs/TarLoad-14-58-9Xog7H.log >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> ==> Loading file from disk >>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> --> mapping DICOM parameter for >>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> --> using user-defined filterParameters for >>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> Candidate Mismatch Error is Visit label does not exist >>>>>>>>>>>>>>>>>>>>>> -> WARNING: This candidate was invalid. Logging to >>>>>>>>>>>>>>>>>>>>>> MRICandidateErrors table with reason >>>>>>>>>>>>>>>>>>>>>> Visit label does not exist >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> ???? ???, 26 ???? 2019 ???? 3:02 ?.?., ?/? Sotirios >>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos ??????: >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> Hi Cecile, >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> The Center error was fixed. Still the insertion of >>>>>>>>>>>>>>>>>>>>>>> mincs fails. Please see the output.txt file i attached. Also is there >>>>>>>>>>>>>>>>>>>>>>> something else i need to change at the paths configuration? >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> ???? ???, 25 ???? 2019 ???? 6:55 ?.?., ?/? Cecile >>>>>>>>>>>>>>>>>>>>>>> Madjar ??????: >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> We are making progress! >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> I have a feeling this error comes from the fact >>>>>>>>>>>>>>>>>>>>>>>> that your psc table does not have the MRI_alias populated for the DCC site. >>>>>>>>>>>>>>>>>>>>>>>> Running the following query in the mysql database should fix this: >>>>>>>>>>>>>>>>>>>>>>>> UPDATE psc SET MRI_alias="DCC", Alias="DCC" WHERE >>>>>>>>>>>>>>>>>>>>>>>> Name="Data Coordinating Center"; >>>>>>>>>>>>>>>>>>>>>>>> Repeat the same with all your sites (make sure to >>>>>>>>>>>>>>>>>>>>>>>> change the Aliases between sites, they should all be unique). >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> Let me know how it goes! >>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> On Thu, Jul 25, 2019 at 11:43 AM Sotirios >>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos wrote: >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> Dear Cecile, >>>>>>>>>>>>>>>>>>>>>>>>> You were right about your guesses. I did the >>>>>>>>>>>>>>>>>>>>>>>>> modifications you suggested, i still get the "no mincs inserted" error, now >>>>>>>>>>>>>>>>>>>>>>>>> i am getting the "No center found this candidate" error ( how do i fix >>>>>>>>>>>>>>>>>>>>>>>>> that? from what i see the .dcm files contains a 'Institution Name', is that >>>>>>>>>>>>>>>>>>>>>>>>> the center? ), so i guess that's why the validation fails, but i changed >>>>>>>>>>>>>>>>>>>>>>>>> the force variable of tarchiveLoader to 1, shouldn't it have inserted the >>>>>>>>>>>>>>>>>>>>>>>>> mincs then? Also it is optional to have a mail server, right? ( from what i >>>>>>>>>>>>>>>>>>>>>>>>> see the mail error does not affect the $valid_study, so i assume we are >>>>>>>>>>>>>>>>>>>>>>>>> okay with that ) >>>>>>>>>>>>>>>>>>>>>>>>> Thank you a lot, >>>>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 25 ???? 2019 ???? 5:48 ?.?., ?/? Cecile >>>>>>>>>>>>>>>>>>>>>>>>> Madjar ??????: >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> From what I understand, I believe you just need >>>>>>>>>>>>>>>>>>>>>>>>>> to update a few config settings from the frontend in the Config module >>>>>>>>>>>>>>>>>>>>>>>>>> (under the Admin menu). >>>>>>>>>>>>>>>>>>>>>>>>>> [image: Screen Shot 2019-07-25 at 10.31.35 AM.png] >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> Then go to the Paths section of the config module >>>>>>>>>>>>>>>>>>>>>>>>>> and update the "LORIS-MRI code" config setting to /data/loris/bin/mri (my >>>>>>>>>>>>>>>>>>>>>>>>>> guess is that currently, it is set to /data/LORIS/data) and click on the >>>>>>>>>>>>>>>>>>>>>>>>>> submit button. >>>>>>>>>>>>>>>>>>>>>>>>>> [image: Screen Shot 2019-07-25 at 10.32.50 AM.png] >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> Then, go to Imaging Pipeline section of the >>>>>>>>>>>>>>>>>>>>>>>>>> Configuration module and update the "Loris-MRI Data Directory" to >>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/ (my guess is that it is empty at the moment in your >>>>>>>>>>>>>>>>>>>>>>>>>> database which is why $data_dir is not defined when you run the >>>>>>>>>>>>>>>>>>>>>>>>>> tarchiveLoader step of the insertion pipeline). >>>>>>>>>>>>>>>>>>>>>>>>>> [image: Screen Shot 2019-07-25 at 10.40.52 AM.png] >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> Finally, I took a look at your environment file >>>>>>>>>>>>>>>>>>>>>>>>>> and it might be a good idea to update your PERL5LIB variable to the >>>>>>>>>>>>>>>>>>>>>>>>>> following (it has been added to the code a few releases ago as we realized >>>>>>>>>>>>>>>>>>>>>>>>>> this was needed for the libraries. Not sure which version of LORIS-MRI you >>>>>>>>>>>>>>>>>>>>>>>>>> are using but it does not hurt to update this variable to what I suggest >>>>>>>>>>>>>>>>>>>>>>>>>> below): >>>>>>>>>>>>>>>>>>>>>>>>>> export >>>>>>>>>>>>>>>>>>>>>>>>>> PERL5LIB=/data/loris/bin/mri/uploadNeuroDB:/data/loris/bin/mri/dicom-archive:$PERL5LIB >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helps. Sorry you are experiencing so >>>>>>>>>>>>>>>>>>>>>>>>>> much trouble setting things up. We probably need to update our WIKI. >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> On Thu, Jul 25, 2019 at 9:48 AM Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos wrote: >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> The "Loris-MRI Data Directory" should be in the >>>>>>>>>>>>>>>>>>>>>>>>>>> environment file? >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 25 ???? 2019 ???? 12:59 ?.?., ?/? >>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos >>>>>>>>>>>>>>>>>>>>>>>>>>> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> The scripts are located in >>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/. Somewhere I might have messed something up but i >>>>>>>>>>>>>>>>>>>>>>>>>>>> remember following the instructions in the wiki.For example when i tried to >>>>>>>>>>>>>>>>>>>>>>>>>>>> execute the batch_uploads_imageuploader perl script the line >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> my $command = "$bin_dir/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl " >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> was pointing to an invalid path, for example: >>>>>>>>>>>>>>>>>>>>>>>>>>>> it was repeating a pattern and had LORIS instead of loris ( i think the >>>>>>>>>>>>>>>>>>>>>>>>>>>> mistake was that in the wiki it suggested to use $PROJECT for the name of >>>>>>>>>>>>>>>>>>>>>>>>>>>> the folder and i choosed 'loris' >>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris/wiki/Imaging-Database >>>>>>>>>>>>>>>>>>>>>>>>>>>> ). See also the in image for the modification i did. Also i didn't find the >>>>>>>>>>>>>>>>>>>>>>>>>>>> section to config the $data_dir variable. >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 24 ???? 2019 ???? 6:05 ?.?., ?/? >>>>>>>>>>>>>>>>>>>>>>>>>>>> Cecile Madjar ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> It looks like you have one Config setting not >>>>>>>>>>>>>>>>>>>>>>>>>>>>> set (based on the first error message you got when running it the first >>>>>>>>>>>>>>>>>>>>>>>>>>>>> time). You need to set a value for "Loris-MRI Data Directory" in the Config >>>>>>>>>>>>>>>>>>>>>>>>>>>>> module under the Imaging pipeline section (from what I can see, it would be >>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/ for your setup). >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> The reason you got that error message the >>>>>>>>>>>>>>>>>>>>>>>>>>>>> second time is that the pipeline checks if the DICOM study was already >>>>>>>>>>>>>>>>>>>>>>>>>>>>> inserted in the tarchive table. Since you ran the study once already, the >>>>>>>>>>>>>>>>>>>>>>>>>>>>> study is inserted into the tarchive, hence the message. However, the >>>>>>>>>>>>>>>>>>>>>>>>>>>>> pipeline did not complete as the MINC files were not created and inserted >>>>>>>>>>>>>>>>>>>>>>>>>>>>> into the files/parameter_file table. In order to continue the insertion, >>>>>>>>>>>>>>>>>>>>>>>>>>>>> you will then need to run the tarchiveLoader command suggested in the >>>>>>>>>>>>>>>>>>>>>>>>>>>>> terminal during the second run: >>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader >>>>>>>>>>>>>>>>>>>>>>>>>>>>> -globLocation -profile prod >>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive//2012/DCM_2012-12-05_ImagingUpload-17-43-ZUEFjb.tar >>>>>>>>>>>>>>>>>>>>>>>>>>>>> -verbose >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Finally, I am a bit confused by your setup. >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Where are the scripts located? In /data/loris/bin/mri or /data/loris/data? >>>>>>>>>>>>>>>>>>>>>>>>>>>>> It feels like the Config setting "LORIS-MRI code" in the Paths section was >>>>>>>>>>>>>>>>>>>>>>>>>>>>> set to "/data/LORIS/data" but it should have been set to the directory >>>>>>>>>>>>>>>>>>>>>>>>>>>>> where the scripts are located (most probably /data/loris/bin/mri). >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helps, >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> On Wed, Jul 24, 2019 at 10:55 AM Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos wrote: >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Ok first i execute this command: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> "lorisadmin at hbp:/data/loris/bin/mri$ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ./batch_uploads_imageuploader -profile prod < ~/Desktop/input.txt > log.txt >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at ./batch_uploads_imageuploader line 143. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at ./batch_uploads_imageuploader line 143. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $_ in pattern >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> match (m//) at ./batch_uploads_imageuploader line 147. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> base is DCC0000_258024_V01 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> path is /data/incoming/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> type is .tar.gz >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> fullpath is >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/incoming/DCC0000_258024_V01.tar.gz >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> source /tmp/ImagingUpload-17-43-ZUEFjb >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> targetlocation /data/loris/data/tarchive >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 256. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 284. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at /data/loris/bin/mri/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> tarchive_validation.pl line 219. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at /data/loris/bin/mri/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl line 270. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 711. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Can't exec "mail": No such file or directory >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 721. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 722. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 723. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 724. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 724. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 725. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 735. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> No Mincs inserted >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The tarchiveLoader insertion script has >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> failed. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Running now the following command: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl -profile prod >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -upload_id 3 /data/incoming/DCC0000_258024_V01.tar.gz -verbose" >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I inserted the VisitLabel, but still the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Mincs are not inserted and i am getting this error >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> "lorisadmin at hbp:/data/loris/bin/mri$ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl -profile prod >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -upload_id 3 /data/incoming/DCC0000_258024_V01.tar.gz -verbose >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> find -path >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> \/tmp\/ImagingUpload\-17\-45\-5MsWEd -name '__MACOSX' -delete >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Spool message is: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The Scan for the uploadID 3 has already been >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> run with tarchiveID: 7. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> To continue with the rest of the insertion >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> pipeline, please run tarchiveLoader from a terminal as follows: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader -globLocation -profile prod >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive//2012/DCM_2012-12-05_ImagingUpload-17-43-ZUEFjb.tar >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -verbose" >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Which files should i delete? I thought that >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> deleting the files from the tarchive was enough. And i executed the last >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> proposed command to continue to rest of the insertion pipeline ( check the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> image ). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 24 ???? 2019 ???? 5:05 ?.?., ?/? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Cecile Madjar ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sorry I was not clear before. Every visits >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> of candidates are created in the session table with one entry per >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID/VisitLabel. So if the imaging pipeline created visits in the session >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> table (that are not attached to instruments) and you want to clean your >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> database completely, you can delete entries in that table as well. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Regarding your point 2, the imaging pipeline >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> can create the visit in the session table as long as the visit label is >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> present in the Visit_Windows table (which means the visit label stored in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the PatientName is a valid visit label). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> However, in your prod file, if the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> variable $subjectID{'createVisitLabel'} is set to 1 for candidates, the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit label should be created in the Visit_Windows table I believe. Here >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> is the line of the prod file you would need to change >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> . >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> In general, we prefer populating the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Visit_Windows table and set the $subjectID{'createVisitLabel'} to 0 for >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> candidate data to avoid insertion of badly labelled MRI data that are >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> complex to relabel. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Finally, regarding the candidate creation, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> if you execute the following steps, the pipeline should be able to create >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> candidates: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - set in the Imaging Pipeline section of the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> config module the config setting "Upload creation of candidates" to Yes >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - manually transfer the scans to the LORIS >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> server instead of uploading it via the imaging browser >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - run batch_imaging_upload.pl as you did >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> until now. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helps! >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> On Wed, Jul 24, 2019 at 8:47 AM Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> wrote: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> About my second question i replaced the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> name of the patient in the .dcm files and now i am getting an error that >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the visit label does not exist. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I thought it was supposed to be >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> automatically created. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> "Done adding archive info into database >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -globLocation -profile prod >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive//DCM_2012-12-05_ImagingUpload-15-42-yUwQQV.tar >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -verbose >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> md5sum >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive/DCM_2012-12-05_ImagingUpload-15-42-yUwQQV.tar >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> candidate id 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> => No Visit labelVisit label does not exist >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Set centerID = 1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Number of MINC files that will be >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> considered for inserting into the database: 1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> log dir is /logs and log file is >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /logs/TarLoad-15-42-L6pocU.log >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> candidate id 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> => No Visit label >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Cleaning up temp files: rm -rf >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-15-42-J2rQms/ImagingUpload-15-42-yUwQQV*" >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 24 ???? 2019 ???? 3:38 ?.?., ?/? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 1) What are the records in the session >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> table? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 2) I tried to upload a non-phantom file >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> like this >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> input_file.txt: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/incoming/DCC0000_258024_V1.tar.gz N >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DCC0000_258024_V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Terminal: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ./batch_uploads_imageuploader -profile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> prod < ~/Desktop/input.txt > log.txt >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and i get the following error in the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> log.txt file >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> "Running now the following command: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl -profile prod >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -upload_id 7 /data/incoming/DCC0000_258024_V1.tar.gz -verbose >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> find -path >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> \/tmp\/ImagingUpload\-14\-56\-FeLCB4 -name '__MACOSX' -delete >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Spool message is: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The PatientName read from the DICOM header >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> does not start with DCC0000_258024_V1 from the mri_upload table >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> " >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and the spool message is repeated for each >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> .dcm file. Should i preprocess every .dcm file and change the PatientName >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> to "DCC0000_258024_V1"? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 3) As far as it concerns the candidate >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> profile i have to create a new one each time before i try to upload a file? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Is there already a way to create a candidate profile and get the DCCID and >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID without the user interface? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 18 ???? 2019 ???? 5:00 ?.?., ?/? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Cecile Madjar >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> See answers to your questions below. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> About the 1st case we had a dicom with a >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> blank studyUID, maybe someone accidentally removed it. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> That is strange. Something must have been >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> done to the DICOM files. I have never seen a study with no StudyUID out of >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the scanner. Usually, you need to manually erase it with some tool. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> However, DICOMs never cease to surprise me... >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Some other questions: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 1) What are the steps to remove all of >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> my patients and uploads?: because i want to try to reupload all the testing >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> dicoms we had with a clean database. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Release 21.0 of LORIS-MRI will offer a >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> script to remove all the entries and files specific to an upload. However, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> this release is not yet out. Hopefully in the next few weeks. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> In the meantime, since your case is >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> particular and that you just want to start with a clean database, the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> following deletes should work (hopefully I won't forget any tables): >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from mri_violations_log; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from mri_protocol_violated_scans; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from MRICandidateErrors; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from parameter_file; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from files_qcstatus; # (if you >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> played with the QC part of the imaging browser for testing) >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from feedback_mri_comments; # (if >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> you played with the QC part of the imaging browser for testing) >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from tarchive_series; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from tarchive_files; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from mri_upload; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from tarchive; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from mri_scanner; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from candidate where >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID="scanner"; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I don't know if you want to also delete >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> entries in the session and candidate table too? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 2) We do not need to create the profile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> of a patient ( are the patients stored in the candidate table? because i >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> can't see the ghosts ), because will it automatically be created when >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> importing a dicom? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I am not sure I understand fully this >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> question. All candidates are stored in the candidate table. The phantom >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> scans however are attached to a scanner candidate depending on where the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> scan happened. It is a bit of a weird concept that we have to redesign >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> eventually but never got a chance to get to it. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hopefully this answered your question, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> otherwise, don't hesitate to let me know. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 3) What is the difference between >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> uploading a dicom as phantom instead of importing as >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCCID_DCCID_VisitLabel? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> When you upload the scan as >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID_DCCID_VisitLabel, there is a check that makes sure the candidate IDs >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and visit label are valid at the time of upload. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> When you upload a scan as phantom, it >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> expects that the DICOM field PatientName and uploaded filename contains the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> string "phantom". We enforced this behaviour on the imaging uploader side >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in recent releases but I can't remember which one. Probably the upcoming >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 21.0 release. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> All those verifications might seem >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> cumbersome but they are here to ensure that the files inserted are all >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> valid and labelled properly as it is a bit messy to have to delete files >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> that were wrongly labelled. At least, the delete script present in release >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 21.0 will make this process easier but it is still good practice to verify >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> those things. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> With pleasure. Hopefully the answers to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> your questions will be helpful. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PS: loris-dev mailing list: you will find >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the initial answer I gave Sotirios below. I forgot to cc the loris-dev in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> my earlier reply... >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 16 ???? 2019 ???? 12:02 ?.?., >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ?/? Cecile Madjar >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Dear Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you for reaching out. Since your >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> email was already organized in points, I will reply directly below your >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> questions below. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 1) What do we do when the StudyUID is >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> blank on the header? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/minor/docs/AppendixA-Troubleshooting_guideline.md >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> There solution provided at the table 3 does not guide us how to find the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> information ( is possible ). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The StudyUID is the field used in our >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> pipeline at the moment to check whether a DICOM study was already inserted >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> into LORIS with that same StudyUID since it is supposed to be unique for >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> every single study. Currently, we do not support insertion of DICOM studies >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> if they do not have a StudyUID associated with them. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Is there a specific reason why the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> StudyUID is blank in the DICOM headers in your DICOM files? Did they go >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> through some processes before upload to LORIS? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 2) When i am about to upload a >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> non-phanton case i need a 'Visit Label'. Is there already a script that can >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> create a new visit label for a specific Candidate, so i can provide it as >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> input afterwards to the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> batch_uploads_imageuploader ( See option 5.1.3 https://github.com/aces/Loris-MRI/blob/minor/docs/05-PipelineLaunchOptions.md ) >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I am not sure if the front-end allows >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> for it but if you use batch_uploads_imageuploader, the insertion scripts >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> could create the visit label for you. However, it does need to be included >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in the patient name in order for the script to know which label it should >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> use. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> For example: you upload V02 for MTL0123 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> (DCCID: 456789) but V02 was not yet created for MTL0123; the insertion >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> scripts will create a V02 visit for MTL0123 if the PatientName field for >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the dataset is MTL0123_456789_V02 with Stage marked as "Not Started". >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> However, *note that for the script to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> create the visit for the candidate, you have to make sure that all the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit label of your projects were inserted in the Visit_Windows table* >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> (otherwise, the visit will never be created as they were not specified as >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> being part of the list of visit label to expect). So in the example above, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> you should have one row in Visit_Windows with Visit_label="V02" set. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 3) Section 4.3 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/minor/docs/04-Scripts.md >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> What do we do when the folder contains multiple mnc files? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> This is a case by case. Most of the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> time, the MINC files that failed insertion into the imaging browser end up >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in the MRI violation module where you can see what went wrong with the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> acquisitions not inserted. If you notice that the MINC file should be >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> inserted as a specific protocol, you can force the insertion as explained >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in section 4.3. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> In your case, I have a feeling that you >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> want to be able to insert MINC files that did not go through the whole >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> pipeline insertion (DICOM archival, then dcm2mnc, then protocol >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> identification, then insertion...). In theory, you could call >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl on any MINC file, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> provided you have at least the following information: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - path to the MINC file >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - uploadID associated with the MINC >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> files or DICOM archive path from which those MINC files were created from >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Then the minc_insertion.pl script will >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> do the subject information and protocol validation etc... >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> If all the MINC files come from the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> same uploadID or TarchiveID, then you could run a loop in bash calling the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl script like this for >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> files deriving from uploadID=1: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ls /path/to/mnc/folder/* | while read >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> f; do minc_insertion.pl -profile prod >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -uploadID 1 -mincPath $f; done >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helped! >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>>>>>> >>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> -- >>>>>>>>>>>> >>>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>>> >>>>>>>>>>> _______________________________________________ >>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> -- >>>>>>>>>> >>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>> Montreal Neurological Institute >>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>> _______________________________________________ >>>>>>>>>> Loris-dev mailing list >>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> -- >>>>>>>>> >>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>> Montreal Neurological Institute >>>>>>>>> McGill University | Montreal | Canada >>>>>>>>> _______________________________________________ >>>>>>>>> Loris-dev mailing list >>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> -- >>>>>>>> >>>>>>>> christine.rogers at mcgill.ca >>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>> Montreal Neurological Institute >>>>>>>> McGill University | Montreal | Canada >>>>>>>> >>>>>>> _______________________________________________ >>>>>>> Loris-dev mailing list >>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>> >>>>>> >>>>>> >>>>>> -- >>>>>> >>>>>> christine.rogers at mcgill.ca >>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>> Montreal Neurological Institute >>>>>> McGill University | Montreal | Canada >>>>>> >>>>> _______________________________________________ >>>>> Loris-dev mailing list >>>>> Loris-dev at bic.mni.mcgill.ca >>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>> >>>> _______________________________________________ >>> Loris-dev mailing list >>> Loris-dev at bic.mni.mcgill.ca >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>> >> >> >> -- >> >> christine.rogers at mcgill.ca >> McGill Centre for Integrative Neuroscience | MCIN.ca >> Montreal Neurological Institute >> McGill University | Montreal | Canada >> > _______________________________________________ > Loris-dev mailing list > Loris-dev at bic.mni.mcgill.ca > https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > -------------- next part -------------- An HTML attachment was scrubbed... URL: From sotirisnik at gmail.com Tue Aug 13 17:21:15 2019 From: sotirisnik at gmail.com (Sotirios Nikoloutsopoulos) Date: Wed, 14 Aug 2019 00:21:15 +0300 Subject: [Loris-dev] Upgrading to Loris 21 - new make file In-Reply-To: References: Message-ID: I think that the files exists although i redownloaded the eslintrc.json i checked others files that had similar errors. lorisadmin at hbp:/var/www/loris$ ls -l ./node_modules/eslint-loader/index.js -rw-rw-r-- 1 lorisadmin lorisadmin 6463 ??? 26 1985 ./node_modules/eslint-loader/index.js lorisadmin at hbp:/var/www/loris$ ls -l .eslintrc.json -rw-rw-r-- 1 lorisadmin lorisadmin 84530 ??? 14 00:04 .eslintrc.json Maybe this can help Module build failed (from ./node_modules/eslint-loader/index.js): SyntaxError: Cannot read config file: /var/www/loris/.eslintrc.json Error: Unexpected token < in JSON at position 6 at JSON.parse () at loadJSONConfigFile (/var/www/loris/node_modules/eslint/lib/config/config-file.js:114:21) at loadConfigFile (/var/www/loris/node_modules/eslint/lib/config/config-file.js:230:26) at loadFromDisk (/var/www/loris/node_modules/eslint/lib/config/config-file.js:500:18) at Object.load (/var/www/loris/node_modules/eslint/lib/config/config-file.js:564:20) at Config.getLocalConfigHierarchy (/var/www/loris/node_modules/eslint/lib/config.js:227:44) at Config.getConfigHierarchy (/var/www/loris/node_modules/eslint/lib/config.js:179:43) at Config.getConfigVector (/var/www/loris/node_modules/eslint/lib/config.js:286:21) at Config.getConfig (/var/www/loris/node_modules/eslint/lib/config.js:329:29) at processText (/var/www/loris/node_modules/eslint/lib/cli-engine.js:162:33) at CLIEngine.executeOnText (/var/www/loris/node_modules/eslint/lib/cli-engine.js:596:17) at lint (/var/www/loris/node_modules/eslint-loader/index.js:237:17) at Object.module.exports (/var/www/loris/node_modules/eslint-loader/index.js:232:21) ERROR in ./modules/imaging_uploader/jsx/index.js Module build failed (from ./node_modules/eslint-loader/index.js): SyntaxError: Cannot read config file: /var/www/loris/.eslintrc.json Error: Unexpected token < in JSON at position 6 at JSON.parse () at loadJSONConfigFile (/var/www/loris/node_modules/eslint/lib/config/config-file.js:114:21) at loadConfigFile (/var/www/loris/node_modules/eslint/lib/config/config-file.js:230:26) at loadFromDisk (/var/www/loris/node_modules/eslint/lib/config/config-file.js:500:18) at Object.load (/var/www/loris/node_modules/eslint/lib/config/config-file.js:564:20) at Config.getLocalConfigHierarchy (/var/www/loris/node_modules/eslint/lib/config.js:227:44) at Config.getConfigHierarchy (/var/www/loris/node_modules/eslint/lib/config.js:179:43) at Config.getConfigVector (/var/www/loris/node_modules/eslint/lib/config.js:286:21) at Config.getConfig (/var/www/loris/node_modules/eslint/lib/config.js:329:29) at processText (/var/www/loris/node_modules/eslint/lib/cli-engine.js:162:33) at CLIEngine.executeOnText (/var/www/loris/node_modules/eslint/lib/cli-engine.js:596:17) at lint (/var/www/loris/node_modules/eslint-loader/index.js:237:17) at Object.module.exports (/var/www/loris/node_modules/eslint-loader/index.js:232:21) ???? ???, 13 ??? 2019 ???? 11:52 ?.?., ?/? John Saigle ??????: > HI Sotirios, > > The make_output.txt file shows webpack failing because it can't find the > ESLint config file. > > Can you confirm whether the file `.eslintrc.json` exists within your loris > root directory (usually `/var/www/loris/`)? When I delete my file I get the > same errors as you. > > If you find that it's missing, you can make a local copy with the contents > found here: > > > https://github.com/aces/Loris/blob/e26a6ad49a73fcffef0cd73bb600c4d17b200b62/.eslintrc.json > > Once you know it exists, try running `make` again. > > Let us know if that moves you forward. > > Best, > John > > On Tue, Aug 13, 2019 at 2:21 PM Sotirios Nikoloutsopoulos < > sotirisnik at gmail.com> wrote: > >> Hi, >> I executed the commands for the node and now i am get the followings: >> >> lorisadmin at hbp:/var/www/loris$ make > ~/make_output >> npm WARN The package prop-types is included as both a dev and production >> dependency. >> npm WARN optional SKIPPING OPTIONAL DEPENDENCY: fsevents at 1.2.4 >> (node_modules/fsevents): >> npm WARN notsup SKIPPING OPTIONAL DEPENDENCY: Unsupported platform for >> fsevents at 1.2.4: wanted {"os":"darwin","arch":"any"} (current: >> {"os":"linux","arch":"x64"}) >> >> npm ERR! code ELIFECYCLE >> npm ERR! errno 2 >> npm ERR! loris at 1.0.0 compile: `webpack` >> npm ERR! Exit status 2 >> npm ERR! >> npm ERR! Failed at the loris at 1.0.0 compile script. >> npm ERR! This is probably not a problem with npm. There is likely >> additional logging output above. >> >> npm ERR! A complete log of this run can be found in: >> npm ERR! >> /home/lorisadmin/.npm/_logs/2019-08-13T18_12_05_378Z-debug.log >> make: *** [javascript] Error 2 >> >> Thanks, >> Sotirios >> >> >> ???? ???, 12 ??? 2019 ???? 10:19 ?.?., ?/? Christine Rogers, Ms. < >> christine.rogers at mcgill.ca> ??????: >> >>> Hi Sotirios, >>> >>> We've seen some users installing LORIS 21 or upgrading to 21 whose >>> version of node doesn't work well with webpack, due to updated packages >>> they're missing. >>> If so, update your node : >>> >>> curl -sL https://deb.nodesource.com/setup_8.x | sudo -E bash - >>> sudo apt-get install -y nodejs >>> >>> Let us know how that goes -- please send us output from the same log if >>> any issues. >>> Best, >>> Christine >>> >>> >>> On Thu, Aug 8, 2019 at 2:38 PM Sotirios Nikoloutsopoulos < >>> sotirisnik at gmail.com> wrote: >>> >>>> It's not a disk space issue, as you can see below i have still 74GB >>>> available. >>>> >>>> lorisadmin at hbp:/var/www/loris$ df -h >>>> Filesystem Size Used Avail Use% Mounted on >>>> udev 2,9G 0 2,9G 0% /dev >>>> tmpfs 597M 8,6M 588M 2% /run >>>> /dev/sda1 98G 19G 74G 21% / >>>> >>>> Maybe we have to pass a flag to get into strict mode? as stated >>>> "SyntaxError: Block-scoped declarations (let, const, function, class) not >>>> yet supported outside strict mode" >>>> >>>> Thanks, >>>> Sotirios >>>> >>>> ???? ???, 8 ??? 2019 ???? 4:32 ?.?., ?/? Dave MacFarlane < >>>> dave.macfarlane at mcin.ca> ??????: >>>> >>>>> It looks like the javascript snippet shown in the error message when >>>>> trying to compile the js is truncated. Have you run out of disk space? >>>>> >>>>> On Thu, Aug 8, 2019 at 8:37 AM Sotirios Nikoloutsopoulos < >>>>> sotirisnik at gmail.com> wrote: >>>>> >>>>>> Hi, >>>>>> >>>>>> I runned make and also included the file it reports at the end. >>>>>> >>>>>> lorisadmin at hbp:/var/www/loris$ make >>>>>> npm install >>>>>> npm WARN optional Skipping failed optional dependency >>>>>> /chokidar/fsevents: >>>>>> npm WARN notsup Not compatible with your operating system or >>>>>> architecture: fsevents at 1.2.9 >>>>>> npm WARN optional Skipping failed optional dependency >>>>>> /watchpack/chokidar/fsevents: >>>>>> npm WARN notsup Not compatible with your operating system or >>>>>> architecture: fsevents at 1.2.9 >>>>>> npm run compile >>>>>> >>>>>> > loris at 1.0.0 compile /var/www/loris >>>>>> > webpack >>>>>> >>>>>> /var/www/loris/node_modules/webpack/bin/webpack.js:86 >>>>>> let notify = >>>>>> ^^^ >>>>>> >>>>>> SyntaxError: Block-scoped declarations (let, const, function, class) >>>>>> not yet supported outside strict mode >>>>>> at exports.runInThisContext (vm.js:53:16) >>>>>> at Module._compile (module.js:374:25) >>>>>> at Object.Module._extensions..js (module.js:417:10) >>>>>> at Module.load (module.js:344:32) >>>>>> at Function.Module._load (module.js:301:12) >>>>>> at Function.Module.runMain (module.js:442:10) >>>>>> at startup (node.js:136:18) >>>>>> at node.js:966:3 >>>>>> >>>>>> npm ERR! Linux 4.15.0-55-generic >>>>>> npm ERR! argv "/usr/bin/nodejs" "/usr/bin/npm" "run" "compile" >>>>>> npm ERR! node v4.2.6 >>>>>> npm ERR! npm v3.5.2 >>>>>> npm ERR! code ELIFECYCLE >>>>>> npm ERR! loris at 1.0.0 compile: `webpack` >>>>>> npm ERR! Exit status 1 >>>>>> npm ERR! >>>>>> npm ERR! Failed at the loris at 1.0.0 compile script 'webpack'. >>>>>> npm ERR! Make sure you have the latest version of node.js and npm >>>>>> installed. >>>>>> npm ERR! If you do, this is most likely a problem with the loris >>>>>> package, >>>>>> npm ERR! not with npm itself. >>>>>> npm ERR! Tell the author that this fails on your system: >>>>>> npm ERR! webpack >>>>>> npm ERR! You can get information on how to open an issue for this >>>>>> project with: >>>>>> npm ERR! npm bugs loris >>>>>> npm ERR! Or if that isn't available, you can get their info via: >>>>>> npm ERR! npm owner ls loris >>>>>> npm ERR! There is likely additional logging output above. >>>>>> >>>>>> npm ERR! Please include the following file with any support request: >>>>>> npm ERR! /var/www/loris/npm-debug.log >>>>>> Makefile:14: recipe for target 'javascript' failed >>>>>> make: *** [javascript] Error 1 >>>>>> >>>>>> Thanks, >>>>>> >>>>>> Sotirios >>>>>> >>>>>> ???? ???, 7 ??? 2019 ???? 5:41 ?.?., ?/? Christine Rogers, Ms. < >>>>>> christine.rogers at mcgill.ca> ??????: >>>>>> >>>>>>> Hi Sotirios, >>>>>>> >>>>>>> Thanks, have you tried all of these steps? >>>>>>> - clear your browser cache (and refresh a few times) >>>>>>> - delete any files in your smarty/templates_c directory (this will >>>>>>> clear the template cache - do Not touch smarty/templates/) >>>>>>> - run `make` (per the 21 release notes, this replaces the composer >>>>>>> commands used in previous releases to update your dependencies) >>>>>>> - restart apache (doesn't hurt) >>>>>>> >>>>>>> Let us know how it goes -- let us know what difference you see >>>>>>> after, with your logs. A >>>>>>> lso please send us your Config path settings (see these >>>>>>> Troubleshooting Queries >>>>>>> ) >>>>>>> if you're still seeing front-end issues. >>>>>>> >>>>>>> Thanks, >>>>>>> Christine >>>>>>> >>>>>>> On Wed, Aug 7, 2019 at 8:02 AM Sotirios Nikoloutsopoulos < >>>>>>> sotirisnik at gmail.com> wrote: >>>>>>> >>>>>>>> Hi, >>>>>>>> >>>>>>>> lorisadmin at hbp:/var/www/loris$ sudo cat /var/log/apache2/error.log >>>>>>>> [Wed Aug 07 07:35:02.422501 2019] [mpm_prefork:notice] [pid 1267] >>>>>>>> AH00163: Apache/2.4.18 (Ubuntu) OpenSSL/1.0.2g configured -- resuming >>>>>>>> normal operations >>>>>>>> [Wed Aug 07 07:35:02.422514 2019] [core:notice] [pid 1267] AH00094: >>>>>>>> Command line: '/usr/sbin/apache2' >>>>>>>> >>>>>>>> And as for the access.log the content are empty >>>>>>>> lorisadmin at hbp:/var/www/loris$ sudo ls -l >>>>>>>> /var/log/apache2/access.log >>>>>>>> lorisadmin at hbp:/var/www/loris$ sudo ls -l >>>>>>>> /var/log/apache2/access.log >>>>>>>> -rw-r----- 1 root adm 0 ???? 28 14:09 /var/log/apache2/access.log >>>>>>>> >>>>>>>> Also i noticed a loris_access.log. >>>>>>>> >>>>>>>> The only non-blank pages are: >>>>>>>> mri_violations, dataquery does not exist at all, statistics, >>>>>>>> data_team_helper, genomic_browser, configuration and >>>>>>>> server_processes_manager/ prints "Required configuration settings for >>>>>>>> Server Processes Manager are missing. Cannot continue." >>>>>>>> >>>>>>>> Thanks, >>>>>>>> Sotirios >>>>>>>> >>>>>>>> ???? ???, 6 ??? 2019 ???? 10:13 ?.?., ?/? Christine Rogers, Ms. < >>>>>>>> christine.rogers at mcgill.ca> ??????: >>>>>>>> >>>>>>>>> Hi Sotirios and LORIS community -- >>>>>>>>> >>>>>>>>> When upgrading to brand-new release 21 -- just a reminder to >>>>>>>>> follow the release notes and run the new *make* file to update >>>>>>>>> your dependencies (instead of using *composer* commands). >>>>>>>>> We've also updated the Wiki page >>>>>>>>> to >>>>>>>>> clarify that the release notes for each version will tell you what to run. >>>>>>>>> >>>>>>>>> If your current version is not the last release (20.3), it's still >>>>>>>>> important to upgrade to each minor release increment (e.g. 20.2, 20.3) >>>>>>>>> before making the leap to 21.0. >>>>>>>>> >>>>>>>>> If you're getting blank pages, post-upgrade -- Try clearing your >>>>>>>>> cache. >>>>>>>>> >>>>>>>>> Got questions or feedback e.g. on the Release Notes? please don't >>>>>>>>> hesitate to let us know. >>>>>>>>> Thanks, >>>>>>>>> Christine >>>>>>>>> The LORIS team >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> On Tue, Aug 6, 2019 at 10:09 AM Christine Rogers, Ms. < >>>>>>>>> christine.rogers at mcgill.ca> wrote: >>>>>>>>> >>>>>>>>>> Hi Sotirios, >>>>>>>>>> Could you also let us know -- on which pages is content visible, >>>>>>>>>> and on which pages/modules is content not visible for you? >>>>>>>>>> Thanks, >>>>>>>>>> Christine >>>>>>>>>> >>>>>>>>>> On Tue, Aug 6, 2019 at 9:54 AM Christine Rogers, Ms. < >>>>>>>>>> christine.rogers at mcgill.ca> wrote: >>>>>>>>>> >>>>>>>>>>> Thanks Sotirios, >>>>>>>>>>> That's good to know. It sounds like you've checked that your >>>>>>>>>>> /var/www/loris/project/config.xml file get populated properly. >>>>>>>>>>> >>>>>>>>>>> Please send us the last few errors you're seeing in your apache >>>>>>>>>>> error log file, and your config paths and we can see what's happening with >>>>>>>>>>> your front end -- >>>>>>>>>>> Run these Troubleshooting Queries >>>>>>>>>>> >>>>>>>>>>> to get your config path settings, given your front end is not displaying >>>>>>>>>>> fully. >>>>>>>>>>> >>>>>>>>>>> The Loris-MRI repo >>>>>>>>>>> 21 >>>>>>>>>>> install/upgrade would then be your next steps. >>>>>>>>>>> Best, >>>>>>>>>>> Christine >>>>>>>>>>> >>>>>>>>>>> On Tue, Aug 6, 2019 at 7:53 AM Sotirios Nikoloutsopoulos < >>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>> >>>>>>>>>>>> I am using a VM. What i did was: >>>>>>>>>>>> 1) Download the files from https://github.com/aces/Loris and >>>>>>>>>>>> replace them to my existing /vaw/www/loris folder. >>>>>>>>>>>> 2) Execute the composer install --no-dev and then composer >>>>>>>>>>>> dump-autoload as mentioned here >>>>>>>>>>>> https://github.com/aces/Loris/wiki/Updating-your-LORIS. >>>>>>>>>>>> 3) Execute install.sh from /var/www/loris/tools and because >>>>>>>>>>>> LORIS already existed i moved a .config file, then re-executed the >>>>>>>>>>>> install.sh successfully >>>>>>>>>>>> 4 ) As for the database, i dropped the schema and i executed >>>>>>>>>>>> the installdb.php >>>>>>>>>>>> >>>>>>>>>>>> ???? ???, 5 ??? 2019 ???? 5:22 ?.?., ?/? Christine Rogers, Ms. < >>>>>>>>>>>> christine.rogers at mcgill.ca> ??????: >>>>>>>>>>>> >>>>>>>>>>>>> Hi Sotorios, >>>>>>>>>>>>> >>>>>>>>>>>>> Thanks - when you re-installed did you start on a fresh root >>>>>>>>>>>>> path / VM or might some of your old system setting still apply? >>>>>>>>>>>>> (And if you did any steps similar to an upgrade, did you >>>>>>>>>>>>> follow the Upgrade steps in the Release Notes, from both repos?) >>>>>>>>>>>>> >>>>>>>>>>>>> About the TR_range column - it was recently split (MRI pr339 >>>>>>>>>>>>> ) split into >>>>>>>>>>>>> TR_min and _max columns. Given the code was trying to query TR_range which >>>>>>>>>>>>> does not exist in your mri_protocol table, double-check which version of >>>>>>>>>>>>> the Loris repo (tables) and the Loris-MRI repo (code) you have installed to >>>>>>>>>>>>> ensure they match. >>>>>>>>>>>>> >>>>>>>>>>>>> Christine >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> On Mon, Aug 5, 2019 at 9:06 AM Sotirios Nikoloutsopoulos < >>>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>> >>>>>>>>>>>>>> I reinstalled LORIS to 21 version and now the content is not >>>>>>>>>>>>>> visible at all at most pages. >>>>>>>>>>>>>> >>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>> >>>>>>>>>>>>>> ???? ???, 5 ??? 2019 ???? 3:19 ?.?., ?/? Sotirios >>>>>>>>>>>>>> Nikoloutsopoulos ??????: >>>>>>>>>>>>>> >>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> Is it easy to upgrade to Loris 21? Also the following fails >>>>>>>>>>>>>>> because the line 1985 of NeuroDB/MRIProcessingUtility.pm query mri_protocol >>>>>>>>>>>>>>> which doesn't have TR_range >>>>>>>>>>>>>>> https://github.com/aces/Loris/blob/21.0-release/SQL/0000-00-00-schema.sql#L556 >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> lorisadmin at hbp:/data/loris/bin/mri$ >>>>>>>>>>>>>>> ./batch_uploads_imageuploader -profile prod < ~/Desktop/input.txt > log.txt >>>>>>>>>>>>>>> Use of uninitialized value $_ in pattern match (m//) at >>>>>>>>>>>>>>> ./batch_uploads_imageuploader line 147. >>>>>>>>>>>>>>> base is DCC0000_258024_V1 >>>>>>>>>>>>>>> path is /data/incoming/ >>>>>>>>>>>>>>> type is .tar.gz >>>>>>>>>>>>>>> fullpath is /data/incoming/DCC0000_258024_V1.tar.gz >>>>>>>>>>>>>>> DBD::mysql::st execute failed: Unknown column 'TR_range' in >>>>>>>>>>>>>>> 'where clause' at >>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line 1985. >>>>>>>>>>>>>>> DBD::mysql::st fetchrow_array failed: fetch() without >>>>>>>>>>>>>>> execute() at >>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line 1986. >>>>>>>>>>>>>>> Use of uninitialized value $count_mri_protocol in numeric gt >>>>>>>>>>>>>>> (>) at /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm >>>>>>>>>>>>>>> line 1995. >>>>>>>>>>>>>>> DBD::mysql::st execute failed: Unknown column 'TR_range' in >>>>>>>>>>>>>>> 'field list' at /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 562. >>>>>>>>>>>>>>> Can't exec "mail": No such file or directory at >>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 721. >>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 722. >>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 723. >>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 724. >>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 725. >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> No Mincs inserted >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> Thanks, >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> ???? ???, 3 ??? 2019 ???? 1:08 ?.?., ?/? Christine Rogers, >>>>>>>>>>>>>>> Ms. ??????: >>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> First, just a note: we've released LORIS 21 this week with >>>>>>>>>>>>>>>> some major new features and cleanup -- especially if you are early in your >>>>>>>>>>>>>>>> setup phase, check out the Release notes for both the LORIS >>>>>>>>>>>>>>>> and >>>>>>>>>>>>>>>> Loris-MRI >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> repos. >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Thanks for your screenshots -- your empty mri_protocol >>>>>>>>>>>>>>>> table should be at the root of these issues : >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> The mri_protocol table must be populated >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> in order for your scans to be registered in LORIS -- it serves as a >>>>>>>>>>>>>>>> whitelist for the insertion pipeline which filters out scans that aren't >>>>>>>>>>>>>>>> identified or matched to scan types in this table. >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> By default, this table is populated with entries for t1, >>>>>>>>>>>>>>>> t2, fMRI and DTI (Insert statements for 21 release branch >>>>>>>>>>>>>>>> are here >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> ) >>>>>>>>>>>>>>>> Feel free to restore our default records and broaden their >>>>>>>>>>>>>>>> parameters to match all your scan types. >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> re Defaced, native, selected -- these filter the scans >>>>>>>>>>>>>>>> displayed as you move to the next page (View Session), instead of viewing >>>>>>>>>>>>>>>> "all types" of scans from a given session : >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> - "defaced" means that a defacing script >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> has masked the subject's face in the volume (for patient privacy) >>>>>>>>>>>>>>>> - "native" means that no pre-processing has been >>>>>>>>>>>>>>>> performed on the scan (it's raw data), >>>>>>>>>>>>>>>> - "selected" will show only volumes that have been >>>>>>>>>>>>>>>> QC'd and "selected" as the best of their type -- used to display only the >>>>>>>>>>>>>>>> best quality T1 image instead of all T1s acquired in a session, e.g. >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> re QC Comments -- >>>>>>>>>>>>>>>> Once you have successfully loaded scans (matched to the >>>>>>>>>>>>>>>> mri_protocol table), you'll be able to use the Imaging Browser's View >>>>>>>>>>>>>>>> Session subpage to enter/view QC comments on each volume, or for each >>>>>>>>>>>>>>>> visit. >>>>>>>>>>>>>>>> These are stored directly in the database, and linked to >>>>>>>>>>>>>>>> each scan. (Table name: feedback_mri_comments) >>>>>>>>>>>>>>>> (Visit-level QC comments are linked to the session.) >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> For a walkthrough of the Imaging setup - please see the Imaging >>>>>>>>>>>>>>>> Setup guide >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> - >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> An old LORIS walkthrough video >>>>>>>>>>>>>>>> can also >>>>>>>>>>>>>>>> walk you through some of the Imaging front-end features, starting at 8:00 >>>>>>>>>>>>>>>> LORIS' imaging modules have been updated many times since >>>>>>>>>>>>>>>> this video, but the functionality and workflow is similar. >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Let us know how it goes once you have entries in your >>>>>>>>>>>>>>>> mri_protocol table - >>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>> Christine >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> On Fri, Aug 2, 2019 at 7:58 AM Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Hi Christine, >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> In the candidate_list page i can see this patient >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> If i press the link under PSCID i get to see >>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> and if i press the link under Scan Done it redirects me to >>>>>>>>>>>>>>>>> imaging_browser >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> At the mri_violations page i also see No results ( neither >>>>>>>>>>>>>>>>> on resolved / not resolved ). >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> At the imaging_uploader i can see the record that failed. >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> If i click on the tarchive info i get to see the Protocol >>>>>>>>>>>>>>>>> Name which i think is the acquisition we wanted? >>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Also my mri_protocol table is empty. >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Furthermore i would like to ask about the defaced, native, >>>>>>>>>>>>>>>>> selected. What exactly is native and selected? And where are the qc >>>>>>>>>>>>>>>>> comments stored? >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Finally a walkthrough would be helpful. >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Thanks, >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> ???? ???, 30 ???? 2019 ???? 8:29 ?.?., ?/? Christine >>>>>>>>>>>>>>>>> Rogers, Ms. ??????: >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>> Glad to hear you're making progress with the visit >>>>>>>>>>>>>>>>>> labels. To follow up on your last few emails: >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> a- The Wiki's Setup Guide contains Sample insert >>>>>>>>>>>>>>>>>> statements for the Visit Windows table >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> . >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> As Cecile mentioned, the consistency of visit label >>>>>>>>>>>>>>>>>> format is important: V01, v01, V1, 01 -- whichever you select to use is >>>>>>>>>>>>>>>>>> fine; we use V01 by default across all documentation. >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> b- For Password reset, there is a script in the tools/ >>>>>>>>>>>>>>>>>> directory so that a back-end administrator can reset any front-end user >>>>>>>>>>>>>>>>>> password, including Admin. (See info on setting up / resetting User >>>>>>>>>>>>>>>>>> passwords in the Wiki's Setup Guide >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> ) >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> c- The minc file not being registered -- due to >>>>>>>>>>>>>>>>>> AcquisitionProtocol unknown. >>>>>>>>>>>>>>>>>> This means the SeriesDescription (Acquisition Protocol) >>>>>>>>>>>>>>>>>> in you Dicom header was not matched to any scan listed in the mri_protocol >>>>>>>>>>>>>>>>>> database table. >>>>>>>>>>>>>>>>>> (In the online Loris-MRI Troubleshooting Guide, >>>>>>>>>>>>>>>>>> this >>>>>>>>>>>>>>>>>> is Table 3, 2nd-last item "no MINCs inserted"). >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> The MRI Violations module (Readme here) >>>>>>>>>>>>>>>>>> will show >>>>>>>>>>>>>>>>>> you the details of this mismatch -- >>>>>>>>>>>>>>>>>> Go to the module (under the Imaging menu), find your scan >>>>>>>>>>>>>>>>>> and click the link "Could not identify scan type" -- in the next subpage >>>>>>>>>>>>>>>>>> you can compare the scan's actual parameters against the mri_protocol >>>>>>>>>>>>>>>>>> table. >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> To resolve this, adjust your mri_protocol table values or >>>>>>>>>>>>>>>>>> perhaps ensure your DICOMs are labelled consistently. >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Let us know if this works for you -- we can also walk you >>>>>>>>>>>>>>>>>> through an example of non-identified scans on >>>>>>>>>>>>>>>>>> Demo.loris.ca (MRI Violations module). >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>> Christine >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> The LORIS team >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> On Tue, Jul 30, 2019 at 10:47 AM Sotirios >>>>>>>>>>>>>>>>>> Nikoloutsopoulos wrote: >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> I hope this is sufficient as the error for the visit >>>>>>>>>>>>>>>>>>> label disappeared. >>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Please see the attached file. Also something i found. >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> lorisadmin at hbp:/data/loris/bin/mri$ cat >>>>>>>>>>>>>>>>>>> /data/loris/data//logs/TarLoad-17-39-xubBdv.log >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> ==> Loading file from disk >>>>>>>>>>>>>>>>>>> /tmp/TarLoad-17-39-UyQcG2/dcc0000_258024_v1_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> --> mapping DICOM parameter for >>>>>>>>>>>>>>>>>>> /tmp/TarLoad-17-39-UyQcG2/dcc0000_258024_v1_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> ==> computing md5 hash for MINC body. >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> --> md5: 6b1202fd63e29de4c9be1cd9925888a5 >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> ==> verifying acquisition protocol >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Acquisition protocol is unknown >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> --> The minc file cannot be registered since the >>>>>>>>>>>>>>>>>>> AcquisitionProtocol is unknown >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> ???? ???, 30 ???? 2019 ???? 4:58 ?.?., ?/? Sotirios >>>>>>>>>>>>>>>>>>> Nikoloutsopoulos ??????: >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Ok I fixed the login problem by using a known hash and >>>>>>>>>>>>>>>>>>>> by deleting the rows from the login_history i was able to login. >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> ???? ???, 30 ???? 2019 ???? 4:50 ?.?., ?/? Sotirios >>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos ??????: >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> there was no visit label 01 in the Visit_Windows table >>>>>>>>>>>>>>>>>>>>> and i don't know how to insert it because the record requires lots of >>>>>>>>>>>>>>>>>>>>> attributes. Also the system for a reason asked me to update my password and >>>>>>>>>>>>>>>>>>>>> now i don't remember it and my account got suspended. Is there a way to >>>>>>>>>>>>>>>>>>>>> reset it or set a simple password? I updated the password hash in the >>>>>>>>>>>>>>>>>>>>> users table by using the hash from another LORIS setup we had and i still >>>>>>>>>>>>>>>>>>>>> couldn't login ( also the attribute password is always NULL and the >>>>>>>>>>>>>>>>>>>>> expiration date is 1999-01-01 for some reason ). >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> Thanks >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> ???? ???, 29 ???? 2019 ???? 5:21 ?.?., ?/? Cecile >>>>>>>>>>>>>>>>>>>>> Madjar ??????: >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> Can you try adding the visit label v01 to the >>>>>>>>>>>>>>>>>>>>>> Visit_Windows table? >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> However, I noticed that in a previous dataset, the >>>>>>>>>>>>>>>>>>>>>> label was V1. Does that refer to the same visit? If so, you might want to >>>>>>>>>>>>>>>>>>>>>> harmonize the visit labels so they are all the same across datasets for a >>>>>>>>>>>>>>>>>>>>>> given timepoint, meaning you will need to relabel scans when the visit >>>>>>>>>>>>>>>>>>>>>> label is different but referring to the same visit label (v01 = V1 etc...). >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> Hope this helps, >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> On Mon, Jul 29, 2019 at 10:15 AM Sotirios >>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos wrote: >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> Could you help me with the "Visit label does not >>>>>>>>>>>>>>>>>>>>>>> exist"? I had changed $subjectID{'createVisitLabel'} to 1 as you had >>>>>>>>>>>>>>>>>>>>>>> suggested but it appears that this problem hasn't been resolved yet. >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> lorisadmin at hbp:/data/loris/bin/mri$ cat >>>>>>>>>>>>>>>>>>>>>>> /data/loris/data//logs/TarLoad-14-58-9Xog7H.log >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> ==> Loading file from disk >>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> --> mapping DICOM parameter for >>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> --> using user-defined filterParameters for >>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> Candidate Mismatch Error is Visit label does not >>>>>>>>>>>>>>>>>>>>>>> exist >>>>>>>>>>>>>>>>>>>>>>> -> WARNING: This candidate was invalid. Logging to >>>>>>>>>>>>>>>>>>>>>>> MRICandidateErrors table with reason >>>>>>>>>>>>>>>>>>>>>>> Visit label does not exist >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> ???? ???, 26 ???? 2019 ???? 3:02 ?.?., ?/? Sotirios >>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos ??????: >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> Hi Cecile, >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> The Center error was fixed. Still the insertion of >>>>>>>>>>>>>>>>>>>>>>>> mincs fails. Please see the output.txt file i attached. Also is there >>>>>>>>>>>>>>>>>>>>>>>> something else i need to change at the paths configuration? >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 25 ???? 2019 ???? 6:55 ?.?., ?/? Cecile >>>>>>>>>>>>>>>>>>>>>>>> Madjar ??????: >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> We are making progress! >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> I have a feeling this error comes from the fact >>>>>>>>>>>>>>>>>>>>>>>>> that your psc table does not have the MRI_alias populated for the DCC site. >>>>>>>>>>>>>>>>>>>>>>>>> Running the following query in the mysql database should fix this: >>>>>>>>>>>>>>>>>>>>>>>>> UPDATE psc SET MRI_alias="DCC", Alias="DCC" WHERE >>>>>>>>>>>>>>>>>>>>>>>>> Name="Data Coordinating Center"; >>>>>>>>>>>>>>>>>>>>>>>>> Repeat the same with all your sites (make sure to >>>>>>>>>>>>>>>>>>>>>>>>> change the Aliases between sites, they should all be unique). >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> Let me know how it goes! >>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> On Thu, Jul 25, 2019 at 11:43 AM Sotirios >>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos wrote: >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> Dear Cecile, >>>>>>>>>>>>>>>>>>>>>>>>>> You were right about your guesses. I did the >>>>>>>>>>>>>>>>>>>>>>>>>> modifications you suggested, i still get the "no mincs inserted" error, now >>>>>>>>>>>>>>>>>>>>>>>>>> i am getting the "No center found this candidate" error ( how do i fix >>>>>>>>>>>>>>>>>>>>>>>>>> that? from what i see the .dcm files contains a 'Institution Name', is that >>>>>>>>>>>>>>>>>>>>>>>>>> the center? ), so i guess that's why the validation fails, but i changed >>>>>>>>>>>>>>>>>>>>>>>>>> the force variable of tarchiveLoader to 1, shouldn't it have inserted the >>>>>>>>>>>>>>>>>>>>>>>>>> mincs then? Also it is optional to have a mail server, right? ( from what i >>>>>>>>>>>>>>>>>>>>>>>>>> see the mail error does not affect the $valid_study, so i assume we are >>>>>>>>>>>>>>>>>>>>>>>>>> okay with that ) >>>>>>>>>>>>>>>>>>>>>>>>>> Thank you a lot, >>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 25 ???? 2019 ???? 5:48 ?.?., ?/? Cecile >>>>>>>>>>>>>>>>>>>>>>>>>> Madjar ??????: >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> From what I understand, I believe you just need >>>>>>>>>>>>>>>>>>>>>>>>>>> to update a few config settings from the frontend in the Config module >>>>>>>>>>>>>>>>>>>>>>>>>>> (under the Admin menu). >>>>>>>>>>>>>>>>>>>>>>>>>>> [image: Screen Shot 2019-07-25 at 10.31.35 >>>>>>>>>>>>>>>>>>>>>>>>>>> AM.png] >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> Then go to the Paths section of the config >>>>>>>>>>>>>>>>>>>>>>>>>>> module and update the "LORIS-MRI code" config setting to >>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri (my guess is that currently, it is set to >>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data) and click on the submit button. >>>>>>>>>>>>>>>>>>>>>>>>>>> [image: Screen Shot 2019-07-25 at 10.32.50 >>>>>>>>>>>>>>>>>>>>>>>>>>> AM.png] >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> Then, go to Imaging Pipeline section of the >>>>>>>>>>>>>>>>>>>>>>>>>>> Configuration module and update the "Loris-MRI Data Directory" to >>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/ (my guess is that it is empty at the moment in your >>>>>>>>>>>>>>>>>>>>>>>>>>> database which is why $data_dir is not defined when you run the >>>>>>>>>>>>>>>>>>>>>>>>>>> tarchiveLoader step of the insertion pipeline). >>>>>>>>>>>>>>>>>>>>>>>>>>> [image: Screen Shot 2019-07-25 at 10.40.52 >>>>>>>>>>>>>>>>>>>>>>>>>>> AM.png] >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> Finally, I took a look at your environment file >>>>>>>>>>>>>>>>>>>>>>>>>>> and it might be a good idea to update your PERL5LIB variable to the >>>>>>>>>>>>>>>>>>>>>>>>>>> following (it has been added to the code a few releases ago as we realized >>>>>>>>>>>>>>>>>>>>>>>>>>> this was needed for the libraries. Not sure which version of LORIS-MRI you >>>>>>>>>>>>>>>>>>>>>>>>>>> are using but it does not hurt to update this variable to what I suggest >>>>>>>>>>>>>>>>>>>>>>>>>>> below): >>>>>>>>>>>>>>>>>>>>>>>>>>> export >>>>>>>>>>>>>>>>>>>>>>>>>>> PERL5LIB=/data/loris/bin/mri/uploadNeuroDB:/data/loris/bin/mri/dicom-archive:$PERL5LIB >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helps. Sorry you are experiencing so >>>>>>>>>>>>>>>>>>>>>>>>>>> much trouble setting things up. We probably need to update our WIKI. >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> On Thu, Jul 25, 2019 at 9:48 AM Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos wrote: >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> The "Loris-MRI Data Directory" should be in the >>>>>>>>>>>>>>>>>>>>>>>>>>>> environment file? >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 25 ???? 2019 ???? 12:59 ?.?., ?/? >>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos >>>>>>>>>>>>>>>>>>>>>>>>>>>> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> The scripts are located in >>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/. Somewhere I might have messed something up but i >>>>>>>>>>>>>>>>>>>>>>>>>>>>> remember following the instructions in the wiki.For example when i tried to >>>>>>>>>>>>>>>>>>>>>>>>>>>>> execute the batch_uploads_imageuploader perl script the line >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> my $command = "$bin_dir/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl " >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> was pointing to an invalid path, for example: >>>>>>>>>>>>>>>>>>>>>>>>>>>>> it was repeating a pattern and had LORIS instead of loris ( i think the >>>>>>>>>>>>>>>>>>>>>>>>>>>>> mistake was that in the wiki it suggested to use $PROJECT for the name of >>>>>>>>>>>>>>>>>>>>>>>>>>>>> the folder and i choosed 'loris' >>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris/wiki/Imaging-Database >>>>>>>>>>>>>>>>>>>>>>>>>>>>> ). See also the in image for the modification i did. Also i didn't find the >>>>>>>>>>>>>>>>>>>>>>>>>>>>> section to config the $data_dir variable. >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 24 ???? 2019 ???? 6:05 ?.?., ?/? >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Cecile Madjar ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> It looks like you have one Config setting not >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> set (based on the first error message you got when running it the first >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> time). You need to set a value for "Loris-MRI Data Directory" in the Config >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> module under the Imaging pipeline section (from what I can see, it would be >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/ for your setup). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The reason you got that error message the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> second time is that the pipeline checks if the DICOM study was already >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> inserted in the tarchive table. Since you ran the study once already, the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> study is inserted into the tarchive, hence the message. However, the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> pipeline did not complete as the MINC files were not created and inserted >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> into the files/parameter_file table. In order to continue the insertion, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> you will then need to run the tarchiveLoader command suggested in the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> terminal during the second run: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -globLocation -profile prod >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive//2012/DCM_2012-12-05_ImagingUpload-17-43-ZUEFjb.tar >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -verbose >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Finally, I am a bit confused by your setup. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Where are the scripts located? In /data/loris/bin/mri or /data/loris/data? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> It feels like the Config setting "LORIS-MRI code" in the Paths section was >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> set to "/data/LORIS/data" but it should have been set to the directory >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> where the scripts are located (most probably /data/loris/bin/mri). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helps, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> On Wed, Jul 24, 2019 at 10:55 AM Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> wrote: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Ok first i execute this command: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> "lorisadmin at hbp:/data/loris/bin/mri$ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ./batch_uploads_imageuploader -profile prod < ~/Desktop/input.txt > log.txt >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at ./batch_uploads_imageuploader line 143. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at ./batch_uploads_imageuploader line 143. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $_ in pattern >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> match (m//) at ./batch_uploads_imageuploader line 147. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> base is DCC0000_258024_V01 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> path is /data/incoming/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> type is .tar.gz >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> fullpath is >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/incoming/DCC0000_258024_V01.tar.gz >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> source /tmp/ImagingUpload-17-43-ZUEFjb >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> targetlocation /data/loris/data/tarchive >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 256. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 284. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at /data/loris/bin/mri/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> tarchive_validation.pl line 219. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at /data/loris/bin/mri/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl line 270. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 711. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Can't exec "mail": No such file or directory >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 721. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 722. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 723. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 724. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 724. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 725. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 735. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> No Mincs inserted >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The tarchiveLoader insertion script has >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> failed. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Running now the following command: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl -profile prod >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -upload_id 3 /data/incoming/DCC0000_258024_V01.tar.gz -verbose" >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I inserted the VisitLabel, but still the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Mincs are not inserted and i am getting this error >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> "lorisadmin at hbp:/data/loris/bin/mri$ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl -profile prod >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -upload_id 3 /data/incoming/DCC0000_258024_V01.tar.gz -verbose >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> find -path >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> \/tmp\/ImagingUpload\-17\-45\-5MsWEd -name '__MACOSX' -delete >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Spool message is: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The Scan for the uploadID 3 has already been >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> run with tarchiveID: 7. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> To continue with the rest of the insertion >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> pipeline, please run tarchiveLoader from a terminal as follows: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader -globLocation -profile prod >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive//2012/DCM_2012-12-05_ImagingUpload-17-43-ZUEFjb.tar >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -verbose" >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Which files should i delete? I thought that >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> deleting the files from the tarchive was enough. And i executed the last >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> proposed command to continue to rest of the insertion pipeline ( check the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> image ). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 24 ???? 2019 ???? 5:05 ?.?., ?/? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Cecile Madjar >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sorry I was not clear before. Every visits >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> of candidates are created in the session table with one entry per >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID/VisitLabel. So if the imaging pipeline created visits in the session >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> table (that are not attached to instruments) and you want to clean your >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> database completely, you can delete entries in that table as well. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Regarding your point 2, the imaging >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> pipeline can create the visit in the session table as long as the visit >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> label is present in the Visit_Windows table (which means the visit label >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> stored in the PatientName is a valid visit label). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> However, in your prod file, if the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> variable $subjectID{'createVisitLabel'} is set to 1 for candidates, the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit label should be created in the Visit_Windows table I believe. Here >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> is the line of the prod file you would need to change >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> . >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> In general, we prefer populating the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Visit_Windows table and set the $subjectID{'createVisitLabel'} to 0 for >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> candidate data to avoid insertion of badly labelled MRI data that are >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> complex to relabel. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Finally, regarding the candidate creation, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> if you execute the following steps, the pipeline should be able to create >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> candidates: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - set in the Imaging Pipeline section of >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the config module the config setting "Upload creation of candidates" to Yes >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - manually transfer the scans to the LORIS >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> server instead of uploading it via the imaging browser >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - run batch_imaging_upload.pl as you did >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> until now. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helps! >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> On Wed, Jul 24, 2019 at 8:47 AM Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> wrote: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> About my second question i replaced the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> name of the patient in the .dcm files and now i am getting an error that >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the visit label does not exist. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I thought it was supposed to be >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> automatically created. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> "Done adding archive info into database >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -globLocation -profile prod >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive//DCM_2012-12-05_ImagingUpload-15-42-yUwQQV.tar >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -verbose >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> md5sum >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive/DCM_2012-12-05_ImagingUpload-15-42-yUwQQV.tar >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> candidate id 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> => No Visit labelVisit label does not >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> exist >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Set centerID = 1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Number of MINC files that will be >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> considered for inserting into the database: 1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> log dir is /logs and log file is >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /logs/TarLoad-15-42-L6pocU.log >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> candidate id 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> => No Visit label >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Cleaning up temp files: rm -rf >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-15-42-J2rQms/ImagingUpload-15-42-yUwQQV*" >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 24 ???? 2019 ???? 3:38 ?.?., ?/? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 1) What are the records in the session >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> table? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 2) I tried to upload a non-phantom file >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> like this >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> input_file.txt: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/incoming/DCC0000_258024_V1.tar.gz N >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DCC0000_258024_V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Terminal: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ./batch_uploads_imageuploader -profile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> prod < ~/Desktop/input.txt > log.txt >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and i get the following error in the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> log.txt file >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> "Running now the following command: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl -profile prod >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -upload_id 7 /data/incoming/DCC0000_258024_V1.tar.gz -verbose >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> find -path >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> \/tmp\/ImagingUpload\-14\-56\-FeLCB4 -name '__MACOSX' -delete >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Spool message is: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The PatientName read from the DICOM >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> header does not start with DCC0000_258024_V1 from the mri_upload table >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> " >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and the spool message is repeated for >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> each .dcm file. Should i preprocess every .dcm file and change the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PatientName to "DCC0000_258024_V1"? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 3) As far as it concerns the candidate >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> profile i have to create a new one each time before i try to upload a file? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Is there already a way to create a candidate profile and get the DCCID and >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID without the user interface? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 18 ???? 2019 ???? 5:00 ?.?., >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ?/? Cecile Madjar >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> See answers to your questions below. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> About the 1st case we had a dicom with a >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> blank studyUID, maybe someone accidentally removed it. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> That is strange. Something must have >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> been done to the DICOM files. I have never seen a study with no StudyUID >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> out of the scanner. Usually, you need to manually erase it with some tool. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> However, DICOMs never cease to surprise me... >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Some other questions: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 1) What are the steps to remove all of >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> my patients and uploads?: because i want to try to reupload all the testing >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> dicoms we had with a clean database. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Release 21.0 of LORIS-MRI will offer a >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> script to remove all the entries and files specific to an upload. However, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> this release is not yet out. Hopefully in the next few weeks. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> In the meantime, since your case is >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> particular and that you just want to start with a clean database, the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> following deletes should work (hopefully I won't forget any tables): >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from mri_violations_log; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from mri_protocol_violated_scans; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from MRICandidateErrors; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from parameter_file; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from files_qcstatus; # (if you >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> played with the QC part of the imaging browser for testing) >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from feedback_mri_comments; # (if >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> you played with the QC part of the imaging browser for testing) >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from tarchive_series; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from tarchive_files; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from mri_upload; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from tarchive; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from mri_scanner; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from candidate where >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID="scanner"; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I don't know if you want to also delete >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> entries in the session and candidate table too? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 2) We do not need to create the profile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> of a patient ( are the patients stored in the candidate table? because i >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> can't see the ghosts ), because will it automatically be created when >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> importing a dicom? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I am not sure I understand fully this >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> question. All candidates are stored in the candidate table. The phantom >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> scans however are attached to a scanner candidate depending on where the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> scan happened. It is a bit of a weird concept that we have to redesign >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> eventually but never got a chance to get to it. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hopefully this answered your question, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> otherwise, don't hesitate to let me know. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 3) What is the difference between >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> uploading a dicom as phantom instead of importing as >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCCID_DCCID_VisitLabel? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> When you upload the scan as >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID_DCCID_VisitLabel, there is a check that makes sure the candidate IDs >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and visit label are valid at the time of upload. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> When you upload a scan as phantom, it >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> expects that the DICOM field PatientName and uploaded filename contains the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> string "phantom". We enforced this behaviour on the imaging uploader side >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in recent releases but I can't remember which one. Probably the upcoming >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 21.0 release. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> All those verifications might seem >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> cumbersome but they are here to ensure that the files inserted are all >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> valid and labelled properly as it is a bit messy to have to delete files >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> that were wrongly labelled. At least, the delete script present in release >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 21.0 will make this process easier but it is still good practice to verify >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> those things. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> With pleasure. Hopefully the answers to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> your questions will be helpful. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PS: loris-dev mailing list: you will >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> find the initial answer I gave Sotirios below. I forgot to cc the loris-dev >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in my earlier reply... >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 16 ???? 2019 ???? 12:02 ?.?., >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ?/? Cecile Madjar < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> cecile.madjar at mcin.ca> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Dear Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you for reaching out. Since your >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> email was already organized in points, I will reply directly below your >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> questions below. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 1) What do we do when the StudyUID is >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> blank on the header? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/minor/docs/AppendixA-Troubleshooting_guideline.md >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> There solution provided at the table 3 does not guide us how to find the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> information ( is possible ). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The StudyUID is the field used in our >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> pipeline at the moment to check whether a DICOM study was already inserted >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> into LORIS with that same StudyUID since it is supposed to be unique for >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> every single study. Currently, we do not support insertion of DICOM studies >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> if they do not have a StudyUID associated with them. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Is there a specific reason why the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> StudyUID is blank in the DICOM headers in your DICOM files? Did they go >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> through some processes before upload to LORIS? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 2) When i am about to upload a >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> non-phanton case i need a 'Visit Label'. Is there already a script that can >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> create a new visit label for a specific Candidate, so i can provide it as >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> input afterwards to the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> batch_uploads_imageuploader ( See option 5.1.3 https://github.com/aces/Loris-MRI/blob/minor/docs/05-PipelineLaunchOptions.md ) >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I am not sure if the front-end allows >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> for it but if you use batch_uploads_imageuploader, the insertion scripts >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> could create the visit label for you. However, it does need to be included >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in the patient name in order for the script to know which label it should >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> use. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> For example: you upload V02 for >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> MTL0123 (DCCID: 456789) but V02 was not yet created for MTL0123; the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> insertion scripts will create a V02 visit for MTL0123 if the PatientName >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> field for the dataset is MTL0123_456789_V02 with Stage marked as "Not >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Started". >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> However, *note that for the script to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> create the visit for the candidate, you have to make sure that all the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit label of your projects were inserted in the Visit_Windows table* >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> (otherwise, the visit will never be created as they were not specified as >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> being part of the list of visit label to expect). So in the example above, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> you should have one row in Visit_Windows with Visit_label="V02" set. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 3) Section 4.3 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/minor/docs/04-Scripts.md >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> What do we do when the folder contains multiple mnc files? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> This is a case by case. Most of the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> time, the MINC files that failed insertion into the imaging browser end up >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in the MRI violation module where you can see what went wrong with the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> acquisitions not inserted. If you notice that the MINC file should be >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> inserted as a specific protocol, you can force the insertion as explained >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in section 4.3. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> In your case, I have a feeling that >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> you want to be able to insert MINC files that did not go through the whole >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> pipeline insertion (DICOM archival, then dcm2mnc, then protocol >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> identification, then insertion...). In theory, you could call >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl on any MINC file, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> provided you have at least the following information: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - path to the MINC file >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - uploadID associated with the MINC >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> files or DICOM archive path from which those MINC files were created from >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Then the minc_insertion.pl script >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> will do the subject information and protocol validation etc... >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> If all the MINC files come from the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> same uploadID or TarchiveID, then you could run a loop in bash calling the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl script like this >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> for files deriving from uploadID=1: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ls /path/to/mnc/folder/* | while read >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> f; do minc_insertion.pl -profile prod >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -uploadID 1 -mincPath $f; done >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helped! >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> -- >>>>>>>>>>>>> >>>>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>>>> >>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> -- >>>>>>>>>>> >>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>> _______________________________________________ >>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> -- >>>>>>>>>> >>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>> Montreal Neurological Institute >>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>> _______________________________________________ >>>>>>>>>> Loris-dev mailing list >>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> -- >>>>>>>>> >>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>> Montreal Neurological Institute >>>>>>>>> McGill University | Montreal | Canada >>>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> Loris-dev mailing list >>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>> >>>>>>> >>>>>>> >>>>>>> -- >>>>>>> >>>>>>> christine.rogers at mcgill.ca >>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>> Montreal Neurological Institute >>>>>>> McGill University | Montreal | Canada >>>>>>> >>>>>> _______________________________________________ >>>>>> Loris-dev mailing list >>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>> >>>>> _______________________________________________ >>>> Loris-dev mailing list >>>> Loris-dev at bic.mni.mcgill.ca >>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>> >>> >>> >>> -- >>> >>> christine.rogers at mcgill.ca >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>> Montreal Neurological Institute >>> McGill University | Montreal | Canada >>> >> _______________________________________________ >> Loris-dev mailing list >> Loris-dev at bic.mni.mcgill.ca >> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From wangshen.mcin at gmail.com Tue Aug 13 19:29:08 2019 From: wangshen.mcin at gmail.com (Shen Wang) Date: Tue, 13 Aug 2019 19:29:08 -0400 Subject: [Loris-dev] Upgrading to Loris 21 - new make file In-Reply-To: References: Message-ID: Hi Sotirios, When you do make command, please make sure with sudo at the beginning. [sudo make] If it still doesn't work for you. Then try the solutions below. solution 1: [image: ???? 2019-08-13 19.21.15.png] Regards Shen On Tue, 13 Aug 2019 at 17:22, Sotirios Nikoloutsopoulos < sotirisnik at gmail.com> wrote: > I think that the files exists although i redownloaded the eslintrc.json i > checked others files that had similar errors. > > lorisadmin at hbp:/var/www/loris$ ls -l ./node_modules/eslint-loader/index.js > -rw-rw-r-- 1 lorisadmin lorisadmin 6463 ??? 26 1985 > ./node_modules/eslint-loader/index.js > > lorisadmin at hbp:/var/www/loris$ ls -l .eslintrc.json > -rw-rw-r-- 1 lorisadmin lorisadmin 84530 ??? 14 00:04 .eslintrc.json > > Maybe this can help > > Module build failed (from ./node_modules/eslint-loader/index.js): > SyntaxError: Cannot read config file: /var/www/loris/.eslintrc.json > Error: Unexpected token < in JSON at position 6 > at JSON.parse () > at loadJSONConfigFile > (/var/www/loris/node_modules/eslint/lib/config/config-file.js:114:21) > at loadConfigFile > (/var/www/loris/node_modules/eslint/lib/config/config-file.js:230:26) > at loadFromDisk > (/var/www/loris/node_modules/eslint/lib/config/config-file.js:500:18) > at Object.load > (/var/www/loris/node_modules/eslint/lib/config/config-file.js:564:20) > at Config.getLocalConfigHierarchy > (/var/www/loris/node_modules/eslint/lib/config.js:227:44) > at Config.getConfigHierarchy > (/var/www/loris/node_modules/eslint/lib/config.js:179:43) > at Config.getConfigVector > (/var/www/loris/node_modules/eslint/lib/config.js:286:21) > at Config.getConfig > (/var/www/loris/node_modules/eslint/lib/config.js:329:29) > at processText > (/var/www/loris/node_modules/eslint/lib/cli-engine.js:162:33) > at CLIEngine.executeOnText > (/var/www/loris/node_modules/eslint/lib/cli-engine.js:596:17) > at lint (/var/www/loris/node_modules/eslint-loader/index.js:237:17) > at Object.module.exports > (/var/www/loris/node_modules/eslint-loader/index.js:232:21) > > ERROR in ./modules/imaging_uploader/jsx/index.js > Module build failed (from ./node_modules/eslint-loader/index.js): > SyntaxError: Cannot read config file: /var/www/loris/.eslintrc.json > Error: Unexpected token < in JSON at position 6 > at JSON.parse () > at loadJSONConfigFile > (/var/www/loris/node_modules/eslint/lib/config/config-file.js:114:21) > at loadConfigFile > (/var/www/loris/node_modules/eslint/lib/config/config-file.js:230:26) > at loadFromDisk > (/var/www/loris/node_modules/eslint/lib/config/config-file.js:500:18) > at Object.load > (/var/www/loris/node_modules/eslint/lib/config/config-file.js:564:20) > at Config.getLocalConfigHierarchy > (/var/www/loris/node_modules/eslint/lib/config.js:227:44) > at Config.getConfigHierarchy > (/var/www/loris/node_modules/eslint/lib/config.js:179:43) > at Config.getConfigVector > (/var/www/loris/node_modules/eslint/lib/config.js:286:21) > at Config.getConfig > (/var/www/loris/node_modules/eslint/lib/config.js:329:29) > at processText > (/var/www/loris/node_modules/eslint/lib/cli-engine.js:162:33) > at CLIEngine.executeOnText > (/var/www/loris/node_modules/eslint/lib/cli-engine.js:596:17) > at lint (/var/www/loris/node_modules/eslint-loader/index.js:237:17) > at Object.module.exports > (/var/www/loris/node_modules/eslint-loader/index.js:232:21) > > > > ???? ???, 13 ??? 2019 ???? 11:52 ?.?., ?/? John Saigle < > john.saigle at mcin.ca> ??????: > >> HI Sotirios, >> >> The make_output.txt file shows webpack failing because it can't find the >> ESLint config file. >> >> Can you confirm whether the file `.eslintrc.json` exists within your >> loris root directory (usually `/var/www/loris/`)? When I delete my file I >> get the same errors as you. >> >> If you find that it's missing, you can make a local copy with the >> contents found here: >> >> >> https://github.com/aces/Loris/blob/e26a6ad49a73fcffef0cd73bb600c4d17b200b62/.eslintrc.json >> >> Once you know it exists, try running `make` again. >> >> Let us know if that moves you forward. >> >> Best, >> John >> >> On Tue, Aug 13, 2019 at 2:21 PM Sotirios Nikoloutsopoulos < >> sotirisnik at gmail.com> wrote: >> >>> Hi, >>> I executed the commands for the node and now i am get the followings: >>> >>> lorisadmin at hbp:/var/www/loris$ make > ~/make_output >>> npm WARN The package prop-types is included as both a dev and production >>> dependency. >>> npm WARN optional SKIPPING OPTIONAL DEPENDENCY: fsevents at 1.2.4 >>> (node_modules/fsevents): >>> npm WARN notsup SKIPPING OPTIONAL DEPENDENCY: Unsupported platform for >>> fsevents at 1.2.4: wanted {"os":"darwin","arch":"any"} (current: >>> {"os":"linux","arch":"x64"}) >>> >>> npm ERR! code ELIFECYCLE >>> npm ERR! errno 2 >>> npm ERR! loris at 1.0.0 compile: `webpack` >>> npm ERR! Exit status 2 >>> npm ERR! >>> npm ERR! Failed at the loris at 1.0.0 compile script. >>> npm ERR! This is probably not a problem with npm. There is likely >>> additional logging output above. >>> >>> npm ERR! A complete log of this run can be found in: >>> npm ERR! >>> /home/lorisadmin/.npm/_logs/2019-08-13T18_12_05_378Z-debug.log >>> make: *** [javascript] Error 2 >>> >>> Thanks, >>> Sotirios >>> >>> >>> ???? ???, 12 ??? 2019 ???? 10:19 ?.?., ?/? Christine Rogers, Ms. < >>> christine.rogers at mcgill.ca> ??????: >>> >>>> Hi Sotirios, >>>> >>>> We've seen some users installing LORIS 21 or upgrading to 21 whose >>>> version of node doesn't work well with webpack, due to updated packages >>>> they're missing. >>>> If so, update your node : >>>> >>>> curl -sL https://deb.nodesource.com/setup_8.x | sudo -E bash - >>>> sudo apt-get install -y nodejs >>>> >>>> Let us know how that goes -- please send us output from the same log if >>>> any issues. >>>> Best, >>>> Christine >>>> >>>> >>>> On Thu, Aug 8, 2019 at 2:38 PM Sotirios Nikoloutsopoulos < >>>> sotirisnik at gmail.com> wrote: >>>> >>>>> It's not a disk space issue, as you can see below i have still 74GB >>>>> available. >>>>> >>>>> lorisadmin at hbp:/var/www/loris$ df -h >>>>> Filesystem Size Used Avail Use% Mounted on >>>>> udev 2,9G 0 2,9G 0% /dev >>>>> tmpfs 597M 8,6M 588M 2% /run >>>>> /dev/sda1 98G 19G 74G 21% / >>>>> >>>>> Maybe we have to pass a flag to get into strict mode? as stated >>>>> "SyntaxError: Block-scoped declarations (let, const, function, class) not >>>>> yet supported outside strict mode" >>>>> >>>>> Thanks, >>>>> Sotirios >>>>> >>>>> ???? ???, 8 ??? 2019 ???? 4:32 ?.?., ?/? Dave MacFarlane < >>>>> dave.macfarlane at mcin.ca> ??????: >>>>> >>>>>> It looks like the javascript snippet shown in the error message when >>>>>> trying to compile the js is truncated. Have you run out of disk space? >>>>>> >>>>>> On Thu, Aug 8, 2019 at 8:37 AM Sotirios Nikoloutsopoulos < >>>>>> sotirisnik at gmail.com> wrote: >>>>>> >>>>>>> Hi, >>>>>>> >>>>>>> I runned make and also included the file it reports at the end. >>>>>>> >>>>>>> lorisadmin at hbp:/var/www/loris$ make >>>>>>> npm install >>>>>>> npm WARN optional Skipping failed optional dependency >>>>>>> /chokidar/fsevents: >>>>>>> npm WARN notsup Not compatible with your operating system or >>>>>>> architecture: fsevents at 1.2.9 >>>>>>> npm WARN optional Skipping failed optional dependency >>>>>>> /watchpack/chokidar/fsevents: >>>>>>> npm WARN notsup Not compatible with your operating system or >>>>>>> architecture: fsevents at 1.2.9 >>>>>>> npm run compile >>>>>>> >>>>>>> > loris at 1.0.0 compile /var/www/loris >>>>>>> > webpack >>>>>>> >>>>>>> /var/www/loris/node_modules/webpack/bin/webpack.js:86 >>>>>>> let notify = >>>>>>> ^^^ >>>>>>> >>>>>>> SyntaxError: Block-scoped declarations (let, const, function, class) >>>>>>> not yet supported outside strict mode >>>>>>> at exports.runInThisContext (vm.js:53:16) >>>>>>> at Module._compile (module.js:374:25) >>>>>>> at Object.Module._extensions..js (module.js:417:10) >>>>>>> at Module.load (module.js:344:32) >>>>>>> at Function.Module._load (module.js:301:12) >>>>>>> at Function.Module.runMain (module.js:442:10) >>>>>>> at startup (node.js:136:18) >>>>>>> at node.js:966:3 >>>>>>> >>>>>>> npm ERR! Linux 4.15.0-55-generic >>>>>>> npm ERR! argv "/usr/bin/nodejs" "/usr/bin/npm" "run" "compile" >>>>>>> npm ERR! node v4.2.6 >>>>>>> npm ERR! npm v3.5.2 >>>>>>> npm ERR! code ELIFECYCLE >>>>>>> npm ERR! loris at 1.0.0 compile: `webpack` >>>>>>> npm ERR! Exit status 1 >>>>>>> npm ERR! >>>>>>> npm ERR! Failed at the loris at 1.0.0 compile script 'webpack'. >>>>>>> npm ERR! Make sure you have the latest version of node.js and npm >>>>>>> installed. >>>>>>> npm ERR! If you do, this is most likely a problem with the loris >>>>>>> package, >>>>>>> npm ERR! not with npm itself. >>>>>>> npm ERR! Tell the author that this fails on your system: >>>>>>> npm ERR! webpack >>>>>>> npm ERR! You can get information on how to open an issue for this >>>>>>> project with: >>>>>>> npm ERR! npm bugs loris >>>>>>> npm ERR! Or if that isn't available, you can get their info via: >>>>>>> npm ERR! npm owner ls loris >>>>>>> npm ERR! There is likely additional logging output above. >>>>>>> >>>>>>> npm ERR! Please include the following file with any support request: >>>>>>> npm ERR! /var/www/loris/npm-debug.log >>>>>>> Makefile:14: recipe for target 'javascript' failed >>>>>>> make: *** [javascript] Error 1 >>>>>>> >>>>>>> Thanks, >>>>>>> >>>>>>> Sotirios >>>>>>> >>>>>>> ???? ???, 7 ??? 2019 ???? 5:41 ?.?., ?/? Christine Rogers, Ms. < >>>>>>> christine.rogers at mcgill.ca> ??????: >>>>>>> >>>>>>>> Hi Sotirios, >>>>>>>> >>>>>>>> Thanks, have you tried all of these steps? >>>>>>>> - clear your browser cache (and refresh a few times) >>>>>>>> - delete any files in your smarty/templates_c directory (this will >>>>>>>> clear the template cache - do Not touch smarty/templates/) >>>>>>>> - run `make` (per the 21 release notes, this replaces the composer >>>>>>>> commands used in previous releases to update your dependencies) >>>>>>>> - restart apache (doesn't hurt) >>>>>>>> >>>>>>>> Let us know how it goes -- let us know what difference you see >>>>>>>> after, with your logs. A >>>>>>>> lso please send us your Config path settings (see these >>>>>>>> Troubleshooting Queries >>>>>>>> ) >>>>>>>> if you're still seeing front-end issues. >>>>>>>> >>>>>>>> Thanks, >>>>>>>> Christine >>>>>>>> >>>>>>>> On Wed, Aug 7, 2019 at 8:02 AM Sotirios Nikoloutsopoulos < >>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>> >>>>>>>>> Hi, >>>>>>>>> >>>>>>>>> lorisadmin at hbp:/var/www/loris$ sudo cat /var/log/apache2/error.log >>>>>>>>> [Wed Aug 07 07:35:02.422501 2019] [mpm_prefork:notice] [pid 1267] >>>>>>>>> AH00163: Apache/2.4.18 (Ubuntu) OpenSSL/1.0.2g configured -- resuming >>>>>>>>> normal operations >>>>>>>>> [Wed Aug 07 07:35:02.422514 2019] [core:notice] [pid 1267] >>>>>>>>> AH00094: Command line: '/usr/sbin/apache2' >>>>>>>>> >>>>>>>>> And as for the access.log the content are empty >>>>>>>>> lorisadmin at hbp:/var/www/loris$ sudo ls -l >>>>>>>>> /var/log/apache2/access.log >>>>>>>>> lorisadmin at hbp:/var/www/loris$ sudo ls -l >>>>>>>>> /var/log/apache2/access.log >>>>>>>>> -rw-r----- 1 root adm 0 ???? 28 14:09 /var/log/apache2/access.log >>>>>>>>> >>>>>>>>> Also i noticed a loris_access.log. >>>>>>>>> >>>>>>>>> The only non-blank pages are: >>>>>>>>> mri_violations, dataquery does not exist at all, statistics, >>>>>>>>> data_team_helper, genomic_browser, configuration and >>>>>>>>> server_processes_manager/ prints "Required configuration settings for >>>>>>>>> Server Processes Manager are missing. Cannot continue." >>>>>>>>> >>>>>>>>> Thanks, >>>>>>>>> Sotirios >>>>>>>>> >>>>>>>>> ???? ???, 6 ??? 2019 ???? 10:13 ?.?., ?/? Christine Rogers, Ms. < >>>>>>>>> christine.rogers at mcgill.ca> ??????: >>>>>>>>> >>>>>>>>>> Hi Sotirios and LORIS community -- >>>>>>>>>> >>>>>>>>>> When upgrading to brand-new release 21 -- just a reminder to >>>>>>>>>> follow the release notes and run the new *make* file to update >>>>>>>>>> your dependencies (instead of using *composer* commands). >>>>>>>>>> We've also updated the Wiki page >>>>>>>>>> to >>>>>>>>>> clarify that the release notes for each version will tell you what to run. >>>>>>>>>> >>>>>>>>>> If your current version is not the last release (20.3), it's >>>>>>>>>> still important to upgrade to each minor release increment (e.g. 20.2, >>>>>>>>>> 20.3) before making the leap to 21.0. >>>>>>>>>> >>>>>>>>>> If you're getting blank pages, post-upgrade -- Try clearing your >>>>>>>>>> cache. >>>>>>>>>> >>>>>>>>>> Got questions or feedback e.g. on the Release Notes? please don't >>>>>>>>>> hesitate to let us know. >>>>>>>>>> Thanks, >>>>>>>>>> Christine >>>>>>>>>> The LORIS team >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> On Tue, Aug 6, 2019 at 10:09 AM Christine Rogers, Ms. < >>>>>>>>>> christine.rogers at mcgill.ca> wrote: >>>>>>>>>> >>>>>>>>>>> Hi Sotirios, >>>>>>>>>>> Could you also let us know -- on which pages is content visible, >>>>>>>>>>> and on which pages/modules is content not visible for you? >>>>>>>>>>> Thanks, >>>>>>>>>>> Christine >>>>>>>>>>> >>>>>>>>>>> On Tue, Aug 6, 2019 at 9:54 AM Christine Rogers, Ms. < >>>>>>>>>>> christine.rogers at mcgill.ca> wrote: >>>>>>>>>>> >>>>>>>>>>>> Thanks Sotirios, >>>>>>>>>>>> That's good to know. It sounds like you've checked that your >>>>>>>>>>>> /var/www/loris/project/config.xml file get populated properly. >>>>>>>>>>>> >>>>>>>>>>>> Please send us the last few errors you're seeing in your apache >>>>>>>>>>>> error log file, and your config paths and we can see what's happening with >>>>>>>>>>>> your front end -- >>>>>>>>>>>> Run these Troubleshooting Queries >>>>>>>>>>>> >>>>>>>>>>>> to get your config path settings, given your front end is not displaying >>>>>>>>>>>> fully. >>>>>>>>>>>> >>>>>>>>>>>> The Loris-MRI repo >>>>>>>>>>>> 21 >>>>>>>>>>>> install/upgrade would then be your next steps. >>>>>>>>>>>> Best, >>>>>>>>>>>> Christine >>>>>>>>>>>> >>>>>>>>>>>> On Tue, Aug 6, 2019 at 7:53 AM Sotirios Nikoloutsopoulos < >>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>> >>>>>>>>>>>>> I am using a VM. What i did was: >>>>>>>>>>>>> 1) Download the files from https://github.com/aces/Loris and >>>>>>>>>>>>> replace them to my existing /vaw/www/loris folder. >>>>>>>>>>>>> 2) Execute the composer install --no-dev and then composer >>>>>>>>>>>>> dump-autoload as mentioned here >>>>>>>>>>>>> https://github.com/aces/Loris/wiki/Updating-your-LORIS. >>>>>>>>>>>>> 3) Execute install.sh from /var/www/loris/tools and because >>>>>>>>>>>>> LORIS already existed i moved a .config file, then re-executed the >>>>>>>>>>>>> install.sh successfully >>>>>>>>>>>>> 4 ) As for the database, i dropped the schema and i executed >>>>>>>>>>>>> the installdb.php >>>>>>>>>>>>> >>>>>>>>>>>>> ???? ???, 5 ??? 2019 ???? 5:22 ?.?., ?/? Christine Rogers, Ms. >>>>>>>>>>>>> ??????: >>>>>>>>>>>>> >>>>>>>>>>>>>> Hi Sotorios, >>>>>>>>>>>>>> >>>>>>>>>>>>>> Thanks - when you re-installed did you start on a fresh root >>>>>>>>>>>>>> path / VM or might some of your old system setting still apply? >>>>>>>>>>>>>> (And if you did any steps similar to an upgrade, did you >>>>>>>>>>>>>> follow the Upgrade steps in the Release Notes, from both repos?) >>>>>>>>>>>>>> >>>>>>>>>>>>>> About the TR_range column - it was recently split (MRI pr339 >>>>>>>>>>>>>> ) split into >>>>>>>>>>>>>> TR_min and _max columns. Given the code was trying to query TR_range which >>>>>>>>>>>>>> does not exist in your mri_protocol table, double-check which version of >>>>>>>>>>>>>> the Loris repo (tables) and the Loris-MRI repo (code) you have installed to >>>>>>>>>>>>>> ensure they match. >>>>>>>>>>>>>> >>>>>>>>>>>>>> Christine >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> On Mon, Aug 5, 2019 at 9:06 AM Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>> >>>>>>>>>>>>>>> I reinstalled LORIS to 21 version and now the content is not >>>>>>>>>>>>>>> visible at all at most pages. >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> ???? ???, 5 ??? 2019 ???? 3:19 ?.?., ?/? Sotirios >>>>>>>>>>>>>>> Nikoloutsopoulos ??????: >>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Is it easy to upgrade to Loris 21? Also the following fails >>>>>>>>>>>>>>>> because the line 1985 of NeuroDB/MRIProcessingUtility.pm query mri_protocol >>>>>>>>>>>>>>>> which doesn't have TR_range >>>>>>>>>>>>>>>> https://github.com/aces/Loris/blob/21.0-release/SQL/0000-00-00-schema.sql#L556 >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> lorisadmin at hbp:/data/loris/bin/mri$ >>>>>>>>>>>>>>>> ./batch_uploads_imageuploader -profile prod < ~/Desktop/input.txt > log.txt >>>>>>>>>>>>>>>> Use of uninitialized value $_ in pattern match (m//) at >>>>>>>>>>>>>>>> ./batch_uploads_imageuploader line 147. >>>>>>>>>>>>>>>> base is DCC0000_258024_V1 >>>>>>>>>>>>>>>> path is /data/incoming/ >>>>>>>>>>>>>>>> type is .tar.gz >>>>>>>>>>>>>>>> fullpath is /data/incoming/DCC0000_258024_V1.tar.gz >>>>>>>>>>>>>>>> DBD::mysql::st execute failed: Unknown column 'TR_range' in >>>>>>>>>>>>>>>> 'where clause' at >>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line 1985. >>>>>>>>>>>>>>>> DBD::mysql::st fetchrow_array failed: fetch() without >>>>>>>>>>>>>>>> execute() at >>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line 1986. >>>>>>>>>>>>>>>> Use of uninitialized value $count_mri_protocol in numeric >>>>>>>>>>>>>>>> gt (>) at /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm >>>>>>>>>>>>>>>> line 1995. >>>>>>>>>>>>>>>> DBD::mysql::st execute failed: Unknown column 'TR_range' in >>>>>>>>>>>>>>>> 'field list' at /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 562. >>>>>>>>>>>>>>>> Can't exec "mail": No such file or directory at >>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 721. >>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 722. >>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 723. >>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 724. >>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 725. >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> No Mincs inserted >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Thanks, >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> ???? ???, 3 ??? 2019 ???? 1:08 ?.?., ?/? Christine Rogers, >>>>>>>>>>>>>>>> Ms. ??????: >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> First, just a note: we've released LORIS 21 this week >>>>>>>>>>>>>>>>> with some major new features and cleanup -- especially if you are early in >>>>>>>>>>>>>>>>> your setup phase, check out the Release notes for both the >>>>>>>>>>>>>>>>> LORIS >>>>>>>>>>>>>>>>> and Loris-MRI >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> repos. >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Thanks for your screenshots -- your empty mri_protocol >>>>>>>>>>>>>>>>> table should be at the root of these issues : >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> The mri_protocol table must be populated >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> in order for your scans to be registered in LORIS -- it serves as a >>>>>>>>>>>>>>>>> whitelist for the insertion pipeline which filters out scans that aren't >>>>>>>>>>>>>>>>> identified or matched to scan types in this table. >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> By default, this table is populated with entries for t1, >>>>>>>>>>>>>>>>> t2, fMRI and DTI (Insert statements for 21 release branch >>>>>>>>>>>>>>>>> are here >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> ) >>>>>>>>>>>>>>>>> Feel free to restore our default records and broaden their >>>>>>>>>>>>>>>>> parameters to match all your scan types. >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> re Defaced, native, selected -- these filter the scans >>>>>>>>>>>>>>>>> displayed as you move to the next page (View Session), instead of viewing >>>>>>>>>>>>>>>>> "all types" of scans from a given session : >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> - "defaced" means that a defacing script >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> has masked the subject's face in the volume (for patient privacy) >>>>>>>>>>>>>>>>> - "native" means that no pre-processing has been >>>>>>>>>>>>>>>>> performed on the scan (it's raw data), >>>>>>>>>>>>>>>>> - "selected" will show only volumes that have been >>>>>>>>>>>>>>>>> QC'd and "selected" as the best of their type -- used to display only the >>>>>>>>>>>>>>>>> best quality T1 image instead of all T1s acquired in a session, e.g. >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> re QC Comments -- >>>>>>>>>>>>>>>>> Once you have successfully loaded scans (matched to the >>>>>>>>>>>>>>>>> mri_protocol table), you'll be able to use the Imaging Browser's View >>>>>>>>>>>>>>>>> Session subpage to enter/view QC comments on each volume, or for each >>>>>>>>>>>>>>>>> visit. >>>>>>>>>>>>>>>>> These are stored directly in the database, and linked to >>>>>>>>>>>>>>>>> each scan. (Table name: feedback_mri_comments) >>>>>>>>>>>>>>>>> (Visit-level QC comments are linked to the session.) >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> For a walkthrough of the Imaging setup - please see the Imaging >>>>>>>>>>>>>>>>> Setup guide >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> - >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> An old LORIS walkthrough video >>>>>>>>>>>>>>>>> can also >>>>>>>>>>>>>>>>> walk you through some of the Imaging front-end features, starting at 8:00 >>>>>>>>>>>>>>>>> LORIS' imaging modules have been updated many times since >>>>>>>>>>>>>>>>> this video, but the functionality and workflow is similar. >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Let us know how it goes once you have entries in your >>>>>>>>>>>>>>>>> mri_protocol table - >>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>> Christine >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> On Fri, Aug 2, 2019 at 7:58 AM Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Hi Christine, >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> In the candidate_list page i can see this patient >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> If i press the link under PSCID i get to see >>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> and if i press the link under Scan Done it redirects me >>>>>>>>>>>>>>>>>> to imaging_browser >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> At the mri_violations page i also see No results ( >>>>>>>>>>>>>>>>>> neither on resolved / not resolved ). >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> At the imaging_uploader i can see the record that failed. >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> If i click on the tarchive info i get to see the Protocol >>>>>>>>>>>>>>>>>> Name which i think is the acquisition we wanted? >>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Also my mri_protocol table is empty. >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Furthermore i would like to ask about the defaced, >>>>>>>>>>>>>>>>>> native, selected. What exactly is native and selected? And where are the qc >>>>>>>>>>>>>>>>>> comments stored? >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Finally a walkthrough would be helpful. >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Thanks, >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> ???? ???, 30 ???? 2019 ???? 8:29 ?.?., ?/? Christine >>>>>>>>>>>>>>>>>> Rogers, Ms. ??????: >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>> Glad to hear you're making progress with the visit >>>>>>>>>>>>>>>>>>> labels. To follow up on your last few emails: >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> a- The Wiki's Setup Guide contains Sample insert >>>>>>>>>>>>>>>>>>> statements for the Visit Windows table >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> . >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> As Cecile mentioned, the consistency of visit label >>>>>>>>>>>>>>>>>>> format is important: V01, v01, V1, 01 -- whichever you select to use is >>>>>>>>>>>>>>>>>>> fine; we use V01 by default across all documentation. >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> b- For Password reset, there is a script in the tools/ >>>>>>>>>>>>>>>>>>> directory so that a back-end administrator can reset any front-end user >>>>>>>>>>>>>>>>>>> password, including Admin. (See info on setting up / resetting User >>>>>>>>>>>>>>>>>>> passwords in the Wiki's Setup Guide >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> ) >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> c- The minc file not being registered -- due to >>>>>>>>>>>>>>>>>>> AcquisitionProtocol unknown. >>>>>>>>>>>>>>>>>>> This means the SeriesDescription (Acquisition Protocol) >>>>>>>>>>>>>>>>>>> in you Dicom header was not matched to any scan listed in the mri_protocol >>>>>>>>>>>>>>>>>>> database table. >>>>>>>>>>>>>>>>>>> (In the online Loris-MRI Troubleshooting Guide, >>>>>>>>>>>>>>>>>>> this >>>>>>>>>>>>>>>>>>> is Table 3, 2nd-last item "no MINCs inserted"). >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> The MRI Violations module (Readme here) >>>>>>>>>>>>>>>>>>> will show >>>>>>>>>>>>>>>>>>> you the details of this mismatch -- >>>>>>>>>>>>>>>>>>> Go to the module (under the Imaging menu), find your >>>>>>>>>>>>>>>>>>> scan and click the link "Could not identify scan type" -- in the next >>>>>>>>>>>>>>>>>>> subpage you can compare the scan's actual parameters against the >>>>>>>>>>>>>>>>>>> mri_protocol table. >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> To resolve this, adjust your mri_protocol table values >>>>>>>>>>>>>>>>>>> or perhaps ensure your DICOMs are labelled consistently. >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Let us know if this works for you -- we can also walk >>>>>>>>>>>>>>>>>>> you through an example of non-identified scans on >>>>>>>>>>>>>>>>>>> Demo.loris.ca (MRI Violations module). >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>> Christine >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> The LORIS team >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> On Tue, Jul 30, 2019 at 10:47 AM Sotirios >>>>>>>>>>>>>>>>>>> Nikoloutsopoulos wrote: >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> I hope this is sufficient as the error for the visit >>>>>>>>>>>>>>>>>>>> label disappeared. >>>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Please see the attached file. Also something i found. >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> lorisadmin at hbp:/data/loris/bin/mri$ cat >>>>>>>>>>>>>>>>>>>> /data/loris/data//logs/TarLoad-17-39-xubBdv.log >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> ==> Loading file from disk >>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-17-39-UyQcG2/dcc0000_258024_v1_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> --> mapping DICOM parameter for >>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-17-39-UyQcG2/dcc0000_258024_v1_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> ==> computing md5 hash for MINC body. >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> --> md5: 6b1202fd63e29de4c9be1cd9925888a5 >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> ==> verifying acquisition protocol >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Acquisition protocol is unknown >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> --> The minc file cannot be registered since the >>>>>>>>>>>>>>>>>>>> AcquisitionProtocol is unknown >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> ???? ???, 30 ???? 2019 ???? 4:58 ?.?., ?/? Sotirios >>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos ??????: >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> Ok I fixed the login problem by using a known hash and >>>>>>>>>>>>>>>>>>>>> by deleting the rows from the login_history i was able to login. >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> ???? ???, 30 ???? 2019 ???? 4:50 ?.?., ?/? Sotirios >>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos ??????: >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> there was no visit label 01 in the Visit_Windows >>>>>>>>>>>>>>>>>>>>>> table and i don't know how to insert it because the record requires lots of >>>>>>>>>>>>>>>>>>>>>> attributes. Also the system for a reason asked me to update my password and >>>>>>>>>>>>>>>>>>>>>> now i don't remember it and my account got suspended. Is there a way to >>>>>>>>>>>>>>>>>>>>>> reset it or set a simple password? I updated the password hash in the >>>>>>>>>>>>>>>>>>>>>> users table by using the hash from another LORIS setup we had and i still >>>>>>>>>>>>>>>>>>>>>> couldn't login ( also the attribute password is always NULL and the >>>>>>>>>>>>>>>>>>>>>> expiration date is 1999-01-01 for some reason ). >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> Thanks >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> ???? ???, 29 ???? 2019 ???? 5:21 ?.?., ?/? Cecile >>>>>>>>>>>>>>>>>>>>>> Madjar ??????: >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> Can you try adding the visit label v01 to the >>>>>>>>>>>>>>>>>>>>>>> Visit_Windows table? >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> However, I noticed that in a previous dataset, the >>>>>>>>>>>>>>>>>>>>>>> label was V1. Does that refer to the same visit? If so, you might want to >>>>>>>>>>>>>>>>>>>>>>> harmonize the visit labels so they are all the same across datasets for a >>>>>>>>>>>>>>>>>>>>>>> given timepoint, meaning you will need to relabel scans when the visit >>>>>>>>>>>>>>>>>>>>>>> label is different but referring to the same visit label (v01 = V1 etc...). >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> Hope this helps, >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> On Mon, Jul 29, 2019 at 10:15 AM Sotirios >>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos wrote: >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> Could you help me with the "Visit label does not >>>>>>>>>>>>>>>>>>>>>>>> exist"? I had changed $subjectID{'createVisitLabel'} to 1 as you had >>>>>>>>>>>>>>>>>>>>>>>> suggested but it appears that this problem hasn't been resolved yet. >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> lorisadmin at hbp:/data/loris/bin/mri$ cat >>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data//logs/TarLoad-14-58-9Xog7H.log >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> ==> Loading file from disk >>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> --> mapping DICOM parameter for >>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> --> using user-defined filterParameters for >>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> Candidate Mismatch Error is Visit label does not >>>>>>>>>>>>>>>>>>>>>>>> exist >>>>>>>>>>>>>>>>>>>>>>>> -> WARNING: This candidate was invalid. Logging to >>>>>>>>>>>>>>>>>>>>>>>> MRICandidateErrors table with reason >>>>>>>>>>>>>>>>>>>>>>>> Visit label does not exist >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 26 ???? 2019 ???? 3:02 ?.?., ?/? Sotirios >>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos ??????: >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> Hi Cecile, >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> The Center error was fixed. Still the insertion of >>>>>>>>>>>>>>>>>>>>>>>>> mincs fails. Please see the output.txt file i attached. Also is there >>>>>>>>>>>>>>>>>>>>>>>>> something else i need to change at the paths configuration? >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 25 ???? 2019 ???? 6:55 ?.?., ?/? Cecile >>>>>>>>>>>>>>>>>>>>>>>>> Madjar ??????: >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> We are making progress! >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> I have a feeling this error comes from the fact >>>>>>>>>>>>>>>>>>>>>>>>>> that your psc table does not have the MRI_alias populated for the DCC site. >>>>>>>>>>>>>>>>>>>>>>>>>> Running the following query in the mysql database should fix this: >>>>>>>>>>>>>>>>>>>>>>>>>> UPDATE psc SET MRI_alias="DCC", Alias="DCC" WHERE >>>>>>>>>>>>>>>>>>>>>>>>>> Name="Data Coordinating Center"; >>>>>>>>>>>>>>>>>>>>>>>>>> Repeat the same with all your sites (make sure to >>>>>>>>>>>>>>>>>>>>>>>>>> change the Aliases between sites, they should all be unique). >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> Let me know how it goes! >>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> On Thu, Jul 25, 2019 at 11:43 AM Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos wrote: >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> Dear Cecile, >>>>>>>>>>>>>>>>>>>>>>>>>>> You were right about your guesses. I did the >>>>>>>>>>>>>>>>>>>>>>>>>>> modifications you suggested, i still get the "no mincs inserted" error, now >>>>>>>>>>>>>>>>>>>>>>>>>>> i am getting the "No center found this candidate" error ( how do i fix >>>>>>>>>>>>>>>>>>>>>>>>>>> that? from what i see the .dcm files contains a 'Institution Name', is that >>>>>>>>>>>>>>>>>>>>>>>>>>> the center? ), so i guess that's why the validation fails, but i changed >>>>>>>>>>>>>>>>>>>>>>>>>>> the force variable of tarchiveLoader to 1, shouldn't it have inserted the >>>>>>>>>>>>>>>>>>>>>>>>>>> mincs then? Also it is optional to have a mail server, right? ( from what i >>>>>>>>>>>>>>>>>>>>>>>>>>> see the mail error does not affect the $valid_study, so i assume we are >>>>>>>>>>>>>>>>>>>>>>>>>>> okay with that ) >>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you a lot, >>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 25 ???? 2019 ???? 5:48 ?.?., ?/? >>>>>>>>>>>>>>>>>>>>>>>>>>> Cecile Madjar ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> From what I understand, I believe you just need >>>>>>>>>>>>>>>>>>>>>>>>>>>> to update a few config settings from the frontend in the Config module >>>>>>>>>>>>>>>>>>>>>>>>>>>> (under the Admin menu). >>>>>>>>>>>>>>>>>>>>>>>>>>>> [image: Screen Shot 2019-07-25 at 10.31.35 >>>>>>>>>>>>>>>>>>>>>>>>>>>> AM.png] >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> Then go to the Paths section of the config >>>>>>>>>>>>>>>>>>>>>>>>>>>> module and update the "LORIS-MRI code" config setting to >>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri (my guess is that currently, it is set to >>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data) and click on the submit button. >>>>>>>>>>>>>>>>>>>>>>>>>>>> [image: Screen Shot 2019-07-25 at 10.32.50 >>>>>>>>>>>>>>>>>>>>>>>>>>>> AM.png] >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> Then, go to Imaging Pipeline section of the >>>>>>>>>>>>>>>>>>>>>>>>>>>> Configuration module and update the "Loris-MRI Data Directory" to >>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/ (my guess is that it is empty at the moment in your >>>>>>>>>>>>>>>>>>>>>>>>>>>> database which is why $data_dir is not defined when you run the >>>>>>>>>>>>>>>>>>>>>>>>>>>> tarchiveLoader step of the insertion pipeline). >>>>>>>>>>>>>>>>>>>>>>>>>>>> [image: Screen Shot 2019-07-25 at 10.40.52 >>>>>>>>>>>>>>>>>>>>>>>>>>>> AM.png] >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> Finally, I took a look at your environment file >>>>>>>>>>>>>>>>>>>>>>>>>>>> and it might be a good idea to update your PERL5LIB variable to the >>>>>>>>>>>>>>>>>>>>>>>>>>>> following (it has been added to the code a few releases ago as we realized >>>>>>>>>>>>>>>>>>>>>>>>>>>> this was needed for the libraries. Not sure which version of LORIS-MRI you >>>>>>>>>>>>>>>>>>>>>>>>>>>> are using but it does not hurt to update this variable to what I suggest >>>>>>>>>>>>>>>>>>>>>>>>>>>> below): >>>>>>>>>>>>>>>>>>>>>>>>>>>> export >>>>>>>>>>>>>>>>>>>>>>>>>>>> PERL5LIB=/data/loris/bin/mri/uploadNeuroDB:/data/loris/bin/mri/dicom-archive:$PERL5LIB >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helps. Sorry you are experiencing so >>>>>>>>>>>>>>>>>>>>>>>>>>>> much trouble setting things up. We probably need to update our WIKI. >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> On Thu, Jul 25, 2019 at 9:48 AM Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos wrote: >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> The "Loris-MRI Data Directory" should be in >>>>>>>>>>>>>>>>>>>>>>>>>>>>> the environment file? >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 25 ???? 2019 ???? 12:59 ?.?., ?/? >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The scripts are located in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/. Somewhere I might have messed something up but i >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> remember following the instructions in the wiki.For example when i tried to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> execute the batch_uploads_imageuploader perl script the line >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> my $command = "$bin_dir/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl " >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> was pointing to an invalid path, for example: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> it was repeating a pattern and had LORIS instead of loris ( i think the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> mistake was that in the wiki it suggested to use $PROJECT for the name of >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the folder and i choosed 'loris' >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris/wiki/Imaging-Database >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ). See also the in image for the modification i did. Also i didn't find the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> section to config the $data_dir variable. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 24 ???? 2019 ???? 6:05 ?.?., ?/? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Cecile Madjar ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> It looks like you have one Config setting >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> not set (based on the first error message you got when running it the first >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> time). You need to set a value for "Loris-MRI Data Directory" in the Config >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> module under the Imaging pipeline section (from what I can see, it would be >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/ for your setup). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The reason you got that error message the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> second time is that the pipeline checks if the DICOM study was already >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> inserted in the tarchive table. Since you ran the study once already, the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> study is inserted into the tarchive, hence the message. However, the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> pipeline did not complete as the MINC files were not created and inserted >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> into the files/parameter_file table. In order to continue the insertion, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> you will then need to run the tarchiveLoader command suggested in the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> terminal during the second run: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -globLocation -profile prod >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive//2012/DCM_2012-12-05_ImagingUpload-17-43-ZUEFjb.tar >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -verbose >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Finally, I am a bit confused by your setup. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Where are the scripts located? In /data/loris/bin/mri or /data/loris/data? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> It feels like the Config setting "LORIS-MRI code" in the Paths section was >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> set to "/data/LORIS/data" but it should have been set to the directory >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> where the scripts are located (most probably /data/loris/bin/mri). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helps, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> On Wed, Jul 24, 2019 at 10:55 AM Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> wrote: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Ok first i execute this command: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> "lorisadmin at hbp:/data/loris/bin/mri$ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ./batch_uploads_imageuploader -profile prod < ~/Desktop/input.txt > log.txt >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at ./batch_uploads_imageuploader line 143. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at ./batch_uploads_imageuploader line 143. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $_ in pattern >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> match (m//) at ./batch_uploads_imageuploader line 147. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> base is DCC0000_258024_V01 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> path is /data/incoming/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> type is .tar.gz >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> fullpath is >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/incoming/DCC0000_258024_V01.tar.gz >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> source /tmp/ImagingUpload-17-43-ZUEFjb >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> targetlocation /data/loris/data/tarchive >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 256. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 284. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at /data/loris/bin/mri/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> tarchive_validation.pl line 219. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at /data/loris/bin/mri/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl line 270. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 711. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Can't exec "mail": No such file or >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> directory at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 721. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 722. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 723. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 724. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 724. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 725. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 735. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> No Mincs inserted >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The tarchiveLoader insertion script has >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> failed. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Running now the following command: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl -profile prod >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -upload_id 3 /data/incoming/DCC0000_258024_V01.tar.gz -verbose" >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I inserted the VisitLabel, but still the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Mincs are not inserted and i am getting this error >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> "lorisadmin at hbp:/data/loris/bin/mri$ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl -profile prod >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -upload_id 3 /data/incoming/DCC0000_258024_V01.tar.gz -verbose >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> find -path >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> \/tmp\/ImagingUpload\-17\-45\-5MsWEd -name '__MACOSX' -delete >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Spool message is: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The Scan for the uploadID 3 has already >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> been run with tarchiveID: 7. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> To continue with the rest of the insertion >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> pipeline, please run tarchiveLoader from a terminal as follows: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader -globLocation -profile prod >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive//2012/DCM_2012-12-05_ImagingUpload-17-43-ZUEFjb.tar >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -verbose" >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Which files should i delete? I thought that >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> deleting the files from the tarchive was enough. And i executed the last >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> proposed command to continue to rest of the insertion pipeline ( check the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> image ). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 24 ???? 2019 ???? 5:05 ?.?., ?/? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Cecile Madjar >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sorry I was not clear before. Every visits >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> of candidates are created in the session table with one entry per >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID/VisitLabel. So if the imaging pipeline created visits in the session >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> table (that are not attached to instruments) and you want to clean your >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> database completely, you can delete entries in that table as well. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Regarding your point 2, the imaging >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> pipeline can create the visit in the session table as long as the visit >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> label is present in the Visit_Windows table (which means the visit label >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> stored in the PatientName is a valid visit label). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> However, in your prod file, if the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> variable $subjectID{'createVisitLabel'} is set to 1 for candidates, the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit label should be created in the Visit_Windows table I believe. Here >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> is the line of the prod file you would need to change >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> . >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> In general, we prefer populating the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Visit_Windows table and set the $subjectID{'createVisitLabel'} to 0 for >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> candidate data to avoid insertion of badly labelled MRI data that are >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> complex to relabel. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Finally, regarding the candidate creation, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> if you execute the following steps, the pipeline should be able to create >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> candidates: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - set in the Imaging Pipeline section of >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the config module the config setting "Upload creation of candidates" to Yes >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - manually transfer the scans to the LORIS >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> server instead of uploading it via the imaging browser >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - run batch_imaging_upload.pl as you did >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> until now. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helps! >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> On Wed, Jul 24, 2019 at 8:47 AM Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> wrote: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> About my second question i replaced the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> name of the patient in the .dcm files and now i am getting an error that >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the visit label does not exist. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I thought it was supposed to be >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> automatically created. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> "Done adding archive info into database >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -globLocation -profile prod >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive//DCM_2012-12-05_ImagingUpload-15-42-yUwQQV.tar >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -verbose >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> md5sum >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive/DCM_2012-12-05_ImagingUpload-15-42-yUwQQV.tar >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> candidate id 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> => No Visit labelVisit label does not >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> exist >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Set centerID = 1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Number of MINC files that will be >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> considered for inserting into the database: 1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> log dir is /logs and log file is >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /logs/TarLoad-15-42-L6pocU.log >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> candidate id 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> => No Visit label >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Cleaning up temp files: rm -rf >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-15-42-J2rQms/ImagingUpload-15-42-yUwQQV*" >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 24 ???? 2019 ???? 3:38 ?.?., >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ?/? Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 1) What are the records in the session >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> table? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 2) I tried to upload a non-phantom file >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> like this >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> input_file.txt: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/incoming/DCC0000_258024_V1.tar.gz >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> N DCC0000_258024_V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Terminal: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ./batch_uploads_imageuploader -profile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> prod < ~/Desktop/input.txt > log.txt >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and i get the following error in the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> log.txt file >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> "Running now the following command: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl -profile prod >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -upload_id 7 /data/incoming/DCC0000_258024_V1.tar.gz -verbose >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> find -path >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> \/tmp\/ImagingUpload\-14\-56\-FeLCB4 -name '__MACOSX' -delete >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Spool message is: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The PatientName read from the DICOM >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> header does not start with DCC0000_258024_V1 from the mri_upload table >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> " >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and the spool message is repeated for >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> each .dcm file. Should i preprocess every .dcm file and change the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PatientName to "DCC0000_258024_V1"? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 3) As far as it concerns the candidate >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> profile i have to create a new one each time before i try to upload a file? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Is there already a way to create a candidate profile and get the DCCID and >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID without the user interface? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 18 ???? 2019 ???? 5:00 ?.?., >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ?/? Cecile Madjar >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> See answers to your questions below. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> About the 1st case we had a dicom with >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> a blank studyUID, maybe someone accidentally removed it. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> That is strange. Something must have >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> been done to the DICOM files. I have never seen a study with no StudyUID >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> out of the scanner. Usually, you need to manually erase it with some tool. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> However, DICOMs never cease to surprise me... >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Some other questions: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 1) What are the steps to remove all of >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> my patients and uploads?: because i want to try to reupload all the testing >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> dicoms we had with a clean database. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Release 21.0 of LORIS-MRI will offer a >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> script to remove all the entries and files specific to an upload. However, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> this release is not yet out. Hopefully in the next few weeks. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> In the meantime, since your case is >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> particular and that you just want to start with a clean database, the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> following deletes should work (hopefully I won't forget any tables): >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from mri_violations_log; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from mri_protocol_violated_scans; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from MRICandidateErrors; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from parameter_file; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from files_qcstatus; # (if you >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> played with the QC part of the imaging browser for testing) >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from feedback_mri_comments; # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> (if you played with the QC part of the imaging browser for testing) >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from tarchive_series; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from tarchive_files; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from mri_upload; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from tarchive; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from mri_scanner; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from candidate where >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID="scanner"; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I don't know if you want to also delete >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> entries in the session and candidate table too? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 2) We do not need to create the profile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> of a patient ( are the patients stored in the candidate table? because i >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> can't see the ghosts ), because will it automatically be created when >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> importing a dicom? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I am not sure I understand fully this >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> question. All candidates are stored in the candidate table. The phantom >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> scans however are attached to a scanner candidate depending on where the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> scan happened. It is a bit of a weird concept that we have to redesign >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> eventually but never got a chance to get to it. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hopefully this answered your question, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> otherwise, don't hesitate to let me know. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 3) What is the difference between >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> uploading a dicom as phantom instead of importing as >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCCID_DCCID_VisitLabel? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> When you upload the scan as >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID_DCCID_VisitLabel, there is a check that makes sure the candidate IDs >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and visit label are valid at the time of upload. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> When you upload a scan as phantom, it >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> expects that the DICOM field PatientName and uploaded filename contains the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> string "phantom". We enforced this behaviour on the imaging uploader side >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in recent releases but I can't remember which one. Probably the upcoming >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 21.0 release. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> All those verifications might seem >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> cumbersome but they are here to ensure that the files inserted are all >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> valid and labelled properly as it is a bit messy to have to delete files >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> that were wrongly labelled. At least, the delete script present in release >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 21.0 will make this process easier but it is still good practice to verify >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> those things. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> With pleasure. Hopefully the answers to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> your questions will be helpful. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PS: loris-dev mailing list: you will >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> find the initial answer I gave Sotirios below. I forgot to cc the loris-dev >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in my earlier reply... >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 16 ???? 2019 ???? 12:02 ?.?., >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ?/? Cecile Madjar < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> cecile.madjar at mcin.ca> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Dear Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you for reaching out. Since >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> your email was already organized in points, I will reply directly below >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> your questions below. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 1) What do we do when the StudyUID is >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> blank on the header? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/minor/docs/AppendixA-Troubleshooting_guideline.md >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> There solution provided at the table 3 does not guide us how to find the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> information ( is possible ). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The StudyUID is the field used in our >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> pipeline at the moment to check whether a DICOM study was already inserted >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> into LORIS with that same StudyUID since it is supposed to be unique for >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> every single study. Currently, we do not support insertion of DICOM studies >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> if they do not have a StudyUID associated with them. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Is there a specific reason why the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> StudyUID is blank in the DICOM headers in your DICOM files? Did they go >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> through some processes before upload to LORIS? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 2) When i am about to upload a >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> non-phanton case i need a 'Visit Label'. Is there already a script that can >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> create a new visit label for a specific Candidate, so i can provide it as >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> input afterwards to the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> batch_uploads_imageuploader ( See option 5.1.3 https://github.com/aces/Loris-MRI/blob/minor/docs/05-PipelineLaunchOptions.md ) >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I am not sure if the front-end allows >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> for it but if you use batch_uploads_imageuploader, the insertion scripts >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> could create the visit label for you. However, it does need to be included >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in the patient name in order for the script to know which label it should >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> use. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> For example: you upload V02 for >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> MTL0123 (DCCID: 456789) but V02 was not yet created for MTL0123; the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> insertion scripts will create a V02 visit for MTL0123 if the PatientName >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> field for the dataset is MTL0123_456789_V02 with Stage marked as "Not >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Started". >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> However, *note that for the script >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> to create the visit for the candidate, you have to make sure that all the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit label of your projects were inserted in the Visit_Windows table* >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> (otherwise, the visit will never be created as they were not specified as >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> being part of the list of visit label to expect). So in the example above, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> you should have one row in Visit_Windows with Visit_label="V02" set. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 3) Section 4.3 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/minor/docs/04-Scripts.md >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> What do we do when the folder contains multiple mnc files? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> This is a case by case. Most of the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> time, the MINC files that failed insertion into the imaging browser end up >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in the MRI violation module where you can see what went wrong with the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> acquisitions not inserted. If you notice that the MINC file should be >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> inserted as a specific protocol, you can force the insertion as explained >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in section 4.3. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> In your case, I have a feeling that >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> you want to be able to insert MINC files that did not go through the whole >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> pipeline insertion (DICOM archival, then dcm2mnc, then protocol >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> identification, then insertion...). In theory, you could call >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl on any MINC file, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> provided you have at least the following information: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - path to the MINC file >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - uploadID associated with the MINC >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> files or DICOM archive path from which those MINC files were created from >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Then the minc_insertion.pl script >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> will do the subject information and protocol validation etc... >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> If all the MINC files come from the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> same uploadID or TarchiveID, then you could run a loop in bash calling the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl script like this >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> for files deriving from uploadID=1: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ls /path/to/mnc/folder/* | while read >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> f; do minc_insertion.pl -profile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> prod -uploadID 1 -mincPath $f; done >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helped! >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> -- >>>>>>>>>>>>>> >>>>>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>>>>> >>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> -- >>>>>>>>>>>> >>>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> -- >>>>>>>>>>> >>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>> _______________________________________________ >>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> -- >>>>>>>>>> >>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>> Montreal Neurological Institute >>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>> >>>>>>>>> _______________________________________________ >>>>>>>>> Loris-dev mailing list >>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> -- >>>>>>>> >>>>>>>> christine.rogers at mcgill.ca >>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>> Montreal Neurological Institute >>>>>>>> McGill University | Montreal | Canada >>>>>>>> >>>>>>> _______________________________________________ >>>>>>> Loris-dev mailing list >>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>> >>>>>> _______________________________________________ >>>>> Loris-dev mailing list >>>>> Loris-dev at bic.mni.mcgill.ca >>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>> >>>> >>>> >>>> -- >>>> >>>> christine.rogers at mcgill.ca >>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>> Montreal Neurological Institute >>>> McGill University | Montreal | Canada >>>> >>> _______________________________________________ >>> Loris-dev mailing list >>> Loris-dev at bic.mni.mcgill.ca >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>> >> _______________________________________________ > Loris-dev mailing list > Loris-dev at bic.mni.mcgill.ca > https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > -- Shen Wang Loris Developer Montreal Neurological Institute McGill University -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: ???? 2019-08-13 19.21.15.png Type: image/png Size: 508603 bytes Desc: not available URL: From sotirisnik at gmail.com Tue Aug 13 19:54:41 2019 From: sotirisnik at gmail.com (Sotirios Nikoloutsopoulos) Date: Wed, 14 Aug 2019 02:54:41 +0300 Subject: [Loris-dev] Upgrading to Loris 21 - new make file In-Reply-To: References: Message-ID: No, it didn't work, i also tried space/tabs because most of the errors where about indentation, also there are some errors about React. Thanks lorisadmin at hbp:/var/www/loris$ sudo ./node_modules/.bin/eslint --init ? How would you like to configure ESLint? Answer questions about your style ? Which version of ECMAScript do you use? ES2015 ? Are you using ES6 modules? Yes ? Where will your code run? Browser ? Do you use CommonJS? Yes ? Do you use JSX? Yes ? Do you use React? Yes ? What style of indentation do you use? Spaces ? What quotes do you use for strings? Single ? What line endings do you use? Unix ? Do you require semicolons? Yes ? What format do you want your config file to be in? JSON The config that you've selected requires the following dependencies: eslint-plugin-react at latest Successfully created .eslintrc.json file in /var/www/loris lorisadmin at hbp:/var/www/loris$ sudo make > sudo_make_output npm WARN The package prop-types is included as both a dev and production dependency. npm WARN optional SKIPPING OPTIONAL DEPENDENCY: fsevents at 1.2.4 (node_modules/fsevents): npm WARN notsup SKIPPING OPTIONAL DEPENDENCY: Unsupported platform for fsevents at 1.2.4: wanted {"os":"darwin","arch":"any"} (current: {"os":"linux","arch":"x64"}) npm ERR! code ELIFECYCLE npm ERR! errno 2 npm ERR! loris at 1.0.0 compile: `webpack` npm ERR! Exit status 2 npm ERR! npm ERR! Failed at the loris at 1.0.0 compile script. npm ERR! This is probably not a problem with npm. There is likely additional logging output above. npm ERR! A complete log of this run can be found in: npm ERR! /home/lorisadmin/.npm/_logs/2019-08-13T23_40_58_841Z-debug.log ???? ???, 14 ??? 2019 ???? 2:29 ?.?., ?/? Shen Wang ??????: > Hi Sotirios, > When you do make command, please make sure with sudo at the beginning. > [sudo make] > If it still doesn't work for you. > Then try the solutions below. > solution 1: > [image: ???? 2019-08-13 19.21.15.png] > Regards > Shen > > > > > On Tue, 13 Aug 2019 at 17:22, Sotirios Nikoloutsopoulos < > sotirisnik at gmail.com> wrote: > >> I think that the files exists although i redownloaded the eslintrc.json i >> checked others files that had similar errors. >> >> lorisadmin at hbp:/var/www/loris$ ls -l >> ./node_modules/eslint-loader/index.js >> -rw-rw-r-- 1 lorisadmin lorisadmin 6463 ??? 26 1985 >> ./node_modules/eslint-loader/index.js >> >> lorisadmin at hbp:/var/www/loris$ ls -l .eslintrc.json >> -rw-rw-r-- 1 lorisadmin lorisadmin 84530 ??? 14 00:04 .eslintrc.json >> >> Maybe this can help >> >> Module build failed (from ./node_modules/eslint-loader/index.js): >> SyntaxError: Cannot read config file: /var/www/loris/.eslintrc.json >> Error: Unexpected token < in JSON at position 6 >> at JSON.parse () >> at loadJSONConfigFile >> (/var/www/loris/node_modules/eslint/lib/config/config-file.js:114:21) >> at loadConfigFile >> (/var/www/loris/node_modules/eslint/lib/config/config-file.js:230:26) >> at loadFromDisk >> (/var/www/loris/node_modules/eslint/lib/config/config-file.js:500:18) >> at Object.load >> (/var/www/loris/node_modules/eslint/lib/config/config-file.js:564:20) >> at Config.getLocalConfigHierarchy >> (/var/www/loris/node_modules/eslint/lib/config.js:227:44) >> at Config.getConfigHierarchy >> (/var/www/loris/node_modules/eslint/lib/config.js:179:43) >> at Config.getConfigVector >> (/var/www/loris/node_modules/eslint/lib/config.js:286:21) >> at Config.getConfig >> (/var/www/loris/node_modules/eslint/lib/config.js:329:29) >> at processText >> (/var/www/loris/node_modules/eslint/lib/cli-engine.js:162:33) >> at CLIEngine.executeOnText >> (/var/www/loris/node_modules/eslint/lib/cli-engine.js:596:17) >> at lint >> (/var/www/loris/node_modules/eslint-loader/index.js:237:17) >> at Object.module.exports >> (/var/www/loris/node_modules/eslint-loader/index.js:232:21) >> >> ERROR in ./modules/imaging_uploader/jsx/index.js >> Module build failed (from ./node_modules/eslint-loader/index.js): >> SyntaxError: Cannot read config file: /var/www/loris/.eslintrc.json >> Error: Unexpected token < in JSON at position 6 >> at JSON.parse () >> at loadJSONConfigFile >> (/var/www/loris/node_modules/eslint/lib/config/config-file.js:114:21) >> at loadConfigFile >> (/var/www/loris/node_modules/eslint/lib/config/config-file.js:230:26) >> at loadFromDisk >> (/var/www/loris/node_modules/eslint/lib/config/config-file.js:500:18) >> at Object.load >> (/var/www/loris/node_modules/eslint/lib/config/config-file.js:564:20) >> at Config.getLocalConfigHierarchy >> (/var/www/loris/node_modules/eslint/lib/config.js:227:44) >> at Config.getConfigHierarchy >> (/var/www/loris/node_modules/eslint/lib/config.js:179:43) >> at Config.getConfigVector >> (/var/www/loris/node_modules/eslint/lib/config.js:286:21) >> at Config.getConfig >> (/var/www/loris/node_modules/eslint/lib/config.js:329:29) >> at processText >> (/var/www/loris/node_modules/eslint/lib/cli-engine.js:162:33) >> at CLIEngine.executeOnText >> (/var/www/loris/node_modules/eslint/lib/cli-engine.js:596:17) >> at lint >> (/var/www/loris/node_modules/eslint-loader/index.js:237:17) >> at Object.module.exports >> (/var/www/loris/node_modules/eslint-loader/index.js:232:21) >> >> >> >> ???? ???, 13 ??? 2019 ???? 11:52 ?.?., ?/? John Saigle < >> john.saigle at mcin.ca> ??????: >> >>> HI Sotirios, >>> >>> The make_output.txt file shows webpack failing because it can't find the >>> ESLint config file. >>> >>> Can you confirm whether the file `.eslintrc.json` exists within your >>> loris root directory (usually `/var/www/loris/`)? When I delete my file I >>> get the same errors as you. >>> >>> If you find that it's missing, you can make a local copy with the >>> contents found here: >>> >>> >>> https://github.com/aces/Loris/blob/e26a6ad49a73fcffef0cd73bb600c4d17b200b62/.eslintrc.json >>> >>> Once you know it exists, try running `make` again. >>> >>> Let us know if that moves you forward. >>> >>> Best, >>> John >>> >>> On Tue, Aug 13, 2019 at 2:21 PM Sotirios Nikoloutsopoulos < >>> sotirisnik at gmail.com> wrote: >>> >>>> Hi, >>>> I executed the commands for the node and now i am get the followings: >>>> >>>> lorisadmin at hbp:/var/www/loris$ make > ~/make_output >>>> npm WARN The package prop-types is included as both a dev and >>>> production dependency. >>>> npm WARN optional SKIPPING OPTIONAL DEPENDENCY: fsevents at 1.2.4 >>>> (node_modules/fsevents): >>>> npm WARN notsup SKIPPING OPTIONAL DEPENDENCY: Unsupported platform for >>>> fsevents at 1.2.4: wanted {"os":"darwin","arch":"any"} (current: >>>> {"os":"linux","arch":"x64"}) >>>> >>>> npm ERR! code ELIFECYCLE >>>> npm ERR! errno 2 >>>> npm ERR! loris at 1.0.0 compile: `webpack` >>>> npm ERR! Exit status 2 >>>> npm ERR! >>>> npm ERR! Failed at the loris at 1.0.0 compile script. >>>> npm ERR! This is probably not a problem with npm. There is likely >>>> additional logging output above. >>>> >>>> npm ERR! A complete log of this run can be found in: >>>> npm ERR! >>>> /home/lorisadmin/.npm/_logs/2019-08-13T18_12_05_378Z-debug.log >>>> make: *** [javascript] Error 2 >>>> >>>> Thanks, >>>> Sotirios >>>> >>>> >>>> ???? ???, 12 ??? 2019 ???? 10:19 ?.?., ?/? Christine Rogers, Ms. < >>>> christine.rogers at mcgill.ca> ??????: >>>> >>>>> Hi Sotirios, >>>>> >>>>> We've seen some users installing LORIS 21 or upgrading to 21 whose >>>>> version of node doesn't work well with webpack, due to updated packages >>>>> they're missing. >>>>> If so, update your node : >>>>> >>>>> curl -sL https://deb.nodesource.com/setup_8.x | sudo -E bash - >>>>> sudo apt-get install -y nodejs >>>>> >>>>> Let us know how that goes -- please send us output from the same log >>>>> if any issues. >>>>> Best, >>>>> Christine >>>>> >>>>> >>>>> On Thu, Aug 8, 2019 at 2:38 PM Sotirios Nikoloutsopoulos < >>>>> sotirisnik at gmail.com> wrote: >>>>> >>>>>> It's not a disk space issue, as you can see below i have still 74GB >>>>>> available. >>>>>> >>>>>> lorisadmin at hbp:/var/www/loris$ df -h >>>>>> Filesystem Size Used Avail Use% Mounted on >>>>>> udev 2,9G 0 2,9G 0% /dev >>>>>> tmpfs 597M 8,6M 588M 2% /run >>>>>> /dev/sda1 98G 19G 74G 21% / >>>>>> >>>>>> Maybe we have to pass a flag to get into strict mode? as stated >>>>>> "SyntaxError: Block-scoped declarations (let, const, function, class) not >>>>>> yet supported outside strict mode" >>>>>> >>>>>> Thanks, >>>>>> Sotirios >>>>>> >>>>>> ???? ???, 8 ??? 2019 ???? 4:32 ?.?., ?/? Dave MacFarlane < >>>>>> dave.macfarlane at mcin.ca> ??????: >>>>>> >>>>>>> It looks like the javascript snippet shown in the error message when >>>>>>> trying to compile the js is truncated. Have you run out of disk space? >>>>>>> >>>>>>> On Thu, Aug 8, 2019 at 8:37 AM Sotirios Nikoloutsopoulos < >>>>>>> sotirisnik at gmail.com> wrote: >>>>>>> >>>>>>>> Hi, >>>>>>>> >>>>>>>> I runned make and also included the file it reports at the end. >>>>>>>> >>>>>>>> lorisadmin at hbp:/var/www/loris$ make >>>>>>>> npm install >>>>>>>> npm WARN optional Skipping failed optional dependency >>>>>>>> /chokidar/fsevents: >>>>>>>> npm WARN notsup Not compatible with your operating system or >>>>>>>> architecture: fsevents at 1.2.9 >>>>>>>> npm WARN optional Skipping failed optional dependency >>>>>>>> /watchpack/chokidar/fsevents: >>>>>>>> npm WARN notsup Not compatible with your operating system or >>>>>>>> architecture: fsevents at 1.2.9 >>>>>>>> npm run compile >>>>>>>> >>>>>>>> > loris at 1.0.0 compile /var/www/loris >>>>>>>> > webpack >>>>>>>> >>>>>>>> /var/www/loris/node_modules/webpack/bin/webpack.js:86 >>>>>>>> let notify = >>>>>>>> ^^^ >>>>>>>> >>>>>>>> SyntaxError: Block-scoped declarations (let, const, function, >>>>>>>> class) not yet supported outside strict mode >>>>>>>> at exports.runInThisContext (vm.js:53:16) >>>>>>>> at Module._compile (module.js:374:25) >>>>>>>> at Object.Module._extensions..js (module.js:417:10) >>>>>>>> at Module.load (module.js:344:32) >>>>>>>> at Function.Module._load (module.js:301:12) >>>>>>>> at Function.Module.runMain (module.js:442:10) >>>>>>>> at startup (node.js:136:18) >>>>>>>> at node.js:966:3 >>>>>>>> >>>>>>>> npm ERR! Linux 4.15.0-55-generic >>>>>>>> npm ERR! argv "/usr/bin/nodejs" "/usr/bin/npm" "run" "compile" >>>>>>>> npm ERR! node v4.2.6 >>>>>>>> npm ERR! npm v3.5.2 >>>>>>>> npm ERR! code ELIFECYCLE >>>>>>>> npm ERR! loris at 1.0.0 compile: `webpack` >>>>>>>> npm ERR! Exit status 1 >>>>>>>> npm ERR! >>>>>>>> npm ERR! Failed at the loris at 1.0.0 compile script 'webpack'. >>>>>>>> npm ERR! Make sure you have the latest version of node.js and npm >>>>>>>> installed. >>>>>>>> npm ERR! If you do, this is most likely a problem with the loris >>>>>>>> package, >>>>>>>> npm ERR! not with npm itself. >>>>>>>> npm ERR! Tell the author that this fails on your system: >>>>>>>> npm ERR! webpack >>>>>>>> npm ERR! You can get information on how to open an issue for this >>>>>>>> project with: >>>>>>>> npm ERR! npm bugs loris >>>>>>>> npm ERR! Or if that isn't available, you can get their info via: >>>>>>>> npm ERR! npm owner ls loris >>>>>>>> npm ERR! There is likely additional logging output above. >>>>>>>> >>>>>>>> npm ERR! Please include the following file with any support request: >>>>>>>> npm ERR! /var/www/loris/npm-debug.log >>>>>>>> Makefile:14: recipe for target 'javascript' failed >>>>>>>> make: *** [javascript] Error 1 >>>>>>>> >>>>>>>> Thanks, >>>>>>>> >>>>>>>> Sotirios >>>>>>>> >>>>>>>> ???? ???, 7 ??? 2019 ???? 5:41 ?.?., ?/? Christine Rogers, Ms. < >>>>>>>> christine.rogers at mcgill.ca> ??????: >>>>>>>> >>>>>>>>> Hi Sotirios, >>>>>>>>> >>>>>>>>> Thanks, have you tried all of these steps? >>>>>>>>> - clear your browser cache (and refresh a few times) >>>>>>>>> - delete any files in your smarty/templates_c directory (this will >>>>>>>>> clear the template cache - do Not touch smarty/templates/) >>>>>>>>> - run `make` (per the 21 release notes, this replaces the composer >>>>>>>>> commands used in previous releases to update your dependencies) >>>>>>>>> - restart apache (doesn't hurt) >>>>>>>>> >>>>>>>>> Let us know how it goes -- let us know what difference you see >>>>>>>>> after, with your logs. A >>>>>>>>> lso please send us your Config path settings (see these >>>>>>>>> Troubleshooting Queries >>>>>>>>> ) >>>>>>>>> if you're still seeing front-end issues. >>>>>>>>> >>>>>>>>> Thanks, >>>>>>>>> Christine >>>>>>>>> >>>>>>>>> On Wed, Aug 7, 2019 at 8:02 AM Sotirios Nikoloutsopoulos < >>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>> >>>>>>>>>> Hi, >>>>>>>>>> >>>>>>>>>> lorisadmin at hbp:/var/www/loris$ sudo cat >>>>>>>>>> /var/log/apache2/error.log >>>>>>>>>> [Wed Aug 07 07:35:02.422501 2019] [mpm_prefork:notice] [pid 1267] >>>>>>>>>> AH00163: Apache/2.4.18 (Ubuntu) OpenSSL/1.0.2g configured -- resuming >>>>>>>>>> normal operations >>>>>>>>>> [Wed Aug 07 07:35:02.422514 2019] [core:notice] [pid 1267] >>>>>>>>>> AH00094: Command line: '/usr/sbin/apache2' >>>>>>>>>> >>>>>>>>>> And as for the access.log the content are empty >>>>>>>>>> lorisadmin at hbp:/var/www/loris$ sudo ls -l >>>>>>>>>> /var/log/apache2/access.log >>>>>>>>>> lorisadmin at hbp:/var/www/loris$ sudo ls -l >>>>>>>>>> /var/log/apache2/access.log >>>>>>>>>> -rw-r----- 1 root adm 0 ???? 28 14:09 /var/log/apache2/access.log >>>>>>>>>> >>>>>>>>>> Also i noticed a loris_access.log. >>>>>>>>>> >>>>>>>>>> The only non-blank pages are: >>>>>>>>>> mri_violations, dataquery does not exist at all, statistics, >>>>>>>>>> data_team_helper, genomic_browser, configuration and >>>>>>>>>> server_processes_manager/ prints "Required configuration settings for >>>>>>>>>> Server Processes Manager are missing. Cannot continue." >>>>>>>>>> >>>>>>>>>> Thanks, >>>>>>>>>> Sotirios >>>>>>>>>> >>>>>>>>>> ???? ???, 6 ??? 2019 ???? 10:13 ?.?., ?/? Christine Rogers, Ms. < >>>>>>>>>> christine.rogers at mcgill.ca> ??????: >>>>>>>>>> >>>>>>>>>>> Hi Sotirios and LORIS community -- >>>>>>>>>>> >>>>>>>>>>> When upgrading to brand-new release 21 -- just a reminder to >>>>>>>>>>> follow the release notes and run the new *make* file to update >>>>>>>>>>> your dependencies (instead of using *composer* commands). >>>>>>>>>>> We've also updated the Wiki page >>>>>>>>>>> to >>>>>>>>>>> clarify that the release notes for each version will tell you what to run. >>>>>>>>>>> >>>>>>>>>>> If your current version is not the last release (20.3), it's >>>>>>>>>>> still important to upgrade to each minor release increment (e.g. 20.2, >>>>>>>>>>> 20.3) before making the leap to 21.0. >>>>>>>>>>> >>>>>>>>>>> If you're getting blank pages, post-upgrade -- Try clearing your >>>>>>>>>>> cache. >>>>>>>>>>> >>>>>>>>>>> Got questions or feedback e.g. on the Release Notes? please >>>>>>>>>>> don't hesitate to let us know. >>>>>>>>>>> Thanks, >>>>>>>>>>> Christine >>>>>>>>>>> The LORIS team >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> On Tue, Aug 6, 2019 at 10:09 AM Christine Rogers, Ms. < >>>>>>>>>>> christine.rogers at mcgill.ca> wrote: >>>>>>>>>>> >>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>> Could you also let us know -- on which pages is content >>>>>>>>>>>> visible, and on which pages/modules is content not visible for you? >>>>>>>>>>>> Thanks, >>>>>>>>>>>> Christine >>>>>>>>>>>> >>>>>>>>>>>> On Tue, Aug 6, 2019 at 9:54 AM Christine Rogers, Ms. < >>>>>>>>>>>> christine.rogers at mcgill.ca> wrote: >>>>>>>>>>>> >>>>>>>>>>>>> Thanks Sotirios, >>>>>>>>>>>>> That's good to know. It sounds like you've checked that your >>>>>>>>>>>>> /var/www/loris/project/config.xml file get populated properly. >>>>>>>>>>>>> >>>>>>>>>>>>> Please send us the last few errors you're seeing in your >>>>>>>>>>>>> apache error log file, and your config paths and we can see what's >>>>>>>>>>>>> happening with your front end -- >>>>>>>>>>>>> Run these Troubleshooting Queries >>>>>>>>>>>>> >>>>>>>>>>>>> to get your config path settings, given your front end is not displaying >>>>>>>>>>>>> fully. >>>>>>>>>>>>> >>>>>>>>>>>>> The Loris-MRI repo >>>>>>>>>>>>> 21 >>>>>>>>>>>>> install/upgrade would then be your next steps. >>>>>>>>>>>>> Best, >>>>>>>>>>>>> Christine >>>>>>>>>>>>> >>>>>>>>>>>>> On Tue, Aug 6, 2019 at 7:53 AM Sotirios Nikoloutsopoulos < >>>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>> >>>>>>>>>>>>>> I am using a VM. What i did was: >>>>>>>>>>>>>> 1) Download the files from https://github.com/aces/Loris and >>>>>>>>>>>>>> replace them to my existing /vaw/www/loris folder. >>>>>>>>>>>>>> 2) Execute the composer install --no-dev and then composer >>>>>>>>>>>>>> dump-autoload as mentioned here >>>>>>>>>>>>>> https://github.com/aces/Loris/wiki/Updating-your-LORIS. >>>>>>>>>>>>>> 3) Execute install.sh from /var/www/loris/tools and because >>>>>>>>>>>>>> LORIS already existed i moved a .config file, then re-executed the >>>>>>>>>>>>>> install.sh successfully >>>>>>>>>>>>>> 4 ) As for the database, i dropped the schema and i executed >>>>>>>>>>>>>> the installdb.php >>>>>>>>>>>>>> >>>>>>>>>>>>>> ???? ???, 5 ??? 2019 ???? 5:22 ?.?., ?/? Christine Rogers, >>>>>>>>>>>>>> Ms. ??????: >>>>>>>>>>>>>> >>>>>>>>>>>>>>> Hi Sotorios, >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> Thanks - when you re-installed did you start on a fresh root >>>>>>>>>>>>>>> path / VM or might some of your old system setting still apply? >>>>>>>>>>>>>>> (And if you did any steps similar to an upgrade, did you >>>>>>>>>>>>>>> follow the Upgrade steps in the Release Notes, from both repos?) >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> About the TR_range column - it was recently split (MRI pr339 >>>>>>>>>>>>>>> ) split into >>>>>>>>>>>>>>> TR_min and _max columns. Given the code was trying to query TR_range which >>>>>>>>>>>>>>> does not exist in your mri_protocol table, double-check which version of >>>>>>>>>>>>>>> the Loris repo (tables) and the Loris-MRI repo (code) you have installed to >>>>>>>>>>>>>>> ensure they match. >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> Christine >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> On Mon, Aug 5, 2019 at 9:06 AM Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> I reinstalled LORIS to 21 version and now the content is >>>>>>>>>>>>>>>> not visible at all at most pages. >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> ???? ???, 5 ??? 2019 ???? 3:19 ?.?., ?/? Sotirios >>>>>>>>>>>>>>>> Nikoloutsopoulos ??????: >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Is it easy to upgrade to Loris 21? Also the following >>>>>>>>>>>>>>>>> fails because the line 1985 of NeuroDB/MRIProcessingUtility.pm query >>>>>>>>>>>>>>>>> mri_protocol which doesn't have TR_range >>>>>>>>>>>>>>>>> https://github.com/aces/Loris/blob/21.0-release/SQL/0000-00-00-schema.sql#L556 >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> lorisadmin at hbp:/data/loris/bin/mri$ >>>>>>>>>>>>>>>>> ./batch_uploads_imageuploader -profile prod < ~/Desktop/input.txt > log.txt >>>>>>>>>>>>>>>>> Use of uninitialized value $_ in pattern match (m//) at >>>>>>>>>>>>>>>>> ./batch_uploads_imageuploader line 147. >>>>>>>>>>>>>>>>> base is DCC0000_258024_V1 >>>>>>>>>>>>>>>>> path is /data/incoming/ >>>>>>>>>>>>>>>>> type is .tar.gz >>>>>>>>>>>>>>>>> fullpath is /data/incoming/DCC0000_258024_V1.tar.gz >>>>>>>>>>>>>>>>> DBD::mysql::st execute failed: Unknown column 'TR_range' >>>>>>>>>>>>>>>>> in 'where clause' at >>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line 1985. >>>>>>>>>>>>>>>>> DBD::mysql::st fetchrow_array failed: fetch() without >>>>>>>>>>>>>>>>> execute() at >>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line 1986. >>>>>>>>>>>>>>>>> Use of uninitialized value $count_mri_protocol in numeric >>>>>>>>>>>>>>>>> gt (>) at /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm >>>>>>>>>>>>>>>>> line 1995. >>>>>>>>>>>>>>>>> DBD::mysql::st execute failed: Unknown column 'TR_range' >>>>>>>>>>>>>>>>> in 'field list' at /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line >>>>>>>>>>>>>>>>> 562. >>>>>>>>>>>>>>>>> Can't exec "mail": No such file or directory at >>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 721. >>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 722. >>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 723. >>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 724. >>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 725. >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> No Mincs inserted >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Thanks, >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> ???? ???, 3 ??? 2019 ???? 1:08 ?.?., ?/? Christine Rogers, >>>>>>>>>>>>>>>>> Ms. ??????: >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> First, just a note: we've released LORIS 21 this week >>>>>>>>>>>>>>>>>> with some major new features and cleanup -- especially if you are early in >>>>>>>>>>>>>>>>>> your setup phase, check out the Release notes for both the >>>>>>>>>>>>>>>>>> LORIS >>>>>>>>>>>>>>>>>> and >>>>>>>>>>>>>>>>>> Loris-MRI >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> repos. >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Thanks for your screenshots -- your empty mri_protocol >>>>>>>>>>>>>>>>>> table should be at the root of these issues : >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> The mri_protocol table must be populated >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> in order for your scans to be registered in LORIS -- it serves as a >>>>>>>>>>>>>>>>>> whitelist for the insertion pipeline which filters out scans that aren't >>>>>>>>>>>>>>>>>> identified or matched to scan types in this table. >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> By default, this table is populated with entries for t1, >>>>>>>>>>>>>>>>>> t2, fMRI and DTI (Insert statements for 21 release >>>>>>>>>>>>>>>>>> branch are here >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> ) >>>>>>>>>>>>>>>>>> Feel free to restore our default records and broaden >>>>>>>>>>>>>>>>>> their parameters to match all your scan types. >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> re Defaced, native, selected -- these filter the scans >>>>>>>>>>>>>>>>>> displayed as you move to the next page (View Session), instead of viewing >>>>>>>>>>>>>>>>>> "all types" of scans from a given session : >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> - "defaced" means that a defacing script >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> has masked the subject's face in the volume (for patient privacy) >>>>>>>>>>>>>>>>>> - "native" means that no pre-processing has been >>>>>>>>>>>>>>>>>> performed on the scan (it's raw data), >>>>>>>>>>>>>>>>>> - "selected" will show only volumes that have been >>>>>>>>>>>>>>>>>> QC'd and "selected" as the best of their type -- used to display only the >>>>>>>>>>>>>>>>>> best quality T1 image instead of all T1s acquired in a session, e.g. >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> re QC Comments -- >>>>>>>>>>>>>>>>>> Once you have successfully loaded scans (matched to the >>>>>>>>>>>>>>>>>> mri_protocol table), you'll be able to use the Imaging Browser's View >>>>>>>>>>>>>>>>>> Session subpage to enter/view QC comments on each volume, or for each >>>>>>>>>>>>>>>>>> visit. >>>>>>>>>>>>>>>>>> These are stored directly in the database, and linked to >>>>>>>>>>>>>>>>>> each scan. (Table name: feedback_mri_comments) >>>>>>>>>>>>>>>>>> (Visit-level QC comments are linked to the session.) >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> For a walkthrough of the Imaging setup - please see the Imaging >>>>>>>>>>>>>>>>>> Setup guide >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> - >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> An old LORIS walkthrough video >>>>>>>>>>>>>>>>>> can also >>>>>>>>>>>>>>>>>> walk you through some of the Imaging front-end features, starting at 8:00 >>>>>>>>>>>>>>>>>> LORIS' imaging modules have been updated many times since >>>>>>>>>>>>>>>>>> this video, but the functionality and workflow is similar. >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Let us know how it goes once you have entries in your >>>>>>>>>>>>>>>>>> mri_protocol table - >>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>> Christine >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> On Fri, Aug 2, 2019 at 7:58 AM Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Hi Christine, >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> In the candidate_list page i can see this patient >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> If i press the link under PSCID i get to see >>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> and if i press the link under Scan Done it redirects me >>>>>>>>>>>>>>>>>>> to imaging_browser >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> At the mri_violations page i also see No results ( >>>>>>>>>>>>>>>>>>> neither on resolved / not resolved ). >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> At the imaging_uploader i can see the record that failed. >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> If i click on the tarchive info i get to see the >>>>>>>>>>>>>>>>>>> Protocol Name which i think is the acquisition we wanted? >>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Also my mri_protocol table is empty. >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Furthermore i would like to ask about the defaced, >>>>>>>>>>>>>>>>>>> native, selected. What exactly is native and selected? And where are the qc >>>>>>>>>>>>>>>>>>> comments stored? >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Finally a walkthrough would be helpful. >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Thanks, >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> ???? ???, 30 ???? 2019 ???? 8:29 ?.?., ?/? Christine >>>>>>>>>>>>>>>>>>> Rogers, Ms. ??????: >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>> Glad to hear you're making progress with the visit >>>>>>>>>>>>>>>>>>>> labels. To follow up on your last few emails: >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> a- The Wiki's Setup Guide contains Sample insert >>>>>>>>>>>>>>>>>>>> statements for the Visit Windows table >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> . >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> As Cecile mentioned, the consistency of visit label >>>>>>>>>>>>>>>>>>>> format is important: V01, v01, V1, 01 -- whichever you select to use is >>>>>>>>>>>>>>>>>>>> fine; we use V01 by default across all documentation. >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> b- For Password reset, there is a script in the tools/ >>>>>>>>>>>>>>>>>>>> directory so that a back-end administrator can reset any front-end user >>>>>>>>>>>>>>>>>>>> password, including Admin. (See info on setting up / resetting User >>>>>>>>>>>>>>>>>>>> passwords in the Wiki's Setup Guide >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> ) >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> c- The minc file not being registered -- due to >>>>>>>>>>>>>>>>>>>> AcquisitionProtocol unknown. >>>>>>>>>>>>>>>>>>>> This means the SeriesDescription (Acquisition Protocol) >>>>>>>>>>>>>>>>>>>> in you Dicom header was not matched to any scan listed in the mri_protocol >>>>>>>>>>>>>>>>>>>> database table. >>>>>>>>>>>>>>>>>>>> (In the online Loris-MRI Troubleshooting Guide, >>>>>>>>>>>>>>>>>>>> this >>>>>>>>>>>>>>>>>>>> is Table 3, 2nd-last item "no MINCs inserted"). >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> The MRI Violations module (Readme here) >>>>>>>>>>>>>>>>>>>> will show >>>>>>>>>>>>>>>>>>>> you the details of this mismatch -- >>>>>>>>>>>>>>>>>>>> Go to the module (under the Imaging menu), find your >>>>>>>>>>>>>>>>>>>> scan and click the link "Could not identify scan type" -- in the next >>>>>>>>>>>>>>>>>>>> subpage you can compare the scan's actual parameters against the >>>>>>>>>>>>>>>>>>>> mri_protocol table. >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> To resolve this, adjust your mri_protocol table values >>>>>>>>>>>>>>>>>>>> or perhaps ensure your DICOMs are labelled consistently. >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Let us know if this works for you -- we can also walk >>>>>>>>>>>>>>>>>>>> you through an example of non-identified scans on >>>>>>>>>>>>>>>>>>>> Demo.loris.ca (MRI Violations module). >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>> Christine >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> The LORIS team >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> On Tue, Jul 30, 2019 at 10:47 AM Sotirios >>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos wrote: >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> I hope this is sufficient as the error for the visit >>>>>>>>>>>>>>>>>>>>> label disappeared. >>>>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> Please see the attached file. Also something i found. >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> lorisadmin at hbp:/data/loris/bin/mri$ cat >>>>>>>>>>>>>>>>>>>>> /data/loris/data//logs/TarLoad-17-39-xubBdv.log >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> ==> Loading file from disk >>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-17-39-UyQcG2/dcc0000_258024_v1_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> --> mapping DICOM parameter for >>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-17-39-UyQcG2/dcc0000_258024_v1_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> ==> computing md5 hash for MINC body. >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> --> md5: 6b1202fd63e29de4c9be1cd9925888a5 >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> ==> verifying acquisition protocol >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> Acquisition protocol is unknown >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> --> The minc file cannot be registered since the >>>>>>>>>>>>>>>>>>>>> AcquisitionProtocol is unknown >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> ???? ???, 30 ???? 2019 ???? 4:58 ?.?., ?/? Sotirios >>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos ??????: >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> Ok I fixed the login problem by using a known hash >>>>>>>>>>>>>>>>>>>>>> and by deleting the rows from the login_history i was able to login. >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> ???? ???, 30 ???? 2019 ???? 4:50 ?.?., ?/? Sotirios >>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos ??????: >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> there was no visit label 01 in the Visit_Windows >>>>>>>>>>>>>>>>>>>>>>> table and i don't know how to insert it because the record requires lots of >>>>>>>>>>>>>>>>>>>>>>> attributes. Also the system for a reason asked me to update my password and >>>>>>>>>>>>>>>>>>>>>>> now i don't remember it and my account got suspended. Is there a way to >>>>>>>>>>>>>>>>>>>>>>> reset it or set a simple password? I updated the password hash in the >>>>>>>>>>>>>>>>>>>>>>> users table by using the hash from another LORIS setup we had and i still >>>>>>>>>>>>>>>>>>>>>>> couldn't login ( also the attribute password is always NULL and the >>>>>>>>>>>>>>>>>>>>>>> expiration date is 1999-01-01 for some reason ). >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> Thanks >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> ???? ???, 29 ???? 2019 ???? 5:21 ?.?., ?/? Cecile >>>>>>>>>>>>>>>>>>>>>>> Madjar ??????: >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> Can you try adding the visit label v01 to the >>>>>>>>>>>>>>>>>>>>>>>> Visit_Windows table? >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> However, I noticed that in a previous dataset, the >>>>>>>>>>>>>>>>>>>>>>>> label was V1. Does that refer to the same visit? If so, you might want to >>>>>>>>>>>>>>>>>>>>>>>> harmonize the visit labels so they are all the same across datasets for a >>>>>>>>>>>>>>>>>>>>>>>> given timepoint, meaning you will need to relabel scans when the visit >>>>>>>>>>>>>>>>>>>>>>>> label is different but referring to the same visit label (v01 = V1 etc...). >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> Hope this helps, >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> On Mon, Jul 29, 2019 at 10:15 AM Sotirios >>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos wrote: >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> Could you help me with the "Visit label does not >>>>>>>>>>>>>>>>>>>>>>>>> exist"? I had changed $subjectID{'createVisitLabel'} to 1 as you had >>>>>>>>>>>>>>>>>>>>>>>>> suggested but it appears that this problem hasn't been resolved yet. >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> lorisadmin at hbp:/data/loris/bin/mri$ cat >>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data//logs/TarLoad-14-58-9Xog7H.log >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> ==> Loading file from disk >>>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> --> mapping DICOM parameter for >>>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> --> using user-defined filterParameters for >>>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> Candidate Mismatch Error is Visit label does not >>>>>>>>>>>>>>>>>>>>>>>>> exist >>>>>>>>>>>>>>>>>>>>>>>>> -> WARNING: This candidate was invalid. Logging to >>>>>>>>>>>>>>>>>>>>>>>>> MRICandidateErrors table with reason >>>>>>>>>>>>>>>>>>>>>>>>> Visit label does not exist >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 26 ???? 2019 ???? 3:02 ?.?., ?/? >>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos >>>>>>>>>>>>>>>>>>>>>>>>> ??????: >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> Hi Cecile, >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> The Center error was fixed. Still the insertion >>>>>>>>>>>>>>>>>>>>>>>>>> of mincs fails. Please see the output.txt file i attached. Also is there >>>>>>>>>>>>>>>>>>>>>>>>>> something else i need to change at the paths configuration? >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 25 ???? 2019 ???? 6:55 ?.?., ?/? Cecile >>>>>>>>>>>>>>>>>>>>>>>>>> Madjar ??????: >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> We are making progress! >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> I have a feeling this error comes from the fact >>>>>>>>>>>>>>>>>>>>>>>>>>> that your psc table does not have the MRI_alias populated for the DCC site. >>>>>>>>>>>>>>>>>>>>>>>>>>> Running the following query in the mysql database should fix this: >>>>>>>>>>>>>>>>>>>>>>>>>>> UPDATE psc SET MRI_alias="DCC", Alias="DCC" >>>>>>>>>>>>>>>>>>>>>>>>>>> WHERE Name="Data Coordinating Center"; >>>>>>>>>>>>>>>>>>>>>>>>>>> Repeat the same with all your sites (make sure >>>>>>>>>>>>>>>>>>>>>>>>>>> to change the Aliases between sites, they should all be unique). >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> Let me know how it goes! >>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> On Thu, Jul 25, 2019 at 11:43 AM Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos wrote: >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> Dear Cecile, >>>>>>>>>>>>>>>>>>>>>>>>>>>> You were right about your guesses. I did the >>>>>>>>>>>>>>>>>>>>>>>>>>>> modifications you suggested, i still get the "no mincs inserted" error, now >>>>>>>>>>>>>>>>>>>>>>>>>>>> i am getting the "No center found this candidate" error ( how do i fix >>>>>>>>>>>>>>>>>>>>>>>>>>>> that? from what i see the .dcm files contains a 'Institution Name', is that >>>>>>>>>>>>>>>>>>>>>>>>>>>> the center? ), so i guess that's why the validation fails, but i changed >>>>>>>>>>>>>>>>>>>>>>>>>>>> the force variable of tarchiveLoader to 1, shouldn't it have inserted the >>>>>>>>>>>>>>>>>>>>>>>>>>>> mincs then? Also it is optional to have a mail server, right? ( from what i >>>>>>>>>>>>>>>>>>>>>>>>>>>> see the mail error does not affect the $valid_study, so i assume we are >>>>>>>>>>>>>>>>>>>>>>>>>>>> okay with that ) >>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you a lot, >>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 25 ???? 2019 ???? 5:48 ?.?., ?/? >>>>>>>>>>>>>>>>>>>>>>>>>>>> Cecile Madjar ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> From what I understand, I believe you just >>>>>>>>>>>>>>>>>>>>>>>>>>>>> need to update a few config settings from the frontend in the Config module >>>>>>>>>>>>>>>>>>>>>>>>>>>>> (under the Admin menu). >>>>>>>>>>>>>>>>>>>>>>>>>>>>> [image: Screen Shot 2019-07-25 at 10.31.35 >>>>>>>>>>>>>>>>>>>>>>>>>>>>> AM.png] >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Then go to the Paths section of the config >>>>>>>>>>>>>>>>>>>>>>>>>>>>> module and update the "LORIS-MRI code" config setting to >>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri (my guess is that currently, it is set to >>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data) and click on the submit button. >>>>>>>>>>>>>>>>>>>>>>>>>>>>> [image: Screen Shot 2019-07-25 at 10.32.50 >>>>>>>>>>>>>>>>>>>>>>>>>>>>> AM.png] >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Then, go to Imaging Pipeline section of the >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Configuration module and update the "Loris-MRI Data Directory" to >>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/ (my guess is that it is empty at the moment in your >>>>>>>>>>>>>>>>>>>>>>>>>>>>> database which is why $data_dir is not defined when you run the >>>>>>>>>>>>>>>>>>>>>>>>>>>>> tarchiveLoader step of the insertion pipeline). >>>>>>>>>>>>>>>>>>>>>>>>>>>>> [image: Screen Shot 2019-07-25 at 10.40.52 >>>>>>>>>>>>>>>>>>>>>>>>>>>>> AM.png] >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Finally, I took a look at your environment >>>>>>>>>>>>>>>>>>>>>>>>>>>>> file and it might be a good idea to update your PERL5LIB variable to the >>>>>>>>>>>>>>>>>>>>>>>>>>>>> following (it has been added to the code a few releases ago as we realized >>>>>>>>>>>>>>>>>>>>>>>>>>>>> this was needed for the libraries. Not sure which version of LORIS-MRI you >>>>>>>>>>>>>>>>>>>>>>>>>>>>> are using but it does not hurt to update this variable to what I suggest >>>>>>>>>>>>>>>>>>>>>>>>>>>>> below): >>>>>>>>>>>>>>>>>>>>>>>>>>>>> export >>>>>>>>>>>>>>>>>>>>>>>>>>>>> PERL5LIB=/data/loris/bin/mri/uploadNeuroDB:/data/loris/bin/mri/dicom-archive:$PERL5LIB >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helps. Sorry you are experiencing so >>>>>>>>>>>>>>>>>>>>>>>>>>>>> much trouble setting things up. We probably need to update our WIKI. >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> On Thu, Jul 25, 2019 at 9:48 AM Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos wrote: >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The "Loris-MRI Data Directory" should be in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the environment file? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 25 ???? 2019 ???? 12:59 ?.?., ?/? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The scripts are located in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/. Somewhere I might have messed something up but i >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> remember following the instructions in the wiki.For example when i tried to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> execute the batch_uploads_imageuploader perl script the line >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> my $command = "$bin_dir/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl " >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> was pointing to an invalid path, for >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> example: it was repeating a pattern and had LORIS instead of loris ( i >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> think the mistake was that in the wiki it suggested to use $PROJECT for >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the name of the folder and i choosed 'loris' >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris/wiki/Imaging-Database >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ). See also the in image for the modification i did. Also i didn't find the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> section to config the $data_dir variable. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 24 ???? 2019 ???? 6:05 ?.?., ?/? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Cecile Madjar >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> It looks like you have one Config setting >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> not set (based on the first error message you got when running it the first >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> time). You need to set a value for "Loris-MRI Data Directory" in the Config >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> module under the Imaging pipeline section (from what I can see, it would be >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/ for your setup). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The reason you got that error message the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> second time is that the pipeline checks if the DICOM study was already >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> inserted in the tarchive table. Since you ran the study once already, the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> study is inserted into the tarchive, hence the message. However, the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> pipeline did not complete as the MINC files were not created and inserted >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> into the files/parameter_file table. In order to continue the insertion, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> you will then need to run the tarchiveLoader command suggested in the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> terminal during the second run: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -globLocation -profile prod >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive//2012/DCM_2012-12-05_ImagingUpload-17-43-ZUEFjb.tar >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -verbose >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Finally, I am a bit confused by your setup. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Where are the scripts located? In /data/loris/bin/mri or /data/loris/data? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> It feels like the Config setting "LORIS-MRI code" in the Paths section was >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> set to "/data/LORIS/data" but it should have been set to the directory >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> where the scripts are located (most probably /data/loris/bin/mri). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helps, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> On Wed, Jul 24, 2019 at 10:55 AM Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> wrote: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Ok first i execute this command: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> "lorisadmin at hbp:/data/loris/bin/mri$ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ./batch_uploads_imageuploader -profile prod < ~/Desktop/input.txt > log.txt >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at ./batch_uploads_imageuploader line 143. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at ./batch_uploads_imageuploader line 143. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $_ in pattern >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> match (m//) at ./batch_uploads_imageuploader line 147. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> base is DCC0000_258024_V01 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> path is /data/incoming/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> type is .tar.gz >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> fullpath is >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/incoming/DCC0000_258024_V01.tar.gz >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> source /tmp/ImagingUpload-17-43-ZUEFjb >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> targetlocation /data/loris/data/tarchive >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 256. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 284. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at /data/loris/bin/mri/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> tarchive_validation.pl line 219. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at /data/loris/bin/mri/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl line 270. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 711. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Can't exec "mail": No such file or >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> directory at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 721. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 722. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 723. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 724. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 724. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 725. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 735. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> No Mincs inserted >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The tarchiveLoader insertion script has >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> failed. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Running now the following command: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl -profile prod >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -upload_id 3 /data/incoming/DCC0000_258024_V01.tar.gz -verbose" >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I inserted the VisitLabel, but still the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Mincs are not inserted and i am getting this error >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> "lorisadmin at hbp:/data/loris/bin/mri$ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl -profile prod >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -upload_id 3 /data/incoming/DCC0000_258024_V01.tar.gz -verbose >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> find -path >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> \/tmp\/ImagingUpload\-17\-45\-5MsWEd -name '__MACOSX' -delete >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Spool message is: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The Scan for the uploadID 3 has already >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> been run with tarchiveID: 7. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> To continue with the rest of the insertion >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> pipeline, please run tarchiveLoader from a terminal as follows: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader -globLocation -profile prod >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive//2012/DCM_2012-12-05_ImagingUpload-17-43-ZUEFjb.tar >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -verbose" >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Which files should i delete? I thought >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> that deleting the files from the tarchive was enough. And i executed the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> last proposed command to continue to rest of the insertion pipeline ( check >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the image ). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 24 ???? 2019 ???? 5:05 ?.?., ?/? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Cecile Madjar >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sorry I was not clear before. Every >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visits of candidates are created in the session table with one entry per >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID/VisitLabel. So if the imaging pipeline created visits in the session >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> table (that are not attached to instruments) and you want to clean your >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> database completely, you can delete entries in that table as well. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Regarding your point 2, the imaging >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> pipeline can create the visit in the session table as long as the visit >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> label is present in the Visit_Windows table (which means the visit label >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> stored in the PatientName is a valid visit label). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> However, in your prod file, if the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> variable $subjectID{'createVisitLabel'} is set to 1 for candidates, the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit label should be created in the Visit_Windows table I believe. Here >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> is the line of the prod file you would need to change >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> . >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> In general, we prefer populating the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Visit_Windows table and set the $subjectID{'createVisitLabel'} to 0 for >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> candidate data to avoid insertion of badly labelled MRI data that are >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> complex to relabel. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Finally, regarding the candidate >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> creation, if you execute the following steps, the pipeline should be able >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> to create candidates: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - set in the Imaging Pipeline section of >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the config module the config setting "Upload creation of candidates" to Yes >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - manually transfer the scans to the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> LORIS server instead of uploading it via the imaging browser >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - run batch_imaging_upload.pl as you did >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> until now. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helps! >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> On Wed, Jul 24, 2019 at 8:47 AM Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> wrote: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> About my second question i replaced the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> name of the patient in the .dcm files and now i am getting an error that >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the visit label does not exist. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I thought it was supposed to be >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> automatically created. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> "Done adding archive info into database >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -globLocation -profile prod >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive//DCM_2012-12-05_ImagingUpload-15-42-yUwQQV.tar >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -verbose >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> md5sum >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive/DCM_2012-12-05_ImagingUpload-15-42-yUwQQV.tar >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> candidate id 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> => No Visit labelVisit label does not >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> exist >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Set centerID = 1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Number of MINC files that will be >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> considered for inserting into the database: 1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> log dir is /logs and log file is >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /logs/TarLoad-15-42-L6pocU.log >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> candidate id 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> => No Visit label >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Cleaning up temp files: rm -rf >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-15-42-J2rQms/ImagingUpload-15-42-yUwQQV*" >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 24 ???? 2019 ???? 3:38 ?.?., >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ?/? Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 1) What are the records in the session >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> table? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 2) I tried to upload a non-phantom file >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> like this >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> input_file.txt: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/incoming/DCC0000_258024_V1.tar.gz >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> N DCC0000_258024_V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Terminal: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ./batch_uploads_imageuploader -profile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> prod < ~/Desktop/input.txt > log.txt >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and i get the following error in the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> log.txt file >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> "Running now the following command: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl -profile prod >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -upload_id 7 /data/incoming/DCC0000_258024_V1.tar.gz -verbose >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> find -path >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> \/tmp\/ImagingUpload\-14\-56\-FeLCB4 -name '__MACOSX' -delete >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Spool message is: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The PatientName read from the DICOM >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> header does not start with DCC0000_258024_V1 from the mri_upload table >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> " >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and the spool message is repeated for >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> each .dcm file. Should i preprocess every .dcm file and change the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PatientName to "DCC0000_258024_V1"? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 3) As far as it concerns the candidate >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> profile i have to create a new one each time before i try to upload a file? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Is there already a way to create a candidate profile and get the DCCID and >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID without the user interface? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 18 ???? 2019 ???? 5:00 ?.?., >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ?/? Cecile Madjar < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> cecile.madjar at mcin.ca> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> See answers to your questions below. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> About the 1st case we had a dicom with >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> a blank studyUID, maybe someone accidentally removed it. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> That is strange. Something must have >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> been done to the DICOM files. I have never seen a study with no StudyUID >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> out of the scanner. Usually, you need to manually erase it with some tool. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> However, DICOMs never cease to surprise me... >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Some other questions: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 1) What are the steps to remove all >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> of my patients and uploads?: because i want to try to reupload all the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> testing dicoms we had with a clean database. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Release 21.0 of LORIS-MRI will offer a >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> script to remove all the entries and files specific to an upload. However, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> this release is not yet out. Hopefully in the next few weeks. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> In the meantime, since your case is >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> particular and that you just want to start with a clean database, the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> following deletes should work (hopefully I won't forget any tables): >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from mri_violations_log; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> mri_protocol_violated_scans; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from MRICandidateErrors; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from parameter_file; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from files_qcstatus; # (if you >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> played with the QC part of the imaging browser for testing) >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from feedback_mri_comments; # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> (if you played with the QC part of the imaging browser for testing) >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from tarchive_series; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from tarchive_files; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from mri_upload; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from tarchive; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from mri_scanner; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from candidate where >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID="scanner"; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I don't know if you want to also >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete entries in the session and candidate table too? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 2) We do not need to create the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> profile of a patient ( are the patients stored in the candidate table? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> because i can't see the ghosts ), because will it automatically be created >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> when importing a dicom? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I am not sure I understand fully this >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> question. All candidates are stored in the candidate table. The phantom >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> scans however are attached to a scanner candidate depending on where the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> scan happened. It is a bit of a weird concept that we have to redesign >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> eventually but never got a chance to get to it. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hopefully this answered your question, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> otherwise, don't hesitate to let me know. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 3) What is the difference between >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> uploading a dicom as phantom instead of importing as >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCCID_DCCID_VisitLabel? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> When you upload the scan as >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID_DCCID_VisitLabel, there is a check that makes sure the candidate IDs >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and visit label are valid at the time of upload. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> When you upload a scan as phantom, it >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> expects that the DICOM field PatientName and uploaded filename contains the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> string "phantom". We enforced this behaviour on the imaging uploader side >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in recent releases but I can't remember which one. Probably the upcoming >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 21.0 release. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> All those verifications might seem >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> cumbersome but they are here to ensure that the files inserted are all >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> valid and labelled properly as it is a bit messy to have to delete files >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> that were wrongly labelled. At least, the delete script present in release >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 21.0 will make this process easier but it is still good practice to verify >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> those things. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> With pleasure. Hopefully the answers >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> to your questions will be helpful. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PS: loris-dev mailing list: you will >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> find the initial answer I gave Sotirios below. I forgot to cc the loris-dev >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in my earlier reply... >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 16 ???? 2019 ???? 12:02 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ?.?., ?/? Cecile Madjar < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> cecile.madjar at mcin.ca> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Dear Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you for reaching out. Since >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> your email was already organized in points, I will reply directly below >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> your questions below. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 1) What do we do when the StudyUID >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> is blank on the header? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/minor/docs/AppendixA-Troubleshooting_guideline.md >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> There solution provided at the table 3 does not guide us how to find the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> information ( is possible ). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The StudyUID is the field used in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> our pipeline at the moment to check whether a DICOM study was already >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> inserted into LORIS with that same StudyUID since it is supposed to be >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> unique for every single study. Currently, we do not support insertion of >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DICOM studies if they do not have a StudyUID associated with them. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Is there a specific reason why the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> StudyUID is blank in the DICOM headers in your DICOM files? Did they go >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> through some processes before upload to LORIS? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 2) When i am about to upload a >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> non-phanton case i need a 'Visit Label'. Is there already a script that can >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> create a new visit label for a specific Candidate, so i can provide it as >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> input afterwards to the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> batch_uploads_imageuploader ( See option 5.1.3 https://github.com/aces/Loris-MRI/blob/minor/docs/05-PipelineLaunchOptions.md ) >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I am not sure if the front-end >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> allows for it but if you use batch_uploads_imageuploader, the insertion >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> scripts could create the visit label for you. However, it does need to be >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> included in the patient name in order for the script to know which label it >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> should use. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> For example: you upload V02 for >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> MTL0123 (DCCID: 456789) but V02 was not yet created for MTL0123; the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> insertion scripts will create a V02 visit for MTL0123 if the PatientName >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> field for the dataset is MTL0123_456789_V02 with Stage marked as "Not >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Started". >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> However, *note that for the script >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> to create the visit for the candidate, you have to make sure that all the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit label of your projects were inserted in the Visit_Windows table* >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> (otherwise, the visit will never be created as they were not specified as >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> being part of the list of visit label to expect). So in the example above, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> you should have one row in Visit_Windows with Visit_label="V02" set. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 3) Section 4.3 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/minor/docs/04-Scripts.md >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> What do we do when the folder contains multiple mnc files? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> This is a case by case. Most of the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> time, the MINC files that failed insertion into the imaging browser end up >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in the MRI violation module where you can see what went wrong with the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> acquisitions not inserted. If you notice that the MINC file should be >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> inserted as a specific protocol, you can force the insertion as explained >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in section 4.3. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> In your case, I have a feeling that >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> you want to be able to insert MINC files that did not go through the whole >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> pipeline insertion (DICOM archival, then dcm2mnc, then protocol >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> identification, then insertion...). In theory, you could call >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl on any MINC file, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> provided you have at least the following information: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - path to the MINC file >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - uploadID associated with the MINC >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> files or DICOM archive path from which those MINC files were created from >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Then the minc_insertion.pl script >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> will do the subject information and protocol validation etc... >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> If all the MINC files come from the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> same uploadID or TarchiveID, then you could run a loop in bash calling the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl script like this >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> for files deriving from uploadID=1: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ls /path/to/mnc/folder/* | while >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> read f; do minc_insertion.pl >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -profile prod -uploadID 1 -mincPath $f; done >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helped! >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>>>>>> >>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> -- >>>>>>>>>>>>> >>>>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> -- >>>>>>>>>>>> >>>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> -- >>>>>>>>>>> >>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>> >>>>>>>>>> _______________________________________________ >>>>>>>>>> Loris-dev mailing list >>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> -- >>>>>>>>> >>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>> Montreal Neurological Institute >>>>>>>>> McGill University | Montreal | Canada >>>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> Loris-dev mailing list >>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>> >>>>>>> _______________________________________________ >>>>>> Loris-dev mailing list >>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>> >>>>> >>>>> >>>>> -- >>>>> >>>>> christine.rogers at mcgill.ca >>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>> Montreal Neurological Institute >>>>> McGill University | Montreal | Canada >>>>> >>>> _______________________________________________ >>>> Loris-dev mailing list >>>> Loris-dev at bic.mni.mcgill.ca >>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>> >>> _______________________________________________ >> Loris-dev mailing list >> Loris-dev at bic.mni.mcgill.ca >> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >> > > > -- > Shen Wang > Loris Developer > Montreal Neurological Institute > McGill University > > -------------- next part -------------- An HTML attachment was scrubbed... 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Name: ???? 2019-08-13 19.21.15.png Type: image/png Size: 508603 bytes Desc: not available URL: -------------- next part -------------- 0 info it worked if it ends with ok 1 verbose cli [ '/usr/bin/node', '/usr/bin/npm', 'run', 'compile' ] 2 info using npm at 6.4.1 3 info using node at v8.16.0 4 verbose run-script [ 'precompile', 'compile', 'postcompile' ] 5 info lifecycle loris at 1.0.0~precompile: loris at 1.0.0 6 info lifecycle loris at 1.0.0~compile: loris at 1.0.0 7 verbose lifecycle loris at 1.0.0~compile: unsafe-perm in lifecycle true 8 verbose lifecycle loris at 1.0.0~compile: PATH: /usr/lib/node_modules/npm/node_modules/npm-lifecycle/node-gyp-bin:/var/www/loris/node_modules/.bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/snap/bin 9 verbose lifecycle loris at 1.0.0~compile: CWD: /var/www/loris 10 silly lifecycle loris at 1.0.0~compile: Args: [ '-c', 'webpack' ] 11 silly lifecycle loris at 1.0.0~compile: Returned: code: 2 signal: null 12 info lifecycle loris at 1.0.0~compile: Failed to exec compile script 13 verbose stack Error: loris at 1.0.0 compile: `webpack` 13 verbose stack Exit status 2 13 verbose stack at EventEmitter. (/usr/lib/node_modules/npm/node_modules/npm-lifecycle/index.js:301:16) 13 verbose stack at emitTwo (events.js:126:13) 13 verbose stack at EventEmitter.emit (events.js:214:7) 13 verbose stack at ChildProcess. (/usr/lib/node_modules/npm/node_modules/npm-lifecycle/lib/spawn.js:55:14) 13 verbose stack at emitTwo (events.js:126:13) 13 verbose stack at ChildProcess.emit (events.js:214:7) 13 verbose stack at maybeClose (internal/child_process.js:915:16) 13 verbose stack at Process.ChildProcess._handle.onexit (internal/child_process.js:209:5) 14 verbose pkgid loris at 1.0.0 15 verbose cwd /var/www/loris 16 verbose Linux 4.15.0-55-generic 17 verbose argv "/usr/bin/node" "/usr/bin/npm" "run" "compile" 18 verbose node v8.16.0 19 verbose npm v6.4.1 20 error code ELIFECYCLE 21 error errno 2 22 error loris at 1.0.0 compile: `webpack` 22 error Exit status 2 23 error Failed at the loris at 1.0.0 compile script. 23 error This is probably not a problem with npm. There is likely additional logging output above. 24 verbose exit [ 2, true ] -------------- next part -------------- A non-text attachment was scrubbed... Name: sudo_make_output Type: application/octet-stream Size: 1066491 bytes Desc: not available URL: From wangshen.mcin at gmail.com Tue Aug 13 20:22:44 2019 From: wangshen.mcin at gmail.com (Shen Wang) Date: Tue, 13 Aug 2019 20:22:44 -0400 Subject: [Loris-dev] Upgrading to Loris 21 - new make file In-Reply-To: References: Message-ID: Hi Sotirios, I saw your output file, the config issue is gone. you can use [sudo npm run lintfix:javascript ] to fix these indent issues. If it still has errors. Then try modify this file .eslintignore with this # Ignore until ESLint is run modules/* modules/dataquery/ node_modules/* htdocs/js/components/* jsx/* # Ignore external libs htdocs/js/flot/* htdocs/js/jquery/* htdocs/js/jszip/* htdocs/js/modernizr/* htdocs/js/modules/* htdocs/js/react/* htdocs/js/shims/* htdocs/js/c3.min.js htdocs/js/d3.min.js htdocs/js/FileSaver.min.js then do sudo make. It should work. Regards Shen Sotirios Nikoloutsopoulos ?2019?8?13? ????7:54??? > No, it didn't work, i also tried space/tabs because most of the errors > where about indentation, also there are some errors about React. > > Thanks > > lorisadmin at hbp:/var/www/loris$ sudo ./node_modules/.bin/eslint --init > ? How would you like to configure ESLint? Answer questions about your style > ? Which version of ECMAScript do you use? ES2015 > ? Are you using ES6 modules? Yes > ? Where will your code run? Browser > ? Do you use CommonJS? Yes > ? Do you use JSX? Yes > ? Do you use React? Yes > ? What style of indentation do you use? Spaces > ? What quotes do you use for strings? Single > ? What line endings do you use? Unix > ? Do you require semicolons? Yes > ? What format do you want your config file to be in? JSON > The config that you've selected requires the following dependencies: > > eslint-plugin-react at latest > Successfully created .eslintrc.json file in /var/www/loris > > lorisadmin at hbp:/var/www/loris$ sudo make > sudo_make_output > npm WARN The package prop-types is included as both a dev and production > dependency. > npm WARN optional SKIPPING OPTIONAL DEPENDENCY: fsevents at 1.2.4 > (node_modules/fsevents): > npm WARN notsup SKIPPING OPTIONAL DEPENDENCY: Unsupported platform for > fsevents at 1.2.4: wanted {"os":"darwin","arch":"any"} (current: > {"os":"linux","arch":"x64"}) > > npm ERR! code ELIFECYCLE > npm ERR! errno 2 > npm ERR! loris at 1.0.0 compile: `webpack` > npm ERR! Exit status 2 > npm ERR! > npm ERR! Failed at the loris at 1.0.0 compile script. > npm ERR! This is probably not a problem with npm. There is likely > additional logging output above. > > npm ERR! A complete log of this run can be found in: > npm ERR! /home/lorisadmin/.npm/_logs/2019-08-13T23_40_58_841Z-debug.log > > ???? ???, 14 ??? 2019 ???? 2:29 ?.?., ?/? Shen Wang < > wangshen.mcin at gmail.com> ??????: > >> Hi Sotirios, >> When you do make command, please make sure with sudo at the beginning. >> [sudo make] >> If it still doesn't work for you. >> Then try the solutions below. >> solution 1: >> [image: ???? 2019-08-13 19.21.15.png] >> Regards >> Shen >> >> >> >> >> On Tue, 13 Aug 2019 at 17:22, Sotirios Nikoloutsopoulos < >> sotirisnik at gmail.com> wrote: >> >>> I think that the files exists although i redownloaded the eslintrc.json >>> i checked others files that had similar errors. >>> >>> lorisadmin at hbp:/var/www/loris$ ls -l >>> ./node_modules/eslint-loader/index.js >>> -rw-rw-r-- 1 lorisadmin lorisadmin 6463 ??? 26 1985 >>> ./node_modules/eslint-loader/index.js >>> >>> lorisadmin at hbp:/var/www/loris$ ls -l .eslintrc.json >>> -rw-rw-r-- 1 lorisadmin lorisadmin 84530 ??? 14 00:04 .eslintrc.json >>> >>> Maybe this can help >>> >>> Module build failed (from ./node_modules/eslint-loader/index.js): >>> SyntaxError: Cannot read config file: /var/www/loris/.eslintrc.json >>> Error: Unexpected token < in JSON at position 6 >>> at JSON.parse () >>> at loadJSONConfigFile >>> (/var/www/loris/node_modules/eslint/lib/config/config-file.js:114:21) >>> at loadConfigFile >>> (/var/www/loris/node_modules/eslint/lib/config/config-file.js:230:26) >>> at loadFromDisk >>> (/var/www/loris/node_modules/eslint/lib/config/config-file.js:500:18) >>> at Object.load >>> (/var/www/loris/node_modules/eslint/lib/config/config-file.js:564:20) >>> at Config.getLocalConfigHierarchy >>> (/var/www/loris/node_modules/eslint/lib/config.js:227:44) >>> at Config.getConfigHierarchy >>> (/var/www/loris/node_modules/eslint/lib/config.js:179:43) >>> at Config.getConfigVector >>> (/var/www/loris/node_modules/eslint/lib/config.js:286:21) >>> at Config.getConfig >>> (/var/www/loris/node_modules/eslint/lib/config.js:329:29) >>> at processText >>> (/var/www/loris/node_modules/eslint/lib/cli-engine.js:162:33) >>> at CLIEngine.executeOnText >>> (/var/www/loris/node_modules/eslint/lib/cli-engine.js:596:17) >>> at lint >>> (/var/www/loris/node_modules/eslint-loader/index.js:237:17) >>> at Object.module.exports >>> (/var/www/loris/node_modules/eslint-loader/index.js:232:21) >>> >>> ERROR in ./modules/imaging_uploader/jsx/index.js >>> Module build failed (from ./node_modules/eslint-loader/index.js): >>> SyntaxError: Cannot read config file: /var/www/loris/.eslintrc.json >>> Error: Unexpected token < in JSON at position 6 >>> at JSON.parse () >>> at loadJSONConfigFile >>> (/var/www/loris/node_modules/eslint/lib/config/config-file.js:114:21) >>> at loadConfigFile >>> (/var/www/loris/node_modules/eslint/lib/config/config-file.js:230:26) >>> at loadFromDisk >>> (/var/www/loris/node_modules/eslint/lib/config/config-file.js:500:18) >>> at Object.load >>> (/var/www/loris/node_modules/eslint/lib/config/config-file.js:564:20) >>> at Config.getLocalConfigHierarchy >>> (/var/www/loris/node_modules/eslint/lib/config.js:227:44) >>> at Config.getConfigHierarchy >>> (/var/www/loris/node_modules/eslint/lib/config.js:179:43) >>> at Config.getConfigVector >>> (/var/www/loris/node_modules/eslint/lib/config.js:286:21) >>> at Config.getConfig >>> (/var/www/loris/node_modules/eslint/lib/config.js:329:29) >>> at processText >>> (/var/www/loris/node_modules/eslint/lib/cli-engine.js:162:33) >>> at CLIEngine.executeOnText >>> (/var/www/loris/node_modules/eslint/lib/cli-engine.js:596:17) >>> at lint >>> (/var/www/loris/node_modules/eslint-loader/index.js:237:17) >>> at Object.module.exports >>> (/var/www/loris/node_modules/eslint-loader/index.js:232:21) >>> >>> >>> >>> ???? ???, 13 ??? 2019 ???? 11:52 ?.?., ?/? John Saigle < >>> john.saigle at mcin.ca> ??????: >>> >>>> HI Sotirios, >>>> >>>> The make_output.txt file shows webpack failing because it can't find >>>> the ESLint config file. >>>> >>>> Can you confirm whether the file `.eslintrc.json` exists within your >>>> loris root directory (usually `/var/www/loris/`)? When I delete my file I >>>> get the same errors as you. >>>> >>>> If you find that it's missing, you can make a local copy with the >>>> contents found here: >>>> >>>> >>>> https://github.com/aces/Loris/blob/e26a6ad49a73fcffef0cd73bb600c4d17b200b62/.eslintrc.json >>>> >>>> Once you know it exists, try running `make` again. >>>> >>>> Let us know if that moves you forward. >>>> >>>> Best, >>>> John >>>> >>>> On Tue, Aug 13, 2019 at 2:21 PM Sotirios Nikoloutsopoulos < >>>> sotirisnik at gmail.com> wrote: >>>> >>>>> Hi, >>>>> I executed the commands for the node and now i am get the followings: >>>>> >>>>> lorisadmin at hbp:/var/www/loris$ make > ~/make_output >>>>> npm WARN The package prop-types is included as both a dev and >>>>> production dependency. >>>>> npm WARN optional SKIPPING OPTIONAL DEPENDENCY: fsevents at 1.2.4 >>>>> (node_modules/fsevents): >>>>> npm WARN notsup SKIPPING OPTIONAL DEPENDENCY: Unsupported platform for >>>>> fsevents at 1.2.4: wanted {"os":"darwin","arch":"any"} (current: >>>>> {"os":"linux","arch":"x64"}) >>>>> >>>>> npm ERR! code ELIFECYCLE >>>>> npm ERR! errno 2 >>>>> npm ERR! loris at 1.0.0 compile: `webpack` >>>>> npm ERR! Exit status 2 >>>>> npm ERR! >>>>> npm ERR! Failed at the loris at 1.0.0 compile script. >>>>> npm ERR! This is probably not a problem with npm. There is likely >>>>> additional logging output above. >>>>> >>>>> npm ERR! A complete log of this run can be found in: >>>>> npm ERR! >>>>> /home/lorisadmin/.npm/_logs/2019-08-13T18_12_05_378Z-debug.log >>>>> make: *** [javascript] Error 2 >>>>> >>>>> Thanks, >>>>> Sotirios >>>>> >>>>> >>>>> ???? ???, 12 ??? 2019 ???? 10:19 ?.?., ?/? Christine Rogers, Ms. < >>>>> christine.rogers at mcgill.ca> ??????: >>>>> >>>>>> Hi Sotirios, >>>>>> >>>>>> We've seen some users installing LORIS 21 or upgrading to 21 whose >>>>>> version of node doesn't work well with webpack, due to updated packages >>>>>> they're missing. >>>>>> If so, update your node : >>>>>> >>>>>> curl -sL https://deb.nodesource.com/setup_8.x | sudo -E bash - >>>>>> sudo apt-get install -y nodejs >>>>>> >>>>>> Let us know how that goes -- please send us output from the same log >>>>>> if any issues. >>>>>> Best, >>>>>> Christine >>>>>> >>>>>> >>>>>> On Thu, Aug 8, 2019 at 2:38 PM Sotirios Nikoloutsopoulos < >>>>>> sotirisnik at gmail.com> wrote: >>>>>> >>>>>>> It's not a disk space issue, as you can see below i have still 74GB >>>>>>> available. >>>>>>> >>>>>>> lorisadmin at hbp:/var/www/loris$ df -h >>>>>>> Filesystem Size Used Avail Use% Mounted on >>>>>>> udev 2,9G 0 2,9G 0% /dev >>>>>>> tmpfs 597M 8,6M 588M 2% /run >>>>>>> /dev/sda1 98G 19G 74G 21% / >>>>>>> >>>>>>> Maybe we have to pass a flag to get into strict mode? as stated >>>>>>> "SyntaxError: Block-scoped declarations (let, const, function, class) not >>>>>>> yet supported outside strict mode" >>>>>>> >>>>>>> Thanks, >>>>>>> Sotirios >>>>>>> >>>>>>> ???? ???, 8 ??? 2019 ???? 4:32 ?.?., ?/? Dave MacFarlane < >>>>>>> dave.macfarlane at mcin.ca> ??????: >>>>>>> >>>>>>>> It looks like the javascript snippet shown in the error message >>>>>>>> when trying to compile the js is truncated. Have you run out of disk space? >>>>>>>> >>>>>>>> On Thu, Aug 8, 2019 at 8:37 AM Sotirios Nikoloutsopoulos < >>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>> >>>>>>>>> Hi, >>>>>>>>> >>>>>>>>> I runned make and also included the file it reports at the end. >>>>>>>>> >>>>>>>>> lorisadmin at hbp:/var/www/loris$ make >>>>>>>>> npm install >>>>>>>>> npm WARN optional Skipping failed optional dependency >>>>>>>>> /chokidar/fsevents: >>>>>>>>> npm WARN notsup Not compatible with your operating system or >>>>>>>>> architecture: fsevents at 1.2.9 >>>>>>>>> npm WARN optional Skipping failed optional dependency >>>>>>>>> /watchpack/chokidar/fsevents: >>>>>>>>> npm WARN notsup Not compatible with your operating system or >>>>>>>>> architecture: fsevents at 1.2.9 >>>>>>>>> npm run compile >>>>>>>>> >>>>>>>>> > loris at 1.0.0 compile /var/www/loris >>>>>>>>> > webpack >>>>>>>>> >>>>>>>>> /var/www/loris/node_modules/webpack/bin/webpack.js:86 >>>>>>>>> let notify = >>>>>>>>> ^^^ >>>>>>>>> >>>>>>>>> SyntaxError: Block-scoped declarations (let, const, function, >>>>>>>>> class) not yet supported outside strict mode >>>>>>>>> at exports.runInThisContext (vm.js:53:16) >>>>>>>>> at Module._compile (module.js:374:25) >>>>>>>>> at Object.Module._extensions..js (module.js:417:10) >>>>>>>>> at Module.load (module.js:344:32) >>>>>>>>> at Function.Module._load (module.js:301:12) >>>>>>>>> at Function.Module.runMain (module.js:442:10) >>>>>>>>> at startup (node.js:136:18) >>>>>>>>> at node.js:966:3 >>>>>>>>> >>>>>>>>> npm ERR! Linux 4.15.0-55-generic >>>>>>>>> npm ERR! argv "/usr/bin/nodejs" "/usr/bin/npm" "run" "compile" >>>>>>>>> npm ERR! node v4.2.6 >>>>>>>>> npm ERR! npm v3.5.2 >>>>>>>>> npm ERR! code ELIFECYCLE >>>>>>>>> npm ERR! loris at 1.0.0 compile: `webpack` >>>>>>>>> npm ERR! Exit status 1 >>>>>>>>> npm ERR! >>>>>>>>> npm ERR! Failed at the loris at 1.0.0 compile script 'webpack'. >>>>>>>>> npm ERR! Make sure you have the latest version of node.js and npm >>>>>>>>> installed. >>>>>>>>> npm ERR! If you do, this is most likely a problem with the loris >>>>>>>>> package, >>>>>>>>> npm ERR! not with npm itself. >>>>>>>>> npm ERR! Tell the author that this fails on your system: >>>>>>>>> npm ERR! webpack >>>>>>>>> npm ERR! You can get information on how to open an issue for this >>>>>>>>> project with: >>>>>>>>> npm ERR! npm bugs loris >>>>>>>>> npm ERR! Or if that isn't available, you can get their info via: >>>>>>>>> npm ERR! npm owner ls loris >>>>>>>>> npm ERR! There is likely additional logging output above. >>>>>>>>> >>>>>>>>> npm ERR! Please include the following file with any support >>>>>>>>> request: >>>>>>>>> npm ERR! /var/www/loris/npm-debug.log >>>>>>>>> Makefile:14: recipe for target 'javascript' failed >>>>>>>>> make: *** [javascript] Error 1 >>>>>>>>> >>>>>>>>> Thanks, >>>>>>>>> >>>>>>>>> Sotirios >>>>>>>>> >>>>>>>>> ???? ???, 7 ??? 2019 ???? 5:41 ?.?., ?/? Christine Rogers, Ms. < >>>>>>>>> christine.rogers at mcgill.ca> ??????: >>>>>>>>> >>>>>>>>>> Hi Sotirios, >>>>>>>>>> >>>>>>>>>> Thanks, have you tried all of these steps? >>>>>>>>>> - clear your browser cache (and refresh a few times) >>>>>>>>>> - delete any files in your smarty/templates_c directory (this >>>>>>>>>> will clear the template cache - do Not touch smarty/templates/) >>>>>>>>>> - run `make` (per the 21 release notes, this replaces the >>>>>>>>>> composer commands used in previous releases to update your dependencies) >>>>>>>>>> - restart apache (doesn't hurt) >>>>>>>>>> >>>>>>>>>> Let us know how it goes -- let us know what difference you see >>>>>>>>>> after, with your logs. A >>>>>>>>>> lso please send us your Config path settings (see these >>>>>>>>>> Troubleshooting Queries >>>>>>>>>> ) >>>>>>>>>> if you're still seeing front-end issues. >>>>>>>>>> >>>>>>>>>> Thanks, >>>>>>>>>> Christine >>>>>>>>>> >>>>>>>>>> On Wed, Aug 7, 2019 at 8:02 AM Sotirios Nikoloutsopoulos < >>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>> >>>>>>>>>>> Hi, >>>>>>>>>>> >>>>>>>>>>> lorisadmin at hbp:/var/www/loris$ sudo cat >>>>>>>>>>> /var/log/apache2/error.log >>>>>>>>>>> [Wed Aug 07 07:35:02.422501 2019] [mpm_prefork:notice] [pid >>>>>>>>>>> 1267] AH00163: Apache/2.4.18 (Ubuntu) OpenSSL/1.0.2g configured -- resuming >>>>>>>>>>> normal operations >>>>>>>>>>> [Wed Aug 07 07:35:02.422514 2019] [core:notice] [pid 1267] >>>>>>>>>>> AH00094: Command line: '/usr/sbin/apache2' >>>>>>>>>>> >>>>>>>>>>> And as for the access.log the content are empty >>>>>>>>>>> lorisadmin at hbp:/var/www/loris$ sudo ls -l >>>>>>>>>>> /var/log/apache2/access.log >>>>>>>>>>> lorisadmin at hbp:/var/www/loris$ sudo ls -l >>>>>>>>>>> /var/log/apache2/access.log >>>>>>>>>>> -rw-r----- 1 root adm 0 ???? 28 14:09 /var/log/apache2/access.log >>>>>>>>>>> >>>>>>>>>>> Also i noticed a loris_access.log. >>>>>>>>>>> >>>>>>>>>>> The only non-blank pages are: >>>>>>>>>>> mri_violations, dataquery does not exist at all, statistics, >>>>>>>>>>> data_team_helper, genomic_browser, configuration and >>>>>>>>>>> server_processes_manager/ prints "Required configuration settings for >>>>>>>>>>> Server Processes Manager are missing. Cannot continue." >>>>>>>>>>> >>>>>>>>>>> Thanks, >>>>>>>>>>> Sotirios >>>>>>>>>>> >>>>>>>>>>> ???? ???, 6 ??? 2019 ???? 10:13 ?.?., ?/? Christine Rogers, Ms. < >>>>>>>>>>> christine.rogers at mcgill.ca> ??????: >>>>>>>>>>> >>>>>>>>>>>> Hi Sotirios and LORIS community -- >>>>>>>>>>>> >>>>>>>>>>>> When upgrading to brand-new release 21 -- just a reminder to >>>>>>>>>>>> follow the release notes and run the new *make* file to update >>>>>>>>>>>> your dependencies (instead of using *composer* commands). >>>>>>>>>>>> We've also updated the Wiki page >>>>>>>>>>>> to >>>>>>>>>>>> clarify that the release notes for each version will tell you what to run. >>>>>>>>>>>> >>>>>>>>>>>> If your current version is not the last release (20.3), it's >>>>>>>>>>>> still important to upgrade to each minor release increment (e.g. 20.2, >>>>>>>>>>>> 20.3) before making the leap to 21.0. >>>>>>>>>>>> >>>>>>>>>>>> If you're getting blank pages, post-upgrade -- Try clearing >>>>>>>>>>>> your cache. >>>>>>>>>>>> >>>>>>>>>>>> Got questions or feedback e.g. on the Release Notes? please >>>>>>>>>>>> don't hesitate to let us know. >>>>>>>>>>>> Thanks, >>>>>>>>>>>> Christine >>>>>>>>>>>> The LORIS team >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> On Tue, Aug 6, 2019 at 10:09 AM Christine Rogers, Ms. < >>>>>>>>>>>> christine.rogers at mcgill.ca> wrote: >>>>>>>>>>>> >>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>> Could you also let us know -- on which pages is content >>>>>>>>>>>>> visible, and on which pages/modules is content not visible for you? >>>>>>>>>>>>> Thanks, >>>>>>>>>>>>> Christine >>>>>>>>>>>>> >>>>>>>>>>>>> On Tue, Aug 6, 2019 at 9:54 AM Christine Rogers, Ms. < >>>>>>>>>>>>> christine.rogers at mcgill.ca> wrote: >>>>>>>>>>>>> >>>>>>>>>>>>>> Thanks Sotirios, >>>>>>>>>>>>>> That's good to know. It sounds like you've checked that your >>>>>>>>>>>>>> /var/www/loris/project/config.xml file get populated properly. >>>>>>>>>>>>>> >>>>>>>>>>>>>> Please send us the last few errors you're seeing in your >>>>>>>>>>>>>> apache error log file, and your config paths and we can see what's >>>>>>>>>>>>>> happening with your front end -- >>>>>>>>>>>>>> Run these Troubleshooting Queries >>>>>>>>>>>>>> >>>>>>>>>>>>>> to get your config path settings, given your front end is not displaying >>>>>>>>>>>>>> fully. >>>>>>>>>>>>>> >>>>>>>>>>>>>> The Loris-MRI repo >>>>>>>>>>>>>> 21 >>>>>>>>>>>>>> install/upgrade would then be your next steps. >>>>>>>>>>>>>> Best, >>>>>>>>>>>>>> Christine >>>>>>>>>>>>>> >>>>>>>>>>>>>> On Tue, Aug 6, 2019 at 7:53 AM Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>> >>>>>>>>>>>>>>> I am using a VM. What i did was: >>>>>>>>>>>>>>> 1) Download the files from https://github.com/aces/Loris >>>>>>>>>>>>>>> and replace them to my existing /vaw/www/loris folder. >>>>>>>>>>>>>>> 2) Execute the composer install --no-dev and then composer >>>>>>>>>>>>>>> dump-autoload as mentioned here >>>>>>>>>>>>>>> https://github.com/aces/Loris/wiki/Updating-your-LORIS. >>>>>>>>>>>>>>> 3) Execute install.sh from /var/www/loris/tools and because >>>>>>>>>>>>>>> LORIS already existed i moved a .config file, then re-executed the >>>>>>>>>>>>>>> install.sh successfully >>>>>>>>>>>>>>> 4 ) As for the database, i dropped the schema and i executed >>>>>>>>>>>>>>> the installdb.php >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> ???? ???, 5 ??? 2019 ???? 5:22 ?.?., ?/? Christine Rogers, >>>>>>>>>>>>>>> Ms. ??????: >>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Hi Sotorios, >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Thanks - when you re-installed did you start on a fresh >>>>>>>>>>>>>>>> root path / VM or might some of your old system setting still apply? >>>>>>>>>>>>>>>> (And if you did any steps similar to an upgrade, did you >>>>>>>>>>>>>>>> follow the Upgrade steps in the Release Notes, from both repos?) >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> About the TR_range column - it was recently split (MRI >>>>>>>>>>>>>>>> pr339 ) split >>>>>>>>>>>>>>>> into TR_min and _max columns. Given the code was trying to query TR_range >>>>>>>>>>>>>>>> which does not exist in your mri_protocol table, double-check which version >>>>>>>>>>>>>>>> of the Loris repo (tables) and the Loris-MRI repo (code) you have installed >>>>>>>>>>>>>>>> to ensure they match. >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Christine >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> On Mon, Aug 5, 2019 at 9:06 AM Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> I reinstalled LORIS to 21 version and now the content is >>>>>>>>>>>>>>>>> not visible at all at most pages. >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> ???? ???, 5 ??? 2019 ???? 3:19 ?.?., ?/? Sotirios >>>>>>>>>>>>>>>>> Nikoloutsopoulos ??????: >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Is it easy to upgrade to Loris 21? Also the following >>>>>>>>>>>>>>>>>> fails because the line 1985 of NeuroDB/MRIProcessingUtility.pm query >>>>>>>>>>>>>>>>>> mri_protocol which doesn't have TR_range >>>>>>>>>>>>>>>>>> https://github.com/aces/Loris/blob/21.0-release/SQL/0000-00-00-schema.sql#L556 >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> lorisadmin at hbp:/data/loris/bin/mri$ >>>>>>>>>>>>>>>>>> ./batch_uploads_imageuploader -profile prod < ~/Desktop/input.txt > log.txt >>>>>>>>>>>>>>>>>> Use of uninitialized value $_ in pattern match (m//) at >>>>>>>>>>>>>>>>>> ./batch_uploads_imageuploader line 147. >>>>>>>>>>>>>>>>>> base is DCC0000_258024_V1 >>>>>>>>>>>>>>>>>> path is /data/incoming/ >>>>>>>>>>>>>>>>>> type is .tar.gz >>>>>>>>>>>>>>>>>> fullpath is /data/incoming/DCC0000_258024_V1.tar.gz >>>>>>>>>>>>>>>>>> DBD::mysql::st execute failed: Unknown column 'TR_range' >>>>>>>>>>>>>>>>>> in 'where clause' at >>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line 1985. >>>>>>>>>>>>>>>>>> DBD::mysql::st fetchrow_array failed: fetch() without >>>>>>>>>>>>>>>>>> execute() at >>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line 1986. >>>>>>>>>>>>>>>>>> Use of uninitialized value $count_mri_protocol in numeric >>>>>>>>>>>>>>>>>> gt (>) at /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm >>>>>>>>>>>>>>>>>> line 1995. >>>>>>>>>>>>>>>>>> DBD::mysql::st execute failed: Unknown column 'TR_range' >>>>>>>>>>>>>>>>>> in 'field list' at /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line >>>>>>>>>>>>>>>>>> 562. >>>>>>>>>>>>>>>>>> Can't exec "mail": No such file or directory at >>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 721. >>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 722. >>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 723. >>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 724. >>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 725. >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> No Mincs inserted >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Thanks, >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> ???? ???, 3 ??? 2019 ???? 1:08 ?.?., ?/? Christine >>>>>>>>>>>>>>>>>> Rogers, Ms. ??????: >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> First, just a note: we've released LORIS 21 this week >>>>>>>>>>>>>>>>>>> with some major new features and cleanup -- especially if you are early in >>>>>>>>>>>>>>>>>>> your setup phase, check out the Release notes for both the >>>>>>>>>>>>>>>>>>> LORIS >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> and Loris-MRI >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> repos. >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Thanks for your screenshots -- your empty mri_protocol >>>>>>>>>>>>>>>>>>> table should be at the root of these issues : >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> The mri_protocol table must be populated >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> in order for your scans to be registered in LORIS -- it serves as a >>>>>>>>>>>>>>>>>>> whitelist for the insertion pipeline which filters out scans that aren't >>>>>>>>>>>>>>>>>>> identified or matched to scan types in this table. >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> By default, this table is populated with entries for t1, >>>>>>>>>>>>>>>>>>> t2, fMRI and DTI (Insert statements for 21 release >>>>>>>>>>>>>>>>>>> branch are here >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> ) >>>>>>>>>>>>>>>>>>> Feel free to restore our default records and broaden >>>>>>>>>>>>>>>>>>> their parameters to match all your scan types. >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> re Defaced, native, selected -- these filter the scans >>>>>>>>>>>>>>>>>>> displayed as you move to the next page (View Session), instead of viewing >>>>>>>>>>>>>>>>>>> "all types" of scans from a given session : >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> - "defaced" means that a defacing script >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> has masked the subject's face in the volume (for patient privacy) >>>>>>>>>>>>>>>>>>> - "native" means that no pre-processing has been >>>>>>>>>>>>>>>>>>> performed on the scan (it's raw data), >>>>>>>>>>>>>>>>>>> - "selected" will show only volumes that have been >>>>>>>>>>>>>>>>>>> QC'd and "selected" as the best of their type -- used to display only the >>>>>>>>>>>>>>>>>>> best quality T1 image instead of all T1s acquired in a session, e.g. >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> re QC Comments -- >>>>>>>>>>>>>>>>>>> Once you have successfully loaded scans (matched to the >>>>>>>>>>>>>>>>>>> mri_protocol table), you'll be able to use the Imaging Browser's View >>>>>>>>>>>>>>>>>>> Session subpage to enter/view QC comments on each volume, or for each >>>>>>>>>>>>>>>>>>> visit. >>>>>>>>>>>>>>>>>>> These are stored directly in the database, and linked to >>>>>>>>>>>>>>>>>>> each scan. (Table name: feedback_mri_comments) >>>>>>>>>>>>>>>>>>> (Visit-level QC comments are linked to the session.) >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> For a walkthrough of the Imaging setup - please see the Imaging >>>>>>>>>>>>>>>>>>> Setup guide >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> - >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> An old LORIS walkthrough video >>>>>>>>>>>>>>>>>>> can also >>>>>>>>>>>>>>>>>>> walk you through some of the Imaging front-end features, starting at 8:00 >>>>>>>>>>>>>>>>>>> LORIS' imaging modules have been updated many times >>>>>>>>>>>>>>>>>>> since this video, but the functionality and workflow is similar. >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Let us know how it goes once you have entries in your >>>>>>>>>>>>>>>>>>> mri_protocol table - >>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>> Christine >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> On Fri, Aug 2, 2019 at 7:58 AM Sotirios Nikoloutsopoulos >>>>>>>>>>>>>>>>>>> wrote: >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Hi Christine, >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> In the candidate_list page i can see this patient >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> If i press the link under PSCID i get to see >>>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> and if i press the link under Scan Done it redirects me >>>>>>>>>>>>>>>>>>>> to imaging_browser >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> At the mri_violations page i also see No results ( >>>>>>>>>>>>>>>>>>>> neither on resolved / not resolved ). >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> At the imaging_uploader i can see the record that >>>>>>>>>>>>>>>>>>>> failed. >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> If i click on the tarchive info i get to see the >>>>>>>>>>>>>>>>>>>> Protocol Name which i think is the acquisition we wanted? >>>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Also my mri_protocol table is empty. >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Furthermore i would like to ask about the defaced, >>>>>>>>>>>>>>>>>>>> native, selected. What exactly is native and selected? And where are the qc >>>>>>>>>>>>>>>>>>>> comments stored? >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Finally a walkthrough would be helpful. >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Thanks, >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> ???? ???, 30 ???? 2019 ???? 8:29 ?.?., ?/? Christine >>>>>>>>>>>>>>>>>>>> Rogers, Ms. ??????: >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>> Glad to hear you're making progress with the visit >>>>>>>>>>>>>>>>>>>>> labels. To follow up on your last few emails: >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> a- The Wiki's Setup Guide contains Sample insert >>>>>>>>>>>>>>>>>>>>> statements for the Visit Windows table >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> . >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> As Cecile mentioned, the consistency of visit label >>>>>>>>>>>>>>>>>>>>> format is important: V01, v01, V1, 01 -- whichever you select to use is >>>>>>>>>>>>>>>>>>>>> fine; we use V01 by default across all documentation. >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> b- For Password reset, there is a script in the tools/ >>>>>>>>>>>>>>>>>>>>> directory so that a back-end administrator can reset any front-end user >>>>>>>>>>>>>>>>>>>>> password, including Admin. (See info on setting up / resetting User >>>>>>>>>>>>>>>>>>>>> passwords in the Wiki's Setup Guide >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> ) >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> c- The minc file not being registered -- due to >>>>>>>>>>>>>>>>>>>>> AcquisitionProtocol unknown. >>>>>>>>>>>>>>>>>>>>> This means the SeriesDescription (Acquisition >>>>>>>>>>>>>>>>>>>>> Protocol) in you Dicom header was not matched to any scan listed in the >>>>>>>>>>>>>>>>>>>>> mri_protocol database table. >>>>>>>>>>>>>>>>>>>>> (In the online Loris-MRI Troubleshooting Guide, >>>>>>>>>>>>>>>>>>>>> this >>>>>>>>>>>>>>>>>>>>> is Table 3, 2nd-last item "no MINCs inserted"). >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> The MRI Violations module (Readme here) >>>>>>>>>>>>>>>>>>>>> will show >>>>>>>>>>>>>>>>>>>>> you the details of this mismatch -- >>>>>>>>>>>>>>>>>>>>> Go to the module (under the Imaging menu), find your >>>>>>>>>>>>>>>>>>>>> scan and click the link "Could not identify scan type" -- in the next >>>>>>>>>>>>>>>>>>>>> subpage you can compare the scan's actual parameters against the >>>>>>>>>>>>>>>>>>>>> mri_protocol table. >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> To resolve this, adjust your mri_protocol table values >>>>>>>>>>>>>>>>>>>>> or perhaps ensure your DICOMs are labelled consistently. >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> Let us know if this works for you -- we can also walk >>>>>>>>>>>>>>>>>>>>> you through an example of non-identified scans on >>>>>>>>>>>>>>>>>>>>> Demo.loris.ca (MRI Violations module). >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>> Christine >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> The LORIS team >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> On Tue, Jul 30, 2019 at 10:47 AM Sotirios >>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos wrote: >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> I hope this is sufficient as the error for the visit >>>>>>>>>>>>>>>>>>>>>> label disappeared. >>>>>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> Please see the attached file. Also something i found. >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> lorisadmin at hbp:/data/loris/bin/mri$ cat >>>>>>>>>>>>>>>>>>>>>> /data/loris/data//logs/TarLoad-17-39-xubBdv.log >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> ==> Loading file from disk >>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-17-39-UyQcG2/dcc0000_258024_v1_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> --> mapping DICOM parameter for >>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-17-39-UyQcG2/dcc0000_258024_v1_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> ==> computing md5 hash for MINC body. >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> --> md5: 6b1202fd63e29de4c9be1cd9925888a5 >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> ==> verifying acquisition protocol >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> Acquisition protocol is unknown >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> --> The minc file cannot be registered since the >>>>>>>>>>>>>>>>>>>>>> AcquisitionProtocol is unknown >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> ???? ???, 30 ???? 2019 ???? 4:58 ?.?., ?/? Sotirios >>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos ??????: >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> Ok I fixed the login problem by using a known hash >>>>>>>>>>>>>>>>>>>>>>> and by deleting the rows from the login_history i was able to login. >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> ???? ???, 30 ???? 2019 ???? 4:50 ?.?., ?/? Sotirios >>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos ??????: >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> there was no visit label 01 in the Visit_Windows >>>>>>>>>>>>>>>>>>>>>>>> table and i don't know how to insert it because the record requires lots of >>>>>>>>>>>>>>>>>>>>>>>> attributes. Also the system for a reason asked me to update my password and >>>>>>>>>>>>>>>>>>>>>>>> now i don't remember it and my account got suspended. Is there a way to >>>>>>>>>>>>>>>>>>>>>>>> reset it or set a simple password? I updated the password hash in the >>>>>>>>>>>>>>>>>>>>>>>> users table by using the hash from another LORIS setup we had and i still >>>>>>>>>>>>>>>>>>>>>>>> couldn't login ( also the attribute password is always NULL and the >>>>>>>>>>>>>>>>>>>>>>>> expiration date is 1999-01-01 for some reason ). >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> Thanks >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 29 ???? 2019 ???? 5:21 ?.?., ?/? Cecile >>>>>>>>>>>>>>>>>>>>>>>> Madjar ??????: >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> Can you try adding the visit label v01 to the >>>>>>>>>>>>>>>>>>>>>>>>> Visit_Windows table? >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> However, I noticed that in a previous dataset, the >>>>>>>>>>>>>>>>>>>>>>>>> label was V1. Does that refer to the same visit? If so, you might want to >>>>>>>>>>>>>>>>>>>>>>>>> harmonize the visit labels so they are all the same across datasets for a >>>>>>>>>>>>>>>>>>>>>>>>> given timepoint, meaning you will need to relabel scans when the visit >>>>>>>>>>>>>>>>>>>>>>>>> label is different but referring to the same visit label (v01 = V1 etc...). >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> Hope this helps, >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> On Mon, Jul 29, 2019 at 10:15 AM Sotirios >>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos wrote: >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> Could you help me with the "Visit label does not >>>>>>>>>>>>>>>>>>>>>>>>>> exist"? I had changed $subjectID{'createVisitLabel'} to 1 as you had >>>>>>>>>>>>>>>>>>>>>>>>>> suggested but it appears that this problem hasn't been resolved yet. >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> lorisadmin at hbp:/data/loris/bin/mri$ cat >>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data//logs/TarLoad-14-58-9Xog7H.log >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> ==> Loading file from disk >>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> --> mapping DICOM parameter for >>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> --> using user-defined filterParameters for >>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> Candidate Mismatch Error is Visit label does not >>>>>>>>>>>>>>>>>>>>>>>>>> exist >>>>>>>>>>>>>>>>>>>>>>>>>> -> WARNING: This candidate was invalid. Logging >>>>>>>>>>>>>>>>>>>>>>>>>> to >>>>>>>>>>>>>>>>>>>>>>>>>> MRICandidateErrors table with >>>>>>>>>>>>>>>>>>>>>>>>>> reason Visit label does not exist >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 26 ???? 2019 ???? 3:02 ?.?., ?/? >>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos >>>>>>>>>>>>>>>>>>>>>>>>>> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Cecile, >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> The Center error was fixed. Still the insertion >>>>>>>>>>>>>>>>>>>>>>>>>>> of mincs fails. Please see the output.txt file i attached. Also is there >>>>>>>>>>>>>>>>>>>>>>>>>>> something else i need to change at the paths configuration? >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 25 ???? 2019 ???? 6:55 ?.?., ?/? >>>>>>>>>>>>>>>>>>>>>>>>>>> Cecile Madjar ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> We are making progress! >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> I have a feeling this error comes from the fact >>>>>>>>>>>>>>>>>>>>>>>>>>>> that your psc table does not have the MRI_alias populated for the DCC site. >>>>>>>>>>>>>>>>>>>>>>>>>>>> Running the following query in the mysql database should fix this: >>>>>>>>>>>>>>>>>>>>>>>>>>>> UPDATE psc SET MRI_alias="DCC", Alias="DCC" >>>>>>>>>>>>>>>>>>>>>>>>>>>> WHERE Name="Data Coordinating Center"; >>>>>>>>>>>>>>>>>>>>>>>>>>>> Repeat the same with all your sites (make sure >>>>>>>>>>>>>>>>>>>>>>>>>>>> to change the Aliases between sites, they should all be unique). >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> Let me know how it goes! >>>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> On Thu, Jul 25, 2019 at 11:43 AM Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos wrote: >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Dear Cecile, >>>>>>>>>>>>>>>>>>>>>>>>>>>>> You were right about your guesses. I did the >>>>>>>>>>>>>>>>>>>>>>>>>>>>> modifications you suggested, i still get the "no mincs inserted" error, now >>>>>>>>>>>>>>>>>>>>>>>>>>>>> i am getting the "No center found this candidate" error ( how do i fix >>>>>>>>>>>>>>>>>>>>>>>>>>>>> that? from what i see the .dcm files contains a 'Institution Name', is that >>>>>>>>>>>>>>>>>>>>>>>>>>>>> the center? ), so i guess that's why the validation fails, but i changed >>>>>>>>>>>>>>>>>>>>>>>>>>>>> the force variable of tarchiveLoader to 1, shouldn't it have inserted the >>>>>>>>>>>>>>>>>>>>>>>>>>>>> mincs then? Also it is optional to have a mail server, right? ( from what i >>>>>>>>>>>>>>>>>>>>>>>>>>>>> see the mail error does not affect the $valid_study, so i assume we are >>>>>>>>>>>>>>>>>>>>>>>>>>>>> okay with that ) >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you a lot, >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 25 ???? 2019 ???? 5:48 ?.?., ?/? >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Cecile Madjar ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> From what I understand, I believe you just >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> need to update a few config settings from the frontend in the Config module >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> (under the Admin menu). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [image: Screen Shot 2019-07-25 at 10.31.35 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> AM.png] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Then go to the Paths section of the config >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> module and update the "LORIS-MRI code" config setting to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri (my guess is that currently, it is set to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data) and click on the submit button. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [image: Screen Shot 2019-07-25 at 10.32.50 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> AM.png] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Then, go to Imaging Pipeline section of the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Configuration module and update the "Loris-MRI Data Directory" to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/ (my guess is that it is empty at the moment in your >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> database which is why $data_dir is not defined when you run the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> tarchiveLoader step of the insertion pipeline). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [image: Screen Shot 2019-07-25 at 10.40.52 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> AM.png] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Finally, I took a look at your environment >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> file and it might be a good idea to update your PERL5LIB variable to the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> following (it has been added to the code a few releases ago as we realized >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> this was needed for the libraries. Not sure which version of LORIS-MRI you >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> are using but it does not hurt to update this variable to what I suggest >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> below): >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> export >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PERL5LIB=/data/loris/bin/mri/uploadNeuroDB:/data/loris/bin/mri/dicom-archive:$PERL5LIB >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helps. Sorry you are experiencing >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> so much trouble setting things up. We probably need to update our WIKI. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> On Thu, Jul 25, 2019 at 9:48 AM Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> wrote: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The "Loris-MRI Data Directory" should be in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the environment file? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 25 ???? 2019 ???? 12:59 ?.?., ?/? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The scripts are located in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/. Somewhere I might have messed something up but i >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> remember following the instructions in the wiki.For example when i tried to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> execute the batch_uploads_imageuploader perl script the line >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> my $command = "$bin_dir/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl " >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> was pointing to an invalid path, for >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> example: it was repeating a pattern and had LORIS instead of loris ( i >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> think the mistake was that in the wiki it suggested to use $PROJECT for >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the name of the folder and i choosed 'loris' >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris/wiki/Imaging-Database >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ). See also the in image for the modification i did. Also i didn't find the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> section to config the $data_dir variable. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 24 ???? 2019 ???? 6:05 ?.?., ?/? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Cecile Madjar >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> It looks like you have one Config setting >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> not set (based on the first error message you got when running it the first >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> time). You need to set a value for "Loris-MRI Data Directory" in the Config >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> module under the Imaging pipeline section (from what I can see, it would be >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/ for your setup). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The reason you got that error message the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> second time is that the pipeline checks if the DICOM study was already >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> inserted in the tarchive table. Since you ran the study once already, the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> study is inserted into the tarchive, hence the message. However, the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> pipeline did not complete as the MINC files were not created and inserted >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> into the files/parameter_file table. In order to continue the insertion, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> you will then need to run the tarchiveLoader command suggested in the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> terminal during the second run: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -globLocation -profile prod >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive//2012/DCM_2012-12-05_ImagingUpload-17-43-ZUEFjb.tar >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -verbose >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Finally, I am a bit confused by your >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> setup. Where are the scripts located? In /data/loris/bin/mri or >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data? It feels like the Config setting "LORIS-MRI code" in the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Paths section was set to "/data/LORIS/data" but it should have been set to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the directory where the scripts are located (most probably >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helps, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> On Wed, Jul 24, 2019 at 10:55 AM Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> wrote: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Ok first i execute this command: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> "lorisadmin at hbp:/data/loris/bin/mri$ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ./batch_uploads_imageuploader -profile prod < ~/Desktop/input.txt > log.txt >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at ./batch_uploads_imageuploader line 143. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at ./batch_uploads_imageuploader line 143. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $_ in pattern >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> match (m//) at ./batch_uploads_imageuploader line 147. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> base is DCC0000_258024_V01 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> path is /data/incoming/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> type is .tar.gz >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> fullpath is >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/incoming/DCC0000_258024_V01.tar.gz >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> source /tmp/ImagingUpload-17-43-ZUEFjb >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> targetlocation /data/loris/data/tarchive >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 256. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 284. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at /data/loris/bin/mri/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> tarchive_validation.pl line 219. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at /data/loris/bin/mri/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl line 270. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 711. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Can't exec "mail": No such file or >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> directory at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 721. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 722. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 723. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 724. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 724. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 725. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 735. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> No Mincs inserted >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The tarchiveLoader insertion script has >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> failed. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Running now the following command: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl -profile prod >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -upload_id 3 /data/incoming/DCC0000_258024_V01.tar.gz -verbose" >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I inserted the VisitLabel, but still the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Mincs are not inserted and i am getting this error >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> "lorisadmin at hbp:/data/loris/bin/mri$ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl -profile prod >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -upload_id 3 /data/incoming/DCC0000_258024_V01.tar.gz -verbose >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> find -path >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> \/tmp\/ImagingUpload\-17\-45\-5MsWEd -name '__MACOSX' -delete >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Spool message is: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The Scan for the uploadID 3 has already >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> been run with tarchiveID: 7. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> To continue with the rest of the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> insertion pipeline, please run tarchiveLoader from a terminal as follows: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader -globLocation -profile prod >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive//2012/DCM_2012-12-05_ImagingUpload-17-43-ZUEFjb.tar >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -verbose" >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Which files should i delete? I thought >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> that deleting the files from the tarchive was enough. And i executed the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> last proposed command to continue to rest of the insertion pipeline ( check >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the image ). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 24 ???? 2019 ???? 5:05 ?.?., >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ?/? Cecile Madjar >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sorry I was not clear before. Every >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visits of candidates are created in the session table with one entry per >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID/VisitLabel. So if the imaging pipeline created visits in the session >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> table (that are not attached to instruments) and you want to clean your >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> database completely, you can delete entries in that table as well. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Regarding your point 2, the imaging >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> pipeline can create the visit in the session table as long as the visit >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> label is present in the Visit_Windows table (which means the visit label >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> stored in the PatientName is a valid visit label). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> However, in your prod file, if the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> variable $subjectID{'createVisitLabel'} is set to 1 for candidates, the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit label should be created in the Visit_Windows table I believe. Here >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> is the line of the prod file you would need to change >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> . >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> In general, we prefer populating the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Visit_Windows table and set the $subjectID{'createVisitLabel'} to 0 for >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> candidate data to avoid insertion of badly labelled MRI data that are >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> complex to relabel. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Finally, regarding the candidate >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> creation, if you execute the following steps, the pipeline should be able >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> to create candidates: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - set in the Imaging Pipeline section of >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the config module the config setting "Upload creation of candidates" to Yes >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - manually transfer the scans to the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> LORIS server instead of uploading it via the imaging browser >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - run batch_imaging_upload.pl as you >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> did until now. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helps! >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> On Wed, Jul 24, 2019 at 8:47 AM Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> wrote: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> About my second question i replaced the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> name of the patient in the .dcm files and now i am getting an error that >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the visit label does not exist. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I thought it was supposed to be >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> automatically created. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> "Done adding archive info into database >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -globLocation -profile prod >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive//DCM_2012-12-05_ImagingUpload-15-42-yUwQQV.tar >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -verbose >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> md5sum >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive/DCM_2012-12-05_ImagingUpload-15-42-yUwQQV.tar >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> candidate id 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> => No Visit labelVisit label does not >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> exist >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Set centerID = 1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Number of MINC files that will be >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> considered for inserting into the database: 1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> log dir is /logs and log file is >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /logs/TarLoad-15-42-L6pocU.log >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> candidate id 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> => No Visit label >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Cleaning up temp files: rm -rf >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-15-42-J2rQms/ImagingUpload-15-42-yUwQQV*" >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 24 ???? 2019 ???? 3:38 ?.?., >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ?/? Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 1) What are the records in the session >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> table? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 2) I tried to upload a non-phantom >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> file like this >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> input_file.txt: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/incoming/DCC0000_258024_V1.tar.gz >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> N DCC0000_258024_V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Terminal: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ./batch_uploads_imageuploader >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -profile prod < ~/Desktop/input.txt > log.txt >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and i get the following error in the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> log.txt file >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> "Running now the following command: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl -profile prod >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -upload_id 7 /data/incoming/DCC0000_258024_V1.tar.gz -verbose >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> find -path >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> \/tmp\/ImagingUpload\-14\-56\-FeLCB4 -name '__MACOSX' -delete >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Spool message is: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The PatientName read from the DICOM >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> header does not start with DCC0000_258024_V1 from the mri_upload table >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> " >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and the spool message is repeated for >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> each .dcm file. Should i preprocess every .dcm file and change the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PatientName to "DCC0000_258024_V1"? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 3) As far as it concerns the candidate >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> profile i have to create a new one each time before i try to upload a file? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Is there already a way to create a candidate profile and get the DCCID and >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID without the user interface? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 18 ???? 2019 ???? 5:00 ?.?., >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ?/? Cecile Madjar < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> cecile.madjar at mcin.ca> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> See answers to your questions below. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> About the 1st case we had a dicom >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> with a blank studyUID, maybe someone accidentally removed it. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> That is strange. Something must have >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> been done to the DICOM files. I have never seen a study with no StudyUID >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> out of the scanner. Usually, you need to manually erase it with some tool. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> However, DICOMs never cease to surprise me... >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Some other questions: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 1) What are the steps to remove all >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> of my patients and uploads?: because i want to try to reupload all the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> testing dicoms we had with a clean database. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Release 21.0 of LORIS-MRI will offer >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> a script to remove all the entries and files specific to an upload. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> However, this release is not yet out. Hopefully in the next few weeks. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> In the meantime, since your case is >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> particular and that you just want to start with a clean database, the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> following deletes should work (hopefully I won't forget any tables): >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from mri_violations_log; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> mri_protocol_violated_scans; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from MRICandidateErrors; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from parameter_file; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from files_qcstatus; # (if you >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> played with the QC part of the imaging browser for testing) >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from feedback_mri_comments; # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> (if you played with the QC part of the imaging browser for testing) >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from tarchive_series; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from tarchive_files; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from mri_upload; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from tarchive; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from mri_scanner; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from candidate where >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID="scanner"; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I don't know if you want to also >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete entries in the session and candidate table too? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 2) We do not need to create the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> profile of a patient ( are the patients stored in the candidate table? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> because i can't see the ghosts ), because will it automatically be created >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> when importing a dicom? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I am not sure I understand fully this >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> question. All candidates are stored in the candidate table. The phantom >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> scans however are attached to a scanner candidate depending on where the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> scan happened. It is a bit of a weird concept that we have to redesign >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> eventually but never got a chance to get to it. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hopefully this answered your >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> question, otherwise, don't hesitate to let me know. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 3) What is the difference between >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> uploading a dicom as phantom instead of importing as >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCCID_DCCID_VisitLabel? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> When you upload the scan as >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID_DCCID_VisitLabel, there is a check that makes sure the candidate IDs >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and visit label are valid at the time of upload. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> When you upload a scan as phantom, it >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> expects that the DICOM field PatientName and uploaded filename contains the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> string "phantom". We enforced this behaviour on the imaging uploader side >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in recent releases but I can't remember which one. Probably the upcoming >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 21.0 release. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> All those verifications might seem >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> cumbersome but they are here to ensure that the files inserted are all >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> valid and labelled properly as it is a bit messy to have to delete files >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> that were wrongly labelled. At least, the delete script present in release >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 21.0 will make this process easier but it is still good practice to verify >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> those things. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> With pleasure. Hopefully the answers >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> to your questions will be helpful. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PS: loris-dev mailing list: you will >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> find the initial answer I gave Sotirios below. I forgot to cc the loris-dev >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in my earlier reply... >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 16 ???? 2019 ???? 12:02 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ?.?., ?/? Cecile Madjar < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> cecile.madjar at mcin.ca> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Dear Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you for reaching out. Since >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> your email was already organized in points, I will reply directly below >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> your questions below. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 1) What do we do when the StudyUID >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> is blank on the header? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/minor/docs/AppendixA-Troubleshooting_guideline.md >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> There solution provided at the table 3 does not guide us how to find the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> information ( is possible ). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The StudyUID is the field used in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> our pipeline at the moment to check whether a DICOM study was already >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> inserted into LORIS with that same StudyUID since it is supposed to be >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> unique for every single study. Currently, we do not support insertion of >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DICOM studies if they do not have a StudyUID associated with them. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Is there a specific reason why the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> StudyUID is blank in the DICOM headers in your DICOM files? Did they go >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> through some processes before upload to LORIS? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 2) When i am about to upload a >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> non-phanton case i need a 'Visit Label'. Is there already a script that can >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> create a new visit label for a specific Candidate, so i can provide it as >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> input afterwards to the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> batch_uploads_imageuploader ( See option 5.1.3 https://github.com/aces/Loris-MRI/blob/minor/docs/05-PipelineLaunchOptions.md ) >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I am not sure if the front-end >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> allows for it but if you use batch_uploads_imageuploader, the insertion >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> scripts could create the visit label for you. However, it does need to be >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> included in the patient name in order for the script to know which label it >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> should use. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> For example: you upload V02 for >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> MTL0123 (DCCID: 456789) but V02 was not yet created for MTL0123; the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> insertion scripts will create a V02 visit for MTL0123 if the PatientName >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> field for the dataset is MTL0123_456789_V02 with Stage marked as "Not >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Started". >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> However, *note that for the script >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> to create the visit for the candidate, you have to make sure that all the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit label of your projects were inserted in the Visit_Windows table* >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> (otherwise, the visit will never be created as they were not specified as >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> being part of the list of visit label to expect). So in the example above, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> you should have one row in Visit_Windows with Visit_label="V02" set. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 3) Section 4.3 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/minor/docs/04-Scripts.md >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> What do we do when the folder contains multiple mnc files? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> This is a case by case. Most of >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the time, the MINC files that failed insertion into the imaging browser end >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> up in the MRI violation module where you can see what went wrong with the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> acquisitions not inserted. If you notice that the MINC file should be >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> inserted as a specific protocol, you can force the insertion as explained >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in section 4.3. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> In your case, I have a feeling that >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> you want to be able to insert MINC files that did not go through the whole >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> pipeline insertion (DICOM archival, then dcm2mnc, then protocol >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> identification, then insertion...). In theory, you could call >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl on any MINC >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> file, provided you have at least the following information: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - path to the MINC file >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - uploadID associated with the MINC >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> files or DICOM archive path from which those MINC files were created from >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Then the minc_insertion.pl script >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> will do the subject information and protocol validation etc... >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> If all the MINC files come from the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> same uploadID or TarchiveID, then you could run a loop in bash calling the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl script like this >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> for files deriving from uploadID=1: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ls /path/to/mnc/folder/* | while >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> read f; do minc_insertion.pl >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -profile prod -uploadID 1 -mincPath $f; done >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helped! >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> -- >>>>>>>>>>>>>> >>>>>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> -- >>>>>>>>>>>>> >>>>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> -- >>>>>>>>>>>> >>>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>>> >>>>>>>>>>> _______________________________________________ >>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> -- >>>>>>>>>> >>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>> Montreal Neurological Institute >>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>> >>>>>>>>> _______________________________________________ >>>>>>>>> Loris-dev mailing list >>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>> >>>>>>>> _______________________________________________ >>>>>>> Loris-dev mailing list >>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>> >>>>>> >>>>>> >>>>>> -- >>>>>> >>>>>> christine.rogers at mcgill.ca >>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>> Montreal Neurological Institute >>>>>> McGill University | Montreal | Canada >>>>>> >>>>> _______________________________________________ >>>>> Loris-dev mailing list >>>>> Loris-dev at bic.mni.mcgill.ca >>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>> >>>> _______________________________________________ >>> Loris-dev mailing list >>> Loris-dev at bic.mni.mcgill.ca >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>> >> >> >> -- >> Shen Wang >> Loris Developer >> Montreal Neurological Institute >> McGill University >> >> -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: ???? 2019-08-13 19.21.15.png Type: image/png Size: 508603 bytes Desc: not available URL: From sotirisnik at gmail.com Tue Aug 13 20:33:56 2019 From: sotirisnik at gmail.com (Sotirios Nikoloutsopoulos) Date: Wed, 14 Aug 2019 03:33:56 +0300 Subject: [Loris-dev] Upgrading to Loris 21 - new make file In-Reply-To: References: Message-ID: I did the modifications, still there are errors. Thanks ???? ???, 14 ??? 2019 ???? 3:22 ?.?., ?/? Shen Wang ??????: > Hi Sotirios, > I saw your output file, the config issue is gone. > you can use [sudo npm run lintfix:javascript ] to fix these indent issues. > If it still has errors. > Then try modify this file .eslintignore > with this > > # Ignore until ESLint is run > > modules/* > > modules/dataquery/ > > node_modules/* > > htdocs/js/components/* > > jsx/* > > > # Ignore external libs > > htdocs/js/flot/* > > htdocs/js/jquery/* > > htdocs/js/jszip/* > > htdocs/js/modernizr/* > > htdocs/js/modules/* > > htdocs/js/react/* > > htdocs/js/shims/* > > htdocs/js/c3.min.js > > htdocs/js/d3.min.js > > htdocs/js/FileSaver.min.js > > > then do sudo make. > It should work. > Regards > Shen > > > Sotirios Nikoloutsopoulos ?2019?8?13? ????7:54??? > >> No, it didn't work, i also tried space/tabs because most of the errors >> where about indentation, also there are some errors about React. >> >> Thanks >> >> lorisadmin at hbp:/var/www/loris$ sudo ./node_modules/.bin/eslint --init >> ? How would you like to configure ESLint? Answer questions about your >> style >> ? Which version of ECMAScript do you use? ES2015 >> ? Are you using ES6 modules? Yes >> ? Where will your code run? Browser >> ? Do you use CommonJS? Yes >> ? Do you use JSX? Yes >> ? Do you use React? Yes >> ? What style of indentation do you use? Spaces >> ? What quotes do you use for strings? Single >> ? What line endings do you use? Unix >> ? Do you require semicolons? Yes >> ? What format do you want your config file to be in? JSON >> The config that you've selected requires the following dependencies: >> >> eslint-plugin-react at latest >> Successfully created .eslintrc.json file in /var/www/loris >> >> lorisadmin at hbp:/var/www/loris$ sudo make > sudo_make_output >> npm WARN The package prop-types is included as both a dev and production >> dependency. >> npm WARN optional SKIPPING OPTIONAL DEPENDENCY: fsevents at 1.2.4 >> (node_modules/fsevents): >> npm WARN notsup SKIPPING OPTIONAL DEPENDENCY: Unsupported platform for >> fsevents at 1.2.4: wanted {"os":"darwin","arch":"any"} (current: >> {"os":"linux","arch":"x64"}) >> >> npm ERR! code ELIFECYCLE >> npm ERR! errno 2 >> npm ERR! loris at 1.0.0 compile: `webpack` >> npm ERR! Exit status 2 >> npm ERR! >> npm ERR! Failed at the loris at 1.0.0 compile script. >> npm ERR! This is probably not a problem with npm. There is likely >> additional logging output above. >> >> npm ERR! A complete log of this run can be found in: >> npm ERR! >> /home/lorisadmin/.npm/_logs/2019-08-13T23_40_58_841Z-debug.log >> >> ???? ???, 14 ??? 2019 ???? 2:29 ?.?., ?/? Shen Wang < >> wangshen.mcin at gmail.com> ??????: >> >>> Hi Sotirios, >>> When you do make command, please make sure with sudo at the beginning. >>> [sudo make] >>> If it still doesn't work for you. >>> Then try the solutions below. >>> solution 1: >>> [image: ???? 2019-08-13 19.21.15.png] >>> Regards >>> Shen >>> >>> >>> >>> >>> On Tue, 13 Aug 2019 at 17:22, Sotirios Nikoloutsopoulos < >>> sotirisnik at gmail.com> wrote: >>> >>>> I think that the files exists although i redownloaded the eslintrc.json >>>> i checked others files that had similar errors. >>>> >>>> lorisadmin at hbp:/var/www/loris$ ls -l >>>> ./node_modules/eslint-loader/index.js >>>> -rw-rw-r-- 1 lorisadmin lorisadmin 6463 ??? 26 1985 >>>> ./node_modules/eslint-loader/index.js >>>> >>>> lorisadmin at hbp:/var/www/loris$ ls -l .eslintrc.json >>>> -rw-rw-r-- 1 lorisadmin lorisadmin 84530 ??? 14 00:04 .eslintrc.json >>>> >>>> Maybe this can help >>>> >>>> Module build failed (from ./node_modules/eslint-loader/index.js): >>>> SyntaxError: Cannot read config file: /var/www/loris/.eslintrc.json >>>> Error: Unexpected token < in JSON at position 6 >>>> at JSON.parse () >>>> at loadJSONConfigFile >>>> (/var/www/loris/node_modules/eslint/lib/config/config-file.js:114:21) >>>> at loadConfigFile >>>> (/var/www/loris/node_modules/eslint/lib/config/config-file.js:230:26) >>>> at loadFromDisk >>>> (/var/www/loris/node_modules/eslint/lib/config/config-file.js:500:18) >>>> at Object.load >>>> (/var/www/loris/node_modules/eslint/lib/config/config-file.js:564:20) >>>> at Config.getLocalConfigHierarchy >>>> (/var/www/loris/node_modules/eslint/lib/config.js:227:44) >>>> at Config.getConfigHierarchy >>>> (/var/www/loris/node_modules/eslint/lib/config.js:179:43) >>>> at Config.getConfigVector >>>> (/var/www/loris/node_modules/eslint/lib/config.js:286:21) >>>> at Config.getConfig >>>> (/var/www/loris/node_modules/eslint/lib/config.js:329:29) >>>> at processText >>>> (/var/www/loris/node_modules/eslint/lib/cli-engine.js:162:33) >>>> at CLIEngine.executeOnText >>>> (/var/www/loris/node_modules/eslint/lib/cli-engine.js:596:17) >>>> at lint >>>> (/var/www/loris/node_modules/eslint-loader/index.js:237:17) >>>> at Object.module.exports >>>> (/var/www/loris/node_modules/eslint-loader/index.js:232:21) >>>> >>>> ERROR in ./modules/imaging_uploader/jsx/index.js >>>> Module build failed (from ./node_modules/eslint-loader/index.js): >>>> SyntaxError: Cannot read config file: /var/www/loris/.eslintrc.json >>>> Error: Unexpected token < in JSON at position 6 >>>> at JSON.parse () >>>> at loadJSONConfigFile >>>> (/var/www/loris/node_modules/eslint/lib/config/config-file.js:114:21) >>>> at loadConfigFile >>>> (/var/www/loris/node_modules/eslint/lib/config/config-file.js:230:26) >>>> at loadFromDisk >>>> (/var/www/loris/node_modules/eslint/lib/config/config-file.js:500:18) >>>> at Object.load >>>> (/var/www/loris/node_modules/eslint/lib/config/config-file.js:564:20) >>>> at Config.getLocalConfigHierarchy >>>> (/var/www/loris/node_modules/eslint/lib/config.js:227:44) >>>> at Config.getConfigHierarchy >>>> (/var/www/loris/node_modules/eslint/lib/config.js:179:43) >>>> at Config.getConfigVector >>>> (/var/www/loris/node_modules/eslint/lib/config.js:286:21) >>>> at Config.getConfig >>>> (/var/www/loris/node_modules/eslint/lib/config.js:329:29) >>>> at processText >>>> (/var/www/loris/node_modules/eslint/lib/cli-engine.js:162:33) >>>> at CLIEngine.executeOnText >>>> (/var/www/loris/node_modules/eslint/lib/cli-engine.js:596:17) >>>> at lint >>>> (/var/www/loris/node_modules/eslint-loader/index.js:237:17) >>>> at Object.module.exports >>>> (/var/www/loris/node_modules/eslint-loader/index.js:232:21) >>>> >>>> >>>> >>>> ???? ???, 13 ??? 2019 ???? 11:52 ?.?., ?/? John Saigle < >>>> john.saigle at mcin.ca> ??????: >>>> >>>>> HI Sotirios, >>>>> >>>>> The make_output.txt file shows webpack failing because it can't find >>>>> the ESLint config file. >>>>> >>>>> Can you confirm whether the file `.eslintrc.json` exists within your >>>>> loris root directory (usually `/var/www/loris/`)? When I delete my file I >>>>> get the same errors as you. >>>>> >>>>> If you find that it's missing, you can make a local copy with the >>>>> contents found here: >>>>> >>>>> >>>>> https://github.com/aces/Loris/blob/e26a6ad49a73fcffef0cd73bb600c4d17b200b62/.eslintrc.json >>>>> >>>>> Once you know it exists, try running `make` again. >>>>> >>>>> Let us know if that moves you forward. >>>>> >>>>> Best, >>>>> John >>>>> >>>>> On Tue, Aug 13, 2019 at 2:21 PM Sotirios Nikoloutsopoulos < >>>>> sotirisnik at gmail.com> wrote: >>>>> >>>>>> Hi, >>>>>> I executed the commands for the node and now i am get the followings: >>>>>> >>>>>> lorisadmin at hbp:/var/www/loris$ make > ~/make_output >>>>>> npm WARN The package prop-types is included as both a dev and >>>>>> production dependency. >>>>>> npm WARN optional SKIPPING OPTIONAL DEPENDENCY: fsevents at 1.2.4 >>>>>> (node_modules/fsevents): >>>>>> npm WARN notsup SKIPPING OPTIONAL DEPENDENCY: Unsupported platform >>>>>> for fsevents at 1.2.4: wanted {"os":"darwin","arch":"any"} (current: >>>>>> {"os":"linux","arch":"x64"}) >>>>>> >>>>>> npm ERR! code ELIFECYCLE >>>>>> npm ERR! errno 2 >>>>>> npm ERR! loris at 1.0.0 compile: `webpack` >>>>>> npm ERR! Exit status 2 >>>>>> npm ERR! >>>>>> npm ERR! Failed at the loris at 1.0.0 compile script. >>>>>> npm ERR! This is probably not a problem with npm. There is likely >>>>>> additional logging output above. >>>>>> >>>>>> npm ERR! A complete log of this run can be found in: >>>>>> npm ERR! >>>>>> /home/lorisadmin/.npm/_logs/2019-08-13T18_12_05_378Z-debug.log >>>>>> make: *** [javascript] Error 2 >>>>>> >>>>>> Thanks, >>>>>> Sotirios >>>>>> >>>>>> >>>>>> ???? ???, 12 ??? 2019 ???? 10:19 ?.?., ?/? Christine Rogers, Ms. < >>>>>> christine.rogers at mcgill.ca> ??????: >>>>>> >>>>>>> Hi Sotirios, >>>>>>> >>>>>>> We've seen some users installing LORIS 21 or upgrading to 21 whose >>>>>>> version of node doesn't work well with webpack, due to updated packages >>>>>>> they're missing. >>>>>>> If so, update your node : >>>>>>> >>>>>>> curl -sL https://deb.nodesource.com/setup_8.x | sudo -E bash - >>>>>>> sudo apt-get install -y nodejs >>>>>>> >>>>>>> Let us know how that goes -- please send us output from the same log >>>>>>> if any issues. >>>>>>> Best, >>>>>>> Christine >>>>>>> >>>>>>> >>>>>>> On Thu, Aug 8, 2019 at 2:38 PM Sotirios Nikoloutsopoulos < >>>>>>> sotirisnik at gmail.com> wrote: >>>>>>> >>>>>>>> It's not a disk space issue, as you can see below i have still 74GB >>>>>>>> available. >>>>>>>> >>>>>>>> lorisadmin at hbp:/var/www/loris$ df -h >>>>>>>> Filesystem Size Used Avail Use% Mounted on >>>>>>>> udev 2,9G 0 2,9G 0% /dev >>>>>>>> tmpfs 597M 8,6M 588M 2% /run >>>>>>>> /dev/sda1 98G 19G 74G 21% / >>>>>>>> >>>>>>>> Maybe we have to pass a flag to get into strict mode? as stated >>>>>>>> "SyntaxError: Block-scoped declarations (let, const, function, class) not >>>>>>>> yet supported outside strict mode" >>>>>>>> >>>>>>>> Thanks, >>>>>>>> Sotirios >>>>>>>> >>>>>>>> ???? ???, 8 ??? 2019 ???? 4:32 ?.?., ?/? Dave MacFarlane < >>>>>>>> dave.macfarlane at mcin.ca> ??????: >>>>>>>> >>>>>>>>> It looks like the javascript snippet shown in the error message >>>>>>>>> when trying to compile the js is truncated. Have you run out of disk space? >>>>>>>>> >>>>>>>>> On Thu, Aug 8, 2019 at 8:37 AM Sotirios Nikoloutsopoulos < >>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>> >>>>>>>>>> Hi, >>>>>>>>>> >>>>>>>>>> I runned make and also included the file it reports at the end. >>>>>>>>>> >>>>>>>>>> lorisadmin at hbp:/var/www/loris$ make >>>>>>>>>> npm install >>>>>>>>>> npm WARN optional Skipping failed optional dependency >>>>>>>>>> /chokidar/fsevents: >>>>>>>>>> npm WARN notsup Not compatible with your operating system or >>>>>>>>>> architecture: fsevents at 1.2.9 >>>>>>>>>> npm WARN optional Skipping failed optional dependency >>>>>>>>>> /watchpack/chokidar/fsevents: >>>>>>>>>> npm WARN notsup Not compatible with your operating system or >>>>>>>>>> architecture: fsevents at 1.2.9 >>>>>>>>>> npm run compile >>>>>>>>>> >>>>>>>>>> > loris at 1.0.0 compile /var/www/loris >>>>>>>>>> > webpack >>>>>>>>>> >>>>>>>>>> /var/www/loris/node_modules/webpack/bin/webpack.js:86 >>>>>>>>>> let notify = >>>>>>>>>> ^^^ >>>>>>>>>> >>>>>>>>>> SyntaxError: Block-scoped declarations (let, const, function, >>>>>>>>>> class) not yet supported outside strict mode >>>>>>>>>> at exports.runInThisContext (vm.js:53:16) >>>>>>>>>> at Module._compile (module.js:374:25) >>>>>>>>>> at Object.Module._extensions..js (module.js:417:10) >>>>>>>>>> at Module.load (module.js:344:32) >>>>>>>>>> at Function.Module._load (module.js:301:12) >>>>>>>>>> at Function.Module.runMain (module.js:442:10) >>>>>>>>>> at startup (node.js:136:18) >>>>>>>>>> at node.js:966:3 >>>>>>>>>> >>>>>>>>>> npm ERR! Linux 4.15.0-55-generic >>>>>>>>>> npm ERR! argv "/usr/bin/nodejs" "/usr/bin/npm" "run" "compile" >>>>>>>>>> npm ERR! node v4.2.6 >>>>>>>>>> npm ERR! npm v3.5.2 >>>>>>>>>> npm ERR! code ELIFECYCLE >>>>>>>>>> npm ERR! loris at 1.0.0 compile: `webpack` >>>>>>>>>> npm ERR! Exit status 1 >>>>>>>>>> npm ERR! >>>>>>>>>> npm ERR! Failed at the loris at 1.0.0 compile script 'webpack'. >>>>>>>>>> npm ERR! Make sure you have the latest version of node.js and npm >>>>>>>>>> installed. >>>>>>>>>> npm ERR! If you do, this is most likely a problem with the loris >>>>>>>>>> package, >>>>>>>>>> npm ERR! not with npm itself. >>>>>>>>>> npm ERR! Tell the author that this fails on your system: >>>>>>>>>> npm ERR! webpack >>>>>>>>>> npm ERR! You can get information on how to open an issue for this >>>>>>>>>> project with: >>>>>>>>>> npm ERR! npm bugs loris >>>>>>>>>> npm ERR! Or if that isn't available, you can get their info via: >>>>>>>>>> npm ERR! npm owner ls loris >>>>>>>>>> npm ERR! There is likely additional logging output above. >>>>>>>>>> >>>>>>>>>> npm ERR! Please include the following file with any support >>>>>>>>>> request: >>>>>>>>>> npm ERR! /var/www/loris/npm-debug.log >>>>>>>>>> Makefile:14: recipe for target 'javascript' failed >>>>>>>>>> make: *** [javascript] Error 1 >>>>>>>>>> >>>>>>>>>> Thanks, >>>>>>>>>> >>>>>>>>>> Sotirios >>>>>>>>>> >>>>>>>>>> ???? ???, 7 ??? 2019 ???? 5:41 ?.?., ?/? Christine Rogers, Ms. < >>>>>>>>>> christine.rogers at mcgill.ca> ??????: >>>>>>>>>> >>>>>>>>>>> Hi Sotirios, >>>>>>>>>>> >>>>>>>>>>> Thanks, have you tried all of these steps? >>>>>>>>>>> - clear your browser cache (and refresh a few times) >>>>>>>>>>> - delete any files in your smarty/templates_c directory (this >>>>>>>>>>> will clear the template cache - do Not touch smarty/templates/) >>>>>>>>>>> - run `make` (per the 21 release notes, this replaces the >>>>>>>>>>> composer commands used in previous releases to update your dependencies) >>>>>>>>>>> - restart apache (doesn't hurt) >>>>>>>>>>> >>>>>>>>>>> Let us know how it goes -- let us know what difference you see >>>>>>>>>>> after, with your logs. A >>>>>>>>>>> lso please send us your Config path settings (see these >>>>>>>>>>> Troubleshooting Queries >>>>>>>>>>> ) >>>>>>>>>>> if you're still seeing front-end issues. >>>>>>>>>>> >>>>>>>>>>> Thanks, >>>>>>>>>>> Christine >>>>>>>>>>> >>>>>>>>>>> On Wed, Aug 7, 2019 at 8:02 AM Sotirios Nikoloutsopoulos < >>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>> >>>>>>>>>>>> Hi, >>>>>>>>>>>> >>>>>>>>>>>> lorisadmin at hbp:/var/www/loris$ sudo cat >>>>>>>>>>>> /var/log/apache2/error.log >>>>>>>>>>>> [Wed Aug 07 07:35:02.422501 2019] [mpm_prefork:notice] [pid >>>>>>>>>>>> 1267] AH00163: Apache/2.4.18 (Ubuntu) OpenSSL/1.0.2g configured -- resuming >>>>>>>>>>>> normal operations >>>>>>>>>>>> [Wed Aug 07 07:35:02.422514 2019] [core:notice] [pid 1267] >>>>>>>>>>>> AH00094: Command line: '/usr/sbin/apache2' >>>>>>>>>>>> >>>>>>>>>>>> And as for the access.log the content are empty >>>>>>>>>>>> lorisadmin at hbp:/var/www/loris$ sudo ls -l >>>>>>>>>>>> /var/log/apache2/access.log >>>>>>>>>>>> lorisadmin at hbp:/var/www/loris$ sudo ls -l >>>>>>>>>>>> /var/log/apache2/access.log >>>>>>>>>>>> -rw-r----- 1 root adm 0 ???? 28 14:09 >>>>>>>>>>>> /var/log/apache2/access.log >>>>>>>>>>>> >>>>>>>>>>>> Also i noticed a loris_access.log. >>>>>>>>>>>> >>>>>>>>>>>> The only non-blank pages are: >>>>>>>>>>>> mri_violations, dataquery does not exist at all, statistics, >>>>>>>>>>>> data_team_helper, genomic_browser, configuration and >>>>>>>>>>>> server_processes_manager/ prints "Required configuration settings for >>>>>>>>>>>> Server Processes Manager are missing. Cannot continue." >>>>>>>>>>>> >>>>>>>>>>>> Thanks, >>>>>>>>>>>> Sotirios >>>>>>>>>>>> >>>>>>>>>>>> ???? ???, 6 ??? 2019 ???? 10:13 ?.?., ?/? Christine Rogers, Ms. >>>>>>>>>>>> ??????: >>>>>>>>>>>> >>>>>>>>>>>>> Hi Sotirios and LORIS community -- >>>>>>>>>>>>> >>>>>>>>>>>>> When upgrading to brand-new release 21 -- just a reminder to >>>>>>>>>>>>> follow the release notes and run the new *make* file to >>>>>>>>>>>>> update your dependencies (instead of using *composer* >>>>>>>>>>>>> commands). >>>>>>>>>>>>> We've also updated the Wiki page >>>>>>>>>>>>> to >>>>>>>>>>>>> clarify that the release notes for each version will tell you what to run. >>>>>>>>>>>>> >>>>>>>>>>>>> If your current version is not the last release (20.3), it's >>>>>>>>>>>>> still important to upgrade to each minor release increment (e.g. 20.2, >>>>>>>>>>>>> 20.3) before making the leap to 21.0. >>>>>>>>>>>>> >>>>>>>>>>>>> If you're getting blank pages, post-upgrade -- Try clearing >>>>>>>>>>>>> your cache. >>>>>>>>>>>>> >>>>>>>>>>>>> Got questions or feedback e.g. on the Release Notes? please >>>>>>>>>>>>> don't hesitate to let us know. >>>>>>>>>>>>> Thanks, >>>>>>>>>>>>> Christine >>>>>>>>>>>>> The LORIS team >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> On Tue, Aug 6, 2019 at 10:09 AM Christine Rogers, Ms. < >>>>>>>>>>>>> christine.rogers at mcgill.ca> wrote: >>>>>>>>>>>>> >>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>> Could you also let us know -- on which pages is content >>>>>>>>>>>>>> visible, and on which pages/modules is content not visible for you? >>>>>>>>>>>>>> Thanks, >>>>>>>>>>>>>> Christine >>>>>>>>>>>>>> >>>>>>>>>>>>>> On Tue, Aug 6, 2019 at 9:54 AM Christine Rogers, Ms. < >>>>>>>>>>>>>> christine.rogers at mcgill.ca> wrote: >>>>>>>>>>>>>> >>>>>>>>>>>>>>> Thanks Sotirios, >>>>>>>>>>>>>>> That's good to know. It sounds like you've checked that >>>>>>>>>>>>>>> your /var/www/loris/project/config.xml file get populated properly. >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> Please send us the last few errors you're seeing in your >>>>>>>>>>>>>>> apache error log file, and your config paths and we can see what's >>>>>>>>>>>>>>> happening with your front end -- >>>>>>>>>>>>>>> Run these Troubleshooting Queries >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> to get your config path settings, given your front end is not displaying >>>>>>>>>>>>>>> fully. >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> The Loris-MRI repo >>>>>>>>>>>>>>> 21 >>>>>>>>>>>>>>> install/upgrade would then be your next steps. >>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>> Christine >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> On Tue, Aug 6, 2019 at 7:53 AM Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> I am using a VM. What i did was: >>>>>>>>>>>>>>>> 1) Download the files from https://github.com/aces/Loris >>>>>>>>>>>>>>>> and replace them to my existing /vaw/www/loris folder. >>>>>>>>>>>>>>>> 2) Execute the composer install --no-dev and then composer >>>>>>>>>>>>>>>> dump-autoload as mentioned here >>>>>>>>>>>>>>>> https://github.com/aces/Loris/wiki/Updating-your-LORIS. >>>>>>>>>>>>>>>> 3) Execute install.sh from /var/www/loris/tools and >>>>>>>>>>>>>>>> because LORIS already existed i moved a .config file, then re-executed the >>>>>>>>>>>>>>>> install.sh successfully >>>>>>>>>>>>>>>> 4 ) As for the database, i dropped the schema and i >>>>>>>>>>>>>>>> executed the installdb.php >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> ???? ???, 5 ??? 2019 ???? 5:22 ?.?., ?/? Christine Rogers, >>>>>>>>>>>>>>>> Ms. ??????: >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Hi Sotorios, >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Thanks - when you re-installed did you start on a fresh >>>>>>>>>>>>>>>>> root path / VM or might some of your old system setting still apply? >>>>>>>>>>>>>>>>> (And if you did any steps similar to an upgrade, did you >>>>>>>>>>>>>>>>> follow the Upgrade steps in the Release Notes, from both repos?) >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> About the TR_range column - it was recently split (MRI >>>>>>>>>>>>>>>>> pr339 ) split >>>>>>>>>>>>>>>>> into TR_min and _max columns. Given the code was trying to query TR_range >>>>>>>>>>>>>>>>> which does not exist in your mri_protocol table, double-check which version >>>>>>>>>>>>>>>>> of the Loris repo (tables) and the Loris-MRI repo (code) you have installed >>>>>>>>>>>>>>>>> to ensure they match. >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Christine >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> On Mon, Aug 5, 2019 at 9:06 AM Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> I reinstalled LORIS to 21 version and now the content is >>>>>>>>>>>>>>>>>> not visible at all at most pages. >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> ???? ???, 5 ??? 2019 ???? 3:19 ?.?., ?/? Sotirios >>>>>>>>>>>>>>>>>> Nikoloutsopoulos ??????: >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Is it easy to upgrade to Loris 21? Also the following >>>>>>>>>>>>>>>>>>> fails because the line 1985 of NeuroDB/MRIProcessingUtility.pm query >>>>>>>>>>>>>>>>>>> mri_protocol which doesn't have TR_range >>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris/blob/21.0-release/SQL/0000-00-00-schema.sql#L556 >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> lorisadmin at hbp:/data/loris/bin/mri$ >>>>>>>>>>>>>>>>>>> ./batch_uploads_imageuploader -profile prod < ~/Desktop/input.txt > log.txt >>>>>>>>>>>>>>>>>>> Use of uninitialized value $_ in pattern match (m//) at >>>>>>>>>>>>>>>>>>> ./batch_uploads_imageuploader line 147. >>>>>>>>>>>>>>>>>>> base is DCC0000_258024_V1 >>>>>>>>>>>>>>>>>>> path is /data/incoming/ >>>>>>>>>>>>>>>>>>> type is .tar.gz >>>>>>>>>>>>>>>>>>> fullpath is /data/incoming/DCC0000_258024_V1.tar.gz >>>>>>>>>>>>>>>>>>> DBD::mysql::st execute failed: Unknown column 'TR_range' >>>>>>>>>>>>>>>>>>> in 'where clause' at >>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line 1985. >>>>>>>>>>>>>>>>>>> DBD::mysql::st fetchrow_array failed: fetch() without >>>>>>>>>>>>>>>>>>> execute() at >>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line 1986. >>>>>>>>>>>>>>>>>>> Use of uninitialized value $count_mri_protocol in >>>>>>>>>>>>>>>>>>> numeric gt (>) at >>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line 1995. >>>>>>>>>>>>>>>>>>> DBD::mysql::st execute failed: Unknown column 'TR_range' >>>>>>>>>>>>>>>>>>> in 'field list' at /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line >>>>>>>>>>>>>>>>>>> 562. >>>>>>>>>>>>>>>>>>> Can't exec "mail": No such file or directory at >>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 721. >>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 722. >>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 723. >>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 724. >>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 725. >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> No Mincs inserted >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Thanks, >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> ???? ???, 3 ??? 2019 ???? 1:08 ?.?., ?/? Christine >>>>>>>>>>>>>>>>>>> Rogers, Ms. ??????: >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> First, just a note: we've released LORIS 21 this week >>>>>>>>>>>>>>>>>>>> with some major new features and cleanup -- especially if you are early in >>>>>>>>>>>>>>>>>>>> your setup phase, check out the Release notes for both the >>>>>>>>>>>>>>>>>>>> LORIS >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> and Loris-MRI >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> repos. >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Thanks for your screenshots -- your empty mri_protocol >>>>>>>>>>>>>>>>>>>> table should be at the root of these issues : >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> The mri_protocol table must be populated >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> in order for your scans to be registered in LORIS -- it serves as a >>>>>>>>>>>>>>>>>>>> whitelist for the insertion pipeline which filters out scans that aren't >>>>>>>>>>>>>>>>>>>> identified or matched to scan types in this table. >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> By default, this table is populated with entries for >>>>>>>>>>>>>>>>>>>> t1, t2, fMRI and DTI (Insert statements for 21 release >>>>>>>>>>>>>>>>>>>> branch are here >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> ) >>>>>>>>>>>>>>>>>>>> Feel free to restore our default records and broaden >>>>>>>>>>>>>>>>>>>> their parameters to match all your scan types. >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> re Defaced, native, selected -- these filter the scans >>>>>>>>>>>>>>>>>>>> displayed as you move to the next page (View Session), instead of viewing >>>>>>>>>>>>>>>>>>>> "all types" of scans from a given session : >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> - "defaced" means that a defacing script >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> has masked the subject's face in the volume (for patient privacy) >>>>>>>>>>>>>>>>>>>> - "native" means that no pre-processing has been >>>>>>>>>>>>>>>>>>>> performed on the scan (it's raw data), >>>>>>>>>>>>>>>>>>>> - "selected" will show only volumes that have been >>>>>>>>>>>>>>>>>>>> QC'd and "selected" as the best of their type -- used to display only the >>>>>>>>>>>>>>>>>>>> best quality T1 image instead of all T1s acquired in a session, e.g. >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> re QC Comments -- >>>>>>>>>>>>>>>>>>>> Once you have successfully loaded scans (matched to the >>>>>>>>>>>>>>>>>>>> mri_protocol table), you'll be able to use the Imaging Browser's View >>>>>>>>>>>>>>>>>>>> Session subpage to enter/view QC comments on each volume, or for each >>>>>>>>>>>>>>>>>>>> visit. >>>>>>>>>>>>>>>>>>>> These are stored directly in the database, and linked >>>>>>>>>>>>>>>>>>>> to each scan. (Table name: feedback_mri_comments) >>>>>>>>>>>>>>>>>>>> (Visit-level QC comments are linked to the session.) >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> For a walkthrough of the Imaging setup - please see the Imaging >>>>>>>>>>>>>>>>>>>> Setup guide >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> - >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> An old LORIS walkthrough video >>>>>>>>>>>>>>>>>>>> can also >>>>>>>>>>>>>>>>>>>> walk you through some of the Imaging front-end features, starting at 8:00 >>>>>>>>>>>>>>>>>>>> LORIS' imaging modules have been updated many times >>>>>>>>>>>>>>>>>>>> since this video, but the functionality and workflow is similar. >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Let us know how it goes once you have entries in your >>>>>>>>>>>>>>>>>>>> mri_protocol table - >>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>> Christine >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> On Fri, Aug 2, 2019 at 7:58 AM Sotirios >>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos wrote: >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> Hi Christine, >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> In the candidate_list page i can see this patient >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> If i press the link under PSCID i get to see >>>>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> and if i press the link under Scan Done it redirects >>>>>>>>>>>>>>>>>>>>> me to imaging_browser >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> At the mri_violations page i also see No results ( >>>>>>>>>>>>>>>>>>>>> neither on resolved / not resolved ). >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> At the imaging_uploader i can see the record that >>>>>>>>>>>>>>>>>>>>> failed. >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> If i click on the tarchive info i get to see the >>>>>>>>>>>>>>>>>>>>> Protocol Name which i think is the acquisition we wanted? >>>>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> Also my mri_protocol table is empty. >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> Furthermore i would like to ask about the defaced, >>>>>>>>>>>>>>>>>>>>> native, selected. What exactly is native and selected? And where are the qc >>>>>>>>>>>>>>>>>>>>> comments stored? >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> Finally a walkthrough would be helpful. >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> Thanks, >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> ???? ???, 30 ???? 2019 ???? 8:29 ?.?., ?/? Christine >>>>>>>>>>>>>>>>>>>>> Rogers, Ms. ??????: >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>> Glad to hear you're making progress with the visit >>>>>>>>>>>>>>>>>>>>>> labels. To follow up on your last few emails: >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> a- The Wiki's Setup Guide contains Sample insert >>>>>>>>>>>>>>>>>>>>>> statements for the Visit Windows table >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> . >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> As Cecile mentioned, the consistency of visit label >>>>>>>>>>>>>>>>>>>>>> format is important: V01, v01, V1, 01 -- whichever you select to use is >>>>>>>>>>>>>>>>>>>>>> fine; we use V01 by default across all documentation. >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> b- For Password reset, there is a script in the >>>>>>>>>>>>>>>>>>>>>> tools/ directory so that a back-end administrator can reset any front-end >>>>>>>>>>>>>>>>>>>>>> user password, including Admin. (See info on setting up / resetting User >>>>>>>>>>>>>>>>>>>>>> passwords in the Wiki's Setup Guide >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> ) >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> c- The minc file not being registered -- due to >>>>>>>>>>>>>>>>>>>>>> AcquisitionProtocol unknown. >>>>>>>>>>>>>>>>>>>>>> This means the SeriesDescription (Acquisition >>>>>>>>>>>>>>>>>>>>>> Protocol) in you Dicom header was not matched to any scan listed in the >>>>>>>>>>>>>>>>>>>>>> mri_protocol database table. >>>>>>>>>>>>>>>>>>>>>> (In the online Loris-MRI Troubleshooting Guide, >>>>>>>>>>>>>>>>>>>>>> this >>>>>>>>>>>>>>>>>>>>>> is Table 3, 2nd-last item "no MINCs inserted"). >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> The MRI Violations module (Readme here) >>>>>>>>>>>>>>>>>>>>>> will show >>>>>>>>>>>>>>>>>>>>>> you the details of this mismatch -- >>>>>>>>>>>>>>>>>>>>>> Go to the module (under the Imaging menu), find your >>>>>>>>>>>>>>>>>>>>>> scan and click the link "Could not identify scan type" -- in the next >>>>>>>>>>>>>>>>>>>>>> subpage you can compare the scan's actual parameters against the >>>>>>>>>>>>>>>>>>>>>> mri_protocol table. >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> To resolve this, adjust your mri_protocol table >>>>>>>>>>>>>>>>>>>>>> values or perhaps ensure your DICOMs are labelled consistently. >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> Let us know if this works for you -- we can also walk >>>>>>>>>>>>>>>>>>>>>> you through an example of non-identified scans on >>>>>>>>>>>>>>>>>>>>>> Demo.loris.ca (MRI Violations module). >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>> Christine >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> The LORIS team >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> On Tue, Jul 30, 2019 at 10:47 AM Sotirios >>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos wrote: >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> I hope this is sufficient as the error for the visit >>>>>>>>>>>>>>>>>>>>>>> label disappeared. >>>>>>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> Please see the attached file. Also something i found. >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> lorisadmin at hbp:/data/loris/bin/mri$ cat >>>>>>>>>>>>>>>>>>>>>>> /data/loris/data//logs/TarLoad-17-39-xubBdv.log >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> ==> Loading file from disk >>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-17-39-UyQcG2/dcc0000_258024_v1_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> --> mapping DICOM parameter for >>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-17-39-UyQcG2/dcc0000_258024_v1_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> ==> computing md5 hash for MINC body. >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> --> md5: 6b1202fd63e29de4c9be1cd9925888a5 >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> ==> verifying acquisition protocol >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> Acquisition protocol is unknown >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> --> The minc file cannot be registered since the >>>>>>>>>>>>>>>>>>>>>>> AcquisitionProtocol is unknown >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> ???? ???, 30 ???? 2019 ???? 4:58 ?.?., ?/? Sotirios >>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos ??????: >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> Ok I fixed the login problem by using a known hash >>>>>>>>>>>>>>>>>>>>>>>> and by deleting the rows from the login_history i was able to login. >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 30 ???? 2019 ???? 4:50 ?.?., ?/? Sotirios >>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos ??????: >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> there was no visit label 01 in the Visit_Windows >>>>>>>>>>>>>>>>>>>>>>>>> table and i don't know how to insert it because the record requires lots of >>>>>>>>>>>>>>>>>>>>>>>>> attributes. Also the system for a reason asked me to update my password and >>>>>>>>>>>>>>>>>>>>>>>>> now i don't remember it and my account got suspended. Is there a way to >>>>>>>>>>>>>>>>>>>>>>>>> reset it or set a simple password? I updated the password hash in the >>>>>>>>>>>>>>>>>>>>>>>>> users table by using the hash from another LORIS setup we had and i still >>>>>>>>>>>>>>>>>>>>>>>>> couldn't login ( also the attribute password is always NULL and the >>>>>>>>>>>>>>>>>>>>>>>>> expiration date is 1999-01-01 for some reason ). >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> Thanks >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 29 ???? 2019 ???? 5:21 ?.?., ?/? Cecile >>>>>>>>>>>>>>>>>>>>>>>>> Madjar ??????: >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> Can you try adding the visit label v01 to the >>>>>>>>>>>>>>>>>>>>>>>>>> Visit_Windows table? >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> However, I noticed that in a previous dataset, >>>>>>>>>>>>>>>>>>>>>>>>>> the label was V1. Does that refer to the same visit? If so, you might want >>>>>>>>>>>>>>>>>>>>>>>>>> to harmonize the visit labels so they are all the same across datasets for >>>>>>>>>>>>>>>>>>>>>>>>>> a given timepoint, meaning you will need to relabel scans when the visit >>>>>>>>>>>>>>>>>>>>>>>>>> label is different but referring to the same visit label (v01 = V1 etc...). >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helps, >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> On Mon, Jul 29, 2019 at 10:15 AM Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos wrote: >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> Could you help me with the "Visit label does not >>>>>>>>>>>>>>>>>>>>>>>>>>> exist"? I had changed $subjectID{'createVisitLabel'} to 1 as you had >>>>>>>>>>>>>>>>>>>>>>>>>>> suggested but it appears that this problem hasn't been resolved yet. >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> lorisadmin at hbp:/data/loris/bin/mri$ cat >>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data//logs/TarLoad-14-58-9Xog7H.log >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> ==> Loading file from disk >>>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> --> mapping DICOM parameter for >>>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> --> using user-defined filterParameters for >>>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> Candidate Mismatch Error is Visit label does not >>>>>>>>>>>>>>>>>>>>>>>>>>> exist >>>>>>>>>>>>>>>>>>>>>>>>>>> -> WARNING: This candidate was invalid. Logging >>>>>>>>>>>>>>>>>>>>>>>>>>> to >>>>>>>>>>>>>>>>>>>>>>>>>>> MRICandidateErrors table with >>>>>>>>>>>>>>>>>>>>>>>>>>> reason Visit label does not exist >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 26 ???? 2019 ???? 3:02 ?.?., ?/? >>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos >>>>>>>>>>>>>>>>>>>>>>>>>>> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Cecile, >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> The Center error was fixed. Still the insertion >>>>>>>>>>>>>>>>>>>>>>>>>>>> of mincs fails. Please see the output.txt file i attached. Also is there >>>>>>>>>>>>>>>>>>>>>>>>>>>> something else i need to change at the paths configuration? >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 25 ???? 2019 ???? 6:55 ?.?., ?/? >>>>>>>>>>>>>>>>>>>>>>>>>>>> Cecile Madjar ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> We are making progress! >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> I have a feeling this error comes from the >>>>>>>>>>>>>>>>>>>>>>>>>>>>> fact that your psc table does not have the MRI_alias populated for the DCC >>>>>>>>>>>>>>>>>>>>>>>>>>>>> site. Running the following query in the mysql database should fix this: >>>>>>>>>>>>>>>>>>>>>>>>>>>>> UPDATE psc SET MRI_alias="DCC", Alias="DCC" >>>>>>>>>>>>>>>>>>>>>>>>>>>>> WHERE Name="Data Coordinating Center"; >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Repeat the same with all your sites (make sure >>>>>>>>>>>>>>>>>>>>>>>>>>>>> to change the Aliases between sites, they should all be unique). >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Let me know how it goes! >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> On Thu, Jul 25, 2019 at 11:43 AM Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos wrote: >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Dear Cecile, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> You were right about your guesses. I did the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> modifications you suggested, i still get the "no mincs inserted" error, now >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> i am getting the "No center found this candidate" error ( how do i fix >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> that? from what i see the .dcm files contains a 'Institution Name', is that >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the center? ), so i guess that's why the validation fails, but i changed >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the force variable of tarchiveLoader to 1, shouldn't it have inserted the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> mincs then? Also it is optional to have a mail server, right? ( from what i >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> see the mail error does not affect the $valid_study, so i assume we are >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> okay with that ) >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you a lot, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 25 ???? 2019 ???? 5:48 ?.?., ?/? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Cecile Madjar ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> From what I understand, I believe you just >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> need to update a few config settings from the frontend in the Config module >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> (under the Admin menu). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [image: Screen Shot 2019-07-25 at 10.31.35 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> AM.png] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Then go to the Paths section of the config >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> module and update the "LORIS-MRI code" config setting to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri (my guess is that currently, it is set to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data) and click on the submit button. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [image: Screen Shot 2019-07-25 at 10.32.50 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> AM.png] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Then, go to Imaging Pipeline section of the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Configuration module and update the "Loris-MRI Data Directory" to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/ (my guess is that it is empty at the moment in your >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> database which is why $data_dir is not defined when you run the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> tarchiveLoader step of the insertion pipeline). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [image: Screen Shot 2019-07-25 at 10.40.52 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> AM.png] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Finally, I took a look at your environment >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> file and it might be a good idea to update your PERL5LIB variable to the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> following (it has been added to the code a few releases ago as we realized >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> this was needed for the libraries. Not sure which version of LORIS-MRI you >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> are using but it does not hurt to update this variable to what I suggest >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> below): >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> export >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PERL5LIB=/data/loris/bin/mri/uploadNeuroDB:/data/loris/bin/mri/dicom-archive:$PERL5LIB >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helps. Sorry you are experiencing >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> so much trouble setting things up. We probably need to update our WIKI. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> On Thu, Jul 25, 2019 at 9:48 AM Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> wrote: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The "Loris-MRI Data Directory" should be in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the environment file? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 25 ???? 2019 ???? 12:59 ?.?., ?/? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The scripts are located in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/. Somewhere I might have messed something up but i >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> remember following the instructions in the wiki.For example when i tried to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> execute the batch_uploads_imageuploader perl script the line >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> my $command = "$bin_dir/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl " >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> was pointing to an invalid path, for >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> example: it was repeating a pattern and had LORIS instead of loris ( i >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> think the mistake was that in the wiki it suggested to use $PROJECT for >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the name of the folder and i choosed 'loris' >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris/wiki/Imaging-Database >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ). See also the in image for the modification i did. Also i didn't find the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> section to config the $data_dir variable. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 24 ???? 2019 ???? 6:05 ?.?., ?/? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Cecile Madjar >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> It looks like you have one Config setting >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> not set (based on the first error message you got when running it the first >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> time). You need to set a value for "Loris-MRI Data Directory" in the Config >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> module under the Imaging pipeline section (from what I can see, it would be >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/ for your setup). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The reason you got that error message the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> second time is that the pipeline checks if the DICOM study was already >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> inserted in the tarchive table. Since you ran the study once already, the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> study is inserted into the tarchive, hence the message. However, the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> pipeline did not complete as the MINC files were not created and inserted >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> into the files/parameter_file table. In order to continue the insertion, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> you will then need to run the tarchiveLoader command suggested in the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> terminal during the second run: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -globLocation -profile prod >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive//2012/DCM_2012-12-05_ImagingUpload-17-43-ZUEFjb.tar >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -verbose >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Finally, I am a bit confused by your >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> setup. Where are the scripts located? In /data/loris/bin/mri or >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data? It feels like the Config setting "LORIS-MRI code" in the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Paths section was set to "/data/LORIS/data" but it should have been set to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the directory where the scripts are located (most probably >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helps, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> On Wed, Jul 24, 2019 at 10:55 AM Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> wrote: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Ok first i execute this command: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> "lorisadmin at hbp:/data/loris/bin/mri$ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ./batch_uploads_imageuploader -profile prod < ~/Desktop/input.txt > log.txt >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at ./batch_uploads_imageuploader line 143. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at ./batch_uploads_imageuploader line 143. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $_ in pattern >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> match (m//) at ./batch_uploads_imageuploader line 147. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> base is DCC0000_258024_V01 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> path is /data/incoming/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> type is .tar.gz >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> fullpath is >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/incoming/DCC0000_258024_V01.tar.gz >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> source /tmp/ImagingUpload-17-43-ZUEFjb >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> targetlocation /data/loris/data/tarchive >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 256. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 284. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at /data/loris/bin/mri/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> tarchive_validation.pl line 219. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at /data/loris/bin/mri/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl line 270. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 711. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Can't exec "mail": No such file or >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> directory at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 721. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 722. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 723. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 724. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 724. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 725. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 735. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> No Mincs inserted >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The tarchiveLoader insertion script has >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> failed. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Running now the following command: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl -profile prod >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -upload_id 3 /data/incoming/DCC0000_258024_V01.tar.gz -verbose" >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I inserted the VisitLabel, but still the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Mincs are not inserted and i am getting this error >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> "lorisadmin at hbp:/data/loris/bin/mri$ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl -profile prod >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -upload_id 3 /data/incoming/DCC0000_258024_V01.tar.gz -verbose >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> find -path >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> \/tmp\/ImagingUpload\-17\-45\-5MsWEd -name '__MACOSX' -delete >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Spool message is: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The Scan for the uploadID 3 has already >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> been run with tarchiveID: 7. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> To continue with the rest of the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> insertion pipeline, please run tarchiveLoader from a terminal as follows: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader -globLocation -profile prod >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive//2012/DCM_2012-12-05_ImagingUpload-17-43-ZUEFjb.tar >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -verbose" >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Which files should i delete? I thought >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> that deleting the files from the tarchive was enough. And i executed the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> last proposed command to continue to rest of the insertion pipeline ( check >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the image ). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 24 ???? 2019 ???? 5:05 ?.?., >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ?/? Cecile Madjar >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sorry I was not clear before. Every >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visits of candidates are created in the session table with one entry per >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID/VisitLabel. So if the imaging pipeline created visits in the session >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> table (that are not attached to instruments) and you want to clean your >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> database completely, you can delete entries in that table as well. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Regarding your point 2, the imaging >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> pipeline can create the visit in the session table as long as the visit >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> label is present in the Visit_Windows table (which means the visit label >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> stored in the PatientName is a valid visit label). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> However, in your prod file, if the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> variable $subjectID{'createVisitLabel'} is set to 1 for candidates, the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit label should be created in the Visit_Windows table I believe. Here >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> is the line of the prod file you would need to change >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> . >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> In general, we prefer populating the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Visit_Windows table and set the $subjectID{'createVisitLabel'} to 0 for >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> candidate data to avoid insertion of badly labelled MRI data that are >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> complex to relabel. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Finally, regarding the candidate >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> creation, if you execute the following steps, the pipeline should be able >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> to create candidates: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - set in the Imaging Pipeline section >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> of the config module the config setting "Upload creation of candidates" to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Yes >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - manually transfer the scans to the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> LORIS server instead of uploading it via the imaging browser >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - run batch_imaging_upload.pl as you >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> did until now. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helps! >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> On Wed, Jul 24, 2019 at 8:47 AM >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> About my second question i replaced >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the name of the patient in the .dcm files and now i am getting an error >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> that the visit label does not exist. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I thought it was supposed to be >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> automatically created. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> "Done adding archive info into database >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -globLocation -profile prod >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive//DCM_2012-12-05_ImagingUpload-15-42-yUwQQV.tar >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -verbose >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> md5sum >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive/DCM_2012-12-05_ImagingUpload-15-42-yUwQQV.tar >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> candidate id 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> => No Visit labelVisit label does not >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> exist >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Set centerID = 1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Number of MINC files that will be >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> considered for inserting into the database: 1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> log dir is /logs and log file is >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /logs/TarLoad-15-42-L6pocU.log >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> candidate id 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> => No Visit label >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Cleaning up temp files: rm -rf >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-15-42-J2rQms/ImagingUpload-15-42-yUwQQV*" >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 24 ???? 2019 ???? 3:38 ?.?., >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ?/? Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 1) What are the records in the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> session table? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 2) I tried to upload a non-phantom >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> file like this >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> input_file.txt: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/incoming/DCC0000_258024_V1.tar.gz >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> N DCC0000_258024_V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Terminal: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ./batch_uploads_imageuploader >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -profile prod < ~/Desktop/input.txt > log.txt >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and i get the following error in the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> log.txt file >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> "Running now the following command: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl -profile prod >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -upload_id 7 /data/incoming/DCC0000_258024_V1.tar.gz -verbose >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> find -path >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> \/tmp\/ImagingUpload\-14\-56\-FeLCB4 -name '__MACOSX' -delete >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Spool message is: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The PatientName read from the DICOM >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> header does not start with DCC0000_258024_V1 from the mri_upload table >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> " >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and the spool message is repeated for >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> each .dcm file. Should i preprocess every .dcm file and change the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PatientName to "DCC0000_258024_V1"? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 3) As far as it concerns the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> candidate profile i have to create a new one each time before i try to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> upload a file? Is there already a way to create a candidate profile and get >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the DCCID and PSCID without the user interface? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 18 ???? 2019 ???? 5:00 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ?.?., ?/? Cecile Madjar < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> cecile.madjar at mcin.ca> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> See answers to your questions below. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> About the 1st case we had a dicom >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> with a blank studyUID, maybe someone accidentally removed it. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> That is strange. Something must have >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> been done to the DICOM files. I have never seen a study with no StudyUID >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> out of the scanner. Usually, you need to manually erase it with some tool. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> However, DICOMs never cease to surprise me... >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Some other questions: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 1) What are the steps to remove all >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> of my patients and uploads?: because i want to try to reupload all the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> testing dicoms we had with a clean database. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Release 21.0 of LORIS-MRI will offer >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> a script to remove all the entries and files specific to an upload. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> However, this release is not yet out. Hopefully in the next few weeks. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> In the meantime, since your case is >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> particular and that you just want to start with a clean database, the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> following deletes should work (hopefully I won't forget any tables): >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from mri_violations_log; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> mri_protocol_violated_scans; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from MRICandidateErrors; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from parameter_file; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from files_qcstatus; # (if >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> you played with the QC part of the imaging browser for testing) >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from feedback_mri_comments; # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> (if you played with the QC part of the imaging browser for testing) >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from tarchive_series; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from tarchive_files; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from mri_upload; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from tarchive; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from mri_scanner; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from candidate where >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID="scanner"; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I don't know if you want to also >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete entries in the session and candidate table too? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 2) We do not need to create the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> profile of a patient ( are the patients stored in the candidate table? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> because i can't see the ghosts ), because will it automatically be created >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> when importing a dicom? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I am not sure I understand fully >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> this question. All candidates are stored in the candidate table. The >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> phantom scans however are attached to a scanner candidate depending on >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> where the scan happened. It is a bit of a weird concept that we have to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> redesign eventually but never got a chance to get to it. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hopefully this answered your >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> question, otherwise, don't hesitate to let me know. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 3) What is the difference between >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> uploading a dicom as phantom instead of importing as >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCCID_DCCID_VisitLabel? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> When you upload the scan as >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID_DCCID_VisitLabel, there is a check that makes sure the candidate IDs >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and visit label are valid at the time of upload. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> When you upload a scan as phantom, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> it expects that the DICOM field PatientName and uploaded filename contains >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the string "phantom". We enforced this behaviour on the imaging uploader >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> side in recent releases but I can't remember which one. Probably the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> upcoming 21.0 release. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> All those verifications might seem >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> cumbersome but they are here to ensure that the files inserted are all >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> valid and labelled properly as it is a bit messy to have to delete files >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> that were wrongly labelled. At least, the delete script present in release >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 21.0 will make this process easier but it is still good practice to verify >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> those things. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> With pleasure. Hopefully the answers >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> to your questions will be helpful. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PS: loris-dev mailing list: you will >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> find the initial answer I gave Sotirios below. I forgot to cc the loris-dev >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in my earlier reply... >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 16 ???? 2019 ???? 12:02 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ?.?., ?/? Cecile Madjar < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> cecile.madjar at mcin.ca> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Dear Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you for reaching out. Since >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> your email was already organized in points, I will reply directly below >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> your questions below. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 1) What do we do when the StudyUID >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> is blank on the header? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/minor/docs/AppendixA-Troubleshooting_guideline.md >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> There solution provided at the table 3 does not guide us how to find the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> information ( is possible ). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The StudyUID is the field used in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> our pipeline at the moment to check whether a DICOM study was already >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> inserted into LORIS with that same StudyUID since it is supposed to be >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> unique for every single study. Currently, we do not support insertion of >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DICOM studies if they do not have a StudyUID associated with them. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Is there a specific reason why the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> StudyUID is blank in the DICOM headers in your DICOM files? Did they go >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> through some processes before upload to LORIS? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 2) When i am about to upload a >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> non-phanton case i need a 'Visit Label'. Is there already a script that can >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> create a new visit label for a specific Candidate, so i can provide it as >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> input afterwards to the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> batch_uploads_imageuploader ( See option 5.1.3 https://github.com/aces/Loris-MRI/blob/minor/docs/05-PipelineLaunchOptions.md ) >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I am not sure if the front-end >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> allows for it but if you use batch_uploads_imageuploader, the insertion >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> scripts could create the visit label for you. However, it does need to be >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> included in the patient name in order for the script to know which label it >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> should use. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> For example: you upload V02 for >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> MTL0123 (DCCID: 456789) but V02 was not yet created for MTL0123; the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> insertion scripts will create a V02 visit for MTL0123 if the PatientName >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> field for the dataset is MTL0123_456789_V02 with Stage marked as "Not >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Started". >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> However, *note that for the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> script to create the visit for the candidate, you have to make sure that >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> all the visit label of your projects were inserted in the Visit_Windows >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> table* (otherwise, the visit will >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> never be created as they were not specified as being part of the list of >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit label to expect). So in the example above, you should have one row in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Visit_Windows with Visit_label="V02" set. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 3) Section 4.3 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/minor/docs/04-Scripts.md >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> What do we do when the folder contains multiple mnc files? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> This is a case by case. Most of >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the time, the MINC files that failed insertion into the imaging browser end >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> up in the MRI violation module where you can see what went wrong with the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> acquisitions not inserted. If you notice that the MINC file should be >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> inserted as a specific protocol, you can force the insertion as explained >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in section 4.3. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> In your case, I have a feeling >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> that you want to be able to insert MINC files that did not go through the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> whole pipeline insertion (DICOM archival, then dcm2mnc, then protocol >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> identification, then insertion...). In theory, you could call >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl on any MINC >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> file, provided you have at least the following information: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - path to the MINC file >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - uploadID associated with the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> MINC files or DICOM archive path from which those MINC files were created >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> from >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Then the minc_insertion.pl script >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> will do the subject information and protocol validation etc... >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> If all the MINC files come from >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the same uploadID or TarchiveID, then you could run a loop in bash calling >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the minc_insertion.pl script like >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> this for files deriving from uploadID=1: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ls /path/to/mnc/folder/* | while >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> read f; do minc_insertion.pl >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -profile prod -uploadID 1 -mincPath $f; done >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helped! >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> -- >>>>>>>>>>>>>> >>>>>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> -- >>>>>>>>>>>>> >>>>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>>>> >>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> -- >>>>>>>>>>> >>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>> >>>>>>>>>> _______________________________________________ >>>>>>>>>> Loris-dev mailing list >>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>> >>>>>>>>> _______________________________________________ >>>>>>>> Loris-dev mailing list >>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>> >>>>>>> >>>>>>> >>>>>>> -- >>>>>>> >>>>>>> christine.rogers at mcgill.ca >>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>> Montreal Neurological Institute >>>>>>> McGill University | Montreal | Canada >>>>>>> >>>>>> _______________________________________________ >>>>>> Loris-dev mailing list >>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>> >>>>> _______________________________________________ >>>> Loris-dev mailing list >>>> Loris-dev at bic.mni.mcgill.ca >>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>> >>> >>> >>> -- >>> Shen Wang >>> Loris Developer >>> Montreal Neurological Institute >>> McGill University >>> >>> -------------- next part -------------- An HTML attachment was scrubbed... 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Name: ???? 2019-08-13 19.21.15.png Type: image/png Size: 508603 bytes Desc: not available URL: -------------- next part -------------- lorisadmin at hbp:/var/www/loris$ cat /home/lorisadmin/.npm/_logs/2019-08-14T00_30_55_687Z-debug.log 0 info it worked if it ends with ok 1 verbose cli [ '/usr/bin/node', '/usr/bin/npm', 'run', 'compile' ] 2 info using npm at 6.4.1 3 info using node at v8.16.0 4 verbose run-script [ 'precompile', 'compile', 'postcompile' ] 5 info lifecycle loris at 1.0.0~precompile: loris at 1.0.0 6 info lifecycle loris at 1.0.0~compile: loris at 1.0.0 7 verbose lifecycle loris at 1.0.0~compile: unsafe-perm in lifecycle true 8 verbose lifecycle loris at 1.0.0~compile: PATH: /usr/lib/node_modules/npm/node_modules/npm-lifecycle/node-gyp-bin:/var/www/loris/node_modules/.bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/snap/bin 9 verbose lifecycle loris at 1.0.0~compile: CWD: /var/www/loris 10 silly lifecycle loris at 1.0.0~compile: Args: [ '-c', 'webpack' ] 11 silly lifecycle loris at 1.0.0~compile: Returned: code: 2 signal: null 12 info lifecycle loris at 1.0.0~compile: Failed to exec compile script 13 verbose stack Error: loris at 1.0.0 compile: `webpack` 13 verbose stack Exit status 2 13 verbose stack at EventEmitter. (/usr/lib/node_modules/npm/node_modules/npm-lifecycle/index.js:301:16) 13 verbose stack at emitTwo (events.js:126:13) 13 verbose stack at EventEmitter.emit (events.js:214:7) 13 verbose stack at ChildProcess. (/usr/lib/node_modules/npm/node_modules/npm-lifecycle/lib/spawn.js:55:14) 13 verbose stack at emitTwo (events.js:126:13) 13 verbose stack at ChildProcess.emit (events.js:214:7) 13 verbose stack at maybeClose (internal/child_process.js:915:16) 13 verbose stack at Process.ChildProcess._handle.onexit (internal/child_process.js:209:5) 14 verbose pkgid loris at 1.0.0 15 verbose cwd /var/www/loris 16 verbose Linux 4.15.0-55-generic 17 verbose argv "/usr/bin/node" "/usr/bin/npm" "run" "compile" 18 verbose node v8.16.0 19 verbose npm v6.4.1 20 error code ELIFECYCLE 21 error errno 2 22 error loris at 1.0.0 compile: `webpack` 22 error Exit status 2 23 error Failed at the loris at 1.0.0 compile script. 23 error This is probably not a problem with npm. There is likely additional logging output above. 24 verbose exit [ 2, true ] -------------- next part -------------- npm install audited 7858 packages in 5.349s found 1 low severity vulnerability run `npm audit fix` to fix them, or `npm audit` for details npm run compile > loris at 1.0.0 compile /var/www/loris > webpack Hash: 970783a174b7e73de51c Version: webpack 4.16.5 Child Hash: 970783a174b7e73de51c Time: 3853ms Built at: 2019-08-14 02:47:09 106 assets Entrypoint ./htdocs/js/components/DynamicDataTable.js = ./htdocs/js/components/DynamicDataTable.js ./htdocs/js/components/DynamicDataTable.js.map Entrypoint ./htdocs/js/components/PaginationLinks.js = ./htdocs/js/components/PaginationLinks.js ./htdocs/js/components/PaginationLinks.js.map Entrypoint ./htdocs/js/components/StaticDataTable.js = ./htdocs/js/components/StaticDataTable.js ./htdocs/js/components/StaticDataTable.js.map Entrypoint ./htdocs/js/components/MultiSelectDropdown.js = ./htdocs/js/components/MultiSelectDropdown.js 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Set 'mode' option to 'development' or 'production' to enable defaults for each environment. You can also set it to 'none' to disable any default behavior. Learn more: https://webpack.js.org/concepts/mode/ ERROR in ./jsx/Breadcrumbs.js Module Error (from ./node_modules/eslint-loader/index.js): /var/www/loris/jsx/Breadcrumbs.js 21:1 error Expected indentation of 4 spaces but found 2 indent 22:1 error Expected indentation of 8 spaces but found 4 indent 24:1 error Expected indentation of 8 spaces but found 4 indent 25:1 error Expected indentation of 12 spaces but found 6 indent 26:1 error Expected indentation of 8 spaces but found 4 indent 28:1 error Expected indentation of 8 spaces but found 4 indent 29:1 error Expected indentation of 4 spaces but found 2 indent 31:1 error Expected indentation of 4 spaces but found 2 indent 32:1 error Expected indentation of 8 spaces but found 4 indent 33:1 error Expected indentation of 8 spaces but found 4 indent 34:1 error Expected indentation of 12 spaces but found 6 indent 35:1 error Expected indentation of 8 spaces but found 4 indent 36:1 error Expected indentation of 4 spaces but found 2 indent 38:1 error Expected indentation of 4 spaces but found 2 indent 39:1 error Expected indentation of 8 spaces but found 4 indent 40:1 error Expected indentation of 12 spaces but found 6 indent 41:1 error Expected indentation of 8 spaces but found 4 indent 42:1 error Expected indentation of 4 spaces but found 2 indent 44:1 error Expected indentation of 4 spaces but found 2 indent 47:1 error Expected indentation of 8 spaces but found 4 indent 48:1 error Expected indentation of 8 spaces but found 4 indent 50:1 error Expected indentation of 8 spaces but found 4 indent 51:1 error Expected indentation of 12 spaces but found 6 indent 52:1 error Expected indentation of 8 spaces but found 4 indent 53:1 error Expected indentation of 12 spaces but found 6 indent 54:1 error Expected indentation of 8 spaces but found 4 indent 55:1 error Expected indentation of 12 spaces but found 6 indent 56:1 error Expected indentation of 8 spaces but found 4 indent 57:1 error Expected indentation of 12 spaces but found 6 indent 58:1 error Expected indentation of 8 spaces but found 4 indent 59:1 error Expected indentation of 12 spaces but found 6 indent 60:1 error Expected indentation of 8 spaces but found 4 indent 62:1 error Expected indentation of 8 spaces but found 4 indent 63:1 error Expected indentation of 12 spaces but found 6 indent 64:1 error Expected indentation of 8 spaces but found 4 indent 65:1 error Expected indentation of 4 spaces but found 2 indent 67:1 error Expected indentation of 4 spaces but found 2 indent 68:1 error Expected indentation of 8 spaces but found 4 indent 69:1 error Expected indentation of 8 spaces but found 4 indent 70:1 error Expected indentation of 8 spaces but found 4 indent 71:1 error Expected indentation of 8 spaces but found 4 indent 73:1 error Expected indentation of 8 spaces but found 4 indent 74:1 error Expected indentation of 8 spaces but found 4 indent 75:1 error Expected indentation of 8 spaces but found 4 indent 76:1 error Expected indentation of 12 spaces but found 6 indent 77:1 error Expected indentation of 12 spaces but found 6 indent 78:1 error Expected indentation of 12 spaces but found 6 indent 79:1 error Expected indentation of 16 spaces but found 8 indent 80:1 error Expected indentation of 20 spaces but found 10 indent 81:1 error Expected indentation of 24 spaces but found 12 indent 82:1 error Expected indentation of 28 spaces but found 14 indent 83:1 error Expected indentation of 24 spaces but found 12 indent 84:1 error Expected indentation of 20 spaces but found 10 indent 85:1 error Expected indentation of 16 spaces but found 8 indent 86:1 error Expected indentation of 12 spaces but found 6 indent 87:1 error Expected indentation of 16 spaces but found 8 indent 88:1 error Expected indentation of 20 spaces but found 10 indent 89:1 error Expected indentation of 24 spaces but found 12 indent 90:1 error Expected indentation of 28 spaces but found 14 indent 91:1 error Expected indentation of 24 spaces but found 12 indent 92:1 error Expected indentation of 20 spaces but found 10 indent 93:1 error Expected indentation of 16 spaces but found 8 indent 94:1 error Expected indentation of 12 spaces but found 6 indent 95:1 error Expected indentation of 8 spaces but found 4 indent 97:1 error Expected indentation of 8 spaces but found 4 indent 98:1 error Expected indentation of 12 spaces but found 6 indent 99:1 error Expected indentation of 16 spaces but found 8 indent 100:1 error Expected indentation of 20 spaces but found 10 indent 101:1 error Expected indentation of 24 spaces but found 18 indent 102:1 error Expected indentation of 24 spaces but found 18 indent 103:1 error Expected indentation of 24 spaces but found 18 indent 104:1 error Expected indentation of 24 spaces but found 18 indent 105:1 error Expected indentation of 20 spaces but found 10 indent 107:1 error Expected indentation of 20 spaces but found 10 indent 108:1 error Expected indentation of 20 spaces but found 10 indent 109:1 error Expected indentation of 24 spaces but found 12 indent 110:1 error Expected indentation of 20 spaces but found 10 indent 111:1 error Expected indentation of 16 spaces but found 8 indent 112:1 error Expected indentation of 12 spaces but found 6 indent 113:1 error Expected indentation of 8 spaces but found 4 indent 115:1 error Expected indentation of 8 spaces but found 4 indent 116:1 error Expected indentation of 12 spaces but found 6 indent 117:1 error Expected indentation of 16 spaces but found 8 indent 118:1 error Expected indentation of 20 spaces but found 10 indent 119:1 error Expected indentation of 16 spaces but found 8 indent 120:1 error Expected indentation of 16 spaces but found 8 indent 121:1 error Expected indentation of 16 spaces but found 8 indent 122:1 error Expected indentation of 12 spaces but found 6 indent 123:1 error Expected indentation of 8 spaces but found 4 indent 124:1 error Expected indentation of 4 spaces but found 2 indent 127:1 error Expected indentation of 4 spaces but found 2 indent 128:1 error Expected indentation of 4 spaces but found 2 indent ? 92 problems (92 errors, 0 warnings) 92 errors and 0 warnings potentially fixable with the `--fix` option. ERROR in ./jsx/DynamicDataTable.js Module Error (from ./node_modules/eslint-loader/index.js): /var/www/loris/jsx/DynamicDataTable.js 5:8 error 'StaticDataTable' is defined but never used no-unused-vars 8:1 error Expected indentation of 4 spaces but found 2 indent 9:1 error Expected indentation of 8 spaces but found 4 indent 11:1 error Expected indentation of 8 spaces but found 4 indent 12:1 error Expected indentation of 12 spaces but found 6 indent 13:1 error Expected indentation of 12 spaces but found 6 indent 14:1 error Expected indentation of 12 spaces but found 6 indent 15:1 error Expected indentation of 12 spaces but found 6 indent 16:1 error Expected indentation of 8 spaces but found 4 indent 18:1 error Expected indentation of 8 spaces but found 4 indent 19:1 error Expected indentation of 8 spaces but found 4 indent 20:1 error Expected indentation of 8 spaces but found 4 indent 21:1 error Expected indentation of 8 spaces but found 4 indent 22:1 error Expected indentation of 8 spaces but found 4 indent 23:1 error Expected indentation of 4 spaces but found 2 indent 23:4 error Unnecessary semicolon no-extra-semi 25:1 error Expected indentation of 4 spaces but found 2 indent 26:1 error Expected indentation of 8 spaces but found 4 indent 27:1 error Expected indentation of 8 spaces but found 6 indent 28:1 error Expected indentation of 8 spaces but found 4 indent 29:1 error Expected indentation of 4 spaces but found 2 indent 31:1 error Expected indentation of 4 spaces but found 2 indent 32:1 error Expected indentation of 8 spaces but found 6 indent 33:1 error Expected indentation of 8 spaces but found 4 indent 34:1 error Expected indentation of 4 spaces but found 2 indent 36:1 error Expected indentation of 4 spaces but found 2 indent 37:1 error Expected indentation of 8 spaces but found 4 indent 37:5 error '$' is not defined no-undef 38:1 error Expected indentation of 12 spaces but found 6 indent 39:1 error Expected indentation of 12 spaces but found 6 indent 40:1 error Expected indentation of 12 spaces but found 6 indent 41:1 error Expected indentation of 12 spaces but found 6 indent 42:1 error Expected indentation of 12 spaces but found 6 indent 43:1 error Expected indentation of 8 spaces but found 4 indent 44:1 error Expected indentation of 4 spaces but found 2 indent 46:1 error Expected indentation of 4 spaces but found 2 indent 47:1 error Expected indentation of 8 spaces but found 4 indent 48:1 error Expected indentation of 8 spaces but found 4 indent 49:1 error Expected indentation of 8 spaces but found 4 indent 50:1 error Expected indentation of 4 spaces but found 2 indent 52:1 error Expected indentation of 4 spaces but found 2 indent 53:1 error Expected indentation of 8 spaces but found 4 indent 54:1 error Expected indentation of 12 spaces but found 6 indent 55:1 error Expected indentation of 8 spaces but found 4 indent 56:1 error Expected indentation of 4 spaces but found 2 indent 58:1 error Expected indentation of 4 spaces but found 2 indent 59:1 error Expected indentation of 8 spaces but found 4 indent 60:1 error Expected indentation of 12 spaces but found 6 indent 61:1 error Expected indentation of 12 spaces but found 6 indent 62:1 error Expected indentation of 12 spaces but found 6 indent 63:1 error Expected indentation of 8 spaces but found 4 indent 64:1 error Expected indentation of 4 spaces but found 2 indent 66:1 error Expected indentation of 4 spaces but found 2 indent 67:1 error Expected indentation of 8 spaces but found 4 indent 67:5 error Unexpected console statement no-console 68:1 error Expected indentation of 8 spaces but found 4 indent 69:1 error Expected indentation of 12 spaces but found 6 indent 70:1 error Expected indentation of 8 spaces but found 4 indent 71:1 error Expected indentation of 4 spaces but found 2 indent 73:1 error Expected indentation of 4 spaces but found 2 indent 74:1 error Expected indentation of 8 spaces but found 4 indent 75:1 error Expected indentation of 12 spaces but found 6 indent 76:1 error Expected indentation of 16 spaces but found 8 indent 77:1 error Expected indentation of 20 spaces but found 10 indent 78:1 error Expected indentation of 24 spaces but found 12 indent 79:1 error Expected indentation of 20 spaces but found 10 indent 80:1 error Expected indentation of 16 spaces but found 8 indent 81:1 error Expected indentation of 12 spaces but found 6 indent 83:1 error Expected indentation of 12 spaces but found 6 indent 84:1 error Expected indentation of 16 spaces but found 8 indent 86:1 error Expected indentation of 20 spaces but found 10 indent 87:1 error Expected indentation of 16 spaces but found 8 indent 88:1 error Expected indentation of 12 spaces but found 6 indent 89:1 error Expected indentation of 8 spaces but found 4 indent 91:1 error Expected indentation of 8 spaces but found 4 indent 92:1 error Expected indentation of 12 spaces but found 6 indent 93:1 error Expected indentation of 16 spaces but found 8 indent 94:1 error Expected indentation of 16 spaces but found 8 indent 95:1 error Expected indentation of 16 spaces but found 8 indent 96:1 error Expected indentation of 16 spaces but found 8 indent 97:1 error Expected indentation of 16 spaces but found 8 indent 98:1 error Expected indentation of 16 spaces but found 8 indent 99:1 error Expected indentation of 16 spaces but found 8 indent 100:1 error Expected indentation of 12 spaces but found 6 indent 101:1 error Expected indentation of 8 spaces but found 4 indent 102:1 error Expected indentation of 4 spaces but found 2 indent 106:1 error Expected indentation of 4 spaces but found 2 indent 107:1 error Expected indentation of 4 spaces but found 2 indent 111:1 error Expected indentation of 4 spaces but found 2 indent ? 89 problems (89 errors, 0 warnings) 86 errors and 0 warnings potentially fixable with the `--fix` option. ERROR in ./jsx/Form.js Module Error (from ./node_modules/eslint-loader/index.js): /var/www/loris/jsx/Form.js 30:1 error Expected indentation of 4 spaces but found 2 indent 31:1 error Expected indentation of 8 spaces but found 4 indent 32:1 error Expected indentation of 8 spaces but found 4 indent 33:1 error Expected indentation of 8 spaces but found 4 indent 34:1 error Expected indentation of 4 spaces but found 2 indent 36:1 error Expected indentation of 4 spaces but found 2 indent 37:1 error Expected indentation of 8 spaces but found 4 indent 38:1 error Expected indentation of 8 spaces but found 4 indent 39:1 error Expected indentation of 8 spaces but found 4 indent 40:1 error Expected indentation of 8 spaces but found 4 indent 41:1 error Expected indentation of 8 spaces but found 4 indent 43:1 error Expected indentation of 8 spaces but found 4 indent 44:1 error Expected indentation of 8 spaces but found 4 indent 46:1 error Expected indentation of 8 spaces but found 4 indent 47:1 error Expected indentation of 12 spaces but found 6 indent 48:1 error Expected indentation of 12 spaces but found 6 indent 49:1 error Expected indentation of 12 spaces but found 6 indent 50:1 error Expected indentation of 16 spaces but found 8 indent 51:1 error Expected indentation of 20 spaces but found 10 indent 52:1 error Expected indentation of 24 spaces but found 12 indent 53:1 error Expected indentation of 24 spaces but found 12 indent 54:1 error Expected indentation of 24 spaces but found 12 indent 55:1 error Expected indentation of 20 spaces but found 10 indent 56:1 error Expected indentation of 16 spaces but found 8 indent 57:1 error Expected indentation of 12 spaces but found 6 indent 58:1 error Expected indentation of 8 spaces but found 4 indent 60:1 error Expected indentation of 8 spaces but found 4 indent 61:1 error Expected indentation of 8 spaces but found 4 indent 62:1 error Expected indentation of 12 spaces but found 6 indent 63:1 error Expected indentation of 12 spaces but found 6 indent 64:1 error Expected indentation of 12 spaces but found 6 indent 66:1 error Expected indentation of 12 spaces but found 6 indent 67:1 error Expected indentation of 12 spaces but found 6 indent 68:1 error Expected indentation of 16 spaces but found 8 indent 69:1 error Expected indentation of 12 spaces but found 6 indent 70:1 error Expected indentation of 12 spaces but found 6 indent 71:1 error Expected indentation of 16 spaces but found 8 indent 72:1 error Expected indentation of 12 spaces but found 6 indent 73:1 error Expected indentation of 8 spaces but found 4 indent 75:1 error Expected indentation of 8 spaces but found 4 indent 76:1 error Expected indentation of 4 spaces but found 2 indent 78:1 error Expected indentation of 4 spaces but found 2 indent 80:1 error Expected indentation of 8 spaces but found 4 indent 81:1 error Expected indentation of 12 spaces but found 6 indent 82:1 error Expected indentation of 12 spaces but found 6 indent 83:1 error Expected indentation of 8 spaces but found 4 indent 84:1 error Expected indentation of 4 spaces but found 2 indent 86:1 error Expected indentation of 4 spaces but found 2 indent 87:1 error Expected indentation of 8 spaces but found 4 indent 89:1 error Expected indentation of 8 spaces but found 4 indent 90:1 error Expected indentation of 8 spaces but found 4 indent 92:1 error Expected indentation of 8 spaces but found 4 indent 93:1 error Expected indentation of 8 spaces but found 4 indent 94:1 error Expected indentation of 8 spaces but found 4 indent 95:1 error Expected indentation of 12 spaces but found 6 indent 96:1 error Expected indentation of 12 spaces but found 6 indent 97:1 error Expected indentation of 8 spaces but found 4 indent 99:1 error Expected indentation of 8 spaces but found 4 indent 100:1 error Expected indentation of 12 spaces but found 6 indent 101:1 error Expected indentation of 16 spaces but found 8 indent 102:1 error Expected indentation of 16 spaces but found 8 indent 103:1 error Expected indentation of 16 spaces but found 8 indent 104:1 error Expected indentation of 16 spaces but found 8 indent 105:1 error Expected indentation of 16 spaces but found 8 indent 106:1 error Expected indentation of 16 spaces but found 8 indent 107:1 error Expected indentation of 16 spaces but found 8 indent 108:1 error Expected indentation of 12 spaces but found 6 indent 109:1 error Expected indentation of 16 spaces but found 8 indent 110:1 error Expected indentation of 20 spaces but found 10 indent 111:1 error Expected indentation of 16 spaces but found 8 indent 112:1 error Expected indentation of 12 spaces but found 6 indent 113:1 error Expected indentation of 8 spaces but found 4 indent 114:1 error Expected indentation of 4 spaces but found 2 indent 118:1 error Expected indentation of 4 spaces but found 2 indent 119:1 error Expected indentation of 4 spaces but found 2 indent 120:1 error Expected indentation of 4 spaces but found 2 indent 121:1 error Expected indentation of 4 spaces but found 2 indent 122:1 error Expected indentation of 4 spaces but found 2 indent 123:1 error Expected indentation of 4 spaces but found 2 indent 124:1 error Expected indentation of 4 spaces but found 2 indent 125:1 error Expected indentation of 8 spaces but found 4 indent 126:1 error Expected indentation of 12 spaces but found 6 indent 127:1 error Expected indentation of 12 spaces but found 6 indent 128:1 error Expected indentation of 8 spaces but found 4 indent 129:1 error Expected indentation of 4 spaces but found 2 indent 130:1 error Expected indentation of 4 spaces but found 2 indent 131:1 error Expected indentation of 4 spaces but found 2 indent 135:1 error Expected indentation of 4 spaces but found 2 indent 136:1 error Expected indentation of 4 spaces but found 2 indent 137:1 error Expected indentation of 4 spaces but found 2 indent 138:1 error Expected indentation of 4 spaces but found 2 indent 139:1 error Expected indentation of 4 spaces but found 2 indent 140:1 error Expected indentation of 4 spaces but found 2 indent 141:1 error Expected indentation of 4 spaces but found 2 indent 142:1 error Expected indentation of 4 spaces but found 2 indent 143:1 error Expected indentation of 4 spaces but found 2 indent 144:1 error Expected indentation of 8 spaces but found 4 indent 144:5 error Unexpected console statement no-console 145:1 error Expected indentation of 4 spaces but found 2 indent 157:1 error Expected indentation of 4 spaces but found 2 indent 158:1 error Expected indentation of 8 spaces but found 4 indent 159:1 error Expected indentation of 8 spaces but found 4 indent 160:1 error Expected indentation of 4 spaces but found 2 indent 162:1 error Expected indentation of 4 spaces but found 2 indent 163:1 error Expected indentation of 8 spaces but found 4 indent 164:1 error Expected indentation of 8 spaces but found 4 indent 165:1 error Expected indentation of 8 spaces but found 4 indent 166:1 error Expected indentation of 8 spaces but found 4 indent 167:1 error Expected indentation of 8 spaces but found 4 indent 169:1 error Expected indentation of 8 spaces but found 4 indent 170:1 error Expected indentation of 8 spaces but found 4 indent 171:1 error Expected indentation of 12 spaces but found 6 indent 172:1 error Expected indentation of 12 spaces but found 6 indent 173:1 error Expected indentation of 12 spaces but found 6 indent 175:1 error Expected indentation of 12 spaces but found 6 indent 176:1 error Expected indentation of 12 spaces but found 6 indent 177:1 error Expected indentation of 16 spaces but found 8 indent 178:1 error Expected indentation of 12 spaces but found 6 indent 179:1 error Expected indentation of 12 spaces but found 6 indent 180:1 error Expected indentation of 16 spaces but found 8 indent 181:1 error Expected indentation of 12 spaces but found 6 indent 182:1 error Expected indentation of 8 spaces but found 4 indent 183:1 error Expected indentation of 8 spaces but found 4 indent 184:1 error Expected indentation of 4 spaces but found 2 indent 186:1 error Expected indentation of 4 spaces but found 2 indent 188:1 error Expected indentation of 8 spaces but found 4 indent 190:1 error Expected indentation of 8 spaces but found 4 indent 191:1 error Expected indentation of 12 spaces but found 6 indent 192:1 error Expected indentation of 16 spaces but found 8 indent 193:1 error Expected indentation of 12 spaces but found 6 indent 194:1 error Expected indentation of 16 spaces but found 8 indent 195:1 error Expected indentation of 20 spaces but found 10 indent 196:1 error Expected indentation of 16 spaces but found 8 indent 197:1 error Expected indentation of 16 spaces but found 8 indent 198:1 error Expected indentation of 12 spaces but found 6 indent 199:1 error Expected indentation of 8 spaces but found 4 indent 200:1 error Expected indentation of 4 spaces but found 2 indent 204:1 error Expected indentation of 4 spaces but found 2 indent 205:1 error Expected indentation of 4 spaces but found 2 indent 206:1 error Expected indentation of 4 spaces but found 2 indent 210:1 error Expected indentation of 4 spaces but found 2 indent 211:1 error Expected indentation of 4 spaces but found 2 indent 219:1 error Expected indentation of 4 spaces but found 2 indent 220:1 error Expected indentation of 8 spaces but found 4 indent 221:1 error Expected indentation of 8 spaces but found 4 indent 222:1 error Expected indentation of 8 spaces but found 4 indent 223:1 error Expected indentation of 8 spaces but found 4 indent 224:1 error Expected indentation of 8 spaces but found 4 indent 225:1 error Expected indentation of 4 spaces but found 2 indent 227:1 error Expected indentation of 4 spaces but found 2 indent 228:1 error Expected indentation of 8 spaces but found 4 indent 229:1 error Expected indentation of 8 spaces but found 4 indent 230:1 error Expected indentation of 12 spaces but found 6 indent 231:1 error Expected indentation of 8 spaces but found 4 indent 232:1 error Expected indentation of 4 spaces but found 2 indent 234:1 error Expected indentation of 4 spaces but found 2 indent 235:1 error Expected indentation of 8 spaces but found 4 indent 236:1 error Expected indentation of 8 spaces but found 4 indent 237:1 error Expected indentation of 8 spaces but found 4 indent 238:1 error Expected indentation of 8 spaces but found 4 indent 239:1 error Expected indentation of 12 spaces but found 6 indent 240:1 error Expected indentation of 8 spaces but found 4 indent 241:1 error Expected indentation of 8 spaces but found 4 indent 242:1 error Expected indentation of 8 spaces but found 4 indent 243:1 error Expected indentation of 4 spaces but found 2 indent 245:1 error Expected indentation of 4 spaces but found 2 indent 247:1 error Expected indentation of 8 spaces but found 4 indent 248:1 error Expected indentation of 12 spaces but found 6 indent 249:1 error Expected indentation of 12 spaces but found 6 indent 250:1 error Expected indentation of 12 spaces but found 6 indent 251:1 error Expected indentation of 16 spaces but found 8 indent 252:1 error Expected indentation of 16 spaces but found 8 indent 253:1 error Expected indentation of 16 spaces but found 8 indent 254:1 error Expected indentation of 12 spaces but found 6 indent 255:1 error Expected indentation of 8 spaces but found 4 indent 256:1 error Expected indentation of 4 spaces but found 2 indent 258:1 error Expected indentation of 4 spaces but found 2 indent 262:1 error Expected indentation of 8 spaces but found 4 indent 263:1 error Expected indentation of 12 spaces but found 6 indent 264:1 error Expected indentation of 8 spaces but found 4 indent 265:1 error Expected indentation of 4 spaces but found 2 indent 267:1 error Expected indentation of 4 spaces but found 2 indent 268:1 error Expected indentation of 8 spaces but found 4 indent 269:1 error Expected indentation of 8 spaces but found 4 indent 270:1 error Expected indentation of 8 spaces but found 4 indent 271:1 error Expected indentation of 8 spaces but found 4 indent 272:1 error Expected indentation of 8 spaces but found 4 indent 273:1 error Expected indentation of 8 spaces but found 4 indent 274:1 error Expected indentation of 8 spaces but found 4 indent 275:1 error Expected indentation of 8 spaces but found 4 indent 277:1 error Expected indentation of 8 spaces but found 4 indent 278:1 error Expected indentation of 8 spaces but found 4 indent 279:1 error Expected indentation of 12 spaces but found 6 indent 280:1 error Expected indentation of 8 spaces but found 4 indent 282:1 error Expected indentation of 8 spaces but found 4 indent 283:1 error Expected indentation of 8 spaces but found 4 indent 284:1 error Expected indentation of 12 spaces but found 6 indent 285:1 error Expected indentation of 12 spaces but found 6 indent 286:1 error Expected indentation of 8 spaces but found 4 indent 287:1 error Expected indentation of 12 spaces but found 6 indent 288:1 error Expected indentation of 12 spaces but found 6 indent 289:1 error Expected indentation of 12 spaces but found 6 indent 290:1 error Expected indentation of 12 spaces but found 6 indent 291:1 error Expected indentation of 8 spaces but found 4 indent 292:1 error Expected indentation of 12 spaces but found 6 indent 293:1 error Expected indentation of 12 spaces but found 6 indent 294:1 error Expected indentation of 8 spaces but found 4 indent 296:1 error Expected indentation of 8 spaces but found 4 indent 297:1 error Expected indentation of 8 spaces but found 4 indent 298:1 error Expected indentation of 8 spaces but found 4 indent 299:1 error Expected indentation of 8 spaces but found 4 indent 301:1 error Expected indentation of 12 spaces but found 6 indent 302:1 error Expected indentation of 12 spaces but found 6 indent 303:1 error Expected indentation of 8 spaces but found 4 indent 304:1 error Expected indentation of 12 spaces but found 6 indent 305:1 error Expected indentation of 8 spaces but found 4 indent 307:1 error Expected indentation of 8 spaces but found 4 indent 308:1 error Expected indentation of 8 spaces but found 4 indent 309:1 error Expected indentation of 8 spaces but found 4 indent 310:1 error Expected indentation of 12 spaces but found 6 indent 311:1 error Expected indentation of 16 spaces but found 8 indent 312:1 error Expected indentation of 20 spaces but found 10 indent 313:1 error Expected indentation of 16 spaces but found 8 indent 314:1 error Expected indentation of 12 spaces but found 6 indent 315:1 error Expected indentation of 12 spaces but found 6 indent 316:1 error Expected indentation of 16 spaces but found 8 indent 317:1 error Expected indentation of 20 spaces but found 10 indent 318:1 error Expected indentation of 16 spaces but found 8 indent 319:1 error Expected indentation of 12 spaces but found 6 indent 320:1 error Expected indentation of 8 spaces but found 4 indent 321:1 error Expected indentation of 12 spaces but found 6 indent 322:1 error Expected indentation of 16 spaces but found 8 indent 323:1 error Expected indentation of 20 spaces but found 10 indent 324:1 error Expected indentation of 16 spaces but found 8 indent 325:1 error Expected indentation of 12 spaces but found 6 indent 326:1 error Expected indentation of 8 spaces but found 4 indent 328:1 error Expected indentation of 8 spaces but found 4 indent 329:1 error Expected indentation of 12 spaces but found 6 indent 330:1 error Expected indentation of 16 spaces but found 8 indent 331:1 error Expected indentation of 20 spaces but found 10 indent 332:1 error Expected indentation of 20 spaces but found 10 indent 333:1 error Expected indentation of 16 spaces but found 8 indent 334:1 error Expected indentation of 16 spaces but found 8 indent 335:1 error Expected indentation of 20 spaces but found 10 indent 336:1 error Expected indentation of 24 spaces but found 12 indent 337:1 error Expected indentation of 24 spaces but found 12 indent 338:1 error Expected indentation of 24 spaces but found 12 indent 339:1 error Expected indentation of 24 spaces but found 12 indent 340:1 error Expected indentation of 24 spaces but found 12 indent 341:1 error Expected indentation of 24 spaces but found 12 indent 342:1 error Expected indentation of 24 spaces but found 12 indent 343:1 error Expected indentation of 24 spaces but found 12 indent 344:1 error Expected indentation of 24 spaces but found 12 indent 345:1 error Expected indentation of 24 spaces but found 12 indent 346:1 error Expected indentation of 24 spaces but found 12 indent 347:1 error Expected indentation of 20 spaces but found 10 indent 348:1 error Expected indentation of 20 spaces but found 10 indent 349:1 error Expected indentation of 24 spaces but found 12 indent 350:1 error Expected indentation of 20 spaces but found 10 indent 351:1 error Expected indentation of 20 spaces but found 10 indent 352:1 error Expected indentation of 16 spaces but found 8 indent 353:1 error Expected indentation of 12 spaces but found 6 indent 354:1 error Expected indentation of 8 spaces but found 4 indent 355:1 error Expected indentation of 4 spaces but found 2 indent 359:1 error Expected indentation of 4 spaces but found 2 indent 360:1 error Expected indentation of 4 spaces but found 2 indent 361:1 error Expected indentation of 4 spaces but found 2 indent 362:1 error Expected indentation of 4 spaces but found 2 indent 363:1 error Expected indentation of 4 spaces but found 2 indent 364:1 error Expected indentation of 4 spaces but found 2 indent 365:1 error Expected indentation of 4 spaces but found 2 indent 366:1 error Expected indentation of 4 spaces but found 2 indent 367:1 error Expected indentation of 8 spaces but found 4 indent 368:1 error Expected indentation of 8 spaces but found 4 indent 369:1 error Expected indentation of 4 spaces but found 2 indent 370:1 error Expected indentation of 4 spaces but found 2 indent 371:1 error Expected indentation of 4 spaces but found 2 indent 372:1 error Expected indentation of 4 spaces but found 2 indent 373:1 error Expected indentation of 4 spaces but found 2 indent 374:1 error Expected indentation of 4 spaces but found 2 indent 375:1 error Expected indentation of 4 spaces but found 2 indent 379:1 error Expected indentation of 4 spaces but found 2 indent 380:1 error Expected indentation of 4 spaces but found 2 indent 381:1 error Expected indentation of 4 spaces but found 2 indent 382:1 error Expected indentation of 4 spaces but found 2 indent 383:1 error Expected indentation of 4 spaces but found 2 indent 384:1 error Expected indentation of 4 spaces but found 2 indent 385:1 error Expected indentation of 4 spaces but found 2 indent 386:1 error Expected indentation of 4 spaces but found 2 indent 387:1 error Expected indentation of 4 spaces but found 2 indent 388:1 error Expected indentation of 4 spaces but found 2 indent 389:1 error Expected indentation of 4 spaces but found 2 indent 390:1 error Expected indentation of 4 spaces but found 2 indent 391:1 error Expected indentation of 4 spaces but found 2 indent 392:1 error Expected indentation of 8 spaces but found 4 indent 392:5 error Unexpected console statement no-console 393:1 error Expected indentation of 4 spaces but found 2 indent 401:1 error Expected indentation of 4 spaces but found 2 indent 402:1 error Expected indentation of 8 spaces but found 4 indent 403:1 error Expected indentation of 8 spaces but found 4 indent 404:1 error Expected indentation of 4 spaces but found 2 indent 406:1 error Expected indentation of 4 spaces but found 2 indent 407:1 error Expected indentation of 8 spaces but found 4 indent 408:1 error Expected indentation of 8 spaces but found 4 indent 409:1 error Expected indentation of 8 spaces but found 4 indent 411:1 error Expected indentation of 8 spaces but found 4 indent 412:1 error Expected indentation of 8 spaces but found 4 indent 413:1 error Expected indentation of 12 spaces but found 6 indent 414:1 error Expected indentation of 12 spaces but found 6 indent 415:1 error Expected indentation of 16 spaces but found 8 indent 416:1 error Expected indentation of 20 spaces but found 10 indent 417:1 error Expected indentation of 16 spaces but found 8 indent 418:1 error Expected indentation of 12 spaces but found 6 indent 419:1 error Expected indentation of 8 spaces but found 4 indent 421:1 error Expected indentation of 8 spaces but found 4 indent 422:1 error Expected indentation of 4 spaces but found 2 indent 424:1 error Expected indentation of 4 spaces but found 2 indent 425:1 error Expected indentation of 8 spaces but found 4 indent 426:1 error Expected indentation of 8 spaces but found 4 indent 427:1 error Expected indentation of 8 spaces but found 4 indent 428:1 error Expected indentation of 8 spaces but found 4 indent 429:1 error Expected indentation of 8 spaces but found 4 indent 430:1 error Expected indentation of 8 spaces but found 4 indent 431:1 error Expected indentation of 8 spaces but found 4 indent 432:1 error Expected indentation of 8 spaces but found 4 indent 433:1 error Expected indentation of 8 spaces but found 4 indent 435:1 error Expected indentation of 8 spaces but found 4 indent 436:1 error Expected indentation of 8 spaces but found 4 indent 437:1 error Expected indentation of 12 spaces but found 6 indent 438:1 error Expected indentation of 8 spaces but found 4 indent 440:1 error Expected indentation of 8 spaces but found 4 indent 441:1 error Expected indentation of 8 spaces but found 4 indent 442:1 error Expected indentation of 12 spaces but found 6 indent 443:1 error Expected indentation of 8 spaces but found 4 indent 445:1 error Expected indentation of 8 spaces but found 4 indent 446:1 error Expected indentation of 8 spaces but found 4 indent 447:1 error Expected indentation of 12 spaces but found 6 indent 448:1 error Expected indentation of 12 spaces but found 6 indent 449:1 error Expected indentation of 8 spaces but found 4 indent 451:1 error Expected indentation of 8 spaces but found 4 indent 452:1 error Expected indentation of 8 spaces but found 4 indent 453:1 error Expected indentation of 8 spaces but found 4 indent 454:1 error Expected indentation of 12 spaces but found 6 indent 455:1 error Expected indentation of 16 spaces but found 8 indent 456:1 error Expected indentation of 20 spaces but found 10 indent 457:1 error Expected indentation of 16 spaces but found 8 indent 458:1 error Expected indentation of 12 spaces but found 6 indent 459:1 error Expected indentation of 12 spaces but found 6 indent 460:1 error Expected indentation of 16 spaces but found 8 indent 461:1 error Expected indentation of 20 spaces but found 10 indent 462:1 error Expected indentation of 16 spaces but found 8 indent 463:1 error Expected indentation of 12 spaces but found 6 indent 464:1 error Expected indentation of 8 spaces but found 4 indent 465:1 error Expected indentation of 12 spaces but found 6 indent 466:1 error Expected indentation of 16 spaces but found 8 indent 467:1 error Expected indentation of 20 spaces but found 10 indent 468:1 error Expected indentation of 16 spaces but found 8 indent 469:1 error Expected indentation of 12 spaces but found 6 indent 470:1 error Expected indentation of 8 spaces but found 4 indent 472:1 error Expected indentation of 8 spaces but found 4 indent 473:1 error Expected indentation of 8 spaces but found 4 indent 475:1 error Expected indentation of 8 spaces but found 4 indent 476:1 error Expected indentation of 12 spaces but found 6 indent 477:1 error Expected indentation of 16 spaces but found 8 indent 478:1 error Expected indentation of 20 spaces but found 10 indent 479:1 error Expected indentation of 20 spaces but found 10 indent 480:1 error Expected indentation of 16 spaces but found 8 indent 481:1 error Expected indentation of 16 spaces but found 8 indent 482:1 error Expected indentation of 20 spaces but found 10 indent 483:1 error Expected indentation of 24 spaces but found 12 indent 484:1 error Expected indentation of 24 spaces but found 12 indent 485:1 error Expected indentation of 24 spaces but found 12 indent 486:1 error Expected indentation of 24 spaces but found 12 indent 487:1 error Expected indentation of 24 spaces but found 12 indent 488:1 error Expected indentation of 24 spaces but found 12 indent 489:1 error Expected indentation of 24 spaces but found 12 indent 490:1 error Expected indentation of 24 spaces but found 12 indent 491:1 error Expected indentation of 20 spaces but found 10 indent 492:1 error Expected indentation of 24 spaces but found 12 indent 493:1 error Expected indentation of 24 spaces but found 12 indent 494:1 error Expected indentation of 20 spaces but found 10 indent 495:1 error Expected indentation of 20 spaces but found 10 indent 496:1 error Expected indentation of 16 spaces but found 8 indent 497:1 error Expected indentation of 12 spaces but found 6 indent 498:1 error Expected indentation of 8 spaces but found 4 indent 499:1 error Expected indentation of 4 spaces but found 2 indent 503:1 error Expected indentation of 4 spaces but found 2 indent 504:1 error Expected indentation of 4 spaces but found 2 indent 505:1 error Expected indentation of 4 spaces but found 2 indent 506:1 error Expected indentation of 4 spaces but found 2 indent 507:1 error Expected indentation of 8 spaces but found 4 indent 508:1 error Expected indentation of 8 spaces but found 4 indent 509:1 error Expected indentation of 4 spaces but found 2 indent 510:1 error Expected indentation of 4 spaces but found 2 indent 511:1 error Expected indentation of 4 spaces but found 2 indent 512:1 error Expected indentation of 4 spaces but found 2 indent 513:1 error Expected indentation of 4 spaces but found 2 indent 514:1 error Expected indentation of 4 spaces but found 2 indent 515:1 error Expected indentation of 4 spaces but found 2 indent 516:1 error Expected indentation of 4 spaces but found 2 indent 517:1 error Expected indentation of 4 spaces but found 2 indent 518:1 error Expected indentation of 4 spaces but found 2 indent 522:1 error Expected indentation of 4 spaces but found 2 indent 523:1 error Expected indentation of 4 spaces but found 2 indent 524:1 error Expected indentation of 4 spaces but found 2 indent 525:1 error Expected indentation of 4 spaces but found 2 indent 526:1 error Expected indentation of 4 spaces but found 2 indent 527:1 error Expected indentation of 4 spaces but found 2 indent 528:1 error Expected indentation of 4 spaces but found 2 indent 529:1 error Expected indentation of 4 spaces but found 2 indent 530:1 error Expected indentation of 4 spaces but found 2 indent 531:1 error Expected indentation of 4 spaces but found 2 indent 532:1 error Expected indentation of 4 spaces but found 2 indent 533:1 error Expected indentation of 4 spaces but found 2 indent 534:1 error Expected indentation of 4 spaces but found 2 indent 535:1 error Expected indentation of 4 spaces but found 2 indent 536:1 error Expected indentation of 8 spaces but found 4 indent 536:5 error Unexpected console statement no-console 537:1 error Expected indentation of 4 spaces but found 2 indent 553:1 error Expected indentation of 4 spaces but found 2 indent 554:1 error Expected indentation of 8 spaces but found 4 indent 555:1 error Expected indentation of 8 spaces but found 4 indent 556:1 error Expected indentation of 8 spaces but found 4 indent 557:1 error Expected indentation of 8 spaces but found 4 indent 558:1 error Expected indentation of 8 spaces but found 4 indent 559:1 error Expected indentation of 8 spaces but found 4 indent 560:1 error Expected indentation of 8 spaces but found 4 indent 561:1 error Expected indentation of 4 spaces but found 2 indent 563:1 error Expected indentation of 4 spaces but found 2 indent 564:1 error Expected indentation of 4 spaces but found 2 indent 565:1 error Expected indentation of 4 spaces but found 2 indent 566:1 error Expected indentation of 8 spaces but found 4 indent 567:1 error Expected indentation of 4 spaces but found 2 indent 568:1 error Expected indentation of 4 spaces but found 2 indent 569:1 error Expected indentation of 4 spaces but found 2 indent 570:1 error Expected indentation of 8 spaces but found 4 indent 571:1 error Expected indentation of 12 spaces but found 6 indent 572:1 error Expected indentation of 12 spaces but found 6 indent 573:1 error Expected indentation of 8 spaces but found 4 indent 574:1 error Expected indentation of 4 spaces but found 2 indent 576:1 error Expected indentation of 4 spaces but found 2 indent 577:1 error Expected indentation of 4 spaces but found 2 indent 578:1 error Expected indentation of 8 spaces but found 4 indent 579:1 error Expected indentation of 8 spaces but found 4 indent 580:1 error Expected indentation of 8 spaces but found 4 indent 581:1 error Expected indentation of 8 spaces but found 4 indent 582:1 error Expected indentation of 12 spaces but found 6 indent 583:1 error Expected indentation of 8 spaces but found 4 indent 584:1 error Expected indentation of 8 spaces but found 4 indent 585:1 error Expected indentation of 12 spaces but found 6 indent 586:1 error Expected indentation of 8 spaces but found 4 indent 587:1 error Expected indentation of 4 spaces but found 2 indent 589:1 error Expected indentation of 4 spaces but found 2 indent 590:1 error Expected indentation of 8 spaces but found 4 indent 591:1 error Expected indentation of 8 spaces but found 4 indent 592:1 error Expected indentation of 4 spaces but found 2 indent 594:1 error Expected indentation of 4 spaces but found 2 indent 595:1 error Expected indentation of 8 spaces but found 4 indent 596:1 error Expected indentation of 8 spaces but found 4 indent 597:1 error Expected indentation of 12 spaces but found 6 indent 598:1 error Expected indentation of 8 spaces but found 4 indent 599:1 error Expected indentation of 4 spaces but found 2 indent 601:1 error Expected indentation of 4 spaces but found 2 indent 602:1 error Expected indentation of 4 spaces but found 2 indent 603:1 error Expected indentation of 8 spaces but found 4 indent 604:1 error Expected indentation of 8 spaces but found 4 indent 605:1 error Expected indentation of 8 spaces but found 4 indent 606:1 error Expected indentation of 12 spaces but found 6 indent 607:1 error Expected indentation of 12 spaces but found 6 indent 608:1 error Expected indentation of 8 spaces but found 4 indent 609:1 error Expected indentation of 12 spaces but found 6 indent 610:1 error Expected indentation of 12 spaces but found 6 indent 611:1 error Expected indentation of 8 spaces but found 4 indent 614:1 error Expected indentation of 8 spaces but found 4 indent 615:1 error Expected indentation of 12 spaces but found 6 indent 616:1 error Expected indentation of 8 spaces but found 4 indent 618:1 error Expected indentation of 8 spaces but found 4 indent 619:1 error Expected indentation of 4 spaces but found 2 indent 621:1 error Expected indentation of 4 spaces but found 2 indent 622:1 error Expected indentation of 8 spaces but found 4 indent 623:1 error Expected indentation of 8 spaces but found 4 indent 624:1 error Expected indentation of 8 spaces but found 4 indent 625:1 error Expected indentation of 8 spaces but found 4 indent 626:1 error Expected indentation of 8 spaces but found 4 indent 627:1 error Expected indentation of 8 spaces but found 4 indent 628:1 error Expected indentation of 8 spaces but found 4 indent 629:1 error Expected indentation of 12 spaces but found 6 indent 630:1 error Expected indentation of 8 spaces but found 4 indent 632:1 error Expected indentation of 8 spaces but found 4 indent 633:1 error Expected indentation of 8 spaces but found 4 indent 634:1 error Expected indentation of 12 spaces but found 6 indent 635:1 error Expected indentation of 8 spaces but found 4 indent 637:1 error Expected indentation of 8 spaces but found 4 indent 638:1 error Expected indentation of 12 spaces but found 6 indent 639:1 error Expected indentation of 12 spaces but found 6 indent 640:1 error Expected indentation of 8 spaces but found 4 indent 642:1 error Expected indentation of 8 spaces but found 4 indent 643:1 error Expected indentation of 8 spaces but found 4 indent 644:1 error Expected indentation of 8 spaces but found 4 indent 645:1 error Expected indentation of 8 spaces but found 4 indent 646:1 error Expected indentation of 12 spaces but found 6 indent 647:1 error Expected indentation of 16 spaces but found 8 indent 648:1 error Expected indentation of 20 spaces but found 10 indent 649:1 error Expected indentation of 24 spaces but found 12 indent 650:1 error Expected indentation of 24 spaces but found 12 indent 651:1 error Expected indentation of 24 spaces but found 12 indent 652:1 error Expected indentation of 24 spaces but found 12 indent 653:1 error Expected indentation of 24 spaces but found 12 indent 654:1 error Expected indentation of 24 spaces but found 12 indent 655:1 error Expected indentation of 24 spaces but found 12 indent 656:1 error Expected indentation of 24 spaces but found 12 indent 657:1 error Expected indentation of 24 spaces but found 12 indent 658:1 error Expected indentation of 20 spaces but found 10 indent 659:1 error Expected indentation of 20 spaces but found 10 indent 660:1 error Expected indentation of 24 spaces but found 12 indent 661:1 error Expected indentation of 28 spaces but found 14 indent 662:1 error Expected indentation of 32 spaces but found 16 indent 663:1 error Expected indentation of 28 spaces but found 14 indent 664:1 error Expected indentation of 24 spaces but found 12 indent 665:1 error Expected indentation of 20 spaces but found 10 indent 666:1 error Expected indentation of 16 spaces but found 8 indent 667:1 error Expected indentation of 12 spaces but found 6 indent 668:1 error Expected indentation of 12 spaces but found 6 indent 669:1 error Expected indentation of 8 spaces but found 4 indent 670:1 error Expected indentation of 12 spaces but found 6 indent 671:1 error Expected indentation of 16 spaces but found 8 indent 672:1 error Expected indentation of 16 spaces but found 8 indent 673:1 error Expected indentation of 16 spaces but found 8 indent 674:1 error Expected indentation of 16 spaces but found 8 indent 675:1 error Expected indentation of 16 spaces but found 8 indent 676:1 error Expected indentation of 16 spaces but found 8 indent 677:1 error Expected indentation of 16 spaces but found 8 indent 678:1 error Expected indentation of 12 spaces but found 6 indent 679:1 error Expected indentation of 16 spaces but found 8 indent 680:1 error Expected indentation of 16 spaces but found 8 indent 681:1 error Expected indentation of 20 spaces but found 10 indent 682:1 error Expected indentation of 24 spaces but found 12 indent 683:1 error Expected indentation of 20 spaces but found 10 indent 684:1 error Expected indentation of 16 spaces but found 8 indent 685:1 error Expected indentation of 12 spaces but found 6 indent 686:1 error Expected indentation of 12 spaces but found 6 indent 687:1 error Expected indentation of 8 spaces but found 4 indent 688:1 error Expected indentation of 12 spaces but found 6 indent 689:1 error Expected indentation of 16 spaces but found 8 indent 690:1 error Expected indentation of 16 spaces but found 8 indent 691:1 error Expected indentation of 16 spaces but found 8 indent 692:1 error Expected indentation of 16 spaces but found 8 indent 693:1 error Expected indentation of 16 spaces but found 8 indent 694:1 error Expected indentation of 16 spaces but found 8 indent 695:1 error Expected indentation of 16 spaces but found 8 indent 696:1 error Expected indentation of 16 spaces but found 8 indent 697:1 error Expected indentation of 12 spaces but found 6 indent 698:1 error Expected indentation of 8 spaces but found 4 indent 700:1 error Expected indentation of 8 spaces but found 4 indent 701:1 error Expected indentation of 8 spaces but found 4 indent 702:1 error Expected indentation of 8 spaces but found 4 indent 703:1 error Expected indentation of 12 spaces but found 6 indent 704:1 error Expected indentation of 12 spaces but found 6 indent 705:1 error Expected indentation of 12 spaces but found 6 indent 706:1 error Expected indentation of 12 spaces but found 6 indent 707:1 error Expected indentation of 16 spaces but found 8 indent 708:1 error Expected indentation of 16 spaces but found 8 indent 709:1 error Expected indentation of 12 spaces but found 6 indent 710:1 error Expected indentation of 16 spaces but found 8 indent 711:1 error Expected indentation of 12 spaces but found 6 indent 712:1 error Expected indentation of 12 spaces but found 6 indent 713:1 error Expected indentation of 16 spaces but found 10 indent 714:1 error Expected indentation of 20 spaces but found 12 indent 715:1 error Expected indentation of 20 spaces but found 12 indent 716:1 error Expected indentation of 20 spaces but found 12 indent 717:1 error Expected indentation of 20 spaces but found 12 indent 718:1 error Expected indentation of 16 spaces but found 10 indent 719:1 error Expected indentation of 20 spaces but found 12 indent 721:1 error Expected indentation of 20 spaces but found 12 indent 722:1 error Expected indentation of 24 spaces but found 14 indent 723:1 error Expected indentation of 24 spaces but found 14 indent 724:1 error Expected indentation of 20 spaces but found 12 indent 725:1 error Expected indentation of 16 spaces but found 10 indent 726:1 error Expected indentation of 12 spaces but found 6 indent 727:1 error Expected indentation of 8 spaces but found 4 indent 728:1 error Expected indentation of 8 spaces but found 4 indent 729:1 error Expected indentation of 12 spaces but found 6 indent 730:1 error Expected indentation of 16 spaces but found 8 indent 731:1 error Expected indentation of 20 spaces but found 10 indent 732:1 error Expected indentation of 20 spaces but found 10 indent 733:1 error Expected indentation of 16 spaces but found 8 indent 734:1 error Expected indentation of 16 spaces but found 8 indent 735:1 error Expected indentation of 20 spaces but found 10 indent 736:1 error Expected indentation of 20 spaces but found 10 indent 737:1 error Expected indentation of 20 spaces but found 10 indent 738:1 error Expected indentation of 20 spaces but found 10 indent 739:1 error Expected indentation of 24 spaces but found 12 indent 740:1 error Expected indentation of 24 spaces but found 12 indent 741:1 error Expected indentation of 24 spaces but found 12 indent 742:1 error Expected indentation of 24 spaces but found 12 indent 743:1 error Expected indentation of 20 spaces but found 12 indent 744:1 error Expected indentation of 24 spaces but found 12 indent 745:1 error Expected indentation of 24 spaces but found 12 indent 746:1 error Expected indentation of 20 spaces but found 10 indent 747:1 error Expected indentation of 16 spaces but found 8 indent 748:1 error Expected indentation of 12 spaces but found 6 indent 749:1 error Expected indentation of 8 spaces but found 4 indent 750:1 error Expected indentation of 4 spaces but found 2 indent 754:1 error Expected indentation of 4 spaces but found 2 indent 755:1 error Expected indentation of 4 spaces but found 2 indent 756:1 error Expected indentation of 4 spaces but found 2 indent 757:1 error Expected indentation of 4 spaces but found 2 indent 758:1 error Expected indentation of 4 spaces but found 2 indent 759:1 error Expected indentation of 4 spaces but found 2 indent 760:1 error Expected indentation of 4 spaces but found 2 indent 761:1 error Expected indentation of 4 spaces but found 2 indent 762:1 error Expected indentation of 4 spaces but found 2 indent 763:1 error Expected indentation of 4 spaces but found 2 indent 764:1 error Expected indentation of 4 spaces but found 2 indent 765:1 error Expected indentation of 4 spaces but found 2 indent 766:1 error Expected indentation of 4 spaces but found 2 indent 767:1 error Expected indentation of 4 spaces but found 2 indent 768:1 error Expected indentation of 4 spaces but found 2 indent 769:1 error Expected indentation of 4 spaces but found 2 indent 770:1 error Expected indentation of 4 spaces but found 2 indent 771:1 error Expected indentation of 4 spaces but found 2 indent 772:1 error Expected indentation of 4 spaces but found 2 indent 773:1 error Expected indentation of 4 spaces but found 2 indent 777:1 error Expected indentation of 4 spaces but found 2 indent 778:1 error Expected indentation of 4 spaces but found 2 indent 779:1 error Expected indentation of 4 spaces but found 2 indent 780:1 error Expected indentation of 4 spaces but found 2 indent 781:1 error Expected indentation of 4 spaces but found 2 indent 782:1 error Expected indentation of 4 spaces but found 2 indent 783:1 error Expected indentation of 4 spaces but found 2 indent 784:1 error Expected indentation of 4 spaces but found 2 indent 785:1 error Expected indentation of 4 spaces but found 2 indent 786:1 error Expected indentation of 4 spaces but found 2 indent 787:1 error Expected indentation of 4 spaces but found 2 indent 788:1 error Expected indentation of 4 spaces but found 2 indent 789:1 error Expected indentation of 4 spaces but found 2 indent 790:1 error Expected indentation of 4 spaces but found 2 indent 791:1 error Expected indentation of 4 spaces but found 2 indent 792:1 error Expected indentation of 4 spaces but found 2 indent 793:1 error Expected indentation of 4 spaces but found 2 indent 794:1 error Expected indentation of 4 spaces but found 2 indent 795:1 error Expected indentation of 8 spaces but found 4 indent 795:5 error Unexpected console statement no-console 796:1 error Expected indentation of 4 spaces but found 2 indent 797:1 error Expected indentation of 4 spaces but found 2 indent 798:1 error Expected indentation of 8 spaces but found 4 indent 798:5 error Unexpected console statement no-console 799:1 error Expected indentation of 4 spaces but found 2 indent 800:1 error Expected indentation of 4 spaces but found 2 indent 801:1 error Expected indentation of 8 spaces but found 4 indent 801:5 error Unexpected console statement no-console 802:1 error Expected indentation of 4 spaces but found 2 indent 810:1 error Expected indentation of 4 spaces but found 2 indent 811:1 error Expected indentation of 8 spaces but found 4 indent 812:1 error Expected indentation of 8 spaces but found 4 indent 813:1 error Expected indentation of 4 spaces but found 2 indent 815:1 error Expected indentation of 4 spaces but found 2 indent 816:1 error Expected indentation of 8 spaces but found 4 indent 817:1 error Expected indentation of 4 spaces but found 2 indent 819:1 error Expected indentation of 4 spaces but found 2 indent 820:1 error Expected indentation of 8 spaces but found 4 indent 821:1 error Expected indentation of 8 spaces but found 4 indent 822:1 error Expected indentation of 8 spaces but found 4 indent 824:1 error Expected indentation of 8 spaces but found 4 indent 825:1 error Expected indentation of 8 spaces but found 4 indent 826:1 error Expected indentation of 12 spaces but found 6 indent 827:1 error Expected indentation of 8 spaces but found 4 indent 829:1 error Expected indentation of 8 spaces but found 4 indent 830:1 error Expected indentation of 12 spaces but found 6 indent 831:1 error Expected indentation of 16 spaces but found 8 indent 832:1 error Expected indentation of 20 spaces but found 10 indent 833:1 error Expected indentation of 20 spaces but found 10 indent 834:1 error Expected indentation of 16 spaces but found 8 indent 835:1 error Expected indentation of 16 spaces but found 8 indent 836:1 error Expected indentation of 20 spaces but found 10 indent 837:1 error Expected indentation of 24 spaces but found 12 indent 838:1 error Expected indentation of 24 spaces but found 12 indent 839:1 error Expected indentation of 24 spaces but found 12 indent 840:1 error Expected indentation of 24 spaces but found 12 indent 841:1 error Expected indentation of 24 spaces but found 12 indent 842:1 error Expected indentation of 24 spaces but found 12 indent 843:1 error Expected indentation of 24 spaces but found 12 indent 844:1 error Expected indentation of 24 spaces but found 12 indent 845:1 error Expected indentation of 24 spaces but found 12 indent 846:1 error Expected indentation of 20 spaces but found 10 indent 847:1 error Expected indentation of 20 spaces but found 10 indent 848:1 error Expected indentation of 16 spaces but found 8 indent 849:1 error Expected indentation of 12 spaces but found 6 indent 850:1 error Expected indentation of 8 spaces but found 4 indent 851:1 error Expected indentation of 4 spaces but found 2 indent 855:1 error Expected indentation of 4 spaces but found 2 indent 856:1 error Expected indentation of 4 spaces but found 2 indent 857:1 error Expected indentation of 4 spaces but found 2 indent 858:1 error Expected indentation of 4 spaces but found 2 indent 859:1 error Expected indentation of 4 spaces but found 2 indent 860:1 error Expected indentation of 4 spaces but found 2 indent 861:1 error Expected indentation of 4 spaces but found 2 indent 862:1 error Expected indentation of 4 spaces but found 2 indent 863:1 error Expected indentation of 4 spaces but found 2 indent 867:1 error Expected indentation of 4 spaces but found 2 indent 868:1 error Expected indentation of 4 spaces but found 2 indent 869:1 error Expected indentation of 4 spaces but found 2 indent 870:1 error Expected indentation of 4 spaces but found 2 indent 871:1 error Expected indentation of 4 spaces but found 2 indent 872:1 error Expected indentation of 4 spaces but found 2 indent 873:1 error Expected indentation of 4 spaces but found 2 indent 874:1 error Expected indentation of 4 spaces but found 2 indent 875:1 error Expected indentation of 4 spaces but found 2 indent 876:1 error Expected indentation of 8 spaces but found 4 indent 876:5 error Unexpected console statement no-console 877:1 error Expected indentation of 4 spaces but found 2 indent 885:1 error Expected indentation of 4 spaces but found 2 indent 886:1 error Expected indentation of 8 spaces but found 4 indent 887:1 error Expected indentation of 8 spaces but found 4 indent 888:1 error Expected indentation of 8 spaces but found 4 indent 889:1 error Expected indentation of 4 spaces but found 2 indent 891:1 error Expected indentation of 4 spaces but found 2 indent 892:1 error Expected indentation of 8 spaces but found 4 indent 893:1 error Expected indentation of 4 spaces but found 2 indent 895:1 error Expected indentation of 4 spaces but found 2 indent 896:1 error Expected indentation of 8 spaces but found 4 indent 897:1 error Expected indentation of 4 spaces but found 2 indent 899:1 error Expected indentation of 4 spaces but found 2 indent 900:1 error Expected indentation of 8 spaces but found 4 indent 901:1 error Expected indentation of 8 spaces but found 4 indent 902:1 error Expected indentation of 8 spaces but found 4 indent 903:1 error Expected indentation of 8 spaces but found 4 indent 904:1 error Expected indentation of 8 spaces but found 4 indent 906:1 error Expected indentation of 8 spaces but found 4 indent 907:1 error Expected indentation of 8 spaces but found 4 indent 908:1 error Expected indentation of 12 spaces but found 6 indent 909:1 error Expected indentation of 8 spaces but found 4 indent 911:1 error Expected indentation of 8 spaces but found 4 indent 912:1 error Expected indentation of 8 spaces but found 4 indent 913:1 error Expected indentation of 12 spaces but found 6 indent 914:1 error Expected indentation of 12 spaces but found 6 indent 915:1 error Expected indentation of 8 spaces but found 4 indent 917:1 error Expected indentation of 8 spaces but found 4 indent 918:1 error Expected indentation of 12 spaces but found 6 indent 919:1 error Expected indentation of 16 spaces but found 8 indent 920:1 error Expected indentation of 20 spaces but found 10 indent 921:1 error Expected indentation of 20 spaces but found 10 indent 922:1 error Expected indentation of 16 spaces but found 8 indent 923:1 error Expected indentation of 16 spaces but found 8 indent 924:1 error Expected indentation of 20 spaces but found 10 indent 925:1 error Expected indentation of 24 spaces but found 12 indent 926:1 error Expected indentation of 24 spaces but found 12 indent 927:1 error Expected indentation of 24 spaces but found 12 indent 928:1 error Expected indentation of 24 spaces but found 12 indent 929:1 error Expected indentation of 24 spaces but found 12 indent 930:1 error Expected indentation of 24 spaces but found 12 indent 931:1 error Expected indentation of 24 spaces but found 12 indent 932:1 error Expected indentation of 24 spaces but found 12 indent 933:1 error Expected indentation of 24 spaces but found 12 indent 934:1 error Expected indentation of 20 spaces but found 10 indent 935:1 error Expected indentation of 20 spaces but found 10 indent 936:1 error Expected indentation of 16 spaces but found 8 indent 937:1 error Expected indentation of 12 spaces but found 6 indent 938:1 error Expected indentation of 8 spaces but found 4 indent 939:1 error Expected indentation of 4 spaces but found 2 indent 943:1 error Expected indentation of 4 spaces but found 2 indent 944:1 error Expected indentation of 4 spaces but found 2 indent 945:1 error Expected indentation of 4 spaces but found 2 indent 946:1 error Expected indentation of 4 spaces but found 2 indent 947:1 error Expected indentation of 4 spaces but found 2 indent 948:1 error Expected indentation of 4 spaces but found 2 indent 949:1 error Expected indentation of 4 spaces but found 2 indent 950:1 error Expected indentation of 4 spaces but found 2 indent 951:1 error Expected indentation of 4 spaces but found 2 indent 955:1 error Expected indentation of 4 spaces but found 2 indent 956:1 error Expected indentation of 4 spaces but found 2 indent 957:1 error Expected indentation of 4 spaces but found 2 indent 958:1 error Expected indentation of 4 spaces but found 2 indent 959:1 error Expected indentation of 4 spaces but found 2 indent 960:1 error Expected indentation of 4 spaces but found 2 indent 961:1 error Expected indentation of 4 spaces but found 2 indent 962:1 error Expected indentation of 4 spaces but found 2 indent 963:1 error Expected indentation of 8 spaces but found 4 indent 963:5 error Unexpected console statement no-console 964:1 error Expected indentation of 4 spaces but found 2 indent 965:1 error Expected indentation of 4 spaces but found 2 indent 966:1 error Expected indentation of 4 spaces but found 2 indent 974:1 error Expected indentation of 4 spaces but found 2 indent 975:1 error Expected indentation of 8 spaces but found 4 indent 976:1 error Expected indentation of 8 spaces but found 4 indent 977:1 error Expected indentation of 4 spaces but found 2 indent 979:1 error Expected indentation of 4 spaces but found 2 indent 980:1 error Expected indentation of 8 spaces but found 4 indent 980:10 error 'Modernizr' is not defined no-undef 981:1 error Expected indentation of 12 spaces but found 6 indent 982:1 error Expected indentation of 12 spaces but found 6 indent 983:1 error Expected indentation of 12 spaces but found 6 indent 984:1 error Expected indentation of 12 spaces but found 6 indent 985:1 error Expected indentation of 16 spaces but found 8 indent 986:1 error Expected indentation of 12 spaces but found 6 indent 987:1 error Expected indentation of 12 spaces but found 6 indent 988:1 error Expected indentation of 16 spaces but found 8 indent 989:1 error Expected indentation of 12 spaces but found 6 indent 990:1 error Expected indentation of 12 spaces but found 6 indent 990:25 error '$' is not defined no-undef 991:1 error Expected indentation of 12 spaces but found 6 indent 992:1 error Expected indentation of 16 spaces but found 8 indent 993:1 error Expected indentation of 16 spaces but found 8 indent 994:1 error Expected indentation of 16 spaces but found 8 indent 995:1 error Expected indentation of 16 spaces but found 8 indent 996:1 error Expected indentation of 16 spaces but found 8 indent 997:1 error Expected indentation of 16 spaces but found 8 indent 998:1 error Expected indentation of 20 spaces but found 10 indent 999:1 error Expected indentation of 20 spaces but found 10 indent 999:11 error '$' is not defined no-undef 1000:1 error Expected indentation of 16 spaces but found 8 indent 1001:1 error Expected indentation of 16 spaces but found 8 indent 1001:30 error 'picker' is defined but never used no-unused-vars 1002:1 error Expected indentation of 20 spaces but found 10 indent 1003:1 error Expected indentation of 16 spaces but found 8 indent 1004:1 error Expected indentation of 12 spaces but found 6 indent 1005:1 error Expected indentation of 12 spaces but found 6 indent 1006:1 error Expected indentation of 12 spaces but found 6 indent 1007:1 error Expected indentation of 16 spaces but found 8 indent 1008:1 error Expected indentation of 12 spaces but found 6 indent 1009:1 error Expected indentation of 8 spaces but found 4 indent 1010:1 error Expected indentation of 4 spaces but found 2 indent 1012:1 error Expected indentation of 4 spaces but found 2 indent 1013:1 error Expected indentation of 8 spaces but found 4 indent 1014:1 error Expected indentation of 4 spaces but found 2 indent 1016:1 error Expected indentation of 4 spaces but found 2 indent 1017:1 error Expected indentation of 8 spaces but found 4 indent 1018:1 error Expected indentation of 8 spaces but found 4 indent 1019:1 error Expected indentation of 8 spaces but found 4 indent 1021:1 error Expected indentation of 8 spaces but found 4 indent 1022:1 error Expected indentation of 8 spaces but found 4 indent 1023:1 error Expected indentation of 12 spaces but found 6 indent 1024:1 error Expected indentation of 8 spaces but found 4 indent 1026:1 error Expected indentation of 8 spaces but found 4 indent 1027:1 error Expected indentation of 8 spaces but found 4 indent 1028:1 error Expected indentation of 8 spaces but found 4 indent 1029:1 error Expected indentation of 8 spaces but found 4 indent 1030:1 error Expected indentation of 12 spaces but found 6 indent 1031:1 error Expected indentation of 8 spaces but found 4 indent 1032:1 error Expected indentation of 8 spaces but found 4 indent 1033:1 error Expected indentation of 12 spaces but found 6 indent 1034:1 error Expected indentation of 8 spaces but found 4 indent 1036:1 error Expected indentation of 8 spaces but found 4 indent 1037:1 error Expected indentation of 8 spaces but found 4 indent 1038:1 error Expected indentation of 8 spaces but found 4 indent 1039:1 error Expected indentation of 8 spaces but found 4 indent 1040:1 error Expected indentation of 8 spaces but found 4 indent 1041:1 error Expected indentation of 8 spaces but found 4 indent 1042:1 error Expected indentation of 12 spaces but found 6 indent 1043:1 error Expected indentation of 12 spaces but found 6 indent 1044:1 error Expected indentation of 12 spaces but found 6 indent 1045:1 error Expected indentation of 8 spaces but found 4 indent 1047:1 error Expected indentation of 8 spaces but found 4 indent 1048:1 error Expected indentation of 12 spaces but found 6 indent 1049:1 error Expected indentation of 16 spaces but found 8 indent 1050:1 error Expected indentation of 20 spaces but found 10 indent 1051:1 error Expected indentation of 20 spaces but found 10 indent 1052:1 error Expected indentation of 16 spaces but found 8 indent 1053:1 error Expected indentation of 16 spaces but found 8 indent 1054:1 error Expected indentation of 20 spaces but found 10 indent 1055:1 error Expected indentation of 24 spaces but found 12 indent 1056:1 error Expected indentation of 24 spaces but found 12 indent 1057:1 error Expected indentation of 24 spaces but found 12 indent 1058:1 error Expected indentation of 24 spaces but found 12 indent 1059:1 error Expected indentation of 24 spaces but found 12 indent 1060:1 error Expected indentation of 24 spaces but found 12 indent 1061:1 error Expected indentation of 24 spaces but found 12 indent 1062:1 error Expected indentation of 24 spaces but found 12 indent 1063:1 error Expected indentation of 24 spaces but found 12 indent 1064:1 error Expected indentation of 24 spaces but found 12 indent 1065:1 error Expected indentation of 20 spaces but found 10 indent 1066:1 error Expected indentation of 16 spaces but found 8 indent 1067:1 error Expected indentation of 12 spaces but found 6 indent 1068:1 error Expected indentation of 8 spaces but found 4 indent 1069:1 error Expected indentation of 4 spaces but found 2 indent 1073:1 error Expected indentation of 4 spaces but found 2 indent 1074:1 error Expected indentation of 4 spaces but found 2 indent 1075:1 error Expected indentation of 4 spaces but found 2 indent 1076:1 error Expected indentation of 4 spaces but found 2 indent 1077:1 error Expected indentation of 4 spaces but found 2 indent 1078:1 error Expected indentation of 4 spaces but found 2 indent 1079:1 error Expected indentation of 4 spaces but found 2 indent 1080:1 error Expected indentation of 4 spaces but found 2 indent 1081:1 error Expected indentation of 4 spaces but found 2 indent 1082:1 error Expected indentation of 4 spaces but found 2 indent 1086:1 error Expected indentation of 4 spaces but found 2 indent 1087:1 error Expected indentation of 4 spaces but found 2 indent 1088:1 error Expected indentation of 4 spaces but found 2 indent 1089:1 error Expected indentation of 4 spaces but found 2 indent 1090:1 error Expected indentation of 4 spaces but found 2 indent 1091:1 error Expected indentation of 4 spaces but found 2 indent 1092:1 error Expected indentation of 4 spaces but found 2 indent 1093:1 error Expected indentation of 4 spaces but found 2 indent 1094:1 error Expected indentation of 4 spaces but found 2 indent 1095:1 error Expected indentation of 4 spaces but found 2 indent 1096:1 error Expected indentation of 8 spaces but found 4 indent 1096:5 error Unexpected console statement no-console 1097:1 error Expected indentation of 4 spaces but found 2 indent 1105:1 error Expected indentation of 4 spaces but found 2 indent 1106:1 error Expected indentation of 8 spaces but found 4 indent 1108:1 error Expected indentation of 8 spaces but found 4 indent 1109:1 error Expected indentation of 4 spaces but found 2 indent 1111:1 error Expected indentation of 4 spaces but found 2 indent 1112:1 error Expected indentation of 8 spaces but found 4 indent 1113:1 error Expected indentation of 4 spaces but found 2 indent 1115:1 error Expected indentation of 4 spaces but found 2 indent 1116:1 error Expected indentation of 8 spaces but found 4 indent 1117:1 error Expected indentation of 8 spaces but found 4 indent 1118:1 error Expected indentation of 8 spaces but found 4 indent 1120:1 error Expected indentation of 8 spaces but found 4 indent 1121:1 error Expected indentation of 8 spaces but found 4 indent 1122:1 error Expected indentation of 12 spaces but found 6 indent 1123:1 error Expected indentation of 8 spaces but found 4 indent 1125:1 error Expected indentation of 8 spaces but found 4 indent 1126:1 error Expected indentation of 12 spaces but found 6 indent 1127:1 error Expected indentation of 16 spaces but found 8 indent 1128:1 error Expected indentation of 20 spaces but found 10 indent 1129:1 error Expected indentation of 20 spaces but found 10 indent 1130:1 error Expected indentation of 16 spaces but found 8 indent 1131:1 error Expected indentation of 16 spaces but found 8 indent 1132:1 error Expected indentation of 20 spaces but found 10 indent 1133:1 error Expected indentation of 24 spaces but found 12 indent 1134:1 error Expected indentation of 24 spaces but found 12 indent 1135:1 error Expected indentation of 24 spaces but found 12 indent 1136:1 error Expected indentation of 24 spaces but found 12 indent 1137:1 error Expected indentation of 24 spaces but found 12 indent 1138:1 error Expected indentation of 24 spaces but found 12 indent 1139:1 error Expected indentation of 24 spaces but found 12 indent 1140:1 error Expected indentation of 24 spaces but found 12 indent 1141:1 error Expected indentation of 24 spaces but found 12 indent 1142:1 error Expected indentation of 24 spaces but found 12 indent 1143:1 error Expected indentation of 20 spaces but found 10 indent 1144:1 error Expected indentation of 16 spaces but found 8 indent 1145:1 error Expected indentation of 12 spaces but found 6 indent 1146:1 error Expected indentation of 8 spaces but found 4 indent 1147:1 error Expected indentation of 4 spaces but found 2 indent 1151:1 error Expected indentation of 4 spaces but found 2 indent 1152:1 error Expected indentation of 4 spaces but found 2 indent 1153:1 error Expected indentation of 4 spaces but found 2 indent 1154:1 error Expected indentation of 4 spaces but found 2 indent 1155:1 error Expected indentation of 4 spaces but found 2 indent 1156:1 error Expected indentation of 4 spaces but found 2 indent 1157:1 error Expected indentation of 4 spaces but found 2 indent 1161:1 error Expected indentation of 4 spaces but found 2 indent 1162:1 error Expected indentation of 4 spaces but found 2 indent 1163:1 error Expected indentation of 4 spaces but found 2 indent 1164:1 error Expected indentation of 4 spaces but found 2 indent 1165:1 error Expected indentation of 4 spaces but found 2 indent 1166:1 error Expected indentation of 4 spaces but found 2 indent 1167:1 error Expected indentation of 4 spaces but found 2 indent 1168:1 error Expected indentation of 8 spaces but found 4 indent 1168:5 error Unexpected console statement no-console 1169:1 error Expected indentation of 4 spaces but found 2 indent 1177:1 error Expected indentation of 4 spaces but found 2 indent 1178:1 error Expected indentation of 8 spaces but found 4 indent 1179:1 error Expected indentation of 8 spaces but found 4 indent 1180:1 error Expected indentation of 4 spaces but found 2 indent 1182:1 error Expected indentation of 4 spaces but found 2 indent 1183:1 error Expected indentation of 8 spaces but found 4 indent 1184:1 error Expected indentation of 4 spaces but found 2 indent 1186:1 error Expected indentation of 4 spaces but found 2 indent 1187:1 error Expected indentation of 8 spaces but found 4 indent 1188:1 error Expected indentation of 8 spaces but found 4 indent 1189:1 error Expected indentation of 8 spaces but found 4 indent 1191:1 error Expected indentation of 8 spaces but found 4 indent 1192:1 error Expected indentation of 12 spaces but found 6 indent 1193:1 error Expected indentation of 16 spaces but found 8 indent 1194:1 error Expected indentation of 20 spaces but found 10 indent 1195:1 error Expected indentation of 20 spaces but found 10 indent 1196:1 error Expected indentation of 16 spaces but found 8 indent 1197:1 error Expected indentation of 16 spaces but found 8 indent 1198:1 error Expected indentation of 20 spaces but found 10 indent 1199:1 error Expected indentation of 24 spaces but found 12 indent 1200:1 error Expected indentation of 24 spaces but found 12 indent 1201:1 error Expected indentation of 24 spaces but found 12 indent 1202:1 error Expected indentation of 24 spaces but found 12 indent 1203:1 error Expected indentation of 24 spaces but found 12 indent 1204:1 error Expected indentation of 24 spaces but found 12 indent 1205:1 error Expected indentation of 24 spaces but found 12 indent 1206:1 error Expected indentation of 24 spaces but found 12 indent 1207:1 error Expected indentation of 24 spaces but found 12 indent 1208:1 error Expected indentation of 24 spaces but found 12 indent 1209:1 error Expected indentation of 20 spaces but found 10 indent 1210:1 error Expected indentation of 16 spaces but found 8 indent 1211:1 error Expected indentation of 12 spaces but found 6 indent 1212:1 error Expected indentation of 8 spaces but found 4 indent 1213:1 error Expected indentation of 4 spaces but found 2 indent 1217:1 error Expected indentation of 4 spaces but found 2 indent 1218:1 error Expected indentation of 4 spaces but found 2 indent 1219:1 error Expected indentation of 4 spaces but found 2 indent 1220:1 error Expected indentation of 4 spaces but found 2 indent 1221:1 error Expected indentation of 4 spaces but found 2 indent 1222:1 error Expected indentation of 4 spaces but found 2 indent 1223:1 error Expected indentation of 4 spaces but found 2 indent 1224:1 error Expected indentation of 4 spaces but found 2 indent 1225:1 error Expected indentation of 4 spaces but found 2 indent 1229:1 error Expected indentation of 4 spaces but found 2 indent 1230:1 error Expected indentation of 4 spaces but found 2 indent 1231:1 error Expected indentation of 4 spaces but found 2 indent 1232:1 error Expected indentation of 4 spaces but found 2 indent 1233:1 error Expected indentation of 4 spaces but found 2 indent 1234:1 error Expected indentation of 4 spaces but found 2 indent 1235:1 error Expected indentation of 4 spaces but found 2 indent 1236:1 error Expected indentation of 4 spaces but found 2 indent 1237:1 error Expected indentation of 4 spaces but found 2 indent 1238:1 error Expected indentation of 8 spaces but found 4 indent 1238:5 error Unexpected console statement no-console 1239:1 error Expected indentation of 4 spaces but found 2 indent 1247:1 error Expected indentation of 4 spaces but found 2 indent 1248:1 error Expected indentation of 8 spaces but found 4 indent 1249:1 error Expected indentation of 8 spaces but found 4 indent 1250:1 error Expected indentation of 4 spaces but found 2 indent 1252:1 error Expected indentation of 4 spaces but found 2 indent 1254:1 error Expected indentation of 8 spaces but found 4 indent 1255:1 error Expected indentation of 8 spaces but found 4 indent 1256:1 error Expected indentation of 4 spaces but found 2 indent 1258:1 error Expected indentation of 4 spaces but found 2 indent 1259:1 error Expected indentation of 8 spaces but found 4 indent 1260:1 error Expected indentation of 8 spaces but found 4 indent 1261:1 error Expected indentation of 8 spaces but found 4 indent 1262:1 error Expected indentation of 8 spaces but found 4 indent 1263:1 error Expected indentation of 8 spaces but found 4 indent 1265:1 error Expected indentation of 8 spaces but found 4 indent 1266:1 error Expected indentation of 8 spaces but found 4 indent 1267:1 error Expected indentation of 12 spaces but found 6 indent 1268:1 error Expected indentation of 8 spaces but found 4 indent 1270:1 error Expected indentation of 8 spaces but found 4 indent 1271:1 error Expected indentation of 12 spaces but found 6 indent 1272:1 error Expected indentation of 12 spaces but found 6 indent 1273:1 error Expected indentation of 12 spaces but found 6 indent 1274:1 error Expected indentation of 12 spaces but found 6 indent 1275:1 error Expected indentation of 8 spaces but found 4 indent 1277:1 error Expected indentation of 8 spaces but found 4 indent 1278:1 error Expected indentation of 12 spaces but found 6 indent 1279:1 error Expected indentation of 12 spaces but found 6 indent 1280:1 error Expected indentation of 12 spaces but found 6 indent 1281:1 error Expected indentation of 8 spaces but found 4 indent 1283:1 error Expected indentation of 8 spaces but found 4 indent 1284:1 error Expected indentation of 8 spaces but found 4 indent 1285:1 error Expected indentation of 12 spaces but found 6 indent 1286:1 error Expected indentation of 12 spaces but found 6 indent 1287:1 error Expected indentation of 8 spaces but found 4 indent 1289:1 error Expected indentation of 8 spaces but found 4 indent 1290:1 error Expected indentation of 8 spaces but found 4 indent 1291:1 error Expected indentation of 8 spaces but found 4 indent 1292:1 error Expected indentation of 8 spaces but found 4 indent 1293:1 error Expected indentation of 8 spaces but found 4 indent 1294:1 error Expected indentation of 12 spaces but found 6 indent 1295:1 error Expected indentation of 8 spaces but found 4 indent 1297:1 error Expected indentation of 8 spaces but found 4 indent 1298:1 error Expected indentation of 12 spaces but found 6 indent 1299:1 error Expected indentation of 12 spaces but found 6 indent 1300:1 error Expected indentation of 12 spaces but found 6 indent 1301:1 error Expected indentation of 16 spaces but found 8 indent 1302:1 error Expected indentation of 20 spaces but found 10 indent 1303:1 error Expected indentation of 24 spaces but found 12 indent 1304:1 error Expected indentation of 20 spaces but found 10 indent 1305:1 error Expected indentation of 20 spaces but found 10 indent 1306:1 error Expected indentation of 24 spaces but found 12 indent 1307:1 error Expected indentation of 28 spaces but found 14 indent 1308:1 error Expected indentation of 24 spaces but found 12 indent 1309:1 error Expected indentation of 20 spaces but found 10 indent 1310:1 error Expected indentation of 16 spaces but found 8 indent 1311:1 error Expected indentation of 12 spaces but found 6 indent 1312:1 error Expected indentation of 8 spaces but found 4 indent 1314:1 error Expected indentation of 8 spaces but found 4 indent 1315:1 error Expected indentation of 12 spaces but found 6 indent 1316:1 error Expected indentation of 16 spaces but found 8 indent 1317:1 error Expected indentation of 20 spaces but found 10 indent 1318:1 error Expected indentation of 20 spaces but found 10 indent 1319:1 error Expected indentation of 16 spaces but found 8 indent 1320:1 error Expected indentation of 16 spaces but found 8 indent 1321:1 error Expected indentation of 20 spaces but found 10 indent 1322:1 error Expected indentation of 24 spaces but found 12 indent 1323:1 error Expected indentation of 28 spaces but found 17 indent 1324:1 error Expected indentation of 28 spaces but found 14 indent 1325:1 error Expected indentation of 32 spaces but found 16 indent 1326:1 error Expected indentation of 28 spaces but found 14 indent 1327:1 error Expected indentation of 28 spaces but found 14 indent 1328:1 error Expected indentation of 24 spaces but found 12 indent 1329:1 error Expected indentation of 24 spaces but found 12 indent 1330:1 error Expected indentation of 28 spaces but found 14 indent 1331:1 error Expected indentation of 32 spaces but found 16 indent 1332:1 error Expected indentation of 32 spaces but found 16 indent 1333:1 error Expected indentation of 36 spaces but found 18 indent 1334:1 error Expected indentation of 36 spaces but found 18 indent 1335:1 error Expected indentation of 36 spaces but found 18 indent 1336:1 error Expected indentation of 36 spaces but found 18 indent 1337:1 error Expected indentation of 36 spaces but found 18 indent 1338:1 error Expected indentation of 32 spaces but found 16 indent 1339:1 error Expected indentation of 28 spaces but found 14 indent 1340:1 error Expected indentation of 24 spaces but found 12 indent 1341:1 error Expected indentation of 20 spaces but found 10 indent 1342:1 error Expected indentation of 20 spaces but found 10 indent 1343:1 error Expected indentation of 16 spaces but found 8 indent 1344:1 error Expected indentation of 12 spaces but found 6 indent 1345:1 error Expected indentation of 8 spaces but found 4 indent 1346:1 error Expected indentation of 4 spaces but found 2 indent 1350:1 error Expected indentation of 4 spaces but found 2 indent 1351:1 error Expected indentation of 4 spaces but found 2 indent 1352:1 error Expected indentation of 4 spaces but found 2 indent 1353:1 error Expected indentation of 8 spaces but found 4 indent 1354:1 error Expected indentation of 8 spaces but found 4 indent 1355:1 error Expected indentation of 4 spaces but found 2 indent 1356:1 error Expected indentation of 4 spaces but found 2 indent 1357:1 error Expected indentation of 4 spaces but found 2 indent 1358:1 error Expected indentation of 4 spaces but found 2 indent 1359:1 error Expected indentation of 4 spaces but found 2 indent 1360:1 error Expected indentation of 4 spaces but found 2 indent 1361:1 error Expected indentation of 4 spaces but found 2 indent 1365:1 error Expected indentation of 4 spaces but found 2 indent 1366:1 error Expected indentation of 4 spaces but found 2 indent 1367:1 error Expected indentation of 4 spaces but found 2 indent 1368:1 error Expected indentation of 4 spaces but found 2 indent 1369:1 error Expected indentation of 4 spaces but found 2 indent 1370:1 error Expected indentation of 4 spaces but found 2 indent 1371:1 error Expected indentation of 4 spaces but found 2 indent 1372:1 error Expected indentation of 4 spaces but found 2 indent 1373:1 error Expected indentation of 4 spaces but found 2 indent 1374:1 error Expected indentation of 8 spaces but found 4 indent 1374:5 error Unexpected console statement no-console 1375:1 error Expected indentation of 4 spaces but found 2 indent 1394:1 error Expected indentation of 4 spaces but found 2 indent 1395:1 error Expected indentation of 8 spaces but found 4 indent 1396:1 error Expected indentation of 4 spaces but found 2 indent 1397:1 error Expected indentation of 4 spaces but found 2 indent 1398:1 error Expected indentation of 8 spaces but found 4 indent 1399:1 error Expected indentation of 12 spaces but found 6 indent 1400:1 error Expected indentation of 16 spaces but found 8 indent 1401:1 error Expected indentation of 20 spaces but found 10 indent 1402:1 error Expected indentation of 16 spaces but found 8 indent 1403:1 error Expected indentation of 16 spaces but found 8 indent 1404:1 error Expected indentation of 20 spaces but found 10 indent 1405:1 error Expected indentation of 16 spaces but found 8 indent 1406:1 error Expected indentation of 12 spaces but found 6 indent 1407:1 error Expected indentation of 8 spaces but found 4 indent 1408:1 error Expected indentation of 4 spaces but found 2 indent 1412:1 error Expected indentation of 4 spaces but found 2 indent 1413:1 error Expected indentation of 4 spaces but found 2 indent 1414:1 error Expected indentation of 8 spaces but found 4 indent 1415:1 error Expected indentation of 8 spaces but found 4 indent 1416:1 error Expected indentation of 4 spaces but found 2 indent 1420:1 error Expected indentation of 4 spaces but found 2 indent 1421:1 error Expected indentation of 4 spaces but found 2 indent 1429:1 error Expected indentation of 4 spaces but found 2 indent 1430:1 error Expected indentation of 8 spaces but found 4 indent 1431:1 error Expected indentation of 4 spaces but found 2 indent 1433:1 error Expected indentation of 4 spaces but found 2 indent 1434:1 error Expected indentation of 8 spaces but found 4 indent 1435:1 error Expected indentation of 12 spaces but found 6 indent 1436:1 error Expected indentation of 16 spaces but found 8 indent 1437:1 error Expected indentation of 20 spaces but found 10 indent 1438:1 error Expected indentation of 16 spaces but found 8 indent 1439:1 error Expected indentation of 16 spaces but found 8 indent 1440:1 error Expected indentation of 20 spaces but found 10 indent 1441:1 error Expected indentation of 16 spaces but found 8 indent 1442:1 error Expected indentation of 12 spaces but found 6 indent 1443:1 error Expected indentation of 8 spaces but found 4 indent 1444:1 error Expected indentation of 4 spaces but found 2 indent 1448:1 error Expected indentation of 4 spaces but found 2 indent 1449:1 error Expected indentation of 4 spaces but found 2 indent 1450:1 error Expected indentation of 8 spaces but found 4 indent 1451:1 error Expected indentation of 8 spaces but found 4 indent 1452:1 error Expected indentation of 4 spaces but found 2 indent 1453:1 error Expected indentation of 4 spaces but found 2 indent 1457:1 error Expected indentation of 4 spaces but found 2 indent 1458:1 error Expected indentation of 4 spaces but found 2 indent 1459:1 error Expected indentation of 4 spaces but found 2 indent 1467:1 error Expected indentation of 4 spaces but found 2 indent 1468:1 error Expected indentation of 8 spaces but found 4 indent 1469:1 error Expected indentation of 8 spaces but found 4 indent 1470:1 error Expected indentation of 4 spaces but found 2 indent 1472:1 error Expected indentation of 4 spaces but found 2 indent 1473:1 error Expected indentation of 8 spaces but found 4 indent 1474:1 error Expected indentation of 4 spaces but found 2 indent 1476:1 error Expected indentation of 4 spaces but found 2 indent 1477:1 error Expected indentation of 8 spaces but found 4 indent 1478:1 error Expected indentation of 8 spaces but found 4 indent 1479:1 error Expected indentation of 8 spaces but found 4 indent 1480:1 error Expected indentation of 8 spaces but found 4 indent 1481:1 error Expected indentation of 8 spaces but found 4 indent 1482:1 error Expected indentation of 8 spaces but found 4 indent 1482:9 error 'label' is assigned a value but never used no-unused-vars 1484:1 error Expected indentation of 8 spaces but found 4 indent 1485:1 error Expected indentation of 8 spaces but found 4 indent 1486:1 error Expected indentation of 12 spaces but found 6 indent 1487:1 error Expected indentation of 8 spaces but found 4 indent 1489:1 error Expected indentation of 8 spaces but found 4 indent 1490:1 error Expected indentation of 8 spaces but found 4 indent 1491:1 error Expected indentation of 12 spaces but found 6 indent 1492:1 error Expected indentation of 12 spaces but found 6 indent 1493:1 error Expected indentation of 8 spaces but found 4 indent 1495:1 error Expected indentation of 8 spaces but found 4 indent 1496:1 error Expected indentation of 12 spaces but found 6 indent 1497:1 error Expected indentation of 16 spaces but found 8 indent 1498:1 error Expected indentation of 20 spaces but found 10 indent 1499:1 error Expected indentation of 24 spaces but found 12 indent 1500:1 error Expected indentation of 24 spaces but found 12 indent 1501:1 error Expected indentation of 24 spaces but found 12 indent 1502:1 error Expected indentation of 24 spaces but found 12 indent 1503:1 error Expected indentation of 24 spaces but found 12 indent 1504:1 error Expected indentation of 24 spaces but found 12 indent 1505:1 error Expected indentation of 24 spaces but found 12 indent 1506:1 error Expected indentation of 20 spaces but found 10 indent 1507:1 error Expected indentation of 20 spaces but found 10 indent 1508:1 error Expected indentation of 20 spaces but found 10 indent 1509:1 error Expected indentation of 20 spaces but found 10 indent 1510:1 error Expected indentation of 16 spaces but found 8 indent 1511:1 error Expected indentation of 12 spaces but found 6 indent 1512:1 error Expected indentation of 8 spaces but found 4 indent 1513:1 error Expected indentation of 4 spaces but found 2 indent 1517:1 error Expected indentation of 4 spaces but found 2 indent 1518:1 error Expected indentation of 4 spaces but found 2 indent 1519:1 error Expected indentation of 4 spaces but found 2 indent 1520:1 error Expected indentation of 4 spaces but found 2 indent 1521:1 error Expected indentation of 4 spaces but found 2 indent 1522:1 error Expected indentation of 4 spaces but found 2 indent 1523:1 error Expected indentation of 4 spaces but found 2 indent 1524:1 error Expected indentation of 4 spaces but found 2 indent 1525:1 error Expected indentation of 4 spaces but found 2 indent 1529:1 error Expected indentation of 4 spaces but found 2 indent 1530:1 error Expected indentation of 4 spaces but found 2 indent 1531:1 error Expected indentation of 4 spaces but found 2 indent 1532:1 error Expected indentation of 4 spaces but found 2 indent 1533:1 error Expected indentation of 4 spaces but found 2 indent 1534:1 error Expected indentation of 4 spaces but found 2 indent 1535:1 error Expected indentation of 8 spaces but found 4 indent 1535:5 error Unexpected console statement no-console 1536:1 error Expected indentation of 4 spaces but found 2 indent 1544:1 error Expected indentation of 4 spaces but found 2 indent 1545:1 error Expected indentation of 8 spaces but found 4 indent 1546:1 error Expected indentation of 8 spaces but found 4 indent 1547:1 error Expected indentation of 4 spaces but found 2 indent 1549:1 error Expected indentation of 4 spaces but found 2 indent 1550:1 error Expected indentation of 8 spaces but found 4 indent 1551:1 error Expected indentation of 4 spaces but found 2 indent 1553:1 error Expected indentation of 4 spaces but found 2 indent 1554:1 error Expected indentation of 8 spaces but found 4 indent 1555:1 error Expected indentation of 12 spaces but found 6 indent 1556:1 error Expected indentation of 16 spaces but found 8 indent 1557:1 error Expected indentation of 20 spaces but found 10 indent 1558:1 error Expected indentation of 24 spaces but found 12 indent 1559:1 error Expected indentation of 24 spaces but found 12 indent 1560:1 error Expected indentation of 24 spaces but found 12 indent 1561:1 error Expected indentation of 24 spaces but found 12 indent 1562:1 error Expected indentation of 20 spaces but found 10 indent 1563:1 error Expected indentation of 24 spaces but found 12 indent 1564:1 error Expected indentation of 20 spaces but found 10 indent 1565:1 error Expected indentation of 16 spaces but found 8 indent 1566:1 error Expected indentation of 12 spaces but found 6 indent 1567:1 error Expected indentation of 8 spaces but found 4 indent 1568:1 error Expected indentation of 4 spaces but found 2 indent 1572:1 error Expected indentation of 4 spaces but found 2 indent 1573:1 error Expected indentation of 4 spaces but found 2 indent 1574:1 error Expected indentation of 4 spaces but found 2 indent 1575:1 error Expected indentation of 4 spaces but found 2 indent 1579:1 error Expected indentation of 4 spaces but found 2 indent 1580:1 error Expected indentation of 4 spaces but found 2 indent 1581:1 error Expected indentation of 4 spaces but found 2 indent 1582:1 error Expected indentation of 4 spaces but found 2 indent 1583:1 error Expected indentation of 4 spaces but found 2 indent 1584:1 error Expected indentation of 8 spaces but found 4 indent 1584:5 error Unexpected console statement no-console 1585:1 error Expected indentation of 4 spaces but found 2 indent 1593:1 error Expected indentation of 0 spaces but found 1 indent 1594:1 error Expected indentation of 4 spaces but found 3 indent 1595:1 error Expected indentation of 8 spaces but found 5 indent 1596:1 error Expected indentation of 12 spaces but found 7 indent 1597:1 error Expected indentation of 16 spaces but found 9 indent 1598:1 error Expected indentation of 16 spaces but found 9 indent 1599:1 error Expected indentation of 12 spaces but found 7 indent 1600:1 error Expected indentation of 16 spaces but found 9 indent 1601:1 error Expected indentation of 12 spaces but found 7 indent 1602:1 error Expected indentation of 8 spaces but found 5 indent 1603:1 error Expected indentation of 4 spaces but found 3 indent 1604:1 error Expected indentation of 0 spaces but found 1 indent 1606:1 error Expected indentation of 0 spaces but found 2 indent 1607:1 error Expected indentation of 4 spaces but found 3 indent 1608:1 error Expected indentation of 4 spaces but found 3 indent 1609:1 error Expected indentation of 4 spaces but found 3 indent 1610:1 error Expected indentation of 0 spaces but found 1 indent 1612:1 error Expected indentation of 0 spaces but found 2 indent 1613:1 error Expected indentation of 4 spaces but found 3 indent 1614:1 error Expected indentation of 4 spaces but found 3 indent 1615:1 error Expected indentation of 8 spaces but found 5 indent 1615:6 error Unexpected console statement no-console 1616:1 error Expected indentation of 4 spaces but found 3 indent 1617:1 error Expected indentation of 0 spaces but found 1 indent 1623:1 error Expected indentation of 4 spaces but found 2 indent 1624:1 error Expected indentation of 8 spaces but found 4 indent 1625:1 error Expected indentation of 4 spaces but found 2 indent 1626:1 error Expected indentation of 4 spaces but found 2 indent 1627:1 error Expected indentation of 8 spaces but found 4 indent 1628:1 error Expected indentation of 8 spaces but found 4 indent 1629:1 error Expected indentation of 8 spaces but found 4 indent 1631:1 error Expected indentation of 8 spaces but found 4 indent 1633:1 error Expected indentation of 8 spaces but found 4 indent 1634:1 error Expected indentation of 8 spaces but found 6 indent 1635:1 error Expected indentation of 12 spaces but found 8 indent 1636:1 error Expected indentation of 12 spaces but found 8 indent 1637:1 error Expected indentation of 8 spaces but found 6 indent 1638:1 error Expected indentation of 12 spaces but found 8 indent 1639:1 error Expected indentation of 12 spaces but found 8 indent 1640:1 error Expected indentation of 8 spaces but found 6 indent 1641:1 error Expected indentation of 12 spaces but found 8 indent 1642:1 error Expected indentation of 12 spaces but found 8 indent 1643:1 error Expected indentation of 8 spaces but found 6 indent 1644:1 error Expected indentation of 12 spaces but found 8 indent 1645:1 error Expected indentation of 12 spaces but found 8 indent 1646:1 error Expected indentation of 8 spaces but found 6 indent 1647:1 error Expected indentation of 12 spaces but found 8 indent 1648:1 error Expected indentation of 12 spaces but found 8 indent 1649:1 error Expected indentation of 8 spaces but found 6 indent 1650:1 error Expected indentation of 12 spaces but found 8 indent 1651:1 error Expected indentation of 12 spaces but found 8 indent 1652:1 error Expected indentation of 8 spaces but found 6 indent 1653:1 error Expected indentation of 12 spaces but found 8 indent 1654:1 error Expected indentation of 12 spaces but found 8 indent 1655:1 error Expected indentation of 8 spaces but found 6 indent 1656:1 error Expected indentation of 12 spaces but found 8 indent 1657:1 error Expected indentation of 12 spaces but found 8 indent 1658:1 error Expected indentation of 8 spaces but found 6 indent 1659:1 error Expected indentation of 12 spaces but found 8 indent 1660:1 error Expected indentation of 12 spaces but found 8 indent 1661:1 error Expected indentation of 8 spaces but found 6 indent 1662:1 error Expected indentation of 12 spaces but found 8 indent 1663:1 error Expected indentation of 12 spaces but found 8 indent 1664:1 error Expected indentation of 8 spaces but found 6 indent 1665:1 error Expected indentation of 12 spaces but found 8 indent 1666:1 error Expected indentation of 12 spaces but found 8 indent 1667:1 error Expected indentation of 8 spaces but found 6 indent 1668:1 error Expected indentation of 12 spaces but found 8 indent 1669:1 error Expected indentation of 12 spaces but found 8 indent 1670:1 error Expected indentation of 8 spaces but found 6 indent 1671:1 error Expected indentation of 12 spaces but found 8 indent 1671:9 error Unexpected console statement no-console 1672:1 error Expected indentation of 16 spaces but found 10 indent 1673:1 error Expected indentation of 12 spaces but found 8 indent 1674:1 error Expected indentation of 12 spaces but found 8 indent 1675:1 error Expected indentation of 8 spaces but found 4 indent 1677:1 error Expected indentation of 8 spaces but found 4 indent 1678:1 error Expected indentation of 4 spaces but found 2 indent 1700:1 error Expected indentation of 4 spaces but found 2 indent 1701:1 error Expected indentation of 4 spaces but found 2 indent 1702:1 error Expected indentation of 4 spaces but found 2 indent 1703:1 error Expected indentation of 4 spaces but found 2 indent 1704:1 error Expected indentation of 4 spaces but found 2 indent 1705:1 error Expected indentation of 4 spaces but found 2 indent 1706:1 error Expected indentation of 4 spaces but found 2 indent 1707:1 error Expected indentation of 4 spaces but found 2 indent 1708:1 error Expected indentation of 4 spaces but found 2 indent 1709:1 error Expected indentation of 4 spaces but found 2 indent 1710:1 error Expected indentation of 4 spaces but found 2 indent 1711:1 error Expected indentation of 4 spaces but found 2 indent 1712:1 error Expected indentation of 4 spaces but found 2 indent 1713:1 error Expected indentation of 4 spaces but found 2 indent 1714:1 error Expected indentation of 4 spaces but found 2 indent 1715:1 error Expected indentation of 4 spaces but found 2 indent 1716:1 error Expected indentation of 4 spaces but found 2 indent ? 1359 problems (1359 errors, 0 warnings) 1338 errors and 0 warnings potentially fixable with the `--fix` option. ERROR in ./jsx/Markdown.js Module Error (from ./node_modules/eslint-loader/index.js): /var/www/loris/jsx/Markdown.js 26:1 error Expected indentation of 4 spaces but found 2 indent 27:1 error Expected indentation of 8 spaces but found 4 indent 28:1 error Expected indentation of 12 spaces but found 6 indent 29:1 error Expected indentation of 12 spaces but found 6 indent 30:1 error Expected indentation of 4 spaces but found 2 indent 32:1 error Expected indentation of 4 spaces but found 2 indent 34:1 error Expected indentation of 8 spaces but found 4 indent 36:1 error Expected indentation of 8 spaces but found 4 indent 37:1 error Expected indentation of 8 spaces but found 4 indent 39:1 error Expected indentation of 8 spaces but found 4 indent 40:1 error Expected indentation of 8 spaces but found 4 indent 41:1 error Expected indentation of 8 spaces but found 4 indent 43:1 error Expected indentation of 8 spaces but found 4 indent 44:1 error Expected indentation of 8 spaces but found 4 indent 45:1 error Expected indentation of 8 spaces but found 4 indent 46:1 error Expected indentation of 8 spaces but found 4 indent 47:1 error Expected indentation of 8 spaces but found 4 indent 48:1 error Expected indentation of 8 spaces but found 4 indent 48:50 error 'end' is defined but never used no-unused-vars 48:55 error 'offset' is defined but never used no-unused-vars 48:63 error 'val' is defined but never used no-unused-vars 49:1 error Expected indentation of 12 spaces but found 6 indent 50:1 error Expected indentation of 8 spaces but found 4 indent 52:1 error Expected indentation of 8 spaces but found 4 indent 53:1 error Expected indentation of 8 spaces but found 4 indent 54:1 error Expected indentation of 8 spaces but found 4 indent 54:50 error 'end' is defined but never used no-unused-vars 54:55 error 'offset' is defined but never used no-unused-vars 54:63 error 'val' is defined but never used no-unused-vars 55:1 error Expected indentation of 12 spaces but found 6 indent 56:1 error Expected indentation of 8 spaces but found 4 indent 58:1 error Expected indentation of 8 spaces but found 4 indent 59:1 error Expected indentation of 8 spaces but found 4 indent 59:46 error 'offset' is defined but never used no-unused-vars 59:54 error 'val' is defined but never used no-unused-vars 60:1 error Expected indentation of 12 spaces but found 6 indent 61:1 error Expected indentation of 8 spaces but found 4 indent 62:1 error Expected indentation of 8 spaces but found 4 indent 63:1 error Expected indentation of 8 spaces but found 4 indent 64:1 error Expected indentation of 8 spaces but found 4 indent 65:1 error Expected indentation of 8 spaces but found 4 indent 65:64 error 'offset' is defined but never used no-unused-vars 65:72 error 'val' is defined but never used no-unused-vars 66:1 error Expected indentation of 12 spaces but found 6 indent 67:1 error Expected indentation of 12 spaces but found 6 indent 68:1 error Expected indentation of 8 spaces but found 4 indent 69:1 error Expected indentation of 8 spaces but found 4 indent 70:1 error Expected indentation of 12 spaces but found 6 indent 71:1 error Expected indentation of 12 spaces but found 6 indent 72:1 error Expected indentation of 12 spaces but found 6 indent 73:1 error Expected indentation of 12 spaces but found 6 indent 74:1 error Expected indentation of 12 spaces but found 6 indent 75:1 error Expected indentation of 12 spaces but found 6 indent 76:1 error Expected indentation of 16 spaces but found 8 indent 77:1 error Expected indentation of 16 spaces but found 8 indent 79:1 error Expected indentation of 16 spaces but found 8 indent 80:1 error Expected indentation of 16 spaces but found 10 indent 81:1 error Expected indentation of 20 spaces but found 12 indent 82:1 error Expected indentation of 20 spaces but found 12 indent 84:1 error Expected indentation of 16 spaces but found 10 indent 85:1 error Expected indentation of 20 spaces but found 12 indent 86:1 error Expected indentation of 20 spaces but found 12 indent 88:1 error Expected indentation of 16 spaces but found 10 indent 89:1 error Expected indentation of 20 spaces but found 12 indent 90:1 error Expected indentation of 20 spaces but found 12 indent 92:1 error Expected indentation of 16 spaces but found 10 indent 93:1 error Expected indentation of 20 spaces but found 12 indent 94:1 error Expected indentation of 20 spaces but found 12 indent 96:1 error Expected indentation of 16 spaces but found 10 indent 97:1 error Expected indentation of 20 spaces but found 12 indent 98:1 error Expected indentation of 20 spaces but found 12 indent 99:1 error Expected indentation of 16 spaces but found 10 indent 100:1 error Expected indentation of 16 spaces but found 10 indent 101:1 error Expected indentation of 20 spaces but found 12 indent 102:1 error Expected indentation of 16 spaces but found 8 indent 103:1 error Expected indentation of 12 spaces but found 6 indent 104:1 error Expected indentation of 16 spaces but found 8 indent 105:1 error Expected indentation of 16 spaces but found 8 indent 106:1 error Expected indentation of 16 spaces but found 8 indent 107:1 error Expected indentation of 16 spaces but found 8 indent 108:1 error Expected indentation of 16 spaces but found 8 indent 110:1 error Expected indentation of 16 spaces but found 8 indent 111:1 error Expected indentation of 16 spaces but found 8 indent 113:1 error Expected indentation of 16 spaces but found 8 indent 114:1 error Expected indentation of 16 spaces but found 8 indent 115:1 error Expected indentation of 12 spaces but found 6 indent 116:1 error Expected indentation of 8 spaces but found 4 indent 117:1 error Expected indentation of 8 spaces but found 4 indent 118:1 error Expected indentation of 4 spaces but found 2 indent 122:1 error Expected indentation of 4 spaces but found 2 indent ? 90 problems (90 errors, 0 warnings) 80 errors and 0 warnings potentially fixable with the `--fix` option. ERROR in ./jsx/MultiSelectDropdown.js Module Error (from ./node_modules/eslint-loader/index.js): /var/www/loris/jsx/MultiSelectDropdown.js 8:8 error 'React' is defined but never used no-unused-vars 11:1 error Expected indentation of 4 spaces but found 2 indent 12:1 error Expected indentation of 8 spaces but found 4 indent 14:1 error Expected indentation of 8 spaces but found 4 indent 15:1 error Expected indentation of 4 spaces but found 2 indent 17:1 error Expected indentation of 4 spaces but found 2 indent 18:1 error Expected indentation of 8 spaces but found 4 indent 19:1 error Expected indentation of 4 spaces but found 2 indent 21:1 error Expected indentation of 4 spaces but found 2 indent 22:1 error Expected indentation of 8 spaces but found 4 indent 23:1 error Expected indentation of 8 spaces but found 4 indent 24:1 error Expected indentation of 8 spaces but found 4 indent 25:1 error Expected indentation of 12 spaces but found 6 indent 26:1 error Expected indentation of 16 spaces but found 8 indent 27:1 error Expected indentation of 20 spaces but found 10 indent 28:1 error Expected indentation of 20 spaces but found 10 indent 29:1 error Expected indentation of 20 spaces but found 10 indent 30:1 error Expected indentation of 20 spaces but found 10 indent 31:1 error Expected indentation of 12 spaces but found 6 indent 32:1 error Expected indentation of 8 spaces but found 4 indent 33:1 error Expected indentation of 8 spaces but found 4 indent 34:1 error Expected indentation of 12 spaces but found 6 indent 35:1 error Expected indentation of 16 spaces but found 8 indent 36:1 error Expected indentation of 20 spaces but found 10 indent 37:1 error Expected indentation of 24 spaces but found 12 indent 38:1 error Expected indentation of 20 spaces but found 10 indent 39:1 error Expected indentation of 16 spaces but found 8 indent 40:1 error Expected indentation of 12 spaces but found 6 indent 41:1 error Expected indentation of 8 spaces but found 4 indent 42:1 error Expected indentation of 4 spaces but found 2 indent 46:1 error Expected indentation of 4 spaces but found 2 indent 47:1 error Expected indentation of 8 spaces but found 4 indent 49:1 error Expected indentation of 8 spaces but found 4 indent 50:1 error Expected indentation of 8 spaces but found 4 indent 51:1 error Expected indentation of 4 spaces but found 2 indent 53:1 error Expected indentation of 4 spaces but found 2 indent 54:1 error Expected indentation of 8 spaces but found 4 indent 55:1 error Expected indentation of 4 spaces but found 2 indent 56:1 error Expected indentation of 4 spaces but found 2 indent 57:1 error Expected indentation of 8 spaces but found 4 indent 58:1 error Expected indentation of 4 spaces but found 2 indent 60:1 error Expected indentation of 4 spaces but found 2 indent 61:1 error Expected indentation of 8 spaces but found 4 indent 62:1 error Expected indentation of 12 spaces but found 6 indent 63:1 error Expected indentation of 16 spaces but found 8 indent 64:1 error Expected indentation of 20 spaces but found 10 indent 65:1 error Expected indentation of 24 spaces but found 12 indent 66:1 error Expected indentation of 20 spaces but found 10 indent 67:1 error Expected indentation of 20 spaces but found 10 indent 68:1 error Expected indentation of 24 spaces but found 12 indent 69:1 error Expected indentation of 24 spaces but found 12 indent 70:1 error Expected indentation of 24 spaces but found 12 indent 71:1 error Expected indentation of 24 spaces but found 12 indent 72:1 error Expected indentation of 20 spaces but found 10 indent 73:1 error Expected indentation of 20 spaces but found 10 indent 74:1 error Expected indentation of 24 spaces but found 12 indent 75:1 error Expected indentation of 20 spaces but found 10 indent 76:1 error Expected indentation of 16 spaces but found 8 indent 77:1 error Expected indentation of 12 spaces but found 6 indent 78:1 error Expected indentation of 8 spaces but found 4 indent 79:1 error Expected indentation of 4 spaces but found 2 indent 83:1 error Expected indentation of 4 spaces but found 2 indent 84:1 error Expected indentation of 8 spaces but found 4 indent 86:1 error Expected indentation of 8 spaces but found 4 indent 87:1 error Expected indentation of 12 spaces but found 6 indent 88:1 error Expected indentation of 12 spaces but found 6 indent 89:1 error Expected indentation of 12 spaces but found 6 indent 90:1 error Expected indentation of 16 spaces but found 8 indent 91:1 error Expected indentation of 16 spaces but found 8 indent 92:1 error Expected indentation of 12 spaces but found 6 indent 93:1 error Expected indentation of 8 spaces but found 4 indent 94:1 error Expected indentation of 8 spaces but found 4 indent 95:1 error Expected indentation of 8 spaces but found 4 indent 96:1 error Expected indentation of 8 spaces but found 4 indent 97:1 error Expected indentation of 8 spaces but found 4 indent 98:1 error Expected indentation of 8 spaces but found 4 indent 99:1 error Expected indentation of 4 spaces but found 2 indent 101:1 error Expected indentation of 4 spaces but found 2 indent 102:1 error Expected indentation of 8 spaces but found 4 indent 103:1 error Expected indentation of 8 spaces but found 4 indent 104:1 error Expected indentation of 4 spaces but found 2 indent 106:1 error Expected indentation of 4 spaces but found 2 indent 107:1 error Expected indentation of 8 spaces but found 4 indent 108:1 error Expected indentation of 12 spaces but found 6 indent 109:1 error Expected indentation of 12 spaces but found 6 indent 110:1 error Expected indentation of 8 spaces but found 4 indent 111:1 error Expected indentation of 12 spaces but found 6 indent 112:1 error Expected indentation of 12 spaces but found 6 indent 113:1 error Expected indentation of 8 spaces but found 4 indent 114:1 error Expected indentation of 4 spaces but found 2 indent 116:1 error Expected indentation of 4 spaces but found 2 indent 117:1 error Expected indentation of 8 spaces but found 4 indent 118:1 error Expected indentation of 12 spaces but found 6 indent 119:1 error Expected indentation of 16 spaces but found 8 indent 120:1 error Expected indentation of 12 spaces but found 6 indent 121:1 error Expected indentation of 8 spaces but found 4 indent 122:1 error Expected indentation of 4 spaces but found 2 indent 124:1 error Expected indentation of 4 spaces but found 2 indent 125:1 error Expected indentation of 8 spaces but found 4 indent 126:1 error Expected indentation of 12 spaces but found 6 indent 127:1 error Expected indentation of 16 spaces but found 8 indent 128:1 error Expected indentation of 12 spaces but found 6 indent 129:1 error Expected indentation of 8 spaces but found 4 indent 130:1 error Expected indentation of 4 spaces but found 2 indent 132:1 error Expected indentation of 4 spaces but found 2 indent 133:1 error Expected indentation of 8 spaces but found 4 indent 134:1 error Expected indentation of 4 spaces but found 2 indent 136:1 error Expected indentation of 4 spaces but found 2 indent 137:1 error Expected indentation of 8 spaces but found 4 indent 138:1 error Expected indentation of 8 spaces but found 4 indent 139:1 error Expected indentation of 8 spaces but found 4 indent 140:1 error Expected indentation of 8 spaces but found 4 indent 141:1 error Expected indentation of 8 spaces but found 4 indent 142:1 error Expected indentation of 8 spaces but found 4 indent 143:1 error Expected indentation of 8 spaces but found 4 indent 145:1 error Expected indentation of 8 spaces but found 4 indent 146:1 error Expected indentation of 12 spaces but found 6 indent 147:1 error Expected indentation of 8 spaces but found 4 indent 148:1 error Expected indentation of 8 spaces but found 4 indent 149:1 error Expected indentation of 12 spaces but found 6 indent 150:1 error Expected indentation of 16 spaces but found 8 indent 151:1 error Expected indentation of 16 spaces but found 8 indent 152:1 error Expected indentation of 16 spaces but found 8 indent 153:1 error Expected indentation of 20 spaces but found 10 indent 154:1 error Expected indentation of 20 spaces but found 10 indent 155:1 error Expected indentation of 24 spaces but found 12 indent 156:1 error Expected indentation of 28 spaces but found 14 indent 157:1 error Expected indentation of 28 spaces but found 14 indent 158:1 error Expected indentation of 28 spaces but found 14 indent 159:1 error Expected indentation of 28 spaces but found 14 indent 160:1 error Expected indentation of 28 spaces but found 14 indent 161:1 error Expected indentation of 24 spaces but found 12 indent 162:1 error Expected indentation of 20 spaces but found 10 indent 163:1 error Expected indentation of 20 spaces but found 10 indent 164:1 error Expected indentation of 24 spaces but found 12 indent 165:1 error Expected indentation of 20 spaces but found 10 indent 166:1 error Expected indentation of 16 spaces but found 8 indent 167:1 error Expected indentation of 12 spaces but found 6 indent 168:1 error Expected indentation of 12 spaces but found 6 indent 169:1 error Expected indentation of 16 spaces but found 8 indent 170:1 error Expected indentation of 20 spaces but found 10 indent 171:1 error Expected indentation of 24 spaces but found 12 indent 172:1 error Expected indentation of 24 spaces but found 12 indent 173:1 error Expected indentation of 24 spaces but found 12 indent 174:1 error Expected indentation of 24 spaces but found 12 indent 175:1 error Expected indentation of 24 spaces but found 12 indent 176:1 error Expected indentation of 20 spaces but found 10 indent 177:1 error Expected indentation of 16 spaces but found 8 indent 178:1 error Expected indentation of 12 spaces but found 6 indent 179:1 error Expected indentation of 16 spaces but found 8 indent 180:1 error Expected indentation of 20 spaces but found 10 indent 181:1 error Expected indentation of 24 spaces but found 12 indent 182:1 error Expected indentation of 24 spaces but found 12 indent 183:1 error Expected indentation of 24 spaces but found 12 indent 184:1 error Expected indentation of 24 spaces but found 12 indent 185:1 error Expected indentation of 24 spaces but found 12 indent 186:1 error Expected indentation of 20 spaces but found 10 indent 187:1 error Expected indentation of 16 spaces but found 8 indent 188:1 error Expected indentation of 12 spaces but found 6 indent 189:1 error Expected indentation of 12 spaces but found 6 indent 190:1 error Expected indentation of 16 spaces but found 8 indent 191:1 error Expected indentation of 12 spaces but found 6 indent 192:1 error Expected indentation of 8 spaces but found 4 indent 193:1 error Expected indentation of 12 spaces but found 6 indent 194:1 error Expected indentation of 16 spaces but found 8 indent 195:1 error Expected indentation of 16 spaces but found 8 indent 196:1 error Expected indentation of 16 spaces but found 8 indent 197:1 error Expected indentation of 20 spaces but found 10 indent 198:1 error Expected indentation of 20 spaces but found 10 indent 200:1 error Expected indentation of 24 spaces but found 12 indent 201:1 error Expected indentation of 20 spaces but found 10 indent 202:1 error Expected indentation of 20 spaces but found 10 indent 203:1 error Expected indentation of 24 spaces but found 12 indent 204:1 error Expected indentation of 28 spaces but found 14 indent 205:1 error Expected indentation of 28 spaces but found 14 indent 206:1 error Expected indentation of 28 spaces but found 14 indent 207:1 error Expected indentation of 28 spaces but found 14 indent 208:1 error Expected indentation of 28 spaces but found 14 indent 209:1 error Expected indentation of 24 spaces but found 12 indent 210:1 error Expected indentation of 20 spaces but found 10 indent 211:1 error Expected indentation of 16 spaces but found 8 indent 212:1 error Expected indentation of 12 spaces but found 6 indent 213:1 error Expected indentation of 12 spaces but found 6 indent 214:1 error Expected indentation of 16 spaces but found 8 indent 215:1 error Expected indentation of 20 spaces but found 10 indent 216:1 error Expected indentation of 20 spaces but found 10 indent 217:1 error Expected indentation of 16 spaces but found 8 indent 218:1 error Expected indentation of 12 spaces but found 6 indent 219:1 error Expected indentation of 12 spaces but found 6 indent 220:1 error Expected indentation of 16 spaces but found 8 indent 221:1 error Expected indentation of 12 spaces but found 6 indent 222:1 error Expected indentation of 16 spaces but found 8 indent 223:1 error Expected indentation of 12 spaces but found 6 indent 224:1 error Expected indentation of 8 spaces but found 4 indent 225:1 error Expected indentation of 8 spaces but found 4 indent 226:1 error Expected indentation of 12 spaces but found 6 indent 227:1 error Expected indentation of 16 spaces but found 8 indent 228:1 error Expected indentation of 20 spaces but found 16 indent 229:1 error Expected indentation of 20 spaces but found 16 indent 230:1 error Expected indentation of 20 spaces but found 10 indent 231:1 error Expected indentation of 24 spaces but found 14 indent 232:1 error Expected indentation of 28 spaces but found 16 indent 233:1 error Expected indentation of 24 spaces but found 14 indent 234:1 error Expected indentation of 20 spaces but found 10 indent 235:1 error Expected indentation of 20 spaces but found 10 indent 236:1 error Expected indentation of 24 spaces but found 12 indent 237:1 error Expected indentation of 20 spaces but found 10 indent 238:1 error Expected indentation of 16 spaces but found 8 indent 239:1 error Expected indentation of 16 spaces but found 8 indent 240:1 error Expected indentation of 20 spaces but found 10 indent 241:1 error Expected indentation of 16 spaces but found 8 indent 242:1 error Expected indentation of 12 spaces but found 6 indent 243:1 error Expected indentation of 8 spaces but found 4 indent 244:1 error Expected indentation of 4 spaces but found 2 indent 252:1 error Expected indentation of 4 spaces but found 2 indent 253:1 error Expected indentation of 4 spaces but found 2 indent 254:1 error Expected indentation of 4 spaces but found 2 indent ? 217 problems (217 errors, 0 warnings) 216 errors and 0 warnings potentially fixable with the `--fix` option. ERROR in ./jsx/PaginationLinks.js Module Error (from ./node_modules/eslint-loader/index.js): /var/www/loris/jsx/PaginationLinks.js 7:1 error Expected indentation of 4 spaces but found 2 indent 8:1 error Expected indentation of 8 spaces but found 4 indent 10:1 error Expected indentation of 8 spaces but found 4 indent 12:1 error Expected indentation of 8 spaces but found 4 indent 13:1 error Expected indentation of 8 spaces but found 4 indent 14:1 error Expected indentation of 4 spaces but found 2 indent 16:1 error Expected indentation of 4 spaces but found 2 indent 17:1 error Expected indentation of 8 spaces but found 4 indent 18:1 error Expected indentation of 12 spaces but found 6 indent 19:1 error Expected indentation of 8 spaces but found 4 indent 20:1 error Expected indentation of 4 spaces but found 2 indent 22:1 error Expected indentation of 4 spaces but found 2 indent 23:1 error Expected indentation of 8 spaces but found 4 indent 24:1 error Expected indentation of 12 spaces but found 6 indent 25:1 error Expected indentation of 12 spaces but found 6 indent 27:1 error Expected indentation of 12 spaces but found 6 indent 28:1 error Expected indentation of 16 spaces but found 8 indent 29:1 error Expected indentation of 12 spaces but found 6 indent 30:1 error Expected indentation of 8 spaces but found 4 indent 31:1 error Expected indentation of 4 spaces but found 2 indent 33:1 error Expected indentation of 4 spaces but found 2 indent 34:1 error Expected indentation of 8 spaces but found 4 indent 35:1 error Expected indentation of 8 spaces but found 4 indent 36:1 error Expected indentation of 8 spaces but found 4 indent 37:1 error Expected indentation of 8 spaces but found 4 indent 38:1 error Expected indentation of 8 spaces but found 4 indent 39:1 error Expected indentation of 8 spaces but found 4 indent 41:1 error Expected indentation of 8 spaces but found 4 indent 42:1 error Expected indentation of 12 spaces but found 6 indent 43:1 error Expected indentation of 8 spaces but found 4 indent 44:1 error Expected indentation of 8 spaces but found 4 indent 45:1 error Expected indentation of 12 spaces but found 6 indent 46:1 error Expected indentation of 8 spaces but found 4 indent 48:1 error Expected indentation of 8 spaces but found 4 indent 49:1 error Expected indentation of 12 spaces but found 6 indent 50:1 error Expected indentation of 12 spaces but found 6 indent 51:1 error Expected indentation of 16 spaces but found 8 indent 52:1 error Expected indentation of 16 spaces but found 8 indent 53:1 error Expected indentation of 12 spaces but found 6 indent 54:1 error Expected indentation of 8 spaces but found 4 indent 56:1 error Expected indentation of 8 spaces but found 4 indent 57:1 error Expected indentation of 12 spaces but found 6 indent 58:1 error Expected indentation of 16 spaces but found 8 indent 59:1 error Expected indentation of 12 spaces but found 6 indent 60:1 error Expected indentation of 8 spaces but found 4 indent 61:1 error Expected indentation of 8 spaces but found 4 indent 62:1 error Expected indentation of 12 spaces but found 6 indent 63:1 error Expected indentation of 8 spaces but found 4 indent 64:1 error Expected indentation of 8 spaces but found 4 indent 65:1 error Expected indentation of 12 spaces but found 6 indent 66:1 error Expected indentation of 8 spaces but found 4 indent 69:1 error Expected indentation of 8 spaces but found 4 indent 70:1 error Expected indentation of 12 spaces but found 6 indent 71:1 error Expected indentation of 8 spaces but found 4 indent 73:1 error Expected indentation of 8 spaces but found 4 indent 74:1 error Expected indentation of 12 spaces but found 6 indent 75:1 error Expected indentation of 12 spaces but found 6 indent 76:1 error Expected indentation of 16 spaces but found 8 indent 77:1 error Expected indentation of 12 spaces but found 6 indent 78:1 error Expected indentation of 12 spaces but found 6 indent 79:1 error Expected indentation of 16 spaces but found 8 indent 80:1 error Expected indentation of 20 spaces but found 10 indent 81:1 error Expected indentation of 16 spaces but found 8 indent 82:1 error Expected indentation of 12 spaces but found 6 indent 83:1 error Expected indentation of 8 spaces but found 4 indent 84:1 error Expected indentation of 8 spaces but found 4 indent 85:1 error Expected indentation of 12 spaces but found 6 indent 86:1 error Expected indentation of 16 spaces but found 8 indent 87:1 error Expected indentation of 20 spaces but found 10 indent 88:1 error Expected indentation of 16 spaces but found 8 indent 89:1 error Expected indentation of 12 spaces but found 6 indent 90:1 error Expected indentation of 8 spaces but found 4 indent 92:1 error Expected indentation of 8 spaces but found 4 indent 93:1 error Expected indentation of 12 spaces but found 6 indent 94:1 error Expected indentation of 16 spaces but found 10 indent 95:1 error Expected indentation of 12 spaces but found 6 indent 96:1 error Expected indentation of 8 spaces but found 4 indent 97:1 error Expected indentation of 4 spaces but found 2 indent 100:1 error Expected indentation of 4 spaces but found 2 indent 101:1 error Expected indentation of 4 spaces but found 2 indent 104:1 error Expected indentation of 4 spaces but found 2 indent 105:1 error Expected indentation of 4 spaces but found 2 indent ? 82 problems (82 errors, 0 warnings) 82 errors and 0 warnings potentially fixable with the `--fix` option. ERROR in ./jsx/StaticDataTable.js Module Error (from ./node_modules/eslint-loader/index.js): /var/www/loris/jsx/StaticDataTable.js 13:8 error 'PaginationLinks' is defined but never used no-unused-vars 21:1 error Expected indentation of 4 spaces but found 2 indent 22:1 error Expected indentation of 8 spaces but found 4 indent 24:1 error Expected indentation of 8 spaces but found 4 indent 25:1 error Expected indentation of 12 spaces but found 6 indent 26:1 error Expected indentation of 12 spaces but found 6 indent 27:1 error Expected indentation of 12 spaces but found 6 indent 28:1 error Expected indentation of 12 spaces but found 6 indent 29:1 error Expected indentation of 12 spaces but found 6 indent 30:1 error Expected indentation of 8 spaces but found 4 indent 32:1 error Expected indentation of 8 spaces but found 4 indent 33:1 error Expected indentation of 8 spaces but found 4 indent 34:1 error Expected indentation of 8 spaces but found 4 indent 35:1 error Expected indentation of 8 spaces but found 4 indent 36:1 error Expected indentation of 8 spaces but found 4 indent 37:1 error Expected indentation of 8 spaces but found 4 indent 38:1 error Expected indentation of 8 spaces but found 4 indent 39:1 error Expected indentation of 8 spaces but found 4 indent 40:1 error Expected indentation of 4 spaces but found 2 indent 42:1 error Expected indentation of 4 spaces but found 2 indent 43:1 error Expected indentation of 8 spaces but found 4 indent 43:9 error 'jQuery' is not defined no-undef 44:1 error Expected indentation of 12 spaces but found 6 indent 45:1 error Expected indentation of 16 spaces but found 8 indent 45:9 error '$' is not defined no-undef 46:1 error Expected indentation of 20 spaces but found 10 indent 47:1 error Expected indentation of 16 spaces but found 8 indent 48:1 error Expected indentation of 12 spaces but found 6 indent 49:1 error Expected indentation of 16 spaces but found 8 indent 49:9 error '$' is not defined no-undef 50:1 error Expected indentation of 12 spaces but found 6 indent 51:1 error Expected indentation of 12 spaces but found 6 indent 52:1 error Expected indentation of 16 spaces but found 8 indent 52:9 error '$' is not defined no-undef 53:1 error Expected indentation of 12 spaces but found 6 indent 54:1 error Expected indentation of 8 spaces but found 4 indent 56:1 error Expected indentation of 8 spaces but found 4 indent 57:1 error Expected indentation of 8 spaces but found 4 indent 59:1 error Expected indentation of 8 spaces but found 4 indent 60:1 error Expected indentation of 8 spaces but found 4 indent 61:1 error Expected indentation of 12 spaces but found 6 indent 62:1 error Expected indentation of 8 spaces but found 4 indent 64:1 error Expected indentation of 8 spaces but found 4 indent 65:1 error Expected indentation of 8 spaces but found 4 indent 65:21 error 'loris' is not defined no-undef 66:1 error Expected indentation of 12 spaces but found 6 indent 66:19 error 'loris' is not defined no-undef 67:1 error Expected indentation of 12 spaces but found 6 indent 67:19 error 'loris' is not defined no-undef 68:1 error Expected indentation of 8 spaces but found 4 indent 70:1 error Expected indentation of 8 spaces but found 4 indent 71:1 error Expected indentation of 8 spaces but found 4 indent 71:35 error 'loris' is not defined no-undef 72:1 error Expected indentation of 8 spaces but found 4 indent 73:1 error Expected indentation of 12 spaces but found 6 indent 74:1 error Expected indentation of 8 spaces but found 4 indent 76:1 error Expected indentation of 8 spaces but found 4 indent 77:1 error Expected indentation of 8 spaces but found 4 indent 78:1 error Expected indentation of 4 spaces but found 2 indent 79:1 error Expected indentation of 4 spaces but found 2 indent 80:1 error Expected indentation of 8 spaces but found 4 indent 80:9 error 'jQuery' is not defined no-undef 81:1 error Expected indentation of 12 spaces but found 6 indent 82:1 error Expected indentation of 16 spaces but found 8 indent 82:9 error '$' is not defined no-undef 83:1 error Expected indentation of 20 spaces but found 10 indent 84:1 error Expected indentation of 16 spaces but found 8 indent 85:1 error Expected indentation of 12 spaces but found 6 indent 86:1 error Expected indentation of 16 spaces but found 8 indent 86:9 error '$' is not defined no-undef 87:1 error Expected indentation of 12 spaces but found 6 indent 88:1 error Expected indentation of 8 spaces but found 4 indent 89:1 error Expected indentation of 8 spaces but found 4 indent 92:1 error Expected indentation of 8 spaces but found 4 indent 93:1 error Expected indentation of 12 spaces but found 6 indent 94:1 error Expected indentation of 12 spaces but found 6 indent 95:1 error Expected indentation of 8 spaces but found 4 indent 96:1 error Expected indentation of 4 spaces but found 2 indent 98:1 error Expected indentation of 4 spaces but found 2 indent 99:1 error Expected indentation of 8 spaces but found 4 indent 100:1 error Expected indentation of 12 spaces but found 6 indent 101:1 error Expected indentation of 8 spaces but found 4 indent 102:1 error Expected indentation of 4 spaces but found 2 indent 104:1 error Expected indentation of 4 spaces but found 2 indent 105:1 error Expected indentation of 8 spaces but found 4 indent 105:21 error 'e' is defined but never used no-unused-vars 106:1 error Expected indentation of 12 spaces but found 6 indent 107:1 error Expected indentation of 16 spaces but found 8 indent 108:1 error Expected indentation of 20 spaces but found 10 indent 109:1 error Expected indentation of 16 spaces but found 8 indent 110:1 error Expected indentation of 12 spaces but found 6 indent 111:1 error Expected indentation of 16 spaces but found 8 indent 112:1 error Expected indentation of 20 spaces but found 10 indent 113:1 error Expected indentation of 16 spaces but found 8 indent 114:1 error Expected indentation of 12 spaces but found 6 indent 115:1 error Expected indentation of 8 spaces but found 4 indent 116:1 error Expected indentation of 4 spaces but found 2 indent 118:1 error Expected indentation of 4 spaces but found 2 indent 119:1 error Expected indentation of 8 spaces but found 4 indent 120:1 error Expected indentation of 8 spaces but found 4 indent 122:1 error Expected indentation of 8 spaces but found 4 indent 123:1 error Expected indentation of 8 spaces but found 4 indent 123:17 error 'loris' is not defined no-undef 125:1 error Expected indentation of 8 spaces but found 4 indent 126:1 error Expected indentation of 8 spaces but found 4 indent 128:1 error Expected indentation of 8 spaces but found 4 indent 129:1 error Expected indentation of 12 spaces but found 6 indent 130:1 error Expected indentation of 12 spaces but found 6 indent 131:1 error Expected indentation of 8 spaces but found 4 indent 132:1 error Expected indentation of 4 spaces but found 2 indent 134:1 error Expected indentation of 4 spaces but found 2 indent 135:1 error Expected indentation of 8 spaces but found 4 indent 135:32 error 'loris' is not defined no-undef 137:1 error Expected indentation of 8 spaces but found 4 indent 138:1 error Expected indentation of 12 spaces but found 6 indent 139:1 error Expected indentation of 12 spaces but found 6 indent 140:1 error Expected indentation of 12 spaces but found 6 indent 141:1 error Expected indentation of 12 spaces but found 6 indent 142:1 error Expected indentation of 16 spaces but found 8 indent 143:1 error Expected indentation of 16 spaces but found 8 indent 144:1 error Expected indentation of 16 spaces but found 8 indent 145:1 error Expected indentation of 16 spaces but found 8 indent 146:1 error Expected indentation of 16 spaces but found 8 indent 147:1 error Expected indentation of 16 spaces but found 8 indent 148:1 error Expected indentation of 16 spaces but found 8 indent 149:1 error Expected indentation of 16 spaces but found 8 indent 149:9 error '$' is not defined no-undef 150:1 error Expected indentation of 16 spaces but found 8 indent 151:1 error Expected indentation of 12 spaces but found 6 indent 152:1 error Expected indentation of 8 spaces but found 4 indent 153:1 error Expected indentation of 8 spaces but found 4 indent 154:1 error Expected indentation of 12 spaces but found 6 indent 155:1 error Expected indentation of 12 spaces but found 6 indent 156:1 error Expected indentation of 12 spaces but found 6 indent 157:1 error Expected indentation of 12 spaces but found 6 indent 158:1 error Expected indentation of 8 spaces but found 4 indent 159:1 error Expected indentation of 4 spaces but found 2 indent 161:1 error Expected indentation of 4 spaces but found 2 indent 162:1 error Expected indentation of 8 spaces but found 4 indent 163:1 error Expected indentation of 8 spaces but found 4 indent 164:1 error Expected indentation of 8 spaces but found 4 indent 165:1 error Expected indentation of 12 spaces but found 8 indent 166:1 error Expected indentation of 12 spaces but found 8 indent 167:1 error Expected indentation of 8 spaces but found 4 indent 168:1 error Expected indentation of 8 spaces but found 4 indent 169:1 error Expected indentation of 8 spaces but found 4 indent 171:1 error Expected indentation of 8 spaces but found 4 indent 172:1 error Expected indentation of 12 spaces but found 6 indent 173:1 error Expected indentation of 8 spaces but found 4 indent 175:1 error Expected indentation of 8 spaces but found 4 indent 176:1 error Expected indentation of 12 spaces but found 6 indent 177:1 error Expected indentation of 8 spaces but found 4 indent 179:1 error Expected indentation of 8 spaces but found 4 indent 180:1 error Expected indentation of 12 spaces but found 6 indent 181:1 error Expected indentation of 12 spaces but found 6 indent 182:1 error Expected indentation of 12 spaces but found 6 indent 183:1 error Expected indentation of 16 spaces but found 8 indent 184:1 error Expected indentation of 16 spaces but found 8 indent 185:1 error Expected indentation of 20 spaces but found 10 indent 186:1 error Expected indentation of 16 spaces but found 8 indent 187:1 error Expected indentation of 16 spaces but found 8 indent 188:1 error Expected indentation of 20 spaces but found 10 indent 189:1 error Expected indentation of 24 spaces but found 12 indent 190:1 error Expected indentation of 20 spaces but found 10 indent 191:1 error Expected indentation of 16 spaces but found 8 indent 192:1 error Expected indentation of 12 spaces but found 6 indent 194:1 error Expected indentation of 12 spaces but found 6 indent 197:1 error Expected indentation of 16 spaces but found 8 indent 198:1 error Expected indentation of 12 spaces but found 6 indent 199:1 error Expected indentation of 8 spaces but found 4 indent 201:1 error Expected indentation of 8 spaces but found 4 indent 202:1 error Expected indentation of 8 spaces but found 4 indent 203:1 error Expected indentation of 12 spaces but found 6 indent 204:1 error Expected indentation of 8 spaces but found 4 indent 206:1 error Expected indentation of 8 spaces but found 4 indent 207:1 error Expected indentation of 4 spaces but found 2 indent 209:1 error Expected indentation of 4 spaces but found 2 indent 210:1 error Expected indentation of 8 spaces but found 4 indent 211:1 error Expected indentation of 12 spaces but found 6 indent 212:1 error Expected indentation of 12 spaces but found 6 indent 213:1 error Expected indentation of 8 spaces but found 4 indent 214:1 error Expected indentation of 4 spaces but found 2 indent 216:1 error Expected indentation of 4 spaces but found 2 indent 217:1 error Expected indentation of 8 spaces but found 4 indent 219:1 error Expected indentation of 8 spaces but found 4 indent 220:1 error Expected indentation of 12 spaces but found 6 indent 221:1 error Expected indentation of 12 spaces but found 6 indent 222:1 error Expected indentation of 12 spaces but found 6 indent 223:1 error Expected indentation of 12 spaces but found 6 indent 224:1 error Expected indentation of 16 spaces but found 8 indent 225:1 error Expected indentation of 12 spaces but found 6 indent 226:1 error Expected indentation of 12 spaces but found 6 indent 227:1 error Expected indentation of 12 spaces but found 6 indent 229:1 error Expected indentation of 12 spaces but found 6 indent 230:1 error Expected indentation of 16 spaces but found 8 indent 231:1 error Expected indentation of 16 spaces but found 8 indent 232:1 error Expected indentation of 12 spaces but found 6 indent 233:1 error Expected indentation of 16 spaces but found 8 indent 234:1 error Expected indentation of 16 spaces but found 8 indent 235:1 error Expected indentation of 12 spaces but found 6 indent 236:1 error Expected indentation of 16 spaces but found 8 indent 237:1 error Expected indentation of 16 spaces but found 8 indent 238:1 error Expected indentation of 12 spaces but found 6 indent 239:1 error Expected indentation of 16 spaces but found 8 indent 240:1 error Expected indentation of 12 spaces but found 6 indent 242:1 error Expected indentation of 12 spaces but found 6 indent 243:1 error Expected indentation of 16 spaces but found 8 indent 244:1 error Expected indentation of 12 spaces but found 6 indent 245:1 error Expected indentation of 16 spaces but found 8 indent 246:1 error Expected indentation of 12 spaces but found 6 indent 247:1 error Expected indentation of 8 spaces but found 4 indent 249:1 error Expected indentation of 8 spaces but found 4 indent 250:1 error Expected indentation of 12 spaces but found 6 indent 251:1 error Expected indentation of 16 spaces but found 8 indent 252:1 error Expected indentation of 20 spaces but found 10 indent 253:1 error Expected indentation of 20 spaces but found 10 indent 254:1 error Expected indentation of 20 spaces but found 10 indent 255:1 error Expected indentation of 16 spaces but found 8 indent 256:1 error Expected indentation of 16 spaces but found 8 indent 257:1 error Expected indentation of 16 spaces but found 8 indent 258:1 error Expected indentation of 16 spaces but found 8 indent 260:1 error Expected indentation of 16 spaces but found 8 indent 261:1 error Expected indentation of 16 spaces but found 8 indent 262:1 error Expected indentation of 16 spaces but found 8 indent 263:1 error Expected indentation of 12 spaces but found 6 indent 264:1 error Expected indentation of 16 spaces but found 8 indent 265:1 error Expected indentation of 20 spaces but found 10 indent 266:1 error Expected indentation of 20 spaces but found 10 indent 267:1 error Expected indentation of 20 spaces but found 10 indent 268:1 error Expected indentation of 16 spaces but found 8 indent 269:1 error Expected indentation of 16 spaces but found 8 indent 270:1 error Expected indentation of 16 spaces but found 8 indent 271:1 error Expected indentation of 16 spaces but found 8 indent 273:1 error Expected indentation of 16 spaces but found 8 indent 274:1 error Expected indentation of 16 spaces but found 8 indent 275:1 error Expected indentation of 16 spaces but found 8 indent 276:1 error Expected indentation of 12 spaces but found 6 indent 277:1 error Expected indentation of 12 spaces but found 6 indent 278:1 error Expected indentation of 12 spaces but found 6 indent 279:1 error Expected indentation of 8 spaces but found 4 indent 280:1 error Expected indentation of 8 spaces but found 4 indent 281:1 error Expected indentation of 4 spaces but found 2 indent 283:1 error Expected indentation of 4 spaces but found 2 indent 293:1 error Expected indentation of 4 spaces but found 2 indent 294:1 error Expected indentation of 8 spaces but found 4 indent 295:1 error Expected indentation of 8 spaces but found 4 indent 296:1 error Expected indentation of 8 spaces but found 4 indent 297:1 error Expected indentation of 8 spaces but found 4 indent 298:1 error Expected indentation of 8 spaces but found 4 indent 299:1 error Expected indentation of 8 spaces but found 4 indent 301:1 error Expected indentation of 8 spaces but found 4 indent 302:1 error Expected indentation of 12 spaces but found 6 indent 303:1 error Expected indentation of 12 spaces but found 6 indent 304:1 error Expected indentation of 8 spaces but found 4 indent 306:1 error Expected indentation of 8 spaces but found 4 indent 307:1 error Expected indentation of 8 spaces but found 4 indent 308:1 error Expected indentation of 12 spaces but found 6 indent 309:1 error Expected indentation of 8 spaces but found 4 indent 311:1 error Expected indentation of 8 spaces but found 4 indent 312:1 error Expected indentation of 8 spaces but found 4 indent 313:1 error Expected indentation of 12 spaces but found 6 indent 314:1 error Expected indentation of 12 spaces but found 6 indent 315:1 error Expected indentation of 8 spaces but found 4 indent 317:1 error Expected indentation of 8 spaces but found 4 indent 318:1 error Expected indentation of 8 spaces but found 4 indent 319:1 error Expected indentation of 12 spaces but found 6 indent 320:1 error Expected indentation of 12 spaces but found 6 indent 322:1 error Expected indentation of 12 spaces but found 6 indent 323:1 error Expected indentation of 16 spaces but found 8 indent 324:1 error Expected indentation of 12 spaces but found 6 indent 325:1 error Expected indentation of 16 spaces but found 8 indent 326:1 error Expected indentation of 12 spaces but found 6 indent 327:1 error Expected indentation of 8 spaces but found 4 indent 329:1 error Expected indentation of 8 spaces but found 4 indent 330:1 error Expected indentation of 8 spaces but found 4 indent 331:1 error Expected indentation of 12 spaces but found 6 indent 332:1 error Expected indentation of 12 spaces but found 6 indent 333:1 error Expected indentation of 16 spaces but found 8 indent 334:1 error Expected indentation of 16 spaces but found 8 indent 335:1 error Expected indentation of 16 spaces but found 8 indent 336:1 error Expected indentation of 16 spaces but found 8 indent 337:1 error Expected indentation of 20 spaces but found 10 indent 338:1 error Expected indentation of 16 spaces but found 8 indent 339:1 error Expected indentation of 12 spaces but found 6 indent 340:1 error Expected indentation of 8 spaces but found 4 indent 341:1 error Expected indentation of 8 spaces but found 4 indent 342:1 error Expected indentation of 4 spaces but found 2 indent 343:1 error Expected indentation of 4 spaces but found 2 indent 344:1 error Expected indentation of 8 spaces but found 4 indent 345:1 error Expected indentation of 12 spaces but found 6 indent 346:1 error Expected indentation of 16 spaces but found 8 indent 347:1 error Expected indentation of 20 spaces but found 10 indent 348:1 error Expected indentation of 16 spaces but found 8 indent 349:1 error Expected indentation of 12 spaces but found 6 indent 350:1 error Expected indentation of 8 spaces but found 4 indent 351:1 error Expected indentation of 8 spaces but found 4 indent 352:1 error Expected indentation of 8 spaces but found 4 indent 353:1 error Expected indentation of 12 spaces but found 6 indent 354:1 error Expected indentation of 16 spaces but found 8 indent 355:1 error Expected indentation of 12 spaces but found 6 indent 356:1 error Expected indentation of 8 spaces but found 4 indent 358:1 error Expected indentation of 8 spaces but found 4 indent 359:1 error Expected indentation of 12 spaces but found 6 indent 359:18 error 'loris' is not defined no-undef 360:9 error 'loris' is not defined no-undef 361:1 error Expected indentation of 16 spaces but found 8 indent 362:1 error Expected indentation of 16 spaces but found 8 indent 363:1 error Expected indentation of 20 spaces but found 10 indent 364:1 error Expected indentation of 24 spaces but found 12 indent 365:1 error Expected indentation of 28 spaces but found 16 indent 366:1 error Expected indentation of 28 spaces but found 14 indent 367:1 error Expected indentation of 24 spaces but found 12 indent 368:1 error Expected indentation of 20 spaces but found 10 indent 369:1 error Expected indentation of 16 spaces but found 8 indent 370:1 error Expected indentation of 20 spaces but found 10 indent 371:1 error Expected indentation of 24 spaces but found 12 indent 372:1 error Expected indentation of 28 spaces but found 14 indent 373:1 error Expected indentation of 24 spaces but found 12 indent 374:1 error Expected indentation of 20 spaces but found 10 indent 375:1 error Expected indentation of 16 spaces but found 8 indent 376:1 error Expected indentation of 12 spaces but found 6 indent 377:1 error Expected indentation of 8 spaces but found 4 indent 378:1 error Expected indentation of 8 spaces but found 4 indent 379:1 error Expected indentation of 8 spaces but found 4 indent 380:1 error Expected indentation of 8 spaces but found 4 indent 381:1 error Expected indentation of 8 spaces but found 4 indent 382:1 error Expected indentation of 8 spaces but found 4 indent 383:1 error Expected indentation of 8 spaces but found 4 indent 384:1 error Expected indentation of 8 spaces but found 4 indent 385:1 error Expected indentation of 8 spaces but found 4 indent 387:1 error Expected indentation of 8 spaces but found 4 indent 388:1 error Expected indentation of 12 spaces but found 6 indent 389:1 error Expected indentation of 8 spaces but found 4 indent 391:1 error Expected indentation of 8 spaces but found 4 indent 392:1 error Expected indentation of 8 spaces but found 4 indent 393:1 error Expected indentation of 12 spaces but found 9 indent 394:1 error Expected indentation of 12 spaces but found 9 indent 395:1 error Expected indentation of 8 spaces but found 4 indent 396:1 error Expected indentation of 12 spaces but found 6 indent 398:1 error Expected indentation of 12 spaces but found 6 indent 399:1 error Expected indentation of 12 spaces but found 6 indent 400:1 error Expected indentation of 12 spaces but found 6 indent 401:1 error Expected indentation of 12 spaces but found 6 indent 403:1 error Expected indentation of 12 spaces but found 6 indent 404:1 error Expected indentation of 12 spaces but found 6 indent 405:1 error Expected indentation of 12 spaces but found 6 indent 406:1 error Expected indentation of 16 spaces but found 8 indent 408:1 error Expected indentation of 16 spaces but found 8 indent 409:1 error Expected indentation of 16 spaces but found 8 indent 410:1 error Expected indentation of 20 spaces but found 10 indent 411:1 error Expected indentation of 16 spaces but found 8 indent 413:1 error Expected indentation of 16 spaces but found 8 indent 414:1 error Expected indentation of 20 spaces but found 10 indent 415:1 error Expected indentation of 20 spaces but found 10 indent 416:1 error Expected indentation of 16 spaces but found 8 indent 418:1 error Expected indentation of 16 spaces but found 8 indent 419:1 error Expected indentation of 20 spaces but found 10 indent 420:1 error Expected indentation of 20 spaces but found 10 indent 421:1 error Expected indentation of 24 spaces but found 12 indent 422:1 error Expected indentation of 20 spaces but found 10 indent 423:1 error Expected indentation of 16 spaces but found 8 indent 424:1 error Expected indentation of 20 spaces but found 10 indent 425:1 error Expected indentation of 16 spaces but found 8 indent 427:1 error Expected indentation of 16 spaces but found 8 indent 429:1 error Expected indentation of 16 spaces but found 8 indent 430:1 error Expected indentation of 16 spaces but found 8 indent 431:1 error Expected indentation of 20 spaces but found 10 indent 432:1 error Expected indentation of 24 spaces but found 12 indent 433:1 error Expected indentation of 24 spaces but found 12 indent 434:1 error Expected indentation of 24 spaces but found 12 indent 435:1 error Expected indentation of 24 spaces but found 12 indent 436:1 error Expected indentation of 20 spaces but found 10 indent 437:1 error Expected indentation of 20 spaces but found 10 indent 438:1 error Expected indentation of 24 spaces but found 12 indent 439:1 error Expected indentation of 24 spaces but found 12 indent 440:1 error Expected indentation of 24 spaces but found 12 indent 441:1 error Expected indentation of 20 spaces but found 10 indent 442:1 error Expected indentation of 16 spaces but found 8 indent 443:1 error Expected indentation of 20 spaces but found 10 indent 444:1 error Expected indentation of 16 spaces but found 8 indent 445:1 error Expected indentation of 12 spaces but found 6 indent 447:1 error Expected indentation of 12 spaces but found 6 indent 448:1 error Expected indentation of 12 spaces but found 6 indent 451:1 error Expected indentation of 16 spaces but found 8 indent 452:1 error Expected indentation of 16 spaces but found 8 indent 453:1 error Expected indentation of 20 spaces but found 10 indent 454:1 error Expected indentation of 20 spaces but found 10 indent 455:1 error Expected indentation of 24 spaces but found 12 indent 456:1 error Expected indentation of 28 spaces but found 14 indent 457:1 error Expected indentation of 28 spaces but found 14 indent 458:1 error Expected indentation of 24 spaces but found 12 indent 459:1 error Expected indentation of 20 spaces but found 10 indent 460:1 error Expected indentation of 16 spaces but found 8 indent 461:1 error Expected indentation of 12 spaces but found 6 indent 462:1 error Expected indentation of 8 spaces but found 4 indent 464:1 error Expected indentation of 8 spaces but found 4 indent 465:1 error Expected indentation of 12 spaces but found 6 indent 466:1 error Expected indentation of 16 spaces but found 8 indent 467:1 error Expected indentation of 16 spaces but found 8 indent 468:1 error Expected indentation of 16 spaces but found 8 indent 469:1 error Expected indentation of 12 spaces but found 6 indent 470:1 error Expected indentation of 16 spaces but found 8 indent 471:1 error Expected indentation of 16 spaces but found 8 indent 472:1 error Expected indentation of 16 spaces but found 8 indent 473:1 error Expected indentation of 16 spaces but found 8 indent 474:1 error Expected indentation of 16 spaces but found 8 indent 475:1 error Expected indentation of 16 spaces but found 8 indent 476:1 error Expected indentation of 12 spaces but found 6 indent 477:1 error Expected indentation of 8 spaces but found 4 indent 479:1 error Expected indentation of 8 spaces but found 4 indent 480:1 error Expected indentation of 8 spaces but found 4 indent 481:1 error Expected indentation of 8 spaces but found 4 indent 482:1 error Expected indentation of 12 spaces but found 6 indent 483:1 error Expected indentation of 8 spaces but found 4 indent 485:1 error Expected indentation of 8 spaces but found 4 indent 486:1 error Expected indentation of 12 spaces but found 6 indent 487:1 error Expected indentation of 16 spaces but found 8 indent 488:1 error Expected indentation of 20 spaces but found 10 indent 489:1 error Expected indentation of 24 spaces but found 12 indent 491:1 error Expected indentation of 24 spaces but found 12 indent 492:1 error Expected indentation of 28 spaces but found 14 indent 493:1 error Expected indentation of 32 spaces but found 16 indent 494:1 error Expected indentation of 32 spaces but found 16 indent 495:1 error Expected indentation of 32 spaces but found 16 indent 496:1 error Expected indentation of 32 spaces but found 16 indent 497:1 error Expected indentation of 28 spaces but found 14 indent 498:1 error Expected indentation of 24 spaces but found 12 indent 499:1 error Expected indentation of 20 spaces but found 10 indent 500:1 error Expected indentation of 16 spaces but found 8 indent 501:1 error Expected indentation of 12 spaces but found 6 indent 502:1 error Expected indentation of 8 spaces but found 4 indent 504:1 error Expected indentation of 8 spaces but found 4 indent 505:1 error Expected indentation of 12 spaces but found 6 indent 506:1 error Expected indentation of 16 spaces but found 8 indent 507:1 error Expected indentation of 20 spaces but found 10 indent 508:1 error Expected indentation of 24 spaces but found 12 indent 509:1 error Expected indentation of 28 spaces but found 14 indent 511:1 error Expected indentation of 24 spaces but found 12 indent 512:1 error Expected indentation of 24 spaces but found 12 indent 513:1 error Expected indentation of 28 spaces but found 14 indent 514:1 error Expected indentation of 32 spaces but found 16 indent 515:1 error Expected indentation of 32 spaces but found 16 indent 516:1 error Expected indentation of 28 spaces but found 14 indent 518:1 error Expected indentation of 28 spaces but found 14 indent 519:1 error Expected indentation of 24 spaces but found 12 indent 520:1 error Expected indentation of 24 spaces but found 12 indent 521:1 error Expected indentation of 28 spaces but found 14 indent 522:1 error Expected indentation of 32 spaces but found 16 indent 523:1 error Expected indentation of 32 spaces but found 16 indent 524:1 error Expected indentation of 32 spaces but found 16 indent 525:1 error Expected indentation of 32 spaces but found 16 indent 526:1 error Expected indentation of 28 spaces but found 14 indent 527:1 error Expected indentation of 24 spaces but found 12 indent 528:1 error Expected indentation of 20 spaces but found 10 indent 529:1 error Expected indentation of 16 spaces but found 8 indent 530:1 error Expected indentation of 12 spaces but found 6 indent 531:1 error Expected indentation of 8 spaces but found 4 indent 533:1 error Expected indentation of 8 spaces but found 4 indent 534:1 error Expected indentation of 12 spaces but found 6 indent 535:1 error Expected indentation of 16 spaces but found 8 indent 536:1 error Expected indentation of 16 spaces but found 8 indent 537:1 error Expected indentation of 20 spaces but found 10 indent 538:1 error Expected indentation of 24 spaces but found 12 indent 539:1 error Expected indentation of 20 spaces but found 10 indent 540:1 error Expected indentation of 20 spaces but found 10 indent 541:1 error Expected indentation of 24 spaces but found 12 indent 542:1 error Expected indentation of 20 spaces but found 10 indent 543:1 error Expected indentation of 16 spaces but found 8 indent 544:1 error Expected indentation of 16 spaces but found 8 indent 545:1 error Expected indentation of 12 spaces but found 6 indent 546:1 error Expected indentation of 8 spaces but found 4 indent 547:1 error Expected indentation of 4 spaces but found 2 indent 550:1 error Expected indentation of 4 spaces but found 2 indent 551:1 error Expected indentation of 4 spaces but found 2 indent 552:1 error Expected indentation of 4 spaces but found 2 indent 553:1 error Expected indentation of 4 spaces but found 2 indent 554:1 error Expected indentation of 4 spaces but found 2 indent 555:1 error Expected indentation of 4 spaces but found 2 indent 556:1 error Expected indentation of 4 spaces but found 2 indent 557:1 error Expected indentation of 4 spaces but found 2 indent 558:1 error Expected indentation of 4 spaces but found 2 indent 561:1 error Expected indentation of 4 spaces but found 2 indent 562:1 error Expected indentation of 4 spaces but found 2 indent 563:1 error Expected indentation of 4 spaces but found 2 indent 564:1 error Expected indentation of 4 spaces but found 2 indent 565:1 error Expected indentation of 4 spaces but found 2 indent 566:1 error Expected indentation of 8 spaces but found 4 indent 567:1 error Expected indentation of 8 spaces but found 4 indent 568:1 error Expected indentation of 8 spaces but found 4 indent 569:1 error Expected indentation of 4 spaces but found 2 indent ? 490 problems (490 errors, 0 warnings) 472 errors and 0 warnings potentially fixable with the `--fix` option. ERROR in ./modules/acknowledgements/jsx/acknowledgementsIndex.js Module Error (from ./node_modules/eslint-loader/index.js): /var/www/loris/modules/acknowledgements/jsx/acknowledgementsIndex.js 1:8 error 'React' is defined but never used no-unused-vars 5:8 error 'Modal' is defined but never used no-unused-vars 6:8 error 'Panel' is defined but never used no-unused-vars 7:8 error 'Loader' is defined but never used no-unused-vars 8:8 error 'FilterableDataTable' is defined but never used no-unused-vars 24:1 error Expected indentation of 4 spaces but found 2 indent 25:1 error Expected indentation of 8 spaces but found 4 indent 27:1 error Expected indentation of 8 spaces but found 4 indent 28:1 error Expected indentation of 12 spaces but found 6 indent 29:1 error Expected indentation of 12 spaces but found 6 indent 30:1 error Expected indentation of 12 spaces but found 6 indent 31:1 error Expected indentation of 12 spaces but found 6 indent 32:1 error Expected indentation of 12 spaces but found 6 indent 33:1 error Expected indentation of 16 spaces but found 8 indent 34:1 error Expected indentation of 16 spaces but found 8 indent 35:1 error Expected indentation of 12 spaces but found 6 indent 36:1 error Expected indentation of 12 spaces but found 6 indent 37:1 error Expected indentation of 16 spaces but found 8 indent 38:1 error Expected indentation of 16 spaces but found 8 indent 39:1 error Expected indentation of 16 spaces but found 8 indent 40:1 error Expected indentation of 16 spaces but found 8 indent 41:1 error Expected indentation of 16 spaces but found 8 indent 42:1 error Expected indentation of 16 spaces but found 8 indent 43:1 error Expected indentation of 12 spaces but found 6 indent 44:1 error Expected indentation of 12 spaces but found 6 indent 45:1 error Expected indentation of 16 spaces but found 8 indent 46:1 error Expected indentation of 16 spaces but found 8 indent 47:1 error Expected indentation of 16 spaces but found 8 indent 48:1 error Expected indentation of 16 spaces but found 8 indent 49:1 error Expected indentation of 16 spaces but found 8 indent 50:1 error Expected indentation of 16 spaces but found 8 indent 51:1 error Expected indentation of 16 spaces but found 8 indent 52:1 error Expected indentation of 16 spaces but found 8 indent 53:1 error Expected indentation of 16 spaces but found 8 indent 54:1 error Expected indentation of 16 spaces but found 8 indent 55:1 error Expected indentation of 16 spaces but found 8 indent 56:1 error Expected indentation of 16 spaces but found 8 indent 57:1 error Expected indentation of 16 spaces but found 8 indent 58:1 error Expected indentation of 12 spaces but found 6 indent 59:1 error Expected indentation of 12 spaces but found 6 indent 60:1 error Expected indentation of 8 spaces but found 4 indent 62:1 error Expected indentation of 8 spaces but found 4 indent 63:1 error Expected indentation of 8 spaces but found 4 indent 64:1 error Expected indentation of 8 spaces but found 4 indent 65:1 error Expected indentation of 8 spaces but found 4 indent 66:1 error Expected indentation of 8 spaces but found 4 indent 67:1 error Expected indentation of 8 spaces but found 4 indent 68:1 error Expected indentation of 8 spaces but found 4 indent 69:1 error Expected indentation of 8 spaces but found 4 indent 70:1 error Expected indentation of 8 spaces but found 4 indent 71:1 error Expected indentation of 8 spaces but found 4 indent 72:1 error Expected indentation of 4 spaces but found 2 indent 74:1 error Expected indentation of 4 spaces but found 2 indent 75:1 error Expected indentation of 8 spaces but found 4 indent 76:1 error Expected indentation of 12 spaces but found 6 indent 77:1 error Expected indentation of 4 spaces but found 2 indent 79:1 error Expected indentation of 4 spaces but found 2 indent 86:1 error Expected indentation of 4 spaces but found 2 indent 87:1 error Expected indentation of 8 spaces but found 4 indent 88:1 error Expected indentation of 12 spaces but found 6 indent 89:1 error Expected indentation of 12 spaces but found 6 indent 90:1 error Expected indentation of 12 spaces but found 6 indent 91:1 error Expected indentation of 16 spaces but found 8 indent 92:1 error Expected indentation of 16 spaces but found 8 indent 92:9 error Unexpected console statement no-console 93:1 error Expected indentation of 12 spaces but found 6 indent 94:1 error Expected indentation of 4 spaces but found 2 indent 96:1 error Expected indentation of 4 spaces but found 2 indent 97:1 error Expected indentation of 8 spaces but found 4 indent 98:1 error Expected indentation of 8 spaces but found 4 indent 99:1 error Expected indentation of 12 spaces but found 6 indent 100:1 error Expected indentation of 16 spaces but found 8 indent 101:1 error Expected indentation of 12 spaces but found 6 indent 102:1 error Expected indentation of 8 spaces but found 4 indent 103:1 error Expected indentation of 8 spaces but found 4 indent 104:1 error Expected indentation of 4 spaces but found 2 indent 106:1 error Expected indentation of 4 spaces but found 2 indent 112:1 error Expected indentation of 4 spaces but found 2 indent 113:1 error Expected indentation of 8 spaces but found 4 indent 114:1 error Expected indentation of 8 spaces but found 4 indent 115:1 error Expected indentation of 8 spaces but found 4 indent 116:1 error Expected indentation of 12 spaces but found 6 indent 117:1 error Expected indentation of 8 spaces but found 4 indent 118:1 error Expected indentation of 4 spaces but found 2 indent 120:1 error Expected indentation of 4 spaces but found 2 indent 125:1 error Expected indentation of 4 spaces but found 2 indent 125:16 error 'e' is defined but never used no-unused-vars 126:1 error Expected indentation of 8 spaces but found 4 indent 127:1 error Expected indentation of 8 spaces but found 4 indent 128:1 error Expected indentation of 8 spaces but found 4 indent 129:1 error Expected indentation of 12 spaces but found 6 indent 130:1 error Expected indentation of 16 spaces but found 8 indent 131:1 error Expected indentation of 12 spaces but found 6 indent 132:1 error Expected indentation of 8 spaces but found 4 indent 133:1 error Expected indentation of 8 spaces but found 4 indent 135:1 error Expected indentation of 8 spaces but found 4 indent 136:1 error Expected indentation of 12 spaces but found 6 indent 137:1 error Expected indentation of 12 spaces but found 6 indent 138:1 error Expected indentation of 12 spaces but found 6 indent 139:1 error Expected indentation of 12 spaces but found 6 indent 140:1 error Expected indentation of 8 spaces but found 4 indent 141:1 error Expected indentation of 12 spaces but found 4 indent 142:1 error Expected indentation of 16 spaces but found 6 indent 143:1 error Expected indentation of 20 spaces but found 8 indent 144:1 error Expected indentation of 24 spaces but found 10 indent 145:1 error Expected indentation of 28 spaces but found 12 indent 146:1 error Expected indentation of 28 spaces but found 12 indent 147:1 error Expected indentation of 24 spaces but found 10 indent 148:1 error Expected indentation of 20 spaces but found 8 indent 149:1 error Expected indentation of 16 spaces but found 6 indent 150:1 error Expected indentation of 20 spaces but found 8 indent 151:1 error Expected indentation of 24 spaces but found 10 indent 152:1 error Expected indentation of 20 spaces but found 8 indent 153:1 error Expected indentation of 16 spaces but found 6 indent 154:1 error Expected indentation of 12 spaces but found 4 indent 155:1 error Expected indentation of 12 spaces but found 4 indent 156:1 error Expected indentation of 16 spaces but found 6 indent 156:7 error Unexpected console statement no-console 157:1 error Expected indentation of 12 spaces but found 4 indent 158:1 error Expected indentation of 4 spaces but found 2 indent 160:1 error Expected indentation of 4 spaces but found 2 indent 168:1 error Expected indentation of 4 spaces but found 2 indent 169:1 error Expected indentation of 8 spaces but found 4 indent 170:1 error Expected indentation of 8 spaces but found 4 indent 171:1 error Expected indentation of 12 spaces but found 6 indent 172:1 error Expected indentation of 12 spaces but found 6 indent 173:1 error Expected indentation of 16 spaces but found 8 indent 174:1 error Expected indentation of 20 spaces but found 10 indent 175:1 error Expected indentation of 16 spaces but found 8 indent 176:1 error Expected indentation of 20 spaces but found 10 indent 177:1 error Expected indentation of 16 spaces but found 8 indent 178:1 error Expected indentation of 12 spaces but found 6 indent 179:1 error Expected indentation of 8 spaces but found 4 indent 180:1 error Expected indentation of 12 spaces but found 6 indent 181:1 error Expected indentation of 8 spaces but found 4 indent 182:1 error Expected indentation of 8 spaces but found 4 indent 183:1 error Expected indentation of 4 spaces but found 2 indent 185:1 error Expected indentation of 4 spaces but found 2 indent 194:1 error Expected indentation of 4 spaces but found 2 indent 194:30 error 'row' is defined but never used no-unused-vars 195:1 error Expected indentation of 8 spaces but found 4 indent 197:1 error Expected indentation of 8 spaces but found 4 indent 198:1 error Expected indentation of 8 spaces but found 6 indent 199:1 error Expected indentation of 12 spaces but found 8 indent 200:1 error Expected indentation of 12 spaces but found 8 indent 201:1 error Expected indentation of 8 spaces but found 6 indent 202:1 error Expected indentation of 12 spaces but found 8 indent 203:1 error Expected indentation of 12 spaces but found 8 indent 205:1 error Expected indentation of 8 spaces but found 6 indent 206:1 error Expected indentation of 12 spaces but found 8 indent 207:1 error Expected indentation of 12 spaces but found 8 indent 208:1 error Expected indentation of 8 spaces but found 4 indent 209:1 error Expected indentation of 8 spaces but found 4 indent 210:1 error Expected indentation of 4 spaces but found 2 indent 212:1 error Expected indentation of 4 spaces but found 2 indent 213:1 error Expected indentation of 8 spaces but found 4 indent 214:1 error Expected indentation of 4 spaces but found 2 indent 216:1 error Expected indentation of 4 spaces but found 2 indent 217:1 error Expected indentation of 8 spaces but found 4 indent 218:1 error Expected indentation of 12 spaces but found 6 indent 219:1 error Expected indentation of 12 spaces but found 6 indent 220:1 error Expected indentation of 8 spaces but found 4 indent 221:1 error Expected indentation of 4 spaces but found 2 indent 223:1 error Expected indentation of 4 spaces but found 2 indent 224:1 error Expected indentation of 8 spaces but found 4 indent 225:1 error Expected indentation of 12 spaces but found 6 indent 226:1 error Expected indentation of 16 spaces but found 8 indent 227:1 error Expected indentation of 16 spaces but found 8 indent 228:1 error Expected indentation of 12 spaces but found 6 indent 229:1 error Expected indentation of 16 spaces but found 8 indent 230:1 error Expected indentation of 20 spaces but found 10 indent 231:1 error Expected indentation of 16 spaces but found 8 indent 232:1 error Expected indentation of 12 spaces but found 6 indent 233:1 error Expected indentation of 8 spaces but found 4 indent 234:1 error Expected indentation of 4 spaces but found 2 indent 236:1 error Expected indentation of 4 spaces but found 2 indent 237:1 error Expected indentation of 8 spaces but found 4 indent 238:1 error Expected indentation of 8 spaces but found 4 indent 239:1 error Expected indentation of 8 spaces but found 4 indent 240:1 error Expected indentation of 12 spaces but found 6 indent 241:1 error Expected indentation of 16 spaces but found 8 indent 242:1 error Expected indentation of 16 spaces but found 8 indent 243:1 error Expected indentation of 16 spaces but found 8 indent 244:1 error Expected indentation of 16 spaces but found 8 indent 245:1 error Expected indentation of 12 spaces but found 6 indent 246:1 error Expected indentation of 16 spaces but found 8 indent 247:1 error Expected indentation of 20 spaces but found 10 indent 248:1 error Expected indentation of 20 spaces but found 10 indent 249:1 error Expected indentation of 20 spaces but found 10 indent 250:1 error Expected indentation of 20 spaces but found 10 indent 251:1 error Expected indentation of 20 spaces but found 10 indent 252:1 error Expected indentation of 16 spaces but found 8 indent 253:1 error Expected indentation of 20 spaces but found 10 indent 254:1 error Expected indentation of 24 spaces but found 12 indent 255:1 error Expected indentation of 24 spaces but found 12 indent 256:1 error Expected indentation of 24 spaces but found 12 indent 257:1 error Expected indentation of 24 spaces but found 12 indent 258:1 error Expected indentation of 24 spaces but found 12 indent 259:1 error Expected indentation of 20 spaces but found 10 indent 260:1 error Expected indentation of 20 spaces but found 10 indent 261:1 error Expected indentation of 24 spaces but found 12 indent 262:1 error Expected indentation of 24 spaces but found 12 indent 263:1 error Expected indentation of 24 spaces but found 12 indent 264:1 error Expected indentation of 24 spaces but found 12 indent 265:1 error Expected indentation of 24 spaces but found 12 indent 266:1 error Expected indentation of 20 spaces but found 10 indent 267:1 error Expected indentation of 20 spaces but found 10 indent 268:1 error Expected indentation of 24 spaces but found 12 indent 269:1 error Expected indentation of 24 spaces but found 12 indent 270:1 error Expected indentation of 24 spaces but found 12 indent 271:1 error Expected indentation of 24 spaces but found 12 indent 272:1 error Expected indentation of 24 spaces but found 12 indent 273:1 error Expected indentation of 20 spaces but found 10 indent 274:1 error Expected indentation of 20 spaces but found 10 indent 275:1 error Expected indentation of 24 spaces but found 12 indent 276:1 error Expected indentation of 24 spaces but found 12 indent 277:1 error Expected indentation of 24 spaces but found 12 indent 278:1 error Expected indentation of 24 spaces but found 12 indent 279:1 error Expected indentation of 24 spaces but found 12 indent 280:1 error Expected indentation of 24 spaces but found 12 indent 281:1 error Expected indentation of 24 spaces but found 12 indent 282:1 error Expected indentation of 20 spaces but found 10 indent 283:1 error Expected indentation of 20 spaces but found 10 indent 284:1 error Expected indentation of 24 spaces but found 12 indent 285:1 error Expected indentation of 24 spaces but found 12 indent 286:1 error Expected indentation of 24 spaces but found 12 indent 287:1 error Expected indentation of 24 spaces but found 12 indent 288:1 error Expected indentation of 24 spaces but found 12 indent 289:1 error Expected indentation of 24 spaces but found 12 indent 290:1 error Expected indentation of 24 spaces but found 12 indent 291:1 error Expected indentation of 20 spaces but found 10 indent 292:1 error Expected indentation of 20 spaces but found 10 indent 293:1 error Expected indentation of 24 spaces but found 12 indent 294:1 error Expected indentation of 24 spaces but found 12 indent 295:1 error Expected indentation of 24 spaces but found 12 indent 296:1 error Expected indentation of 24 spaces but found 12 indent 297:1 error Expected indentation of 24 spaces but found 12 indent 298:1 error Expected indentation of 24 spaces but found 12 indent 299:1 error Expected indentation of 24 spaces but found 12 indent 300:1 error Expected indentation of 20 spaces but found 10 indent 301:1 error Expected indentation of 20 spaces but found 10 indent 302:1 error Expected indentation of 24 spaces but found 12 indent 303:1 error Expected indentation of 24 spaces but found 12 indent 304:1 error Expected indentation of 24 spaces but found 12 indent 305:1 error Expected indentation of 24 spaces but found 12 indent 306:1 error Expected indentation of 24 spaces but found 12 indent 307:1 error Expected indentation of 24 spaces but found 12 indent 308:1 error Expected indentation of 24 spaces but found 12 indent 309:1 error Expected indentation of 20 spaces but found 10 indent 310:1 error Expected indentation of 20 spaces but found 10 indent 311:1 error Expected indentation of 24 spaces but found 12 indent 312:1 error Expected indentation of 24 spaces but found 12 indent 313:1 error Expected indentation of 24 spaces but found 12 indent 314:1 error Expected indentation of 24 spaces but found 12 indent 315:1 error Expected indentation of 24 spaces but found 12 indent 316:1 error Expected indentation of 24 spaces but found 12 indent 317:1 error Expected indentation of 24 spaces but found 12 indent 318:1 error Expected indentation of 24 spaces but found 12 indent 319:1 error Expected indentation of 20 spaces but found 10 indent 320:1 error Expected indentation of 20 spaces but found 10 indent 321:1 error Expected indentation of 24 spaces but found 12 indent 322:1 error Expected indentation of 24 spaces but found 12 indent 323:1 error Expected indentation of 24 spaces but found 12 indent 324:1 error Expected indentation of 24 spaces but found 12 indent 325:1 error Expected indentation of 24 spaces but found 12 indent 326:1 error Expected indentation of 24 spaces but found 12 indent 327:1 error Expected indentation of 24 spaces but found 12 indent 328:1 error Expected indentation of 20 spaces but found 10 indent 329:1 error Expected indentation of 20 spaces but found 10 indent 330:1 error Expected indentation of 24 spaces but found 12 indent 331:1 error Expected indentation of 28 spaces but found 14 indent 332:1 error Expected indentation of 28 spaces but found 14 indent 333:1 error Expected indentation of 28 spaces but found 14 indent 334:1 error Expected indentation of 28 spaces but found 14 indent 335:1 error Expected indentation of 24 spaces but found 12 indent 336:1 error Expected indentation of 20 spaces but found 10 indent 337:1 error Expected indentation of 16 spaces but found 8 indent 338:1 error Expected indentation of 12 spaces but found 6 indent 339:1 error Expected indentation of 8 spaces but found 4 indent 340:1 error Expected indentation of 4 spaces but found 2 indent 342:1 error Expected indentation of 4 spaces but found 2 indent 345:1 error Expected indentation of 8 spaces but found 4 indent 346:1 error Expected indentation of 12 spaces but found 6 indent 347:1 error Expected indentation of 8 spaces but found 4 indent 349:1 error Expected indentation of 8 spaces but found 4 indent 350:1 error Expected indentation of 8 spaces but found 4 indent 351:1 error Expected indentation of 12 spaces but found 6 indent 352:1 error Expected indentation of 8 spaces but found 4 indent 354:1 error Expected indentation of 8 spaces but found 3 indent 358:1 error Expected indentation of 8 spaces but found 4 indent 359:1 error Expected indentation of 8 spaces but found 4 indent 360:1 error Expected indentation of 12 spaces but found 6 indent 361:1 error Expected indentation of 12 spaces but found 6 indent 362:1 error Expected indentation of 16 spaces but found 8 indent 363:1 error Expected indentation of 16 spaces but found 8 indent 364:1 error Expected indentation of 12 spaces but found 6 indent 365:1 error Expected indentation of 12 spaces but found 6 indent 366:1 error Expected indentation of 16 spaces but found 8 indent 367:1 error Expected indentation of 16 spaces but found 8 indent 368:1 error Expected indentation of 12 spaces but found 6 indent 369:1 error Expected indentation of 12 spaces but found 6 indent 370:1 error Expected indentation of 12 spaces but found 6 indent 371:1 error Expected indentation of 12 spaces but found 6 indent 372:1 error Expected indentation of 12 spaces but found 6 indent 373:1 error Expected indentation of 16 spaces but found 8 indent 374:1 error Expected indentation of 16 spaces but found 8 indent 375:1 error Expected indentation of 12 spaces but found 6 indent 376:1 error Expected indentation of 12 spaces but found 6 indent 377:1 error Expected indentation of 16 spaces but found 8 indent 378:1 error Expected indentation of 16 spaces but found 8 indent 379:1 error Expected indentation of 12 spaces but found 6 indent 380:1 error Expected indentation of 12 spaces but found 6 indent 381:1 error Expected indentation of 16 spaces but found 8 indent 382:1 error Expected indentation of 16 spaces but found 8 indent 383:1 error Expected indentation of 16 spaces but found 8 indent 384:1 error Expected indentation of 12 spaces but found 6 indent 385:1 error Expected indentation of 8 spaces but found 4 indent 386:1 error Expected indentation of 8 spaces but found 4 indent 387:1 error Expected indentation of 12 spaces but found 6 indent 388:1 error Expected indentation of 8 spaces but found 4 indent 390:1 error Expected indentation of 8 spaces but found 4 indent 391:1 error Expected indentation of 12 spaces but found 6 indent 392:1 error Expected indentation of 16 spaces but found 8 indent 393:1 error Expected indentation of 16 spaces but found 8 indent 394:1 error Expected indentation of 16 spaces but found 8 indent 395:1 error Expected indentation of 20 spaces but found 10 indent 396:1 error Expected indentation of 20 spaces but found 10 indent 397:1 error Expected indentation of 20 spaces but found 10 indent 398:1 error Expected indentation of 20 spaces but found 10 indent 399:1 error Expected indentation of 20 spaces but found 10 indent 400:1 error Expected indentation of 20 spaces but found 10 indent 401:1 error Expected indentation of 16 spaces but found 8 indent 402:1 error Expected indentation of 12 spaces but found 6 indent 403:1 error Expected indentation of 8 spaces but found 4 indent 404:1 error Expected indentation of 4 spaces but found 2 indent 408:1 error Expected indentation of 4 spaces but found 2 indent 409:1 error Expected indentation of 4 spaces but found 2 indent 410:1 error Expected indentation of 4 spaces but found 2 indent 414:1 error Expected indentation of 4 spaces but found 2 indent 414:3 error 'ReactDOM' is not defined no-undef 415:1 error Expected indentation of 8 spaces but found 4 indent 416:1 error Expected indentation of 12 spaces but found 6 indent 416:19 error 'loris' is not defined no-undef 417:1 error Expected indentation of 12 spaces but found 6 indent 417:21 error 'loris' is not defined no-undef 418:1 error Expected indentation of 12 spaces but found 6 indent 418:22 error 'loris' is not defined no-undef 419:1 error Expected indentation of 8 spaces but found 4 indent 420:1 error Expected indentation of 8 spaces but found 4 indent 421:1 error Expected indentation of 4 spaces but found 2 indent ? 350 problems (350 errors, 0 warnings) 337 errors and 0 warnings potentially fixable with the `--fix` option. ERROR in ./modules/brainbrowser/jsx/Brainbrowser.js Module Error (from ./node_modules/eslint-loader/index.js): /var/www/loris/modules/brainbrowser/jsx/Brainbrowser.js 16:1 error Expected indentation of 4 spaces but found 2 indent 17:1 error Expected indentation of 8 spaces but found 4 indent 18:1 error Expected indentation of 8 spaces but found 4 indent 19:1 error Expected indentation of 12 spaces but found 6 indent 20:1 error Expected indentation of 8 spaces but found 4 indent 21:1 error Expected indentation of 8 spaces but found 4 indent 22:1 error Expected indentation of 4 spaces but found 2 indent 24:1 error Expected indentation of 4 spaces but found 2 indent 26:1 error Expected indentation of 8 spaces but found 4 indent 28:1 error Expected indentation of 8 spaces but found 4 indent 29:1 error Expected indentation of 12 spaces but found 6 indent 30:1 error Expected indentation of 8 spaces but found 4 indent 32:1 error Expected indentation of 8 spaces but found 4 indent 32:22 error 'loris' is not defined no-undef 33:1 error Expected indentation of 12 spaces but found 6 indent 33:19 error 'loris' is not defined no-undef 34:1 error Expected indentation of 12 spaces but found 6 indent 34:19 error 'loris' is not defined no-undef 35:1 error Expected indentation of 8 spaces but found 4 indent 37:1 error Expected indentation of 8 spaces but found 4 indent 37:35 error 'loris' is not defined no-undef 38:1 error Expected indentation of 8 spaces but found 4 indent 40:1 error Expected indentation of 8 spaces but found 4 indent 41:1 error Expected indentation of 8 spaces but found 4 indent 42:1 error Expected indentation of 4 spaces but found 2 indent 44:1 error Expected indentation of 4 spaces but found 2 indent 45:1 error Expected indentation of 8 spaces but found 4 indent 47:1 error Expected indentation of 8 spaces but found 4 indent 48:1 error Expected indentation of 8 spaces but found 4 indent 48:22 error 'loris' is not defined no-undef 49:1 error Expected indentation of 8 spaces but found 4 indent 51:1 error Expected indentation of 8 spaces but found 4 indent 52:1 error Expected indentation of 4 spaces but found 2 indent 54:1 error Expected indentation of 4 spaces but found 2 indent 55:1 error Expected indentation of 8 spaces but found 4 indent 56:1 error Expected indentation of 12 spaces but found 6 indent 57:1 error Expected indentation of 12 spaces but found 6 indent 58:1 error Expected indentation of 12 spaces but found 6 indent 59:1 error Expected indentation of 12 spaces but found 6 indent 60:1 error Expected indentation of 12 spaces but found 6 indent 61:1 error Expected indentation of 12 spaces but found 6 indent 62:1 error Expected indentation of 12 spaces but found 6 indent 63:1 error Expected indentation of 12 spaces but found 6 indent 64:1 error Expected indentation of 12 spaces but found 6 indent 65:1 error Expected indentation of 12 spaces but found 6 indent 66:1 error Expected indentation of 12 spaces but found 6 indent 67:1 error Expected indentation of 8 spaces but found 4 indent 69:1 error Expected indentation of 8 spaces but found 4 indent 70:1 error Expected indentation of 12 spaces but found 6 indent 71:1 error Expected indentation of 16 spaces but found 8 indent 72:1 error Expected indentation of 20 spaces but found 10 indent 73:1 error Expected indentation of 24 spaces but found 12 indent 74:1 error Expected indentation of 24 spaces but found 12 indent 75:1 error Expected indentation of 24 spaces but found 12 indent 76:1 error Expected indentation of 28 spaces but found 20 indent 77:1 error Expected indentation of 28 spaces but found 20 indent 78:1 error Expected indentation of 28 spaces but found 20 indent 79:1 error Expected indentation of 28 spaces but found 14 indent 80:1 error Expected indentation of 28 spaces but found 14 indent 81:1 error Expected indentation of 32 spaces but found 16 indent 82:1 error Expected indentation of 36 spaces but found 18 indent 83:1 error Expected indentation of 32 spaces but found 16 indent 84:1 error Expected indentation of 28 spaces but found 14 indent 85:1 error Expected indentation of 24 spaces but found 12 indent 86:1 error Expected indentation of 20 spaces but found 10 indent 87:1 error Expected indentation of 16 spaces but found 8 indent 88:1 error Expected indentation of 16 spaces but found 8 indent 89:1 error Expected indentation of 16 spaces but found 8 indent 90:1 error Expected indentation of 12 spaces but found 6 indent 91:1 error Expected indentation of 8 spaces but found 4 indent 92:1 error Expected indentation of 4 spaces but found 2 indent ? 71 problems (71 errors, 0 warnings) 66 errors and 0 warnings potentially fixable with the `--fix` option. ERROR in ./modules/bvl_feedback/jsx/react.behavioural_feedback_panel.js Module Error (from ./node_modules/eslint-loader/index.js): /var/www/loris/modules/bvl_feedback/jsx/react.behavioural_feedback_panel.js 7:1 error Expected indentation of 4 spaces but found 2 indent 8:1 error Expected indentation of 8 spaces but found 4 indent 9:1 error Expected indentation of 4 spaces but found 2 indent 10:1 error Expected indentation of 4 spaces but found 2 indent 11:1 error Expected indentation of 8 spaces but found 4 indent 12:1 error Expected indentation of 12 spaces but found 6 indent 13:1 error Expected indentation of 16 spaces but found 8 indent 14:1 error Expected indentation of 20 spaces but found 10 indent 16:1 error Expected indentation of 20 spaces but found 10 indent 17:1 error Expected indentation of 16 spaces but found 8 indent 18:1 error Expected indentation of 16 spaces but found 8 indent 19:1 error Expected indentation of 12 spaces but found 6 indent 20:1 error Expected indentation of 8 spaces but found 4 indent 21:1 error Expected indentation of 4 spaces but found 2 indent 24:1 error Expected indentation of 4 spaces but found 2 indent 25:1 error Expected indentation of 4 spaces but found 2 indent 29:1 error Expected indentation of 4 spaces but found 2 indent 30:1 error Expected indentation of 8 spaces but found 4 indent 31:1 error Expected indentation of 8 spaces but found 4 indent 32:1 error Expected indentation of 12 spaces but found 6 indent 33:1 error Expected indentation of 8 spaces but found 4 indent 34:1 error Expected indentation of 8 spaces but found 4 indent 35:1 error Expected indentation of 8 spaces but found 4 indent 36:1 error Expected indentation of 8 spaces but found 4 indent 37:1 error Expected indentation of 4 spaces but found 2 indent 39:1 error Expected indentation of 4 spaces but found 2 indent 40:1 error Expected indentation of 8 spaces but found 4 indent 41:1 error Expected indentation of 12 spaces but found 6 indent 42:1 error Expected indentation of 16 spaces but found 8 indent 43:1 error Expected indentation of 12 spaces but found 6 indent 44:1 error Expected indentation of 8 spaces but found 4 indent 45:1 error Expected indentation of 12 spaces but found 6 indent 46:1 error Expected indentation of 16 spaces but found 8 indent 47:1 error Expected indentation of 12 spaces but found 6 indent 48:1 error Expected indentation of 8 spaces but found 4 indent 49:1 error Expected indentation of 4 spaces but found 2 indent 51:1 error Expected indentation of 4 spaces but found 2 indent 52:1 error Expected indentation of 8 spaces but found 4 indent 53:1 error Expected indentation of 4 spaces but found 2 indent 55:1 error Expected indentation of 4 spaces but found 2 indent 56:1 error Expected indentation of 8 spaces but found 4 indent 57:1 error Expected indentation of 8 spaces but found 4 indent 58:1 error Expected indentation of 12 spaces but found 6 indent 59:1 error Expected indentation of 8 spaces but found 4 indent 60:1 error Expected indentation of 4 spaces but found 2 indent 62:1 error Expected indentation of 4 spaces but found 2 indent 63:1 error Expected indentation of 8 spaces but found 4 indent 65:1 error Expected indentation of 8 spaces but found 4 indent 66:1 error Expected indentation of 12 spaces but found 6 indent 67:1 error Expected indentation of 8 spaces but found 4 indent 69:1 error Expected indentation of 8 spaces but found 4 indent 70:1 error Expected indentation of 12 spaces but found 6 indent 71:1 error Expected indentation of 16 spaces but found 8 indent 72:1 error Expected indentation of 20 spaces but found 10 indent 73:1 error Expected indentation of 16 spaces but found 8 indent 74:1 error Expected indentation of 12 spaces but found 6 indent 75:1 error Expected indentation of 8 spaces but found 4 indent 77:1 error Expected indentation of 8 spaces but found 4 indent 78:1 error Expected indentation of 12 spaces but found 6 indent 79:1 error Expected indentation of 12 spaces but found 6 indent 80:1 error Expected indentation of 16 spaces but found 8 indent 81:1 error Expected indentation of 16 spaces but found 8 indent 82:1 error Expected indentation of 20 spaces but found 10 indent 83:1 error Expected indentation of 24 spaces but found 12 indent 84:1 error Expected indentation of 24 spaces but found 12 indent 85:1 error Expected indentation of 24 spaces but found 12 indent 86:1 error Expected indentation of 24 spaces but found 12 indent 87:1 error Expected indentation of 24 spaces but found 12 indent 88:1 error Expected indentation of 24 spaces but found 12 indent 89:1 error Expected indentation of 24 spaces but found 12 indent 90:1 error Expected indentation of 24 spaces but found 12 indent 91:1 error Expected indentation of 24 spaces but found 12 indent 92:1 error Expected indentation of 24 spaces but found 12 indent 93:1 error Expected indentation of 24 spaces but found 12 indent 94:1 error Expected indentation of 24 spaces but found 12 indent 95:1 error Expected indentation of 24 spaces but found 12 indent 96:1 error Expected indentation of 24 spaces but found 12 indent 97:1 error Expected indentation of 20 spaces but found 10 indent 98:1 error Expected indentation of 16 spaces but found 8 indent 99:1 error Expected indentation of 12 spaces but found 6 indent 101:1 error Expected indentation of 12 spaces but found 6 indent 102:1 error Expected indentation of 16 spaces but found 8 indent 103:1 error Expected indentation of 20 spaces but found 10 indent 104:1 error Expected indentation of 20 spaces but found 10 indent 105:1 error Expected indentation of 16 spaces but found 8 indent 106:1 error Expected indentation of 20 spaces but found 10 indent 107:1 error Expected indentation of 24 spaces but found 12 indent 108:1 error Expected indentation of 20 spaces but found 10 indent 109:1 error Expected indentation of 20 spaces but found 10 indent 110:1 error Expected indentation of 16 spaces but found 8 indent 111:1 error Expected indentation of 12 spaces but found 6 indent 113:1 error Expected indentation of 12 spaces but found 6 indent 114:1 error Expected indentation of 16 spaces but found 8 indent 115:1 error Expected indentation of 20 spaces but found 10 indent 116:1 error Expected indentation of 24 spaces but found 12 indent 117:1 error Expected indentation of 20 spaces but found 10 indent 118:1 error Expected indentation of 16 spaces but found 8 indent 119:1 error Expected indentation of 12 spaces but found 6 indent 120:1 error Expected indentation of 8 spaces but found 4 indent 122:1 error Expected indentation of 8 spaces but found 4 indent 123:1 error Expected indentation of 12 spaces but found 6 indent 124:1 error Expected indentation of 8 spaces but found 4 indent 125:1 error Expected indentation of 4 spaces but found 2 indent 128:1 error Expected indentation of 4 spaces but found 2 indent 129:1 error Expected indentation of 4 spaces but found 2 indent 130:1 error Expected indentation of 4 spaces but found 2 indent 131:1 error Expected indentation of 4 spaces but found 2 indent 132:1 error Expected indentation of 4 spaces but found 2 indent 133:1 error Expected indentation of 4 spaces but found 2 indent 134:1 error Expected indentation of 4 spaces but found 2 indent 138:1 error Expected indentation of 4 spaces but found 2 indent 139:1 error Expected indentation of 8 spaces but found 4 indent 140:1 error Expected indentation of 8 spaces but found 4 indent 141:1 error Expected indentation of 12 spaces but found 6 indent 142:1 error Expected indentation of 12 spaces but found 6 indent 143:1 error Expected indentation of 8 spaces but found 4 indent 144:1 error Expected indentation of 8 spaces but found 4 indent 145:1 error Expected indentation of 8 spaces but found 4 indent 146:1 error Expected indentation of 8 spaces but found 4 indent 147:1 error Expected indentation of 4 spaces but found 2 indent 149:1 error Expected indentation of 4 spaces but found 2 indent 150:1 error Expected indentation of 8 spaces but found 4 indent 151:1 error Expected indentation of 4 spaces but found 2 indent 153:1 error Expected indentation of 4 spaces but found 2 indent 154:1 error Expected indentation of 8 spaces but found 4 indent 155:1 error Expected indentation of 8 spaces but found 4 indent 155:5 error '$' is not defined no-undef 156:1 error Expected indentation of 12 spaces but found 6 indent 157:1 error Expected indentation of 12 spaces but found 6 indent 157:12 error 'loris' is not defined no-undef 158:1 error Expected indentation of 12 spaces but found 6 indent 159:1 error Expected indentation of 12 spaces but found 6 indent 160:1 error Expected indentation of 12 spaces but found 6 indent 161:1 error Expected indentation of 16 spaces but found 8 indent 162:1 error Expected indentation of 12 spaces but found 6 indent 163:1 error Expected indentation of 12 spaces but found 6 indent 164:1 error Expected indentation of 16 spaces but found 8 indent 164:9 error Unexpected console statement no-console 165:1 error Expected indentation of 16 spaces but found 8 indent 165:9 error Unexpected console statement no-console 166:1 error Expected indentation of 12 spaces but found 6 indent 167:1 error Expected indentation of 8 spaces but found 4 indent 168:1 error Expected indentation of 4 spaces but found 2 indent 170:1 error Expected indentation of 4 spaces but found 2 indent 171:1 error Expected indentation of 8 spaces but found 4 indent 172:1 error Expected indentation of 8 spaces but found 4 indent 173:1 error Expected indentation of 12 spaces but found 6 indent 174:1 error Expected indentation of 8 spaces but found 4 indent 175:1 error Expected indentation of 12 spaces but found 6 indent 176:1 error Expected indentation of 8 spaces but found 4 indent 177:1 error Expected indentation of 8 spaces but found 4 indent 178:1 error Expected indentation of 4 spaces but found 2 indent 180:1 error Expected indentation of 4 spaces but found 2 indent 181:1 error Expected indentation of 8 spaces but found 4 indent 182:1 error Expected indentation of 8 spaces but found 4 indent 183:1 error Expected indentation of 8 spaces but found 4 indent 183:5 error '$' is not defined no-undef 184:1 error Expected indentation of 12 spaces but found 6 indent 185:1 error Expected indentation of 12 spaces but found 6 indent 185:12 error 'loris' is not defined no-undef 186:1 error Expected indentation of 12 spaces but found 6 indent 187:1 error Expected indentation of 12 spaces but found 6 indent 188:1 error Expected indentation of 16 spaces but found 8 indent 189:1 error Expected indentation of 16 spaces but found 8 indent 190:1 error Expected indentation of 16 spaces but found 8 indent 191:1 error Expected indentation of 12 spaces but found 6 indent 192:1 error Expected indentation of 12 spaces but found 6 indent 192:25 error 'response' is defined but never used no-unused-vars 193:1 error Expected indentation of 16 spaces but found 8 indent 194:1 error Expected indentation of 16 spaces but found 8 indent 195:1 error Expected indentation of 12 spaces but found 6 indent 196:1 error Expected indentation of 12 spaces but found 6 indent 197:1 error Expected indentation of 16 spaces but found 8 indent 197:9 error Unexpected console statement no-console 198:1 error Expected indentation of 16 spaces but found 8 indent 198:9 error Unexpected console statement no-console 199:1 error Expected indentation of 12 spaces but found 6 indent 200:1 error Expected indentation of 8 spaces but found 4 indent 201:1 error Expected indentation of 4 spaces but found 2 indent 203:1 error Expected indentation of 4 spaces but found 2 indent 204:1 error Expected indentation of 8 spaces but found 4 indent 205:1 error Expected indentation of 8 spaces but found 4 indent 207:1 error Expected indentation of 8 spaces but found 4 indent 208:1 error Expected indentation of 8 spaces but found 4 indent 209:1 error Expected indentation of 8 spaces but found 4 indent 210:1 error Expected indentation of 8 spaces but found 4 indent 212:1 error Expected indentation of 8 spaces but found 4 indent 213:1 error Expected indentation of 12 spaces but found 6 indent 214:1 error Expected indentation of 12 spaces but found 6 indent 215:1 error Expected indentation of 16 spaces but found 8 indent 216:1 error Expected indentation of 20 spaces but found 10 indent 217:1 error Expected indentation of 24 spaces but found 12 indent 218:1 error Expected indentation of 28 spaces but found 14 indent 219:1 error Expected indentation of 28 spaces but found 14 indent 220:1 error Expected indentation of 24 spaces but found 12 indent 221:1 error Expected indentation of 20 spaces but found 10 indent 222:1 error Expected indentation of 16 spaces but found 8 indent 223:1 error Expected indentation of 12 spaces but found 6 indent 224:1 error Expected indentation of 8 spaces but found 4 indent 226:1 error Expected indentation of 8 spaces but found 4 indent 227:1 error Expected indentation of 12 spaces but found 6 indent 228:1 error Expected indentation of 12 spaces but found 6 indent 229:1 error Expected indentation of 12 spaces but found 6 indent 230:1 error Expected indentation of 12 spaces but found 6 indent 231:1 error Expected indentation of 16 spaces but found 8 indent 232:1 error Expected indentation of 20 spaces but found 14 indent 233:1 error Expected indentation of 12 spaces but found 6 indent 234:1 error Expected indentation of 8 spaces but found 4 indent 236:1 error Expected indentation of 8 spaces but found 4 indent 237:1 error Expected indentation of 12 spaces but found 6 indent 238:1 error Expected indentation of 16 spaces but found 6 indent 239:1 error Expected indentation of 20 spaces but found 8 indent 240:1 error Expected indentation of 24 spaces but found 10 indent 241:1 error Expected indentation of 24 spaces but found 10 indent 242:1 error Expected indentation of 20 spaces but found 8 indent 243:1 error Expected indentation of 20 spaces but found 8 indent 244:1 error Expected indentation of 24 spaces but found 10 indent 245:1 error Expected indentation of 28 spaces but found 12 indent 246:1 error Expected indentation of 32 spaces but found 20 indent 247:1 error Expected indentation of 32 spaces but found 20 indent 248:1 error Expected indentation of 32 spaces but found 14 indent 249:1 error Expected indentation of 32 spaces but found 14 indent 250:1 error Expected indentation of 28 spaces but found 12 indent 251:1 error Expected indentation of 28 spaces but found 12 indent 252:1 error Expected indentation of 32 spaces but found 14 indent 253:1 error Expected indentation of 28 spaces but found 12 indent 254:1 error Expected indentation of 24 spaces but found 10 indent 255:1 error Expected indentation of 24 spaces but found 10 indent 256:1 error Expected indentation of 28 spaces but found 16 indent 257:1 error Expected indentation of 24 spaces but found 10 indent 258:1 error Expected indentation of 20 spaces but found 8 indent 259:1 error Expected indentation of 16 spaces but found 6 indent 260:1 error Expected indentation of 16 spaces but found 6 indent 261:1 error Expected indentation of 20 spaces but found 8 indent 262:1 error Expected indentation of 24 spaces but found 10 indent 263:1 error Expected indentation of 24 spaces but found 10 indent 264:1 error Expected indentation of 24 spaces but found 10 indent 265:1 error Expected indentation of 20 spaces but found 8 indent 266:1 error Expected indentation of 20 spaces but found 8 indent 267:1 error Expected indentation of 16 spaces but found 6 indent 268:1 error Expected indentation of 16 spaces but found 6 indent 269:1 error Expected indentation of 12 spaces but found 6 indent 270:1 error Expected indentation of 8 spaces but found 4 indent 271:1 error Expected indentation of 4 spaces but found 2 indent 274:1 error Expected indentation of 4 spaces but found 2 indent 275:1 error Expected indentation of 4 spaces but found 2 indent 276:1 error Expected indentation of 4 spaces but found 2 indent 277:1 error Expected indentation of 4 spaces but found 2 indent 278:1 error Expected indentation of 4 spaces but found 2 indent 279:1 error Expected indentation of 4 spaces but found 2 indent 280:1 error Expected indentation of 4 spaces but found 2 indent 284:1 error Expected indentation of 4 spaces but found 2 indent 285:1 error Expected indentation of 8 spaces but found 4 indent 286:1 error Expected indentation of 8 spaces but found 4 indent 287:1 error Expected indentation of 12 spaces but found 6 indent 288:1 error Expected indentation of 8 spaces but found 4 indent 289:1 error Expected indentation of 8 spaces but found 4 indent 290:1 error Expected indentation of 8 spaces but found 4 indent 291:1 error Expected indentation of 4 spaces but found 2 indent 293:1 error Expected indentation of 4 spaces but found 2 indent 294:1 error Expected indentation of 8 spaces but found 4 indent 295:1 error Expected indentation of 8 spaces but found 4 indent 296:1 error Expected indentation of 12 spaces but found 6 indent 297:1 error Expected indentation of 8 spaces but found 4 indent 298:1 error Expected indentation of 8 spaces but found 4 indent 299:1 error Expected indentation of 4 spaces but found 2 indent 301:1 error Expected indentation of 4 spaces but found 2 indent 302:1 error Expected indentation of 8 spaces but found 4 indent 303:1 error Expected indentation of 4 spaces but found 2 indent 305:1 error Expected indentation of 4 spaces but found 2 indent 306:1 error Expected indentation of 8 spaces but found 4 indent 307:1 error Expected indentation of 12 spaces but found 6 indent 308:1 error Expected indentation of 16 spaces but found 8 indent 309:1 error Expected indentation of 20 spaces but found 10 indent 310:1 error Expected indentation of 24 spaces but found 12 indent 311:1 error Expected indentation of 28 spaces but found 14 indent 312:1 error Expected indentation of 28 spaces but found 14 indent 313:1 error Expected indentation of 28 spaces but found 14 indent 314:1 error Expected indentation of 28 spaces but found 14 indent 315:1 error Expected indentation of 28 spaces but found 14 indent 316:1 error Expected indentation of 28 spaces but found 14 indent 317:1 error Expected indentation of 24 spaces but found 12 indent 318:1 error Expected indentation of 24 spaces but found 12 indent 319:1 error Expected indentation of 28 spaces but found 14 indent 320:1 error Expected indentation of 28 spaces but found 14 indent 321:1 error Expected indentation of 24 spaces but found 12 indent 323:1 error Expected indentation of 24 spaces but found 12 indent 324:1 error Expected indentation of 20 spaces but found 10 indent 325:1 error Expected indentation of 16 spaces but found 8 indent 326:1 error Expected indentation of 12 spaces but found 6 indent 327:1 error Expected indentation of 8 spaces but found 4 indent 328:1 error Expected indentation of 4 spaces but found 2 indent 331:1 error Expected indentation of 4 spaces but found 2 indent 332:1 error Expected indentation of 4 spaces but found 2 indent 336:1 error Expected indentation of 4 spaces but found 2 indent 337:1 error Expected indentation of 8 spaces but found 4 indent 338:1 error Expected indentation of 8 spaces but found 4 indent 339:1 error Expected indentation of 12 spaces but found 6 indent 340:1 error Expected indentation of 8 spaces but found 4 indent 341:1 error Expected indentation of 8 spaces but found 4 indent 342:1 error Expected indentation of 4 spaces but found 2 indent 344:1 error Expected indentation of 4 spaces but found 2 indent 345:1 error Expected indentation of 8 spaces but found 4 indent 346:1 error Expected indentation of 12 spaces but found 6 indent 347:1 error Expected indentation of 8 spaces but found 4 indent 348:1 error Expected indentation of 4 spaces but found 2 indent 350:1 error Expected indentation of 4 spaces but found 2 indent 351:1 error Expected indentation of 8 spaces but found 4 indent 352:1 error Expected indentation of 8 spaces but found 4 indent 354:1 error Expected indentation of 8 spaces but found 4 indent 355:1 error Expected indentation of 12 spaces but found 6 indent 356:1 error Expected indentation of 12 spaces but found 6 indent 357:1 error Expected indentation of 8 spaces but found 4 indent 359:1 error Expected indentation of 8 spaces but found 4 indent 360:1 error Expected indentation of 12 spaces but found 6 indent 361:1 error Expected indentation of 16 spaces but found 8 indent 362:1 error Expected indentation of 20 spaces but found 10 indent 363:1 error Expected indentation of 24 spaces but found 12 indent 364:1 error Expected indentation of 28 spaces but found 14 indent 365:1 error Expected indentation of 32 spaces but found 16 indent 366:1 error Expected indentation of 28 spaces but found 14 indent 367:1 error Expected indentation of 24 spaces but found 12 indent 368:1 error Expected indentation of 20 spaces but found 10 indent 369:1 error Expected indentation of 20 spaces but found 10 indent 370:1 error Expected indentation of 24 spaces but found 12 indent 371:1 error Expected indentation of 20 spaces but found 10 indent 372:1 error Expected indentation of 16 spaces but found 8 indent 373:1 error Expected indentation of 12 spaces but found 6 indent 374:1 error Expected indentation of 8 spaces but found 4 indent 375:1 error Expected indentation of 4 spaces but found 2 indent 378:1 error Expected indentation of 4 spaces but found 2 indent 379:1 error Expected indentation of 4 spaces but found 2 indent 383:1 error Expected indentation of 4 spaces but found 2 indent 384:1 error Expected indentation of 8 spaces but found 4 indent 385:1 error Expected indentation of 8 spaces but found 4 indent 386:1 error Expected indentation of 12 spaces but found 6 indent 387:1 error Expected indentation of 12 spaces but found 6 indent 388:1 error Expected indentation of 12 spaces but found 6 indent 389:1 error Expected indentation of 8 spaces but found 4 indent 390:1 error Expected indentation of 8 spaces but found 4 indent 391:1 error Expected indentation of 8 spaces but found 4 indent 392:1 error Expected indentation of 8 spaces but found 4 indent 393:1 error Expected indentation of 8 spaces but found 4 indent 394:1 error Expected indentation of 4 spaces but found 2 indent 396:1 error Expected indentation of 4 spaces but found 2 indent 397:1 error Expected indentation of 8 spaces but found 4 indent 398:1 error Expected indentation of 4 spaces but found 2 indent 400:1 error Expected indentation of 4 spaces but found 2 indent 401:1 error Expected indentation of 8 spaces but found 4 indent 402:1 error Expected indentation of 4 spaces but found 2 indent 404:1 error Expected indentation of 4 spaces but found 2 indent 405:1 error Expected indentation of 8 spaces but found 4 indent 406:1 error Expected indentation of 4 spaces but found 2 indent 408:1 error Expected indentation of 4 spaces but found 2 indent 409:1 error Expected indentation of 8 spaces but found 4 indent 410:1 error Expected indentation of 12 spaces but found 6 indent 410:7 error '$' is not defined no-undef 411:1 error Expected indentation of 16 spaces but found 8 indent 412:1 error Expected indentation of 16 spaces but found 8 indent 412:14 error 'loris' is not defined no-undef 413:1 error Expected indentation of 16 spaces but found 8 indent 414:1 error Expected indentation of 16 spaces but found 8 indent 415:1 error Expected indentation of 20 spaces but found 10 indent 416:1 error Expected indentation of 20 spaces but found 10 indent 417:1 error Expected indentation of 20 spaces but found 10 indent 418:1 error Expected indentation of 20 spaces but found 10 indent 419:1 error Expected indentation of 20 spaces but found 10 indent 420:1 error Expected indentation of 20 spaces but found 10 indent 421:1 error Expected indentation of 20 spaces but found 10 indent 422:1 error Expected indentation of 16 spaces but found 8 indent 423:1 error Expected indentation of 16 spaces but found 8 indent 424:1 error Expected indentation of 20 spaces but found 10 indent 425:1 error Expected indentation of 20 spaces but found 10 indent 426:1 error Expected indentation of 20 spaces but found 10 indent 427:1 error Expected indentation of 16 spaces but found 8 indent 428:1 error Expected indentation of 16 spaces but found 8 indent 429:1 error Expected indentation of 20 spaces but found 10 indent 429:11 error Unexpected console statement no-console 430:1 error Expected indentation of 20 spaces but found 10 indent 430:11 error Unexpected console statement no-console 431:1 error Expected indentation of 16 spaces but found 8 indent 432:1 error Expected indentation of 12 spaces but found 6 indent 433:1 error Expected indentation of 8 spaces but found 4 indent 434:1 error Expected indentation of 4 spaces but found 2 indent 436:1 error Expected indentation of 4 spaces but found 2 indent 437:1 error Expected indentation of 8 spaces but found 4 indent 438:1 error Expected indentation of 8 spaces but found 4 indent 439:1 error Expected indentation of 8 spaces but found 4 indent 440:1 error Expected indentation of 12 spaces but found 6 indent 441:1 error Expected indentation of 16 spaces but found 8 indent 442:1 error Expected indentation of 20 spaces but found 10 indent 443:1 error Expected indentation of 16 spaces but found 8 indent 444:1 error Expected indentation of 12 spaces but found 6 indent 445:1 error Expected indentation of 8 spaces but found 4 indent 447:1 error Expected indentation of 8 spaces but found 4 indent 448:1 error Expected indentation of 12 spaces but found 6 indent 449:1 error Expected indentation of 16 spaces but found 8 indent 450:1 error Expected indentation of 20 spaces but found 10 indent 451:1 error Expected indentation of 24 spaces but found 12 indent 452:1 error Expected indentation of 24 spaces but found 12 indent 453:1 error Expected indentation of 28 spaces but found 14 indent 454:1 error Expected indentation of 32 spaces but found 16 indent 455:1 error Expected indentation of 32 spaces but found 16 indent 456:1 error Expected indentation of 32 spaces but found 16 indent 457:1 error Expected indentation of 32 spaces but found 16 indent 458:1 error Expected indentation of 28 spaces but found 14 indent 459:1 error Expected indentation of 32 spaces but found 16 indent 460:1 error Expected indentation of 28 spaces but found 14 indent 461:1 error Expected indentation of 24 spaces but found 12 indent 462:1 error Expected indentation of 20 spaces but found 10 indent 463:1 error Expected indentation of 16 spaces but found 8 indent 464:1 error Expected indentation of 12 spaces but found 6 indent 465:1 error Expected indentation of 8 spaces but found 4 indent 467:1 error Expected indentation of 8 spaces but found 4 indent 468:1 error Expected indentation of 8 spaces but found 4 indent 469:1 error Expected indentation of 8 spaces but found 4 indent 470:1 error Expected indentation of 12 spaces but found 6 indent 471:1 error Expected indentation of 16 spaces but found 8 indent 472:1 error Expected indentation of 20 spaces but found 10 indent 473:1 error Expected indentation of 24 spaces but found 12 indent 474:1 error Expected indentation of 20 spaces but found 10 indent 475:1 error Expected indentation of 16 spaces but found 8 indent 476:1 error Expected indentation of 12 spaces but found 6 indent 477:1 error Expected indentation of 8 spaces but found 4 indent 479:1 error Expected indentation of 8 spaces but found 4 indent 480:1 error Expected indentation of 12 spaces but found 6 indent 481:1 error Expected indentation of 16 spaces but found 8 indent 482:1 error Expected indentation of 20 spaces but found 10 indent 483:1 error Expected indentation of 24 spaces but found 12 indent 484:1 error Expected indentation of 24 spaces but found 12 indent 485:1 error Expected indentation of 24 spaces but found 12 indent 486:1 error Expected indentation of 24 spaces but found 12 indent 487:1 error Expected indentation of 24 spaces but found 12 indent 488:1 error Expected indentation of 20 spaces but found 10 indent 489:1 error Expected indentation of 16 spaces but found 8 indent 490:1 error Expected indentation of 16 spaces but found 8 indent 491:1 error Expected indentation of 16 spaces but found 8 indent 492:1 error Expected indentation of 20 spaces but found 10 indent 493:1 error Expected indentation of 24 spaces but found 12 indent 494:1 error Expected indentation of 24 spaces but found 12 indent 495:1 error Expected indentation of 28 spaces but found 14 indent 496:1 error Expected indentation of 32 spaces but found 16 indent 497:1 error Expected indentation of 32 spaces but found 16 indent 498:1 error Expected indentation of 32 spaces but found 16 indent 499:1 error Expected indentation of 32 spaces but found 16 indent 500:1 error Expected indentation of 28 spaces but found 14 indent 501:1 error Expected indentation of 32 spaces but found 16 indent 502:1 error Expected indentation of 28 spaces but found 14 indent 503:1 error Expected indentation of 24 spaces but found 12 indent 504:1 error Expected indentation of 20 spaces but found 10 indent 505:1 error Expected indentation of 16 spaces but found 8 indent 506:1 error Expected indentation of 16 spaces but found 8 indent 507:1 error Expected indentation of 20 spaces but found 10 indent 508:1 error Expected indentation of 24 spaces but found 12 indent 509:1 error Expected indentation of 24 spaces but found 12 indent 510:1 error Expected indentation of 24 spaces but found 12 indent 511:1 error Expected indentation of 20 spaces but found 10 indent 513:1 error Expected indentation of 20 spaces but found 10 indent 514:1 error Expected indentation of 16 spaces but found 8 indent 515:1 error Expected indentation of 12 spaces but found 6 indent 516:1 error Expected indentation of 8 spaces but found 4 indent 517:1 error Expected indentation of 4 spaces but found 2 indent 520:1 error Expected indentation of 4 spaces but found 2 indent 521:1 error Expected indentation of 4 spaces but found 2 indent 522:1 error Expected indentation of 4 spaces but found 2 indent 523:1 error Expected indentation of 4 spaces but found 2 indent 524:1 error Expected indentation of 4 spaces but found 2 indent 525:1 error Expected indentation of 4 spaces but found 2 indent 526:1 error Expected indentation of 4 spaces but found 2 indent 527:1 error Expected indentation of 4 spaces but found 2 indent 528:1 error Expected indentation of 4 spaces but found 2 indent 529:1 error Expected indentation of 4 spaces but found 2 indent 530:1 error Expected indentation of 4 spaces but found 2 indent 531:1 error Expected indentation of 4 spaces but found 2 indent 535:1 error Expected indentation of 4 spaces but found 2 indent 536:1 error Expected indentation of 8 spaces but found 4 indent 537:1 error Expected indentation of 8 spaces but found 4 indent 538:1 error Expected indentation of 12 spaces but found 6 indent 539:1 error Expected indentation of 8 spaces but found 4 indent 540:1 error Expected indentation of 4 spaces but found 2 indent 542:1 error Expected indentation of 4 spaces but found 2 indent 543:1 error Expected indentation of 8 spaces but found 4 indent 545:1 error Expected indentation of 8 spaces but found 4 indent 546:1 error Expected indentation of 12 spaces but found 6 indent 547:1 error Expected indentation of 16 spaces but found 8 indent 548:1 error Expected indentation of 20 spaces but found 10 indent 549:1 error Expected indentation of 24 spaces but found 12 indent 550:1 error Expected indentation of 24 spaces but found 12 indent 551:1 error Expected indentation of 28 spaces but found 14 indent 551:24 error 'loris' is not defined no-undef 554:1 error Expected indentation of 28 spaces but found 14 indent 555:1 error Expected indentation of 32 spaces but found 16 indent 556:1 error Expected indentation of 28 spaces but found 14 indent 557:1 error Expected indentation of 24 spaces but found 12 indent 558:1 error Expected indentation of 24 spaces but found 12 indent 559:1 error Expected indentation of 28 spaces but found 14 indent 559:24 error 'loris' is not defined no-undef 561:1 error Expected indentation of 28 spaces but found 14 indent 562:1 error Expected indentation of 32 spaces but found 16 indent 563:1 error Expected indentation of 28 spaces but found 14 indent 564:1 error Expected indentation of 24 spaces but found 12 indent 565:1 error Expected indentation of 24 spaces but found 12 indent 566:1 error Expected indentation of 20 spaces but found 10 indent 567:1 error Expected indentation of 16 spaces but found 8 indent 568:1 error Expected indentation of 12 spaces but found 6 indent 569:1 error Expected indentation of 8 spaces but found 4 indent 571:1 error Expected indentation of 8 spaces but found 4 indent 572:1 error Expected indentation of 12 spaces but found 6 indent 573:1 error Expected indentation of 16 spaces but found 8 indent 575:1 error Expected indentation of 16 spaces but found 8 indent 576:1 error Expected indentation of 12 spaces but found 6 indent 577:1 error Expected indentation of 8 spaces but found 4 indent 579:1 error Expected indentation of 8 spaces but found 4 indent 580:1 error Expected indentation of 12 spaces but found 6 indent 581:1 error Expected indentation of 16 spaces but found 8 indent 582:1 error Expected indentation of 20 spaces but found 10 indent 583:1 error Expected indentation of 20 spaces but found 10 indent 584:1 error Expected indentation of 24 spaces but found 12 indent 585:1 error Expected indentation of 28 spaces but found 14 indent 586:1 error Expected indentation of 28 spaces but found 14 indent 587:1 error Expected indentation of 28 spaces but found 14 indent 588:1 error Expected indentation of 28 spaces but found 14 indent 589:1 error Expected indentation of 24 spaces but found 12 indent 590:1 error Expected indentation of 20 spaces but found 10 indent 591:1 error Expected indentation of 20 spaces but found 10 indent 592:1 error Expected indentation of 24 spaces but found 12 indent 593:1 error Expected indentation of 20 spaces but found 10 indent 594:1 error Expected indentation of 16 spaces but found 8 indent 595:1 error Expected indentation of 12 spaces but found 6 indent 596:1 error Expected indentation of 8 spaces but found 4 indent 597:1 error Expected indentation of 4 spaces but found 2 indent 600:1 error Expected indentation of 4 spaces but found 2 indent 604:1 error Expected indentation of 4 spaces but found 2 indent 605:1 error Expected indentation of 8 spaces but found 4 indent 606:1 error Expected indentation of 8 spaces but found 4 indent 607:1 error Expected indentation of 12 spaces but found 6 indent 608:1 error Expected indentation of 12 spaces but found 6 indent 609:1 error Expected indentation of 8 spaces but found 4 indent 610:1 error Expected indentation of 8 spaces but found 4 indent 611:1 error Expected indentation of 8 spaces but found 4 indent 612:1 error Expected indentation of 8 spaces but found 4 indent 613:1 error Expected indentation of 8 spaces but found 4 indent 614:1 error Expected indentation of 8 spaces but found 4 indent 615:1 error Expected indentation of 4 spaces but found 2 indent 617:1 error Expected indentation of 4 spaces but found 2 indent 618:1 error Expected indentation of 8 spaces but found 4 indent 619:1 error Expected indentation of 4 spaces but found 2 indent 621:1 error Expected indentation of 4 spaces but found 2 indent 622:1 error Expected indentation of 8 spaces but found 4 indent 622:5 error '$' is not defined no-undef 623:1 error Expected indentation of 12 spaces but found 6 indent 624:1 error Expected indentation of 12 spaces but found 6 indent 624:12 error 'loris' is not defined no-undef 625:1 error Expected indentation of 12 spaces but found 6 indent 626:1 error Expected indentation of 12 spaces but found 6 indent 627:1 error Expected indentation of 16 spaces but found 8 indent 628:1 error Expected indentation of 16 spaces but found 8 indent 629:1 error Expected indentation of 16 spaces but found 8 indent 630:1 error Expected indentation of 12 spaces but found 6 indent 631:1 error Expected indentation of 12 spaces but found 6 indent 632:1 error Expected indentation of 16 spaces but found 8 indent 633:1 error Expected indentation of 12 spaces but found 6 indent 634:1 error Expected indentation of 12 spaces but found 6 indent 635:1 error Expected indentation of 16 spaces but found 8 indent 635:9 error Unexpected console statement no-console 636:1 error Expected indentation of 16 spaces but found 8 indent 636:9 error Unexpected console statement no-console 637:1 error Expected indentation of 12 spaces but found 6 indent 638:1 error Expected indentation of 8 spaces but found 4 indent 639:1 error Expected indentation of 4 spaces but found 2 indent 641:1 error Expected indentation of 4 spaces but found 2 indent 642:1 error Expected indentation of 8 spaces but found 4 indent 642:5 error '$' is not defined no-undef 643:1 error Expected indentation of 12 spaces but found 6 indent 644:1 error Expected indentation of 12 spaces but found 6 indent 644:12 error 'loris' is not defined no-undef 645:1 error Expected indentation of 12 spaces but found 6 indent 646:1 error Expected indentation of 12 spaces but found 6 indent 647:1 error Expected indentation of 16 spaces but found 8 indent 648:1 error Expected indentation of 16 spaces but found 8 indent 649:1 error Expected indentation of 16 spaces but found 8 indent 650:1 error Expected indentation of 16 spaces but found 8 indent 651:1 error Expected indentation of 12 spaces but found 6 indent 652:1 error Expected indentation of 12 spaces but found 6 indent 653:1 error Expected indentation of 16 spaces but found 8 indent 654:1 error Expected indentation of 16 spaces but found 8 indent 655:1 error Expected indentation of 12 spaces but found 6 indent 656:1 error Expected indentation of 12 spaces but found 6 indent 657:1 error Expected indentation of 16 spaces but found 8 indent 657:9 error Unexpected console statement no-console 658:1 error Expected indentation of 16 spaces but found 8 indent 658:9 error Unexpected console statement no-console 659:1 error Expected indentation of 12 spaces but found 6 indent 660:1 error Expected indentation of 8 spaces but found 4 indent 661:1 error Expected indentation of 4 spaces but found 2 indent 663:1 error Expected indentation of 4 spaces but found 2 indent 663:13 error 'data' is defined but never used no-unused-vars 664:1 error Expected indentation of 8 spaces but found 4 indent 665:1 error Expected indentation of 4 spaces but found 2 indent 667:1 error Expected indentation of 4 spaces but found 2 indent 668:1 error Expected indentation of 8 spaces but found 4 indent 669:1 error Expected indentation of 8 spaces but found 4 indent 670:1 error Expected indentation of 8 spaces but found 4 indent 671:1 error Expected indentation of 8 spaces but found 4 indent 672:1 error Expected indentation of 8 spaces but found 4 indent 674:1 error Expected indentation of 8 spaces but found 4 indent 676:1 error Expected indentation of 8 spaces but found 4 indent 676:5 error '$' is not defined no-undef 677:1 error Expected indentation of 12 spaces but found 6 indent 678:1 error Expected indentation of 12 spaces but found 6 indent 678:12 error 'loris' is not defined no-undef 679:1 error Expected indentation of 12 spaces but found 6 indent 680:1 error Expected indentation of 12 spaces but found 6 indent 681:1 error Expected indentation of 16 spaces but found 8 indent 682:1 error Expected indentation of 16 spaces but found 8 indent 683:1 error Expected indentation of 12 spaces but found 6 indent 684:1 error Expected indentation of 12 spaces but found 6 indent 684:25 error 'data' is defined but never used no-unused-vars 685:1 error Expected indentation of 16 spaces but found 8 indent 686:1 error Expected indentation of 16 spaces but found 8 indent 687:1 error Expected indentation of 12 spaces but found 6 indent 688:1 error Expected indentation of 12 spaces but found 6 indent 689:1 error Expected indentation of 16 spaces but found 8 indent 689:9 error Unexpected console statement no-console 690:1 error Expected indentation of 16 spaces but found 8 indent 690:9 error Unexpected console statement no-console 691:1 error Expected indentation of 12 spaces but found 6 indent 692:1 error Expected indentation of 8 spaces but found 4 indent 693:1 error Expected indentation of 4 spaces but found 2 indent 695:1 error Expected indentation of 4 spaces but found 2 indent 696:1 error Expected indentation of 8 spaces but found 4 indent 697:1 error Expected indentation of 8 spaces but found 4 indent 698:1 error Expected indentation of 8 spaces but found 4 indent 700:1 error Expected indentation of 8 spaces but found 4 indent 701:1 error Expected indentation of 8 spaces but found 4 indent 702:1 error Expected indentation of 8 spaces but found 4 indent 704:1 error Expected indentation of 8 spaces but found 4 indent 704:5 error '$' is not defined no-undef 705:1 error Expected indentation of 12 spaces but found 6 indent 706:1 error Expected indentation of 12 spaces but found 6 indent 706:12 error 'loris' is not defined no-undef 707:1 error Expected indentation of 12 spaces but found 6 indent 708:1 error Expected indentation of 12 spaces but found 6 indent 709:1 error Expected indentation of 16 spaces but found 8 indent 710:1 error Expected indentation of 16 spaces but found 8 indent 711:1 error Expected indentation of 12 spaces but found 6 indent 712:1 error Expected indentation of 12 spaces but found 6 indent 712:25 error 'data' is defined but never used no-unused-vars 713:1 error Expected indentation of 16 spaces but found 8 indent 714:1 error Expected indentation of 16 spaces but found 8 indent 715:1 error Expected indentation of 12 spaces but found 6 indent 716:1 error Expected indentation of 12 spaces but found 6 indent 717:1 error Expected indentation of 16 spaces but found 8 indent 717:9 error Unexpected console statement no-console 718:1 error Expected indentation of 16 spaces but found 8 indent 718:9 error Unexpected console statement no-console 719:1 error Expected indentation of 12 spaces but found 6 indent 720:1 error Expected indentation of 8 spaces but found 4 indent 721:1 error Expected indentation of 4 spaces but found 2 indent 723:1 error Expected indentation of 4 spaces but found 2 indent 724:1 error Expected indentation of 8 spaces but found 4 indent 725:1 error Expected indentation of 8 spaces but found 4 indent 726:1 error Expected indentation of 12 spaces but found 6 indent 727:1 error Expected indentation of 16 spaces but found 8 indent 728:1 error Expected indentation of 20 spaces but found 10 indent 729:1 error Expected indentation of 16 spaces but found 8 indent 730:1 error Expected indentation of 16 spaces but found 8 indent 731:1 error Expected indentation of 20 spaces but found 10 indent 732:1 error Expected indentation of 24 spaces but found 12 indent 733:1 error Expected indentation of 24 spaces but found 12 indent 734:1 error Expected indentation of 24 spaces but found 12 indent 735:1 error Expected indentation of 24 spaces but found 12 indent 736:1 error Expected indentation of 24 spaces but found 12 indent 737:1 error Expected indentation of 24 spaces but found 12 indent 738:1 error Expected indentation of 24 spaces but found 12 indent 739:1 error Expected indentation of 20 spaces but found 10 indent 740:1 error Expected indentation of 16 spaces but found 8 indent 741:1 error Expected indentation of 16 spaces but found 8 indent 742:1 error Expected indentation of 20 spaces but found 10 indent 743:1 error Expected indentation of 24 spaces but found 12 indent 744:1 error Expected indentation of 24 spaces but found 12 indent 745:1 error Expected indentation of 24 spaces but found 12 indent 746:1 error Expected indentation of 24 spaces but found 12 indent 747:1 error Expected indentation of 24 spaces but found 12 indent 748:1 error Expected indentation of 24 spaces but found 12 indent 749:1 error Expected indentation of 24 spaces but found 12 indent 750:1 error Expected indentation of 20 spaces but found 10 indent 751:1 error Expected indentation of 16 spaces but found 8 indent 752:1 error Expected indentation of 12 spaces but found 6 indent 753:1 error Expected indentation of 8 spaces but found 4 indent 754:1 error Expected indentation of 4 spaces but found 2 indent 757:1 error Expected indentation of 4 spaces but found 2 indent 758:1 error Expected indentation of 4 spaces but found 2 indent 759:1 error Expected indentation of 4 spaces but found 2 indent 760:1 error Expected indentation of 4 spaces but found 2 indent 761:1 error Expected indentation of 4 spaces but found 2 indent ? 696 problems (696 errors, 0 warnings) 662 errors and 0 warnings potentially fixable with the `--fix` option. ERROR in ./modules/candidate_list/jsx/candidateListIndex.js Module Error (from ./node_modules/eslint-loader/index.js): /var/www/loris/modules/candidate_list/jsx/candidateListIndex.js 1:8 error 'React' is defined but never used no-unused-vars 4:8 error 'Loader' is defined but never used no-unused-vars 5:8 error 'FilterableDataTable' is defined but never used no-unused-vars 6:8 error 'Modal' is defined but never used no-unused-vars 8:8 error 'OpenProfileForm' is defined but never used no-unused-vars 19:1 error Expected indentation of 4 spaces but found 2 indent 20:1 error Expected indentation of 8 spaces but found 4 indent 22:1 error Expected indentation of 8 spaces but found 4 indent 23:1 error Expected indentation of 12 spaces but found 6 indent 24:1 error Expected indentation of 12 spaces but found 6 indent 25:1 error Expected indentation of 12 spaces but found 6 indent 26:1 error Expected indentation of 12 spaces but found 6 indent 27:1 error Expected indentation of 12 spaces but found 6 indent 28:1 error Expected indentation of 8 spaces but found 4 indent 30:1 error Expected indentation of 8 spaces but found 4 indent 31:1 error Expected indentation of 8 spaces but found 4 indent 32:1 error Expected indentation of 8 spaces but found 4 indent 33:1 error Expected indentation of 4 spaces but found 2 indent 35:1 error Expected indentation of 4 spaces but found 2 indent 36:1 error Expected indentation of 8 spaces but found 4 indent 37:1 error Expected indentation of 8 spaces but found 4 indent 38:1 error Expected indentation of 8 spaces but found 4 indent 39:1 error Expected indentation of 4 spaces but found 2 indent 41:1 error Expected indentation of 4 spaces but found 2 indent 42:1 error Expected indentation of 8 spaces but found 4 indent 43:1 error Expected indentation of 8 spaces but found 4 indent 44:1 error Expected indentation of 8 spaces but found 4 indent 45:1 error Expected indentation of 4 spaces but found 2 indent 47:1 error Expected indentation of 4 spaces but found 2 indent 48:1 error Expected indentation of 8 spaces but found 4 indent 49:1 error Expected indentation of 12 spaces but found 6 indent 51:1 error Expected indentation of 8 spaces but found 4 indent 52:1 error Expected indentation of 8 spaces but found 4 indent 53:1 error Expected indentation of 12 spaces but found 6 indent 54:1 error Expected indentation of 8 spaces but found 4 indent 55:1 error Expected indentation of 4 spaces but found 2 indent 57:1 error Expected indentation of 4 spaces but found 2 indent 64:1 error Expected indentation of 4 spaces but found 2 indent 65:1 error Expected indentation of 8 spaces but found 4 indent 66:1 error Expected indentation of 12 spaces but found 6 indent 67:1 error Expected indentation of 12 spaces but found 6 indent 68:1 error Expected indentation of 12 spaces but found 6 indent 69:1 error Expected indentation of 16 spaces but found 8 indent 70:1 error Expected indentation of 16 spaces but found 8 indent 70:9 error Unexpected console statement no-console 71:1 error Expected indentation of 12 spaces but found 6 indent 72:1 error Expected indentation of 4 spaces but found 2 indent 74:1 error Expected indentation of 4 spaces but found 2 indent 75:1 error Expected indentation of 4 spaces but found 2 indent 76:1 error Expected indentation of 8 spaces but found 4 indent 77:1 error Expected indentation of 8 spaces but found 4 indent 79:1 error Expected indentation of 8 spaces but found 4 indent 80:1 error Expected indentation of 8 spaces but found 4 indent 81:1 error Expected indentation of 8 spaces but found 4 indent 82:1 error Expected indentation of 8 spaces but found 4 indent 83:1 error Expected indentation of 4 spaces but found 2 indent 83:4 error Unnecessary semicolon no-extra-semi 85:1 error Expected indentation of 4 spaces but found 2 indent 94:1 error Expected indentation of 4 spaces but found 2 indent 95:1 error Expected indentation of 8 spaces but found 4 indent 96:1 error Expected indentation of 12 spaces but found 6 indent 97:1 error Expected indentation of 12 spaces but found 6 indent 98:1 error Expected indentation of 8 spaces but found 4 indent 99:1 error Expected indentation of 8 spaces but found 4 indent 100:1 error Expected indentation of 12 spaces but found 6 indent 101:1 error Expected indentation of 12 spaces but found 8 indent 102:1 error Expected indentation of 12 spaces but found 8 indent 103:1 error Expected indentation of 12 spaces but found 8 indent 104:1 error Expected indentation of 12 spaces but found 8 indent 105:1 error Expected indentation of 12 spaces but found 8 indent 106:1 error Expected indentation of 12 spaces but found 6 indent 107:1 error Expected indentation of 8 spaces but found 4 indent 108:1 error Expected indentation of 8 spaces but found 4 indent 109:1 error Expected indentation of 12 spaces but found 6 indent 110:1 error Expected indentation of 12 spaces but found 6 indent 111:1 error Expected indentation of 16 spaces but found 8 indent 112:1 error Expected indentation of 20 spaces but found 10 indent 113:1 error Expected indentation of 12 spaces but found 6 indent 114:1 error Expected indentation of 8 spaces but found 4 indent 115:1 error Expected indentation of 8 spaces but found 4 indent 116:1 error Expected indentation of 4 spaces but found 2 indent 118:1 error Expected indentation of 4 spaces but found 2 indent 121:1 error Expected indentation of 8 spaces but found 4 indent 122:1 error Expected indentation of 12 spaces but found 6 indent 123:1 error Expected indentation of 8 spaces but found 4 indent 125:1 error Expected indentation of 8 spaces but found 4 indent 126:1 error Expected indentation of 8 spaces but found 4 indent 127:1 error Expected indentation of 12 spaces but found 6 indent 128:1 error Expected indentation of 8 spaces but found 4 indent 130:1 error Expected indentation of 8 spaces but found 4 indent 134:1 error Expected indentation of 8 spaces but found 4 indent 135:1 error Expected indentation of 8 spaces but found 4 indent 136:1 error Expected indentation of 8 spaces but found 4 indent 137:1 error Expected indentation of 12 spaces but found 6 indent 138:1 error Expected indentation of 16 spaces but found 8 indent 139:1 error Expected indentation of 16 spaces but found 8 indent 140:1 error Expected indentation of 16 spaces but found 8 indent 141:1 error Expected indentation of 20 spaces but found 10 indent 142:1 error Expected indentation of 20 spaces but found 10 indent 143:1 error Expected indentation of 16 spaces but found 8 indent 144:1 error Expected indentation of 12 spaces but found 6 indent 145:1 error Expected indentation of 12 spaces but found 6 indent 146:1 error Expected indentation of 16 spaces but found 8 indent 147:1 error Expected indentation of 16 spaces but found 8 indent 148:1 error Expected indentation of 16 spaces but found 8 indent 149:1 error Expected indentation of 20 spaces but found 10 indent 150:1 error Expected indentation of 20 spaces but found 10 indent 151:1 error Expected indentation of 16 spaces but found 8 indent 152:1 error Expected indentation of 12 spaces but found 6 indent 153:1 error Expected indentation of 12 spaces but found 6 indent 154:1 error Expected indentation of 16 spaces but found 8 indent 155:1 error Expected indentation of 16 spaces but found 8 indent 156:1 error Expected indentation of 16 spaces but found 8 indent 157:1 error Expected indentation of 20 spaces but found 10 indent 158:1 error Expected indentation of 20 spaces but found 10 indent 159:1 error Expected indentation of 16 spaces but found 8 indent 160:1 error Expected indentation of 12 spaces but found 6 indent 161:1 error Expected indentation of 12 spaces but found 6 indent 162:1 error Expected indentation of 16 spaces but found 8 indent 163:1 error Expected indentation of 16 spaces but found 8 indent 164:1 error Expected indentation of 16 spaces but found 8 indent 165:1 error Expected indentation of 20 spaces but found 10 indent 166:1 error Expected indentation of 20 spaces but found 10 indent 167:1 error Expected indentation of 20 spaces but found 10 indent 168:1 error Expected indentation of 16 spaces but found 8 indent 169:1 error Expected indentation of 12 spaces but found 6 indent 170:1 error Expected indentation of 12 spaces but found 6 indent 171:1 error Expected indentation of 16 spaces but found 8 indent 172:1 error Expected indentation of 16 spaces but found 8 indent 173:1 error Expected indentation of 16 spaces but found 8 indent 174:1 error Expected indentation of 20 spaces but found 10 indent 175:1 error Expected indentation of 20 spaces but found 10 indent 176:1 error Expected indentation of 20 spaces but found 10 indent 177:1 error Expected indentation of 16 spaces but found 8 indent 178:1 error Expected indentation of 12 spaces but found 6 indent 179:1 error Expected indentation of 12 spaces but found 6 indent 180:1 error Expected indentation of 16 spaces but found 8 indent 181:1 error Expected indentation of 16 spaces but found 8 indent 182:1 error Expected indentation of 16 spaces but found 8 indent 183:1 error Expected indentation of 20 spaces but found 10 indent 184:1 error Expected indentation of 20 spaces but found 10 indent 185:1 error Expected indentation of 20 spaces but found 10 indent 186:1 error Expected indentation of 24 spaces but found 12 indent 187:1 error Expected indentation of 24 spaces but found 12 indent 188:1 error Expected indentation of 20 spaces but found 10 indent 189:1 error Expected indentation of 16 spaces but found 8 indent 190:1 error Expected indentation of 12 spaces but found 6 indent 191:1 error Expected indentation of 12 spaces but found 6 indent 192:1 error Expected indentation of 16 spaces but found 8 indent 193:1 error Expected indentation of 16 spaces but found 8 indent 194:1 error Expected indentation of 16 spaces but found 8 indent 195:1 error Expected indentation of 20 spaces but found 10 indent 196:1 error Expected indentation of 20 spaces but found 10 indent 197:1 error Expected indentation of 20 spaces but found 10 indent 198:1 error Expected indentation of 20 spaces but found 10 indent 199:1 error Expected indentation of 24 spaces but found 12 indent 200:1 error Expected indentation of 24 spaces but found 12 indent 201:1 error Expected indentation of 20 spaces but found 10 indent 202:1 error Expected indentation of 16 spaces but found 8 indent 203:1 error Expected indentation of 12 spaces but found 6 indent 204:1 error Expected indentation of 12 spaces but found 6 indent 205:1 error Expected indentation of 16 spaces but found 8 indent 206:1 error Expected indentation of 16 spaces but found 8 indent 207:1 error Expected indentation of 16 spaces but found 8 indent 208:1 error Expected indentation of 20 spaces but found 10 indent 209:1 error Expected indentation of 20 spaces but found 10 indent 210:1 error Expected indentation of 20 spaces but found 10 indent 211:1 error Expected indentation of 20 spaces but found 10 indent 212:1 error Expected indentation of 16 spaces but found 8 indent 213:1 error Expected indentation of 12 spaces but found 6 indent 214:1 error Expected indentation of 12 spaces but found 6 indent 215:1 error Expected indentation of 16 spaces but found 8 indent 216:1 error Expected indentation of 16 spaces but found 8 indent 217:1 error Expected indentation of 16 spaces but found 8 indent 218:1 error Expected indentation of 20 spaces but found 10 indent 219:1 error Expected indentation of 20 spaces but found 10 indent 220:1 error Expected indentation of 20 spaces but found 10 indent 221:1 error Expected indentation of 16 spaces but found 8 indent 222:1 error Expected indentation of 12 spaces but found 6 indent 223:1 error Expected indentation of 12 spaces but found 6 indent 224:1 error Expected indentation of 16 spaces but found 8 indent 225:1 error Expected indentation of 16 spaces but found 8 indent 226:1 error Expected indentation of 16 spaces but found 8 indent 227:1 error Expected indentation of 20 spaces but found 10 indent 228:1 error Expected indentation of 20 spaces but found 10 indent 229:1 error Expected indentation of 20 spaces but found 10 indent 230:1 error Expected indentation of 20 spaces but found 10 indent 231:1 error Expected indentation of 24 spaces but found 12 indent 232:1 error Expected indentation of 24 spaces but found 12 indent 233:1 error Expected indentation of 20 spaces but found 10 indent 234:1 error Expected indentation of 16 spaces but found 8 indent 235:1 error Expected indentation of 12 spaces but found 6 indent 236:1 error Expected indentation of 12 spaces but found 6 indent 237:1 error Expected indentation of 16 spaces but found 8 indent 238:1 error Expected indentation of 16 spaces but found 8 indent 239:1 error Expected indentation of 16 spaces but found 8 indent 240:1 error Expected indentation of 20 spaces but found 10 indent 241:1 error Expected indentation of 20 spaces but found 10 indent 242:1 error Expected indentation of 20 spaces but found 10 indent 243:1 error Expected indentation of 16 spaces but found 8 indent 244:1 error Expected indentation of 12 spaces but found 6 indent 245:1 error Expected indentation of 12 spaces but found 6 indent 246:1 error Expected indentation of 16 spaces but found 8 indent 247:1 error Expected indentation of 16 spaces but found 8 indent 248:1 error Expected indentation of 16 spaces but found 8 indent 249:1 error Expected indentation of 20 spaces but found 10 indent 250:1 error Expected indentation of 20 spaces but found 10 indent 251:1 error Expected indentation of 20 spaces but found 10 indent 252:1 error Expected indentation of 20 spaces but found 10 indent 253:1 error Expected indentation of 24 spaces but found 12 indent 254:1 error Expected indentation of 24 spaces but found 12 indent 255:1 error Expected indentation of 24 spaces but found 12 indent 256:1 error Expected indentation of 24 spaces but found 12 indent 257:1 error Expected indentation of 24 spaces but found 12 indent 258:1 error Expected indentation of 20 spaces but found 10 indent 259:1 error Expected indentation of 16 spaces but found 8 indent 260:1 error Expected indentation of 12 spaces but found 6 indent 261:1 error Expected indentation of 12 spaces but found 6 indent 262:1 error Expected indentation of 16 spaces but found 8 indent 263:1 error Expected indentation of 16 spaces but found 8 indent 264:1 error Expected indentation of 16 spaces but found 8 indent 265:1 error Expected indentation of 20 spaces but found 10 indent 266:1 error Expected indentation of 20 spaces but found 10 indent 267:1 error Expected indentation of 20 spaces but found 10 indent 268:1 error Expected indentation of 20 spaces but found 10 indent 269:1 error Expected indentation of 24 spaces but found 12 indent 270:1 error Expected indentation of 24 spaces but found 12 indent 271:1 error Expected indentation of 24 spaces but found 12 indent 272:1 error Expected indentation of 24 spaces but found 12 indent 273:1 error Expected indentation of 24 spaces but found 12 indent 274:1 error Expected indentation of 20 spaces but found 10 indent 275:1 error Expected indentation of 16 spaces but found 8 indent 276:1 error Expected indentation of 12 spaces but found 6 indent 278:1 error Expected indentation of 8 spaces but found 4 indent 279:1 error Expected indentation of 8 spaces but found 5 indent 280:1 error Expected indentation of 12 spaces but found 8 indent 281:1 error Expected indentation of 16 spaces but found 10 indent 282:1 error Expected indentation of 16 spaces but found 10 indent 283:1 error Expected indentation of 16 spaces but found 10 indent 284:1 error Expected indentation of 20 spaces but found 12 indent 285:1 error Expected indentation of 20 spaces but found 12 indent 286:1 error Expected indentation of 20 spaces but found 12 indent 287:1 error Expected indentation of 16 spaces but found 10 indent 288:1 error Expected indentation of 12 spaces but found 8 indent 289:1 error Expected indentation of 8 spaces but found 6 indent 291:1 error Expected indentation of 8 spaces but found 4 indent 292:1 error Expected indentation of 12 spaces but found 6 indent 293:1 error Expected indentation of 16 spaces but found 8 indent 294:1 error Expected indentation of 20 spaces but found 10 indent 295:1 error Expected indentation of 20 spaces but found 10 indent 296:1 error Expected indentation of 20 spaces but found 10 indent 297:1 error Expected indentation of 24 spaces but found 12 indent 298:1 error Expected indentation of 24 spaces but found 12 indent 299:1 error Expected indentation of 24 spaces but found 12 indent 300:1 error Expected indentation of 20 spaces but found 10 indent 301:1 error Expected indentation of 16 spaces but found 8 indent 302:1 error Expected indentation of 12 spaces but found 6 indent 303:1 error Expected indentation of 8 spaces but found 4 indent 305:1 error Expected indentation of 8 spaces but found 4 indent 306:1 error Expected indentation of 8 spaces but found 4 indent 307:1 error Expected indentation of 12 spaces but found 6 indent 308:1 error Expected indentation of 16 spaces but found 8 indent 309:1 error Expected indentation of 16 spaces but found 8 indent 310:1 error Expected indentation of 16 spaces but found 8 indent 311:1 error Expected indentation of 20 spaces but found 10 indent 312:1 error Expected indentation of 16 spaces but found 8 indent 313:1 error Expected indentation of 16 spaces but found 8 indent 314:1 error Expected indentation of 12 spaces but found 6 indent 315:1 error Expected indentation of 16 spaces but found 8 indent 316:1 error Expected indentation of 12 spaces but found 6 indent 317:1 error Expected indentation of 8 spaces but found 4 indent 319:1 error Expected indentation of 8 spaces but found 4 indent 320:1 error Expected indentation of 8 spaces but found 4 indent 321:1 error Expected indentation of 8 spaces but found 4 indent 322:1 error Expected indentation of 12 spaces but found 6 indent 323:1 error Expected indentation of 16 spaces but found 8 indent 324:1 error Expected indentation of 16 spaces but found 8 indent 325:1 error Expected indentation of 16 spaces but found 8 indent 326:1 error Expected indentation of 12 spaces but found 6 indent 327:1 error Expected indentation of 12 spaces but found 6 indent 328:1 error Expected indentation of 16 spaces but found 8 indent 329:1 error Expected indentation of 16 spaces but found 8 indent 330:1 error Expected indentation of 16 spaces but found 8 indent 331:1 error Expected indentation of 12 spaces but found 6 indent 332:1 error Expected indentation of 8 spaces but found 4 indent 334:1 error Expected indentation of 8 spaces but found 4 indent 335:1 error Expected indentation of 12 spaces but found 6 indent 336:1 error Expected indentation of 16 spaces but found 8 indent 337:1 error Expected indentation of 16 spaces but found 8 indent 338:1 error Expected indentation of 20 spaces but found 10 indent 339:1 error Expected indentation of 20 spaces but found 10 indent 340:1 error Expected indentation of 20 spaces but found 10 indent 341:1 error Expected indentation of 20 spaces but found 10 indent 342:1 error Expected indentation of 20 spaces but found 10 indent 343:1 error Expected indentation of 16 spaces but found 8 indent 344:1 error Expected indentation of 12 spaces but found 6 indent 345:1 error Expected indentation of 8 spaces but found 4 indent 346:1 error Expected indentation of 4 spaces but found 2 indent 350:1 error Expected indentation of 4 spaces but found 2 indent 351:1 error Expected indentation of 4 spaces but found 2 indent 355:1 error Expected indentation of 4 spaces but found 2 indent 355:3 error 'ReactDOM' is not defined no-undef 356:1 error Expected indentation of 8 spaces but found 4 indent 357:1 error Expected indentation of 12 spaces but found 6 indent 357:19 error 'loris' is not defined no-undef 358:1 error Expected indentation of 12 spaces but found 6 indent 358:22 error 'loris' is not defined no-undef 359:1 error Expected indentation of 12 spaces but found 6 indent 359:16 error 'loris' is not defined no-undef 360:1 error Expected indentation of 8 spaces but found 4 indent 361:1 error Expected indentation of 8 spaces but found 4 indent 362:1 error Expected indentation of 4 spaces but found 2 indent ? 312 problems (312 errors, 0 warnings) 302 errors and 0 warnings potentially fixable with the `--fix` option. ERROR in ./modules/candidate_list/jsx/onLoad.js Module Error (from ./node_modules/eslint-loader/index.js): /var/www/loris/modules/candidate_list/jsx/onLoad.js 3:1 error '$' is not defined no-undef 4:1 error Expected indentation of 4 spaces but found 2 indent 4:3 error 'ReactDOM' is not defined no-undef 5:1 error Expected indentation of 8 spaces but found 4 indent 5:17 error 'loris' is not defined no-undef 6:1 error Expected indentation of 8 spaces but found 4 indent 7:1 error Expected indentation of 8 spaces but found 4 indent 10:1 error Expected indentation of 4 spaces but found 2 indent ? 8 problems (8 errors, 0 warnings) 5 errors and 0 warnings potentially fixable with the `--fix` option. ERROR in ./modules/candidate_list/jsx/openProfileForm.js Module Error (from ./node_modules/eslint-loader/index.js): /var/www/loris/modules/candidate_list/jsx/openProfileForm.js 1:8 error 'React' is defined but never used no-unused-vars 10:1 error Expected indentation of 4 spaces but found 2 indent 11:1 error Expected indentation of 8 spaces but found 4 indent 13:1 error Expected indentation of 8 spaces but found 4 indent 14:1 error Expected indentation of 12 spaces but found 6 indent 15:1 error Expected indentation of 16 spaces but found 8 indent 16:1 error Expected indentation of 16 spaces but found 8 indent 17:1 error Expected indentation of 12 spaces but found 6 indent 18:1 error Expected indentation of 12 spaces but found 6 indent 19:1 error Expected indentation of 12 spaces but found 6 indent 20:1 error Expected indentation of 8 spaces but found 4 indent 22:1 error Expected indentation of 8 spaces but found 4 indent 23:1 error Expected indentation of 8 spaces but found 4 indent 24:1 error Expected indentation of 4 spaces but found 2 indent 26:1 error Expected indentation of 4 spaces but found 2 indent 27:1 error Expected indentation of 8 spaces but found 4 indent 28:1 error Expected indentation of 8 spaces but found 4 indent 29:1 error Expected indentation of 8 spaces but found 4 indent 30:1 error Expected indentation of 4 spaces but found 2 indent 32:1 error Expected indentation of 4 spaces but found 2 indent 33:1 error Expected indentation of 8 spaces but found 4 indent 34:1 error Expected indentation of 8 spaces but found 4 indent 35:1 error Expected indentation of 12 spaces but found 6 indent 36:1 error Expected indentation of 16 spaces but found 8 indent 37:1 error Expected indentation of 16 spaces but found 8 indent 38:1 error Expected indentation of 12 spaces but found 6 indent 39:1 error Expected indentation of 12 spaces but found 6 indent 40:1 error Expected indentation of 12 spaces but found 6 indent 41:1 error Expected indentation of 8 spaces but found 4 indent 43:1 error Expected indentation of 8 spaces but found 4 indent 44:1 error Expected indentation of 12 spaces but found 6 indent 45:1 error Expected indentation of 16 spaces but found 8 indent 46:1 error Expected indentation of 16 spaces but found 8 indent 47:1 error Expected indentation of 12 spaces but found 6 indent 48:1 error Expected indentation of 12 spaces but found 6 indent 49:1 error Expected indentation of 12 spaces but found 6 indent 50:1 error Expected indentation of 8 spaces but found 4 indent 52:1 error Expected indentation of 8 spaces but found 4 indent 53:1 error Expected indentation of 8 spaces but found 4 indent 54:1 error Expected indentation of 8 spaces but found 4 indent 55:1 error Expected indentation of 12 spaces but found 6 indent 56:1 error Expected indentation of 12 spaces but found 6 indent 57:1 error Expected indentation of 8 spaces but found 4 indent 58:1 error Expected indentation of 8 spaces but found 4 indent 60:1 error Expected indentation of 8 spaces but found 4 indent 60:5 error '$' is not defined no-undef 60:11 error 'loris' is not defined no-undef 61:1 error Expected indentation of 12 spaces but found 6 indent 62:1 error Expected indentation of 16 spaces but found 8 indent 63:1 error Expected indentation of 16 spaces but found 8 indent 64:1 error Expected indentation of 12 spaces but found 6 indent 65:1 error Expected indentation of 12 spaces but found 8 indent 66:1 error Expected indentation of 16 spaces but found 10 indent 67:1 error Expected indentation of 16 spaces but found 10 indent 68:1 error Expected indentation of 20 spaces but found 12 indent 69:1 error Expected indentation of 24 spaces but found 14 indent 70:1 error Expected indentation of 24 spaces but found 14 indent 71:1 error Expected indentation of 20 spaces but found 12 indent 72:1 error Expected indentation of 20 spaces but found 12 indent 72:36 error 'loris' is not defined no-undef 73:1 error Expected indentation of 16 spaces but found 10 indent 74:1 error Expected indentation of 20 spaces but found 12 indent 75:1 error Expected indentation of 20 spaces but found 12 indent 76:1 error Expected indentation of 24 spaces but found 14 indent 77:1 error Expected indentation of 24 spaces but found 14 indent 78:1 error Expected indentation of 20 spaces but found 12 indent 79:1 error Expected indentation of 16 spaces but found 10 indent 80:1 error Expected indentation of 16 spaces but found 10 indent 81:1 error Expected indentation of 12 spaces but found 8 indent 82:1 error Expected indentation of 4 spaces but found 2 indent 84:1 error Expected indentation of 4 spaces but found 2 indent 85:1 error Expected indentation of 8 spaces but found 4 indent 87:1 error Expected indentation of 8 spaces but found 4 indent 88:1 error Expected indentation of 12 spaces but found 6 indent 89:1 error Expected indentation of 16 spaces but found 14 indent 90:1 error Expected indentation of 20 spaces but found 16 indent 91:1 error Expected indentation of 16 spaces but found 14 indent 92:1 error Expected indentation of 12 spaces but found 6 indent 93:1 error Expected indentation of 8 spaces but found 4 indent 94:1 error Expected indentation of 8 spaces but found 4 indent 95:1 error Expected indentation of 12 spaces but found 6 indent 96:1 error Expected indentation of 16 spaces but found 8 indent 97:1 error Expected indentation of 16 spaces but found 8 indent 98:1 error Expected indentation of 16 spaces but found 8 indent 99:1 error Expected indentation of 20 spaces but found 10 indent 100:1 error Expected indentation of 20 spaces but found 10 indent 101:1 error Expected indentation of 20 spaces but found 10 indent 102:1 error Expected indentation of 20 spaces but found 10 indent 103:1 error Expected indentation of 16 spaces but found 8 indent 104:1 error Expected indentation of 16 spaces but found 8 indent 105:1 error Expected indentation of 20 spaces but found 10 indent 106:1 error Expected indentation of 20 spaces but found 10 indent 107:1 error Expected indentation of 20 spaces but found 10 indent 108:1 error Expected indentation of 20 spaces but found 10 indent 109:1 error Expected indentation of 16 spaces but found 8 indent 110:1 error Expected indentation of 16 spaces but found 8 indent 111:1 error Expected indentation of 16 spaces but found 8 indent 112:1 error Expected indentation of 20 spaces but found 10 indent 113:1 error Expected indentation of 20 spaces but found 10 indent 114:1 error Expected indentation of 20 spaces but found 10 indent 115:1 error Expected indentation of 16 spaces but found 8 indent 116:1 error Expected indentation of 12 spaces but found 8 indent 117:1 error Expected indentation of 8 spaces but found 4 indent 118:1 error Expected indentation of 4 spaces but found 2 indent ? 104 problems (104 errors, 0 warnings) 100 errors and 0 warnings potentially fixable with the `--fix` option. ERROR in ./modules/candidate_parameters/jsx/CandidateParameters.js Module Error (from ./node_modules/eslint-loader/index.js): /var/www/loris/modules/candidate_parameters/jsx/CandidateParameters.js 1:8 error 'React' is defined but never used no-unused-vars 8:9 error 'Tabs' is defined but never used no-unused-vars 8:15 error 'TabPane' is defined but never used no-unused-vars 11:1 error Expected indentation of 4 spaces but found 2 indent 12:1 error Expected indentation of 8 spaces but found 4 indent 13:1 error Expected indentation of 8 spaces but found 4 indent 14:1 error Expected indentation of 4 spaces but found 2 indent 16:1 error Expected indentation of 4 spaces but found 2 indent 17:1 error Expected indentation of 8 spaces but found 4 indent 17:26 error 'loris' is not defined no-undef 18:1 error Expected indentation of 8 spaces but found 4 indent 18:24 error 'loris' is not defined no-undef 19:1 error Expected indentation of 8 spaces but found 4 indent 20:1 error Expected indentation of 12 spaces but found 6 indent 20:13 error 'TabContent' is assigned a value but never used no-unused-vars 21:1 error Expected indentation of 12 spaces but found 6 indent 22:1 error Expected indentation of 16 spaces but found 8 indent 23:1 error Expected indentation of 20 spaces but found 10 indent 24:1 error Expected indentation of 24 spaces but found 12 indent 25:1 error Expected indentation of 24 spaces but found 12 indent 26:1 error Expected indentation of 24 spaces but found 12 indent 27:1 error Expected indentation of 20 spaces but found 10 indent 28:1 error Expected indentation of 16 spaces but found 8 indent 29:1 error Expected indentation of 12 spaces but found 6 indent 30:1 error Expected indentation of 8 spaces but found 4 indent 31:1 error Expected indentation of 8 spaces but found 4 indent 32:1 error Expected indentation of 4 spaces but found 2 indent 34:1 error Expected indentation of 4 spaces but found 2 indent 35:1 error Expected indentation of 8 spaces but found 4 indent 36:1 error Expected indentation of 12 spaces but found 6 indent 37:1 error Expected indentation of 12 spaces but found 6 indent 38:1 error Expected indentation of 8 spaces but found 4 indent 40:1 error Expected indentation of 8 spaces but found 4 indent 40:9 error 'loris' is not defined no-undef 41:1 error Expected indentation of 12 spaces but found 6 indent 42:1 error Expected indentation of 8 spaces but found 4 indent 44:1 error Expected indentation of 8 spaces but found 4 indent 44:9 error 'loris' is not defined no-undef 45:1 error Expected indentation of 12 spaces but found 6 indent 46:1 error Expected indentation of 8 spaces but found 4 indent 48:1 error Expected indentation of 8 spaces but found 4 indent 48:9 error 'loris' is not defined no-undef 49:1 error Expected indentation of 12 spaces but found 6 indent 50:1 error Expected indentation of 8 spaces but found 4 indent 52:1 error Expected indentation of 8 spaces but found 4 indent 53:1 error Expected indentation of 12 spaces but found 6 indent 54:1 error Expected indentation of 16 spaces but found 8 indent 55:1 error Expected indentation of 20 spaces but found 11 indent 55:18 error 'loris' is not defined no-undef 56:1 error Expected indentation of 20 spaces but found 11 indent 57:1 error Expected indentation of 16 spaces but found 8 indent 59:1 error Expected indentation of 16 spaces but found 8 indent 60:1 error Expected indentation of 16 spaces but found 8 indent 61:1 error Expected indentation of 16 spaces but found 8 indent 62:1 error Expected indentation of 20 spaces but found 10 indent 63:1 error Expected indentation of 16 spaces but found 8 indent 64:1 error Expected indentation of 12 spaces but found 6 indent 65:1 error Expected indentation of 8 spaces but found 4 indent 66:1 error Expected indentation of 4 spaces but found 2 indent 70:1 error Expected indentation of 4 spaces but found 2 indent 76:14 error 'QueryString' is not defined no-undef 79:1 error Expected indentation of 4 spaces but found 2 indent 80:1 error Expected indentation of 8 spaces but found 4 indent 81:1 error Expected indentation of 12 spaces but found 6 indent 82:1 error Expected indentation of 16 spaces but found 8 indent 83:1 error Expected indentation of 16 spaces but found 8 indent 84:1 error Expected indentation of 12 spaces but found 6 indent 85:1 error Expected indentation of 8 spaces but found 4 indent 86:1 error Expected indentation of 4 spaces but found 2 indent 88:1 error Expected indentation of 4 spaces but found 2 indent 88:3 error 'ReactDOM' is not defined no-undef ? 71 problems (71 errors, 0 warnings) 59 errors and 0 warnings potentially fixable with the `--fix` option. ERROR in ./modules/configuration/jsx/SubprojectRelations.js Module Error (from ./node_modules/eslint-loader/index.js): /var/www/loris/modules/configuration/jsx/SubprojectRelations.js 3:27 error 'React' is not defined no-undef 4:1 error Expected indentation of 4 spaces but found 2 indent 5:1 error Expected indentation of 8 spaces but found 4 indent 6:1 error Expected indentation of 12 spaces but found 6 indent 7:1 error Expected indentation of 8 spaces but found 4 indent 8:1 error Expected indentation of 4 spaces but found 2 indent 9:1 error Expected indentation of 4 spaces but found 2 indent 10:1 error Expected indentation of 8 spaces but found 4 indent 11:1 error Expected indentation of 8 spaces but found 4 indent 12:1 error Expected indentation of 8 spaces but found 4 indent 13:1 error Expected indentation of 12 spaces but found 6 indent 14:1 error Expected indentation of 8 spaces but found 4 indent 16:1 error Expected indentation of 8 spaces but found 4 indent 24:1 error Expected indentation of 4 spaces but found 2 indent 26:28 error 'React' is not defined no-undef ? 15 problems (15 errors, 0 warnings) 13 errors and 0 warnings potentially fixable with the `--fix` option. ERROR in ./modules/conflict_resolver/jsx/conflictResolverIndex.js Module Error (from ./node_modules/eslint-loader/index.js): /var/www/loris/modules/conflict_resolver/jsx/conflictResolverIndex.js 1:8 error 'React' is defined but never used no-unused-vars 3:8 error 'Loader' is defined but never used no-unused-vars 4:9 error 'Tabs' is defined but never used no-unused-vars 4:15 error 'TabPane' is defined but never used no-unused-vars 5:8 error 'FilterForm' is defined but never used no-unused-vars 6:8 error 'DynamicDataTable' is defined but never used no-unused-vars 16:1 error Expected indentation of 4 spaces but found 2 indent 17:1 error Expected indentation of 8 spaces but found 4 indent 18:1 error Expected indentation of 8 spaces but found 4 indent 19:1 error Expected indentation of 12 spaces but found 6 indent 20:1 error Expected indentation of 8 spaces but found 4 indent 21:1 error Expected indentation of 8 spaces but found 4 indent 22:1 error Expected indentation of 4 spaces but found 2 indent 24:1 error Expected indentation of 4 spaces but found 2 indent 25:1 error Expected indentation of 8 spaces but found 4 indent 26:1 error Expected indentation of 4 spaces but found 2 indent 28:1 error Expected indentation of 4 spaces but found 2 indent 29:1 error Expected indentation of 8 spaces but found 4 indent 29:9 error 'loris' is not defined no-undef 30:1 error Expected indentation of 12 spaces but found 6 indent 31:1 error Expected indentation of 8 spaces but found 4 indent 32:1 error Expected indentation of 8 spaces but found 4 indent 33:1 error Expected indentation of 8 spaces but found 4 indent 35:1 error Expected indentation of 8 spaces but found 4 indent 36:1 error Expected indentation of 12 spaces but found 6 indent 37:1 error Expected indentation of 8 spaces but found 4 indent 39:1 error Expected indentation of 8 spaces but found 4 indent 40:1 error Expected indentation of 12 spaces but found 6 indent 41:1 error Expected indentation of 8 spaces but found 4 indent 43:1 error Expected indentation of 8 spaces but found 4 indent 44:1 error Expected indentation of 12 spaces but found 6 indent 45:1 error Expected indentation of 12 spaces but found 6 indent 46:1 error Expected indentation of 12 spaces but found 6 indent 47:1 error Expected indentation of 12 spaces but found 6 indent 48:1 error Expected indentation of 16 spaces but found 8 indent 49:1 error Expected indentation of 20 spaces but found 10 indent 50:1 error Expected indentation of 20 spaces but found 10 indent 51:1 error Expected indentation of 20 spaces but found 10 indent 52:1 error Expected indentation of 16 spaces but found 8 indent 53:1 error Expected indentation of 12 spaces but found 6 indent 54:1 error Expected indentation of 8 spaces but found 4 indent 55:1 error Expected indentation of 8 spaces but found 4 indent 56:1 error Expected indentation of 4 spaces but found 2 indent 57:1 error Expected indentation of 4 spaces but found 2 indent 58:1 error Expected indentation of 4 spaces but found 2 indent 59:1 error Expected indentation of 8 spaces but found 4 indent 60:1 error Expected indentation of 12 spaces but found 6 indent 61:1 error Expected indentation of 16 spaces but found 8 indent 62:1 error Expected indentation of 20 spaces but found 14 indent 63:1 error Expected indentation of 20 spaces but found 14 indent 65:1 error Expected indentation of 20 spaces but found 10 indent 66:1 error Expected indentation of 24 spaces but found 12 indent 67:1 error Expected indentation of 24 spaces but found 12 indent 68:1 error Expected indentation of 24 spaces but found 12 indent 69:1 error Expected indentation of 24 spaces but found 12 indent 70:1 error Expected indentation of 24 spaces but found 12 indent 71:1 error Expected indentation of 24 spaces but found 12 indent 71:28 error 'loris' is not defined no-undef 72:1 error Expected indentation of 20 spaces but found 10 indent 74:1 error Expected indentation of 20 spaces but found 10 indent 75:1 error Expected indentation of 24 spaces but found 12 indent 76:1 error Expected indentation of 24 spaces but found 12 indent 77:1 error Expected indentation of 20 spaces but found 10 indent 79:1 error Expected indentation of 16 spaces but found 8 indent 80:1 error Expected indentation of 12 spaces but found 6 indent 81:1 error Expected indentation of 8 spaces but found 4 indent 82:1 error Expected indentation of 4 spaces but found 2 indent 85:1 error Expected indentation of 4 spaces but found 2 indent 86:1 error Expected indentation of 4 spaces but found 2 indent 89:1 error Expected indentation of 4 spaces but found 2 indent 90:1 error Expected indentation of 4 spaces but found 2 indent 91:1 error Expected indentation of 8 spaces but found 4 indent 92:1 error Expected indentation of 8 spaces but found 4 indent 93:1 error Expected indentation of 12 spaces but found 6 indent 94:1 error Expected indentation of 12 spaces but found 6 indent 95:1 error Expected indentation of 8 spaces but found 4 indent 96:1 error Expected indentation of 4 spaces but found 2 indent 97:1 error Expected indentation of 4 spaces but found 2 indent 104:1 error Expected indentation of 4 spaces but found 2 indent 105:1 error Expected indentation of 8 spaces but found 4 indent 107:1 error Expected indentation of 8 spaces but found 4 indent 107:5 error 'loris' is not defined no-undef 108:1 error Expected indentation of 12 spaces but found 6 indent 109:1 error Expected indentation of 12 spaces but found 6 indent 110:1 error Expected indentation of 12 spaces but found 6 indent 111:1 error Expected indentation of 12 spaces but found 6 indent 112:1 error Expected indentation of 8 spaces but found 4 indent 114:1 error Expected indentation of 8 spaces but found 4 indent 115:1 error Expected indentation of 12 spaces but found 6 indent 116:1 error Expected indentation of 12 spaces but found 6 indent 117:1 error Expected indentation of 12 spaces but found 6 indent 118:1 error Expected indentation of 8 spaces but found 4 indent 119:1 error Expected indentation of 8 spaces but found 4 indent 122:1 error Expected indentation of 8 spaces but found 4 indent 123:1 error Expected indentation of 8 spaces but found 4 indent 124:1 error Expected indentation of 12 spaces but found 6 indent 125:1 error Expected indentation of 8 spaces but found 4 indent 126:1 error Expected indentation of 8 spaces but found 4 indent 129:1 error Expected indentation of 8 spaces but found 4 indent 130:1 error Expected indentation of 8 spaces but found 4 indent 131:1 error Expected indentation of 8 spaces but found 4 indent 132:1 error Expected indentation of 8 spaces but found 4 indent 133:1 error Expected indentation of 4 spaces but found 2 indent 135:1 error Expected indentation of 4 spaces but found 2 indent 136:1 error Expected indentation of 8 spaces but found 4 indent 137:1 error Expected indentation of 4 spaces but found 2 indent 139:1 error Expected indentation of 4 spaces but found 2 indent 144:1 error Expected indentation of 4 spaces but found 2 indent 145:1 error Expected indentation of 8 spaces but found 4 indent 146:1 error Expected indentation of 8 spaces but found 4 indent 147:1 error Expected indentation of 12 spaces but found 6 indent 148:1 error Expected indentation of 16 spaces but found 8 indent 149:1 error Expected indentation of 16 spaces but found 8 indent 150:1 error Expected indentation of 16 spaces but found 8 indent 151:1 error Expected indentation of 16 spaces but found 8 indent 152:1 error Expected indentation of 16 spaces but found 8 indent 153:1 error Expected indentation of 20 spaces but found 10 indent 154:1 error Expected indentation of 20 spaces but found 10 indent 155:1 error Expected indentation of 16 spaces but found 8 indent 156:1 error Expected indentation of 12 spaces but found 6 indent 157:1 error Expected indentation of 8 spaces but found 4 indent 158:1 error Expected indentation of 12 spaces but found 6 indent 159:1 error Expected indentation of 16 spaces but found 8 indent 160:1 error Expected indentation of 20 spaces but found 10 indent 161:1 error Expected indentation of 24 spaces but found 12 indent 162:1 error Expected indentation of 24 spaces but found 12 indent 163:1 error Expected indentation of 20 spaces but found 10 indent 164:1 error Expected indentation of 16 spaces but found 8 indent 164:19 error 'error' is defined but never used no-unused-vars 165:1 error Expected indentation of 16 spaces but found 10 indent 166:1 error Expected indentation of 12 spaces but found 4 indent 167:1 error Expected indentation of 4 spaces but found 2 indent 169:1 error Expected indentation of 4 spaces but found 2 indent 170:1 error Expected indentation of 8 spaces but found 4 indent 171:1 error Expected indentation of 8 spaces but found 4 indent 172:1 error Expected indentation of 12 spaces but found 6 indent 173:1 error Expected indentation of 8 spaces but found 4 indent 174:1 error Expected indentation of 4 spaces but found 2 indent 176:1 error Expected indentation of 4 spaces but found 2 indent 177:1 error Expected indentation of 8 spaces but found 4 indent 178:1 error Expected indentation of 4 spaces but found 2 indent 180:1 error Expected indentation of 4 spaces but found 2 indent 181:1 error Expected indentation of 8 spaces but found 4 indent 182:1 error Expected indentation of 4 spaces but found 2 indent 184:1 error Expected indentation of 4 spaces but found 2 indent 185:1 error Expected indentation of 4 spaces but found 2 indent 187:1 error Expected indentation of 8 spaces but found 4 indent 188:1 error Expected indentation of 12 spaces but found 6 indent 189:1 error Expected indentation of 8 spaces but found 4 indent 191:1 error Expected indentation of 8 spaces but found 4 indent 192:1 error Expected indentation of 8 spaces but found 4 indent 193:1 error Expected indentation of 12 spaces but found 6 indent 194:1 error Expected indentation of 16 spaces but found 8 indent 195:1 error Expected indentation of 16 spaces but found 8 indent 196:1 error Expected indentation of 16 spaces but found 8 indent 197:1 error Expected indentation of 16 spaces but found 8 indent 198:1 error Expected indentation of 16 spaces but found 8 indent 199:1 error Expected indentation of 20 spaces but found 10 indent 200:1 error Expected indentation of 16 spaces but found 8 indent 201:1 error Expected indentation of 12 spaces but found 6 indent 202:1 error Expected indentation of 8 spaces but found 4 indent 203:1 error Expected indentation of 8 spaces but found 4 indent 204:1 error Expected indentation of 12 spaces but found 6 indent 205:1 error Expected indentation of 16 spaces but found 8 indent 206:1 error Expected indentation of 16 spaces but found 8 indent 207:1 error Expected indentation of 12 spaces but found 6 indent 208:1 error Expected indentation of 12 spaces but found 6 indent 209:1 error Expected indentation of 16 spaces but found 8 indent 210:1 error Expected indentation of 16 spaces but found 8 indent 211:1 error Expected indentation of 12 spaces but found 6 indent 212:1 error Expected indentation of 8 spaces but found 4 indent 214:1 error Expected indentation of 8 spaces but found 4 indent 215:1 error Expected indentation of 8 spaces but found 4 indent 216:1 error Expected indentation of 12 spaces but found 6 indent 217:1 error Expected indentation of 16 spaces but found 8 indent 218:1 error Expected indentation of 12 spaces but found 6 indent 219:1 error Expected indentation of 12 spaces but found 6 indent 220:1 error Expected indentation of 16 spaces but found 8 indent 221:1 error Expected indentation of 12 spaces but found 6 indent 222:1 error Expected indentation of 12 spaces but found 6 indent 223:1 error Expected indentation of 16 spaces but found 8 indent 224:1 error Expected indentation of 12 spaces but found 6 indent 225:1 error Expected indentation of 8 spaces but found 4 indent 227:1 error Expected indentation of 8 spaces but found 4 indent 228:1 error Expected indentation of 12 spaces but found 6 indent 229:1 error Expected indentation of 16 spaces but found 8 indent 230:1 error Expected indentation of 20 spaces but found 10 indent 231:1 error Expected indentation of 24 spaces but found 12 indent 232:1 error Expected indentation of 24 spaces but found 12 indent 233:1 error Expected indentation of 24 spaces but found 12 indent 234:1 error Expected indentation of 24 spaces but found 12 indent 235:1 error Expected indentation of 24 spaces but found 12 indent 236:1 error Expected indentation of 24 spaces but found 12 indent 237:1 error Expected indentation of 24 spaces but found 12 indent 238:1 error Expected indentation of 24 spaces but found 12 indent 239:1 error Expected indentation of 20 spaces but found 10 indent 240:1 error Expected indentation of 24 spaces but found 12 indent 241:1 error Expected indentation of 28 spaces but found 14 indent 242:1 error Expected indentation of 28 spaces but found 14 indent 243:1 error Expected indentation of 28 spaces but found 14 indent 244:1 error Expected indentation of 28 spaces but found 14 indent 245:1 error Expected indentation of 24 spaces but found 12 indent 246:1 error Expected indentation of 20 spaces but found 10 indent 247:1 error Expected indentation of 16 spaces but found 8 indent 248:1 error Expected indentation of 16 spaces but found 8 indent 249:1 error Expected indentation of 20 spaces but found 10 indent 250:1 error Expected indentation of 24 spaces but found 12 indent 251:1 error Expected indentation of 20 spaces but found 10 indent 252:1 error Expected indentation of 16 spaces but found 8 indent 253:1 error Expected indentation of 12 spaces but found 6 indent 254:1 error Expected indentation of 8 spaces but found 4 indent 255:1 error Expected indentation of 4 spaces but found 2 indent 258:1 error Expected indentation of 4 spaces but found 2 indent 261:1 error Expected indentation of 4 spaces but found 2 indent 262:1 error Expected indentation of 8 spaces but found 4 indent 263:1 error Expected indentation of 8 spaces but found 4 indent 264:1 error Expected indentation of 12 spaces but found 6 indent 265:1 error Expected indentation of 12 spaces but found 6 indent 266:1 error Expected indentation of 8 spaces but found 4 indent 267:1 error Expected indentation of 4 spaces but found 2 indent 274:1 error Expected indentation of 4 spaces but found 2 indent 274:3 error 'ReactDOM' is not defined no-undef 275:1 error Expected indentation of 8 spaces but found 4 indent 276:1 error Expected indentation of 12 spaces but found 6 indent 277:1 error Expected indentation of 16 spaces but found 8 indent 277:15 error 'loris' is not defined no-undef 278:1 error Expected indentation of 16 spaces but found 8 indent 279:1 error Expected indentation of 20 spaces but found 10 indent 279:23 error 'loris' is not defined no-undef 280:1 error Expected indentation of 20 spaces but found 10 indent 280:21 error 'loris' is not defined no-undef 281:1 error Expected indentation of 16 spaces but found 8 indent 282:1 error Expected indentation of 12 spaces but found 6 indent 283:1 error Expected indentation of 8 spaces but found 4 indent 284:1 error Expected indentation of 8 spaces but found 4 indent 285:1 error Expected indentation of 4 spaces but found 2 indent 286:1 error Expected indentation of 4 spaces but found 2 indent 287:1 error Expected indentation of 4 spaces but found 2 indent 288:1 error Expected indentation of 8 spaces but found 4 indent 289:1 error Expected indentation of 12 spaces but found 6 indent 289:7 error '$' is not defined no-undef 290:1 error Expected indentation of 16 spaces but found 8 indent 291:1 error Expected indentation of 16 spaces but found 8 indent 291:32 error 'loris' is not defined no-undef 292:1 error Expected indentation of 16 spaces but found 8 indent 293:1 error Expected indentation of 12 spaces but found 6 indent 294:1 error Expected indentation of 12 spaces but found 6 indent 295:1 error Expected indentation of 8 spaces but found 4 indent 296:1 error Expected indentation of 4 spaces but found 2 indent ? 249 problems (249 errors, 0 warnings) 233 errors and 0 warnings potentially fixable with the `--fix` option. ERROR in ./modules/conflict_resolver/jsx/resolvedConflictsIndex.js Module Error (from ./node_modules/eslint-loader/index.js): /var/www/loris/modules/conflict_resolver/jsx/resolvedConflictsIndex.js 3:8 error 'Loader' is defined but never used no-unused-vars 4:9 error 'Tabs' is defined but never used no-unused-vars 4:15 error 'TabPane' is defined but never used no-unused-vars 5:8 error 'FilterForm' is defined but never used no-unused-vars 6:8 error 'DynamicDataTable' is defined but never used no-unused-vars 16:1 error Expected indentation of 4 spaces but found 2 indent 17:1 error Expected indentation of 8 spaces but found 4 indent 18:1 error Expected indentation of 8 spaces but found 4 indent 19:1 error Expected indentation of 12 spaces but found 6 indent 20:1 error Expected indentation of 8 spaces but found 4 indent 21:1 error Expected indentation of 8 spaces but found 4 indent 24:1 error Expected indentation of 8 spaces but found 4 indent 25:1 error Expected indentation of 4 spaces but found 2 indent 27:1 error Expected indentation of 4 spaces but found 2 indent 28:1 error Expected indentation of 8 spaces but found 4 indent 29:1 error Expected indentation of 4 spaces but found 2 indent 31:1 error Expected indentation of 4 spaces but found 2 indent 32:1 error Expected indentation of 8 spaces but found 4 indent 32:9 error 'loris' is not defined no-undef 33:1 error Expected indentation of 12 spaces but found 6 indent 34:1 error Expected indentation of 8 spaces but found 4 indent 35:1 error Expected indentation of 8 spaces but found 4 indent 36:1 error Expected indentation of 8 spaces but found 4 indent 38:1 error Expected indentation of 8 spaces but found 4 indent 39:1 error Expected indentation of 12 spaces but found 6 indent 40:1 error Expected indentation of 8 spaces but found 4 indent 42:1 error Expected indentation of 8 spaces but found 4 indent 43:1 error Expected indentation of 12 spaces but found 6 indent 44:1 error Expected indentation of 8 spaces but found 4 indent 46:1 error Expected indentation of 8 spaces but found 4 indent 47:1 error Expected indentation of 12 spaces but found 6 indent 48:1 error Expected indentation of 12 spaces but found 6 indent 49:1 error Expected indentation of 12 spaces but found 6 indent 50:1 error Expected indentation of 12 spaces but found 6 indent 52:1 error Expected indentation of 12 spaces but found 6 indent 53:1 error Expected indentation of 16 spaces but found 8 indent 54:1 error Expected indentation of 12 spaces but found 6 indent 56:1 error Expected indentation of 12 spaces but found 6 indent 57:1 error Expected indentation of 16 spaces but found 8 indent 58:1 error Expected indentation of 12 spaces but found 6 indent 60:1 error Expected indentation of 12 spaces but found 6 indent 61:1 error Expected indentation of 8 spaces but found 4 indent 63:1 error Expected indentation of 8 spaces but found 4 indent 64:1 error Expected indentation of 4 spaces but found 2 indent 66:1 error Expected indentation of 4 spaces but found 2 indent 67:1 error Expected indentation of 4 spaces but found 2 indent 68:1 error Expected indentation of 8 spaces but found 4 indent 69:1 error Expected indentation of 12 spaces but found 6 indent 70:1 error Expected indentation of 16 spaces but found 8 indent 71:1 error Expected indentation of 20 spaces but found 10 indent 72:1 error Expected indentation of 20 spaces but found 10 indent 73:1 error Expected indentation of 20 spaces but found 10 indent 74:1 error Expected indentation of 20 spaces but found 10 indent 75:1 error Expected indentation of 20 spaces but found 10 indent 76:1 error Expected indentation of 20 spaces but found 10 indent 76:26 error 'loris' is not defined no-undef 77:1 error Expected indentation of 16 spaces but found 8 indent 78:1 error Expected indentation of 12 spaces but found 6 indent 79:1 error Expected indentation of 8 spaces but found 4 indent 80:1 error Expected indentation of 4 spaces but found 2 indent 83:1 error Expected indentation of 4 spaces but found 2 indent 84:1 error Expected indentation of 4 spaces but found 2 indent 87:1 error Expected indentation of 4 spaces but found 2 indent 88:1 error Expected indentation of 4 spaces but found 2 indent 89:1 error Expected indentation of 8 spaces but found 4 indent 90:1 error Expected indentation of 8 spaces but found 4 indent 91:1 error Expected indentation of 12 spaces but found 6 indent 92:1 error Expected indentation of 12 spaces but found 6 indent 93:1 error Expected indentation of 8 spaces but found 4 indent 94:1 error Expected indentation of 4 spaces but found 2 indent 95:1 error Expected indentation of 4 spaces but found 2 indent 102:1 error Expected indentation of 4 spaces but found 2 indent 103:1 error Expected indentation of 8 spaces but found 4 indent 105:1 error Expected indentation of 8 spaces but found 4 indent 105:5 error 'loris' is not defined no-undef 106:1 error Expected indentation of 12 spaces but found 6 indent 107:1 error Expected indentation of 12 spaces but found 6 indent 108:1 error Expected indentation of 12 spaces but found 6 indent 109:1 error Expected indentation of 12 spaces but found 6 indent 110:1 error Expected indentation of 8 spaces but found 4 indent 112:1 error Expected indentation of 8 spaces but found 4 indent 113:1 error Expected indentation of 12 spaces but found 6 indent 114:1 error Expected indentation of 12 spaces but found 6 indent 115:1 error Expected indentation of 12 spaces but found 6 indent 116:1 error Expected indentation of 8 spaces but found 4 indent 117:1 error Expected indentation of 8 spaces but found 4 indent 120:1 error Expected indentation of 8 spaces but found 4 indent 121:1 error Expected indentation of 8 spaces but found 4 indent 122:1 error Expected indentation of 12 spaces but found 6 indent 123:1 error Expected indentation of 8 spaces but found 4 indent 124:1 error Expected indentation of 8 spaces but found 4 indent 127:1 error Expected indentation of 8 spaces but found 4 indent 128:1 error Expected indentation of 8 spaces but found 4 indent 129:1 error Expected indentation of 8 spaces but found 4 indent 130:1 error Expected indentation of 8 spaces but found 4 indent 131:1 error Expected indentation of 4 spaces but found 2 indent 133:1 error Expected indentation of 4 spaces but found 2 indent 134:1 error Expected indentation of 8 spaces but found 4 indent 135:1 error Expected indentation of 4 spaces but found 2 indent 137:1 error Expected indentation of 4 spaces but found 2 indent 142:1 error Expected indentation of 4 spaces but found 2 indent 143:1 error Expected indentation of 8 spaces but found 4 indent 144:1 error Expected indentation of 8 spaces but found 4 indent 145:1 error Expected indentation of 12 spaces but found 6 indent 146:1 error Expected indentation of 16 spaces but found 8 indent 147:1 error Expected indentation of 16 spaces but found 8 indent 148:1 error Expected indentation of 16 spaces but found 8 indent 149:1 error Expected indentation of 16 spaces but found 8 indent 150:1 error Expected indentation of 16 spaces but found 8 indent 151:1 error Expected indentation of 20 spaces but found 10 indent 152:1 error Expected indentation of 20 spaces but found 10 indent 153:1 error Expected indentation of 16 spaces but found 8 indent 154:1 error Expected indentation of 12 spaces but found 6 indent 155:1 error Expected indentation of 8 spaces but found 4 indent 156:1 error Expected indentation of 12 spaces but found 6 indent 157:1 error Expected indentation of 16 spaces but found 8 indent 158:1 error Expected indentation of 20 spaces but found 10 indent 159:1 error Expected indentation of 24 spaces but found 12 indent 160:1 error Expected indentation of 24 spaces but found 12 indent 161:1 error Expected indentation of 20 spaces but found 10 indent 162:1 error Expected indentation of 16 spaces but found 8 indent 162:19 error 'error' is defined but never used no-unused-vars 163:1 error Expected indentation of 16 spaces but found 6 indent 164:1 error Expected indentation of 12 spaces but found 4 indent 165:1 error Expected indentation of 4 spaces but found 2 indent 167:1 error Expected indentation of 4 spaces but found 2 indent 168:1 error Expected indentation of 8 spaces but found 4 indent 169:1 error Expected indentation of 8 spaces but found 4 indent 170:1 error Expected indentation of 12 spaces but found 6 indent 171:1 error Expected indentation of 8 spaces but found 4 indent 172:1 error Expected indentation of 4 spaces but found 2 indent 174:1 error Expected indentation of 4 spaces but found 2 indent 175:1 error Expected indentation of 8 spaces but found 4 indent 176:1 error Expected indentation of 4 spaces but found 2 indent 178:1 error Expected indentation of 4 spaces but found 2 indent 179:1 error Expected indentation of 8 spaces but found 4 indent 180:1 error Expected indentation of 4 spaces but found 2 indent 182:1 error Expected indentation of 4 spaces but found 2 indent 183:1 error Expected indentation of 4 spaces but found 2 indent 185:1 error Expected indentation of 8 spaces but found 4 indent 186:1 error Expected indentation of 12 spaces but found 6 indent 187:1 error Expected indentation of 8 spaces but found 4 indent 189:1 error Expected indentation of 8 spaces but found 4 indent 190:1 error Expected indentation of 8 spaces but found 4 indent 191:1 error Expected indentation of 12 spaces but found 6 indent 192:1 error Expected indentation of 16 spaces but found 8 indent 193:1 error Expected indentation of 16 spaces but found 8 indent 194:1 error Expected indentation of 16 spaces but found 8 indent 195:1 error Expected indentation of 16 spaces but found 8 indent 196:1 error Expected indentation of 16 spaces but found 8 indent 197:1 error Expected indentation of 20 spaces but found 10 indent 198:1 error Expected indentation of 16 spaces but found 8 indent 199:1 error Expected indentation of 12 spaces but found 6 indent 200:1 error Expected indentation of 8 spaces but found 4 indent 201:1 error Expected indentation of 8 spaces but found 4 indent 202:1 error Expected indentation of 12 spaces but found 6 indent 203:1 error Expected indentation of 16 spaces but found 8 indent 204:1 error Expected indentation of 16 spaces but found 8 indent 205:1 error Expected indentation of 12 spaces but found 6 indent 206:1 error Expected indentation of 12 spaces but found 6 indent 207:1 error Expected indentation of 16 spaces but found 8 indent 208:1 error Expected indentation of 16 spaces but found 8 indent 209:1 error Expected indentation of 12 spaces but found 6 indent 210:1 error Expected indentation of 8 spaces but found 4 indent 212:1 error Expected indentation of 8 spaces but found 4 indent 213:1 error Expected indentation of 8 spaces but found 4 indent 214:1 error Expected indentation of 12 spaces but found 6 indent 215:1 error Expected indentation of 16 spaces but found 8 indent 216:1 error Expected indentation of 12 spaces but found 6 indent 217:1 error Expected indentation of 12 spaces but found 6 indent 218:1 error Expected indentation of 16 spaces but found 8 indent 219:1 error Expected indentation of 12 spaces but found 6 indent 220:1 error Expected indentation of 12 spaces but found 6 indent 221:1 error Expected indentation of 16 spaces but found 8 indent 222:1 error Expected indentation of 12 spaces but found 6 indent 223:1 error Expected indentation of 8 spaces but found 4 indent 225:1 error Expected indentation of 8 spaces but found 4 indent 226:1 error Expected indentation of 12 spaces but found 6 indent 227:1 error Expected indentation of 16 spaces but found 8 indent 228:1 error Expected indentation of 20 spaces but found 10 indent 229:1 error Expected indentation of 24 spaces but found 12 indent 230:1 error Expected indentation of 24 spaces but found 12 indent 231:1 error Expected indentation of 24 spaces but found 12 indent 232:1 error Expected indentation of 24 spaces but found 12 indent 233:1 error Expected indentation of 24 spaces but found 12 indent 234:1 error Expected indentation of 24 spaces but found 12 indent 235:1 error Expected indentation of 24 spaces but found 12 indent 236:1 error Expected indentation of 24 spaces but found 12 indent 237:1 error Expected indentation of 20 spaces but found 10 indent 238:1 error Expected indentation of 24 spaces but found 12 indent 239:1 error Expected indentation of 28 spaces but found 14 indent 240:1 error Expected indentation of 28 spaces but found 14 indent 241:1 error Expected indentation of 28 spaces but found 14 indent 242:1 error Expected indentation of 28 spaces but found 14 indent 243:1 error Expected indentation of 24 spaces but found 12 indent 244:1 error Expected indentation of 20 spaces but found 10 indent 245:1 error Expected indentation of 16 spaces but found 8 indent 246:1 error Expected indentation of 16 spaces but found 8 indent 247:1 error Expected indentation of 20 spaces but found 10 indent 248:1 error Expected indentation of 24 spaces but found 12 indent 249:1 error Expected indentation of 20 spaces but found 10 indent 250:1 error Expected indentation of 16 spaces but found 8 indent 251:1 error Expected indentation of 12 spaces but found 6 indent 252:1 error Expected indentation of 8 spaces but found 4 indent 253:1 error Expected indentation of 4 spaces but found 2 indent 256:1 error Expected indentation of 4 spaces but found 2 indent 257:1 error Expected indentation of 4 spaces but found 2 indent 260:1 error Expected indentation of 4 spaces but found 2 indent 261:1 error Expected indentation of 4 spaces but found 2 indent 262:1 error Expected indentation of 8 spaces but found 4 indent 263:1 error Expected indentation of 8 spaces but found 4 indent 264:1 error Expected indentation of 12 spaces but found 6 indent 265:1 error Expected indentation of 12 spaces but found 6 indent 266:1 error Expected indentation of 8 spaces but found 4 indent 267:1 error Expected indentation of 4 spaces but found 2 indent 274:1 error Expected indentation of 4 spaces but found 2 indent 274:3 error 'ReactDOM' is not defined no-undef 275:1 error Expected indentation of 8 spaces but found 4 indent 276:1 error Expected indentation of 12 spaces but found 6 indent 277:1 error Expected indentation of 12 spaces but found 6 indent 278:1 error Expected indentation of 16 spaces but found 8 indent 278:15 error 'loris' is not defined no-undef 279:1 error Expected indentation of 16 spaces but found 8 indent 280:1 error Expected indentation of 20 spaces but found 10 indent 280:23 error 'loris' is not defined no-undef 281:1 error Expected indentation of 20 spaces but found 10 indent 281:21 error 'loris' is not defined no-undef 282:1 error Expected indentation of 16 spaces but found 8 indent 283:1 error Expected indentation of 12 spaces but found 6 indent 284:1 error Expected indentation of 8 spaces but found 4 indent 285:1 error Expected indentation of 8 spaces but found 4 indent 286:1 error Expected indentation of 4 spaces but found 2 indent 287:1 error Expected indentation of 4 spaces but found 2 indent 288:1 error Expected indentation of 4 spaces but found 2 indent 289:1 error Expected indentation of 8 spaces but found 4 indent 290:1 error Expected indentation of 12 spaces but found 6 indent 290:7 error '$' is not defined no-undef 291:1 error Expected indentation of 16 spaces but found 8 indent 292:1 error Expected indentation of 16 spaces but found 8 indent 292:32 error 'loris' is not defined no-undef 293:1 error Expected indentation of 16 spaces but found 8 indent 294:1 error Expected indentation of 12 spaces but found 6 indent 295:1 error Expected indentation of 12 spaces but found 6 indent 296:1 error Expected indentation of 8 spaces but found 4 indent 297:1 error Expected indentation of 4 spaces but found 2 indent ? 245 problems (245 errors, 0 warnings) 230 errors and 0 warnings potentially fixable with the `--fix` option. ERROR in ./modules/data_integrity_flag/jsx/dataIntegrityFlagIndex.js Module Error (from ./node_modules/eslint-loader/index.js): /var/www/loris/modules/data_integrity_flag/jsx/dataIntegrityFlagIndex.js 1:8 error 'React' is defined but never used no-unused-vars 4:9 error 'Tabs' is defined but never used no-unused-vars 4:15 error 'TabPane' is defined but never used no-unused-vars 5:8 error 'Loader' is defined but never used no-unused-vars 6:8 error 'FilterableDataTable' is defined but never used no-unused-vars 8:8 error 'SetFlagForm' is defined but never used no-unused-vars 11:1 error Expected indentation of 4 spaces but found 2 indent 12:1 error Expected indentation of 8 spaces but found 4 indent 14:1 error Expected indentation of 8 spaces but found 4 indent 15:1 error Expected indentation of 12 spaces but found 6 indent 16:1 error Expected indentation of 12 spaces but found 6 indent 17:1 error Expected indentation of 12 spaces but found 6 indent 18:1 error Expected indentation of 8 spaces but found 4 indent 20:1 error Expected indentation of 8 spaces but found 4 indent 21:1 error Expected indentation of 8 spaces but found 4 indent 22:1 error Expected indentation of 4 spaces but found 2 indent 24:1 error Expected indentation of 4 spaces but found 2 indent 25:1 error Expected indentation of 8 spaces but found 4 indent 26:1 error Expected indentation of 12 spaces but found 6 indent 27:1 error Expected indentation of 4 spaces but found 2 indent 29:1 error Expected indentation of 4 spaces but found 2 indent 34:1 error Expected indentation of 4 spaces but found 2 indent 35:1 error Expected indentation of 8 spaces but found 4 indent 36:1 error Expected indentation of 12 spaces but found 6 indent 37:1 error Expected indentation of 12 spaces but found 6 indent 38:1 error Expected indentation of 12 spaces but found 6 indent 39:1 error Expected indentation of 16 spaces but found 8 indent 40:1 error Expected indentation of 16 spaces but found 8 indent 40:9 error Unexpected console statement no-console 41:1 error Expected indentation of 12 spaces but found 6 indent 42:1 error Expected indentation of 4 spaces but found 2 indent 44:1 error Expected indentation of 4 spaces but found 2 indent 53:1 error Expected indentation of 4 spaces but found 2 indent 54:1 error Expected indentation of 8 spaces but found 4 indent 55:1 error Expected indentation of 8 spaces but found 4 indent 56:1 error Expected indentation of 8 spaces but found 4 indent 57:1 error Expected indentation of 12 spaces but found 6 indent 57:7 error Unexpected lexical declaration in case block no-case-declarations 57:19 error 'loris' is not defined no-undef 59:1 error Expected indentation of 12 spaces but found 6 indent 60:1 error Expected indentation of 12 spaces but found 6 indent 61:1 error Expected indentation of 8 spaces but found 4 indent 62:1 error Expected indentation of 12 spaces but found 6 indent 62:7 error Unexpected lexical declaration in case block no-case-declarations 63:1 error Expected indentation of 12 spaces but found 6 indent 64:1 error Expected indentation of 16 spaces but found 8 indent 65:1 error Expected indentation of 12 spaces but found 6 indent 66:1 error Expected indentation of 12 spaces but found 6 indent 67:1 error Expected indentation of 8 spaces but found 4 indent 68:1 error Expected indentation of 12 spaces but found 6 indent 69:1 error Expected indentation of 12 spaces but found 6 indent 70:1 error Expected indentation of 8 spaces but found 4 indent 72:1 error Expected indentation of 8 spaces but found 4 indent 73:1 error Expected indentation of 4 spaces but found 2 indent 75:1 error Expected indentation of 4 spaces but found 2 indent 78:1 error Expected indentation of 8 spaces but found 4 indent 79:1 error Expected indentation of 12 spaces but found 6 indent 80:1 error Expected indentation of 8 spaces but found 4 indent 82:1 error Expected indentation of 8 spaces but found 4 indent 83:1 error Expected indentation of 8 spaces but found 4 indent 84:1 error Expected indentation of 12 spaces but found 6 indent 85:1 error Expected indentation of 8 spaces but found 4 indent 87:1 error Expected indentation of 8 spaces but found 3 indent 91:1 error Expected indentation of 8 spaces but found 4 indent 92:1 error Expected indentation of 8 spaces but found 4 indent 93:1 error Expected indentation of 12 spaces but found 6 indent 94:1 error Expected indentation of 12 spaces but found 6 indent 95:1 error Expected indentation of 16 spaces but found 8 indent 96:1 error Expected indentation of 16 spaces but found 8 indent 97:1 error Expected indentation of 16 spaces but found 8 indent 98:1 error Expected indentation of 12 spaces but found 6 indent 99:1 error Expected indentation of 12 spaces but found 6 indent 100:1 error Expected indentation of 16 spaces but found 8 indent 101:1 error Expected indentation of 16 spaces but found 8 indent 102:1 error Expected indentation of 16 spaces but found 8 indent 103:1 error Expected indentation of 12 spaces but found 6 indent 104:1 error Expected indentation of 12 spaces but found 6 indent 105:1 error Expected indentation of 12 spaces but found 6 indent 106:1 error Expected indentation of 16 spaces but found 8 indent 107:1 error Expected indentation of 16 spaces but found 8 indent 108:1 error Expected indentation of 16 spaces but found 8 indent 109:1 error Expected indentation of 12 spaces but found 6 indent 110:1 error Expected indentation of 12 spaces but found 6 indent 111:1 error Expected indentation of 12 spaces but found 6 indent 112:1 error Expected indentation of 16 spaces but found 8 indent 113:1 error Expected indentation of 16 spaces but found 8 indent 114:1 error Expected indentation of 16 spaces but found 8 indent 115:1 error Expected indentation of 12 spaces but found 8 indent 116:1 error Expected indentation of 8 spaces but found 4 indent 117:1 error Expected indentation of 8 spaces but found 4 indent 118:1 error Expected indentation of 12 spaces but found 6 indent 119:1 error Expected indentation of 12 spaces but found 6 indent 120:1 error Expected indentation of 8 spaces but found 4 indent 122:1 error Expected indentation of 8 spaces but found 4 indent 123:1 error Expected indentation of 12 spaces but found 6 indent 124:1 error Expected indentation of 16 spaces but found 8 indent 125:1 error Expected indentation of 20 spaces but found 10 indent 126:1 error Expected indentation of 24 spaces but found 12 indent 127:1 error Expected indentation of 24 spaces but found 12 indent 128:1 error Expected indentation of 24 spaces but found 12 indent 129:1 error Expected indentation of 24 spaces but found 12 indent 130:1 error Expected indentation of 20 spaces but found 10 indent 131:1 error Expected indentation of 16 spaces but found 8 indent 132:1 error Expected indentation of 16 spaces but found 8 indent 133:1 error Expected indentation of 20 spaces but found 10 indent 134:1 error Expected indentation of 24 spaces but found 12 indent 135:1 error Expected indentation of 24 spaces but found 12 indent 136:1 error Expected indentation of 20 spaces but found 10 indent 137:1 error Expected indentation of 16 spaces but found 8 indent 138:1 error Expected indentation of 12 spaces but found 6 indent 139:1 error Expected indentation of 8 spaces but found 4 indent 140:1 error Expected indentation of 4 spaces but found 2 indent 144:1 error Expected indentation of 4 spaces but found 2 indent 145:1 error Expected indentation of 4 spaces but found 2 indent 149:1 error Expected indentation of 4 spaces but found 2 indent 149:3 error 'ReactDOM' is not defined no-undef 150:1 error Expected indentation of 8 spaces but found 4 indent 151:1 error Expected indentation of 12 spaces but found 6 indent 151:19 error 'loris' is not defined no-undef 152:1 error Expected indentation of 12 spaces but found 6 indent 152:22 error 'loris' is not defined no-undef 153:1 error Expected indentation of 8 spaces but found 4 indent 154:1 error Expected indentation of 8 spaces but found 4 indent 155:1 error Expected indentation of 4 spaces but found 2 indent ? 124 problems (124 errors, 0 warnings) 111 errors and 0 warnings potentially fixable with the `--fix` option. ERROR in ./modules/data_team_helper/jsx/behavioural_qc_module.js Module Error (from ./node_modules/eslint-loader/index.js): /var/www/loris/modules/data_team_helper/jsx/behavioural_qc_module.js 10:1 error Expected indentation of 4 spaces but found 2 indent 11:1 error Expected indentation of 8 spaces but found 4 indent 12:1 error Expected indentation of 4 spaces but found 2 indent 14:1 error Expected indentation of 4 spaces but found 2 indent 15:1 error Expected indentation of 8 spaces but found 4 indent 16:1 error Expected indentation of 12 spaces but found 6 indent 17:1 error Expected indentation of 16 spaces but found 6 indent 18:1 error Expected indentation of 20 spaces but found 8 indent 19:1 error Expected indentation of 24 spaces but found 10 indent 20:1 error Expected indentation of 20 spaces but found 8 indent 21:1 error Expected indentation of 16 spaces but found 6 indent 22:1 error Expected indentation of 12 spaces but found 6 indent 23:1 error Expected indentation of 8 spaces but found 4 indent 24:1 error Expected indentation of 4 spaces but found 2 indent 27:1 error Expected indentation of 4 spaces but found 2 indent 31:1 error Expected indentation of 4 spaces but found 2 indent 32:1 error Expected indentation of 8 spaces but found 4 indent 33:1 error Expected indentation of 8 spaces but found 4 indent 34:1 error Expected indentation of 12 spaces but found 6 indent 35:1 error Expected indentation of 12 spaces but found 6 indent 36:1 error Expected indentation of 8 spaces but found 4 indent 38:1 error Expected indentation of 8 spaces but found 4 indent 39:1 error Expected indentation of 8 spaces but found 4 indent 40:1 error Expected indentation of 8 spaces but found 4 indent 41:1 error Expected indentation of 4 spaces but found 2 indent 43:1 error Expected indentation of 4 spaces but found 2 indent 43:29 error 'nextProps' is defined but never used no-unused-vars 44:1 error Expected indentation of 8 spaces but found 4 indent 45:1 error Expected indentation of 12 spaces but found 6 indent 46:1 error Expected indentation of 8 spaces but found 4 indent 47:1 error Expected indentation of 4 spaces but found 2 indent 49:1 error Expected indentation of 4 spaces but found 2 indent 50:1 error Expected indentation of 8 spaces but found 4 indent 51:1 error Expected indentation of 8 spaces but found 4 indent 53:1 error Expected indentation of 8 spaces but found 4 indent 54:1 error Expected indentation of 12 spaces but found 6 indent 55:1 error Expected indentation of 12 spaces but found 6 indent 56:1 error Expected indentation of 12 spaces but found 6 indent 57:1 error Expected indentation of 12 spaces but found 6 indent 58:1 error Expected indentation of 8 spaces but found 4 indent 59:1 error Expected indentation of 4 spaces but found 2 indent 61:1 error Expected indentation of 4 spaces but found 2 indent 62:1 error Expected indentation of 8 spaces but found 4 indent 63:1 error Expected indentation of 12 spaces but found 6 indent 64:1 error Expected indentation of 8 spaces but found 4 indent 65:1 error Expected indentation of 8 spaces but found 4 indent 66:1 error Expected indentation of 12 spaces but found 6 indent 67:1 error Expected indentation of 8 spaces but found 4 indent 68:1 error Expected indentation of 8 spaces but found 4 indent 69:1 error Expected indentation of 4 spaces but found 2 indent 70:1 error Expected indentation of 4 spaces but found 2 indent 71:1 error Expected indentation of 8 spaces but found 4 indent 72:1 error Expected indentation of 4 spaces but found 2 indent 74:1 error Expected indentation of 4 spaces but found 2 indent 75:1 error Expected indentation of 8 spaces but found 4 indent 76:1 error Expected indentation of 8 spaces but found 4 indent 77:1 error Expected indentation of 8 spaces but found 4 indent 78:1 error Expected indentation of 8 spaces but found 4 indent 80:1 error Expected indentation of 8 spaces but found 4 indent 81:1 error Expected indentation of 12 spaces but found 6 indent 82:1 error Expected indentation of 16 spaces but found 8 indent 83:1 error Expected indentation of 20 spaces but found 10 indent 84:1 error Expected indentation of 16 spaces but found 8 indent 85:1 error Expected indentation of 12 spaces but found 6 indent 86:1 error Expected indentation of 12 spaces but found 6 indent 87:1 error Expected indentation of 8 spaces but found 4 indent 89:1 error Expected indentation of 8 spaces but found 4 indent 90:1 error Expected indentation of 12 spaces but found 6 indent 91:1 error Expected indentation of 16 spaces but found 8 indent 92:1 error Expected indentation of 20 spaces but found 10 indent 93:1 error Expected indentation of 20 spaces but found 10 indent 94:1 error Expected indentation of 24 spaces but found 12 indent 95:1 error Expected indentation of 20 spaces but found 10 indent 96:1 error Expected indentation of 16 spaces but found 8 indent 97:1 error Expected indentation of 12 spaces but found 6 indent 98:1 error Expected indentation of 8 spaces but found 4 indent 100:1 error Expected indentation of 8 spaces but found 4 indent 101:1 error Expected indentation of 12 spaces but found 6 indent 102:1 error Expected indentation of 16 spaces but found 8 indent 103:1 error Expected indentation of 16 spaces but found 8 indent 104:1 error Expected indentation of 20 spaces but found 10 indent 105:1 error Expected indentation of 24 spaces but found 12 indent 106:1 error Expected indentation of 20 spaces but found 10 indent 107:1 error Expected indentation of 16 spaces but found 8 indent 108:1 error Expected indentation of 12 spaces but found 6 indent 109:1 error Expected indentation of 8 spaces but found 4 indent 110:1 error Expected indentation of 4 spaces but found 2 indent 113:1 error Expected indentation of 4 spaces but found 2 indent 114:1 error Expected indentation of 4 spaces but found 2 indent 118:1 error Expected indentation of 4 spaces but found 2 indent 119:1 error Expected indentation of 8 spaces but found 4 indent 120:1 error Expected indentation of 8 spaces but found 4 indent 122:1 error Expected indentation of 8 spaces but found 4 indent 123:1 error Expected indentation of 8 spaces but found 4 indent 124:1 error Expected indentation of 4 spaces but found 2 indent 126:1 error Expected indentation of 4 spaces but found 2 indent 127:1 error Expected indentation of 8 spaces but found 4 indent 128:1 error Expected indentation of 8 spaces but found 4 indent 129:1 error Expected indentation of 8 spaces but found 4 indent 130:1 error Expected indentation of 4 spaces but found 2 indent 132:1 error Expected indentation of 4 spaces but found 2 indent 133:1 error Expected indentation of 8 spaces but found 4 indent 134:1 error Expected indentation of 8 spaces but found 4 indent 135:1 error Expected indentation of 12 spaces but found 6 indent 136:1 error Expected indentation of 16 spaces but found 8 indent 137:1 error Expected indentation of 20 spaces but found 10 indent 140:1 error Expected indentation of 20 spaces but found 10 indent 141:1 error Expected indentation of 24 spaces but found 12 indent 142:1 error Expected indentation of 20 spaces but found 10 indent 143:1 error Expected indentation of 16 spaces but found 8 indent 144:1 error Expected indentation of 16 spaces but found 8 indent 145:1 error Expected indentation of 20 spaces but found 10 indent 146:1 error Expected indentation of 24 spaces but found 12 indent 147:1 error Expected indentation of 20 spaces but found 10 indent 148:1 error Expected indentation of 16 spaces but found 8 indent 149:1 error Expected indentation of 16 spaces but found 10 indent 150:1 error Expected indentation of 20 spaces but found 14 indent 151:1 error Expected indentation of 24 spaces but found 18 indent 152:1 error Expected indentation of 20 spaces but found 14 indent 153:1 error Expected indentation of 16 spaces but found 10 indent 154:1 error Expected indentation of 16 spaces but found 8 indent 155:1 error Expected indentation of 20 spaces but found 10 indent 159:1 error Expected indentation of 20 spaces but found 14 indent 160:1 error Expected indentation of 24 spaces but found 12 indent 161:1 error Expected indentation of 20 spaces but found 10 indent 162:1 error Expected indentation of 16 spaces but found 8 indent 163:1 error Expected indentation of 12 spaces but found 6 indent 164:1 error Expected indentation of 8 spaces but found 4 indent 165:1 error Expected indentation of 4 spaces but found 2 indent 168:1 error Expected indentation of 4 spaces but found 2 indent 169:1 error Expected indentation of 4 spaces but found 2 indent 173:1 error Expected indentation of 4 spaces but found 2 indent 174:1 error Expected indentation of 8 spaces but found 4 indent 175:1 error Expected indentation of 8 spaces but found 4 indent 177:1 error Expected indentation of 8 spaces but found 4 indent 178:1 error Expected indentation of 4 spaces but found 2 indent 180:1 error Expected indentation of 4 spaces but found 2 indent 181:1 error Expected indentation of 8 spaces but found 4 indent 182:1 error Expected indentation of 8 spaces but found 4 indent 183:1 error Expected indentation of 8 spaces but found 4 indent 184:1 error Expected indentation of 12 spaces but found 6 indent 185:1 error Expected indentation of 16 spaces but found 8 indent 187:1 error Expected indentation of 16 spaces but found 8 indent 188:1 error Expected indentation of 12 spaces but found 6 indent 189:1 error Expected indentation of 16 spaces but found 8 indent 190:1 error Expected indentation of 16 spaces but found 8 indent 191:1 error Expected indentation of 20 spaces but found 10 indent 192:1 error Expected indentation of 16 spaces but found 8 indent 193:1 error Expected indentation of 16 spaces but found 10 indent 194:1 error Expected indentation of 20 spaces but found 14 indent 195:1 error Expected indentation of 16 spaces but found 10 indent 196:1 error Expected indentation of 16 spaces but found 8 indent 197:1 error Expected indentation of 20 spaces but found 10 indent 197:32 error 'loris' is not defined no-undef 198:1 error Expected indentation of 24 spaces but found 17 indent 199:1 error Expected indentation of 24 spaces but found 18 indent 200:1 error Expected indentation of 28 spaces but found 18 indent 201:1 error Expected indentation of 28 spaces but found 18 indent 202:1 error Expected indentation of 20 spaces but found 10 indent 203:1 error Expected indentation of 16 spaces but found 8 indent 204:1 error Expected indentation of 16 spaces but found 8 indent 205:1 error Expected indentation of 12 spaces but found 6 indent 206:1 error Expected indentation of 8 spaces but found 4 indent 207:1 error Expected indentation of 4 spaces but found 2 indent 210:1 error Expected indentation of 4 spaces but found 2 indent 211:1 error Expected indentation of 4 spaces but found 2 indent 215:1 error Expected indentation of 4 spaces but found 2 indent 216:1 error Expected indentation of 8 spaces but found 4 indent 217:1 error Expected indentation of 8 spaces but found 4 indent 219:1 error Expected indentation of 8 spaces but found 4 indent 220:1 error Expected indentation of 8 spaces but found 4 indent 221:1 error Expected indentation of 4 spaces but found 2 indent 223:1 error Expected indentation of 4 spaces but found 2 indent 224:1 error Expected indentation of 8 spaces but found 4 indent 225:1 error Expected indentation of 8 spaces but found 4 indent 226:1 error Expected indentation of 8 spaces but found 4 indent 227:1 error Expected indentation of 4 spaces but found 2 indent 229:1 error Expected indentation of 4 spaces but found 2 indent 230:1 error Expected indentation of 8 spaces but found 4 indent 231:1 error Expected indentation of 8 spaces but found 4 indent 232:1 error Expected indentation of 8 spaces but found 4 indent 234:1 error Expected indentation of 8 spaces but found 4 indent 235:1 error Expected indentation of 12 spaces but found 6 indent 237:1 error Expected indentation of 12 spaces but found 6 indent 238:1 error Expected indentation of 8 spaces but found 4 indent 240:1 error Expected indentation of 8 spaces but found 4 indent 241:1 error Expected indentation of 12 spaces but found 6 indent 245:1 error Expected indentation of 12 spaces but found 6 indent 246:1 error Expected indentation of 8 spaces but found 4 indent 248:1 error Expected indentation of 8 spaces but found 4 indent 249:1 error Expected indentation of 12 spaces but found 6 indent 250:1 error Expected indentation of 12 spaces but found 6 indent 251:1 error Expected indentation of 8 spaces but found 4 indent 253:1 error Expected indentation of 8 spaces but found 4 indent 254:1 error Expected indentation of 12 spaces but found 6 indent 255:1 error Expected indentation of 16 spaces but found 8 indent 256:1 error Expected indentation of 20 spaces but found 10 indent 257:1 error Expected indentation of 24 spaces but found 12 indent 258:1 error Expected indentation of 20 spaces but found 10 indent 259:1 error Expected indentation of 16 spaces but found 8 indent 260:1 error Expected indentation of 16 spaces but found 10 indent 261:1 error Expected indentation of 20 spaces but found 14 indent 262:1 error Expected indentation of 24 spaces but found 18 indent 263:1 error Expected indentation of 20 spaces but found 14 indent 264:1 error Expected indentation of 16 spaces but found 10 indent 265:1 error Expected indentation of 16 spaces but found 8 indent 266:1 error Expected indentation of 20 spaces but found 10 indent 267:1 error Expected indentation of 24 spaces but found 12 indent 268:1 error Expected indentation of 20 spaces but found 10 indent 269:1 error Expected indentation of 16 spaces but found 8 indent 270:1 error Expected indentation of 16 spaces but found 8 indent 271:1 error Expected indentation of 20 spaces but found 10 indent 272:1 error Expected indentation of 16 spaces but found 8 indent 273:1 error Expected indentation of 12 spaces but found 6 indent 274:1 error Expected indentation of 8 spaces but found 4 indent 275:1 error Expected indentation of 4 spaces but found 2 indent 278:1 error Expected indentation of 4 spaces but found 2 indent 279:1 error Expected indentation of 4 spaces but found 2 indent 283:1 error Expected indentation of 4 spaces but found 2 indent 284:1 error Expected indentation of 8 spaces but found 4 indent 285:1 error Expected indentation of 8 spaces but found 4 indent 286:1 error Expected indentation of 12 spaces but found 6 indent 287:1 error Expected indentation of 8 spaces but found 4 indent 288:1 error Expected indentation of 4 spaces but found 2 indent 290:1 error Expected indentation of 4 spaces but found 2 indent 291:1 error Expected indentation of 8 spaces but found 4 indent 292:1 error Expected indentation of 12 spaces but found 6 indent 293:1 error Expected indentation of 16 spaces but found 8 indent 294:1 error Expected indentation of 16 spaces but found 8 indent 295:1 error Expected indentation of 20 spaces but found 10 indent 296:1 error Expected indentation of 16 spaces but found 8 indent 297:1 error Expected indentation of 12 spaces but found 6 indent 298:1 error Expected indentation of 8 spaces but found 4 indent 299:1 error Expected indentation of 4 spaces but found 2 indent 302:1 error Expected indentation of 4 spaces but found 2 indent 303:1 error Expected indentation of 4 spaces but found 2 indent 307:1 error Expected indentation of 4 spaces but found 2 indent 308:1 error Expected indentation of 8 spaces but found 4 indent 309:1 error Expected indentation of 8 spaces but found 4 indent 310:1 error Expected indentation of 8 spaces but found 4 indent 311:1 error Expected indentation of 4 spaces but found 2 indent 312:1 error Expected indentation of 4 spaces but found 2 indent 314:1 error Expected indentation of 8 spaces but found 4 indent 315:1 error Expected indentation of 8 spaces but found 4 indent 316:1 error Expected indentation of 12 spaces but found 6 indent 317:1 error Expected indentation of 16 spaces but found 8 indent 318:1 error Expected indentation of 20 spaces but found 10 indent 319:1 error Expected indentation of 20 spaces but found 10 indent 320:1 error Expected indentation of 16 spaces but found 8 indent 321:1 error Expected indentation of 20 spaces but found 10 indent 322:1 error Expected indentation of 16 spaces but found 8 indent 323:1 error Expected indentation of 12 spaces but found 6 indent 324:1 error Expected indentation of 8 spaces but found 4 indent 325:1 error Expected indentation of 4 spaces but found 2 indent 328:1 error Expected indentation of 4 spaces but found 2 indent 329:1 error Expected indentation of 4 spaces but found 2 indent 330:1 error Expected indentation of 4 spaces but found 2 indent 331:1 error Expected indentation of 4 spaces but found 2 indent 336:1 error Expected indentation of 4 spaces but found 2 indent 337:1 error Expected indentation of 8 spaces but found 4 indent 338:1 error Expected indentation of 8 spaces but found 4 indent 340:1 error Expected indentation of 8 spaces but found 4 indent 341:1 error Expected indentation of 4 spaces but found 2 indent 343:1 error Expected indentation of 4 spaces but found 2 indent 345:1 error Expected indentation of 8 spaces but found 4 indent 346:1 error Expected indentation of 8 spaces but found 4 indent 347:1 error Expected indentation of 12 spaces but found 6 indent 348:1 error Expected indentation of 16 spaces but found 8 indent 349:1 error Expected indentation of 20 spaces but found 10 indent 350:1 error Expected indentation of 20 spaces but found 10 indent 351:1 error Expected indentation of 16 spaces but found 8 indent 352:1 error Expected indentation of 20 spaces but found 10 indent 353:1 error Expected indentation of 16 spaces but found 8 indent 354:1 error Expected indentation of 12 spaces but found 6 indent 355:1 error Expected indentation of 8 spaces but found 4 indent 356:1 error Expected indentation of 4 spaces but found 2 indent 359:1 error Expected indentation of 4 spaces but found 2 indent 360:1 error Expected indentation of 4 spaces but found 2 indent 361:1 error Expected indentation of 4 spaces but found 2 indent 362:1 error Expected indentation of 4 spaces but found 2 indent 366:1 error Expected indentation of 4 spaces but found 2 indent 367:1 error Expected indentation of 8 spaces but found 4 indent 368:1 error Expected indentation of 8 spaces but found 4 indent 370:1 error Expected indentation of 8 spaces but found 4 indent 371:1 error Expected indentation of 4 spaces but found 2 indent 373:1 error Expected indentation of 4 spaces but found 2 indent 375:1 error Expected indentation of 8 spaces but found 4 indent 376:1 error Expected indentation of 8 spaces but found 4 indent 377:1 error Expected indentation of 12 spaces but found 6 indent 378:1 error Expected indentation of 16 spaces but found 8 indent 379:1 error Expected indentation of 20 spaces but found 10 indent 380:1 error Expected indentation of 20 spaces but found 10 indent 381:1 error Expected indentation of 16 spaces but found 8 indent 382:1 error Expected indentation of 20 spaces but found 10 indent 383:1 error Expected indentation of 16 spaces but found 8 indent 384:1 error Expected indentation of 12 spaces but found 6 indent 385:1 error Expected indentation of 8 spaces but found 4 indent 386:1 error Expected indentation of 4 spaces but found 2 indent 389:1 error Expected indentation of 4 spaces but found 2 indent 390:1 error Expected indentation of 4 spaces but found 2 indent 391:1 error Expected indentation of 4 spaces but found 2 indent 392:1 error Expected indentation of 4 spaces but found 2 indent 396:1 error Expected indentation of 4 spaces but found 2 indent 397:1 error Expected indentation of 8 spaces but found 4 indent 399:1 error Expected indentation of 8 spaces but found 4 indent 400:1 error Expected indentation of 8 spaces but found 4 indent 402:1 error Expected indentation of 8 spaces but found 4 indent 403:1 error Expected indentation of 12 spaces but found 6 indent 404:1 error Expected indentation of 16 spaces but found 8 indent 405:1 error Expected indentation of 20 spaces but found 10 indent 406:1 error Expected indentation of 16 spaces but found 8 indent 407:1 error Expected indentation of 12 spaces but found 6 indent 408:1 error Expected indentation of 12 spaces but found 6 indent 409:1 error Expected indentation of 16 spaces but found 8 indent 410:1 error Expected indentation of 20 spaces but found 10 indent 411:1 error Expected indentation of 24 spaces but found 12 indent 412:1 error Expected indentation of 20 spaces but found 10 indent 413:1 error Expected indentation of 16 spaces but found 8 indent 414:1 error Expected indentation of 16 spaces but found 8 indent 415:1 error Expected indentation of 12 spaces but found 6 indent 416:1 error Expected indentation of 8 spaces but found 4 indent 418:1 error Expected indentation of 8 spaces but found 4 indent 419:1 error Expected indentation of 12 spaces but found 6 indent 420:1 error Expected indentation of 16 spaces but found 8 indent 421:1 error Expected indentation of 12 spaces but found 6 indent 422:1 error Expected indentation of 8 spaces but found 4 indent 424:1 error Expected indentation of 8 spaces but found 4 indent 425:1 error Expected indentation of 12 spaces but found 6 indent 426:1 error Expected indentation of 16 spaces but found 8 indent 427:1 error Expected indentation of 20 spaces but found 10 indent 428:1 error Expected indentation of 16 spaces but found 8 indent 429:1 error Expected indentation of 12 spaces but found 6 indent 431:1 error Expected indentation of 12 spaces but found 6 indent 432:1 error Expected indentation of 16 spaces but found 8 indent 433:1 error Expected indentation of 20 spaces but found 10 indent 434:1 error Expected indentation of 24 spaces but found 12 indent 435:1 error Expected indentation of 20 spaces but found 10 indent 436:1 error Expected indentation of 16 spaces but found 8 indent 437:1 error Expected indentation of 12 spaces but found 6 indent 439:1 error Expected indentation of 12 spaces but found 6 indent 440:1 error Expected indentation of 16 spaces but found 8 indent 441:1 error Expected indentation of 20 spaces but found 10 indent 442:1 error Expected indentation of 24 spaces but found 12 indent 443:1 error Expected indentation of 20 spaces but found 10 indent 444:1 error Expected indentation of 16 spaces but found 8 indent 445:1 error Expected indentation of 12 spaces but found 6 indent 447:1 error Expected indentation of 12 spaces but found 6 indent 448:1 error Expected indentation of 16 spaces but found 8 indent 449:1 error Expected indentation of 16 spaces but found 8 indent 450:1 error Expected indentation of 20 spaces but found 10 indent 451:1 error Expected indentation of 24 spaces but found 12 indent 452:1 error Expected indentation of 20 spaces but found 10 indent 453:1 error Expected indentation of 16 spaces but found 8 indent 454:1 error Expected indentation of 12 spaces but found 6 indent 456:1 error Expected indentation of 12 spaces but found 6 indent 457:1 error Expected indentation of 16 spaces but found 8 indent 458:1 error Expected indentation of 20 spaces but found 10 indent 459:1 error Expected indentation of 16 spaces but found 8 indent 460:1 error Expected indentation of 12 spaces but found 6 indent 461:1 error Expected indentation of 8 spaces but found 4 indent 462:1 error Expected indentation of 8 spaces but found 4 indent 463:1 error Expected indentation of 12 spaces but found 6 indent 464:1 error Expected indentation of 8 spaces but found 4 indent 465:1 error Expected indentation of 4 spaces but found 2 indent 467:1 error Expected indentation of 4 spaces but found 2 indent 468:1 error Expected indentation of 8 spaces but found 4 indent 469:1 error Expected indentation of 12 spaces but found 6 indent 470:1 error Expected indentation of 8 spaces but found 4 indent 471:1 error Expected indentation of 4 spaces but found 2 indent 474:1 error Expected indentation of 4 spaces but found 2 indent 478:1 error Expected indentation of 4 spaces but found 2 indent 479:1 error Expected indentation of 8 spaces but found 4 indent 480:1 error Expected indentation of 8 spaces but found 4 indent 482:1 error Expected indentation of 8 spaces but found 4 indent 483:1 error Expected indentation of 4 spaces but found 2 indent 485:1 error Expected indentation of 4 spaces but found 2 indent 486:1 error Expected indentation of 8 spaces but found 4 indent 487:1 error Expected indentation of 12 spaces but found 6 indent 488:1 error Expected indentation of 12 spaces but found 6 indent 489:1 error Expected indentation of 16 spaces but found 8 indent 490:1 error Expected indentation of 20 spaces but found 10 indent 491:1 error Expected indentation of 16 spaces but found 8 indent 492:1 error Expected indentation of 16 spaces but found 8 indent 493:1 error Expected indentation of 12 spaces but found 6 indent 494:1 error Expected indentation of 12 spaces but found 6 indent 495:1 error Expected indentation of 16 spaces but found 8 indent 496:1 error Expected indentation of 16 spaces but found 8 indent 497:1 error Expected indentation of 16 spaces but found 8 indent 498:1 error Expected indentation of 20 spaces but found 10 indent 499:1 error Expected indentation of 20 spaces but found 10 indent 500:1 error Expected indentation of 20 spaces but found 10 indent 501:1 error Expected indentation of 16 spaces but found 8 indent 502:1 error Expected indentation of 12 spaces but found 6 indent 503:1 error Expected indentation of 8 spaces but found 4 indent 504:1 error Expected indentation of 4 spaces but found 2 indent 505:1 error Expected indentation of 4 spaces but found 2 indent 506:1 error Expected indentation of 8 spaces but found 4 indent 507:1 error Expected indentation of 12 spaces but found 6 indent 508:1 error Expected indentation of 8 spaces but found 4 indent 509:1 error Expected indentation of 8 spaces but found 4 indent 510:1 error Expected indentation of 12 spaces but found 6 indent 511:1 error Expected indentation of 8 spaces but found 4 indent 512:1 error Expected indentation of 8 spaces but found 4 indent 513:1 error Expected indentation of 12 spaces but found 6 indent 514:1 error Expected indentation of 16 spaces but found 8 indent 515:1 error Expected indentation of 8 spaces but found 4 indent 516:1 error Expected indentation of 8 spaces but found 4 indent 517:1 error Expected indentation of 12 spaces but found 6 indent 518:1 error Expected indentation of 16 spaces but found 8 indent 519:1 error Expected indentation of 8 spaces but found 6 indent 520:1 error Expected indentation of 8 spaces but found 4 indent 521:1 error Expected indentation of 12 spaces but found 6 indent 522:1 error Expected indentation of 16 spaces but found 8 indent 523:1 error Expected indentation of 8 spaces but found 6 indent 525:1 error Expected indentation of 8 spaces but found 4 indent 526:1 error Expected indentation of 12 spaces but found 6 indent 527:1 error Expected indentation of 16 spaces but found 8 indent 528:1 error Expected indentation of 20 spaces but found 10 indent 530:1 error Expected indentation of 20 spaces but found 10 indent 531:1 error Expected indentation of 20 spaces but found 10 indent 532:1 error Expected indentation of 24 spaces but found 12 indent 533:1 error Expected indentation of 20 spaces but found 10 indent 534:1 error Expected indentation of 16 spaces but found 8 indent 535:1 error Expected indentation of 12 spaces but found 6 indent 536:1 error Expected indentation of 8 spaces but found 4 indent 537:1 error Expected indentation of 4 spaces but found 2 indent 540:1 error Expected indentation of 4 spaces but found 2 indent 541:1 error Expected indentation of 4 spaces but found 2 indent 542:1 error Expected indentation of 4 spaces but found 2 indent 543:1 error Expected indentation of 4 spaces but found 2 indent 544:1 error Expected indentation of 4 spaces but found 2 indent 545:1 error Expected indentation of 4 spaces but found 2 indent 560:1 error Expected indentation of 4 spaces but found 2 indent 561:1 error Expected indentation of 4 spaces but found 2 indent 562:1 error Expected indentation of 4 spaces but found 2 indent 563:1 error Expected indentation of 4 spaces but found 2 indent ? 436 problems (436 errors, 0 warnings) 434 errors and 0 warnings potentially fixable with the `--fix` option. ERROR in ./modules/datadict/jsx/dataDictIndex.js Module Error (from ./node_modules/eslint-loader/index.js): /var/www/loris/modules/datadict/jsx/dataDictIndex.js 1:8 error 'FilterForm' is defined but never used no-unused-vars 2:8 error 'Loader' is defined but never used no-unused-vars 17:7 error 'DataDictIndex' is defined but never used no-unused-vars 17:29 error 'React' is not defined no-undef 18:1 error Expected indentation of 4 spaces but found 2 indent 19:1 error Expected indentation of 8 spaces but found 4 indent 21:1 error Expected indentation of 8 spaces but found 4 indent 22:1 error Expected indentation of 12 spaces but found 6 indent 23:1 error Expected indentation of 12 spaces but found 6 indent 24:1 error Expected indentation of 12 spaces but found 6 indent 25:1 error Expected indentation of 8 spaces but found 4 indent 27:1 error Expected indentation of 8 spaces but found 4 indent 30:1 error Expected indentation of 8 spaces but found 4 indent 31:1 error Expected indentation of 8 spaces but found 4 indent 32:1 error Expected indentation of 12 spaces but found 6 indent 33:1 error Expected indentation of 8 spaces but found 4 indent 35:1 error Expected indentation of 8 spaces but found 4 indent 38:1 error Expected indentation of 8 spaces but found 4 indent 39:1 error Expected indentation of 8 spaces but found 4 indent 40:1 error Expected indentation of 8 spaces but found 4 indent 41:1 error Expected indentation of 8 spaces but found 4 indent 42:1 error Expected indentation of 4 spaces but found 2 indent 44:1 error Expected indentation of 4 spaces but found 2 indent 45:1 error Expected indentation of 8 spaces but found 4 indent 46:1 error Expected indentation of 4 spaces but found 2 indent 48:1 error Expected indentation of 4 spaces but found 2 indent 53:1 error Expected indentation of 4 spaces but found 2 indent 54:1 error Expected indentation of 8 spaces but found 4 indent 54:5 error '$' is not defined no-undef 55:1 error Expected indentation of 12 spaces but found 6 indent 56:1 error Expected indentation of 12 spaces but found 6 indent 57:1 error Expected indentation of 12 spaces but found 6 indent 58:1 error Expected indentation of 16 spaces but found 8 indent 59:1 error Expected indentation of 20 spaces but found 10 indent 60:1 error Expected indentation of 20 spaces but found 10 indent 61:1 error Expected indentation of 16 spaces but found 8 indent 62:1 error Expected indentation of 12 spaces but found 6 indent 63:1 error Expected indentation of 12 spaces but found 6 indent 63:25 error Unexpected console statement no-console 64:1 error Expected indentation of 8 spaces but found 4 indent 65:1 error Expected indentation of 4 spaces but found 2 indent 67:1 error Expected indentation of 4 spaces but found 2 indent 72:1 error Expected indentation of 4 spaces but found 2 indent 73:1 error Expected indentation of 8 spaces but found 4 indent 74:1 error Expected indentation of 4 spaces but found 2 indent 76:1 error Expected indentation of 4 spaces but found 2 indent 77:1 error Expected indentation of 4 spaces but found 2 indent 80:1 error Expected indentation of 4 spaces but found 2 indent 81:1 error Expected indentation of 8 spaces but found 4 indent 82:1 error Expected indentation of 4 spaces but found 2 indent 84:1 error Expected indentation of 4 spaces but found 2 indent 94:1 error Expected indentation of 4 spaces but found 2 indent 94:39 error 'rowHeaders' is defined but never used no-unused-vars 95:1 error Expected indentation of 8 spaces but found 4 indent 96:1 error Expected indentation of 12 spaces but found 6 indent 97:1 error Expected indentation of 8 spaces but found 4 indent 98:1 error Expected indentation of 8 spaces but found 4 indent 98:31 error 'loris' is not defined no-undef 99:1 error Expected indentation of 8 spaces but found 4 indent 100:1 error Expected indentation of 12 spaces but found 6 indent 101:1 error Expected indentation of 16 spaces but found 8 indent 102:1 error Expected indentation of 20 spaces but found 10 indent 104:1 error Expected indentation of 20 spaces but found 10 indent 105:1 error Expected indentation of 20 spaces but found 10 indent 105:11 error '$' is not defined no-undef 105:18 error 'loris' is not defined no-undef 106:1 error Expected indentation of 24 spaces but found 12 indent 107:1 error Expected indentation of 20 spaces but found 10 indent 107:15 error 'data' is defined but never used no-unused-vars 108:1 error Expected indentation of 16 spaces but found 8 indent 109:1 error Expected indentation of 12 spaces but found 6 indent 110:1 error Expected indentation of 12 spaces but found 6 indent 111:1 error Expected indentation of 16 spaces but found 8 indent 112:1 error Expected indentation of 20 spaces but found 10 indent 113:1 error Expected indentation of 20 spaces but found 10 indent 114:1 error Expected indentation of 20 spaces but found 10 indent 115:1 error Expected indentation of 20 spaces but found 12 indent 116:1 error Expected indentation of 16 spaces but found 8 indent 117:1 error Expected indentation of 12 spaces but found 6 indent 118:1 error Expected indentation of 8 spaces but found 4 indent 119:1 error Expected indentation of 8 spaces but found 4 indent 120:1 error Expected indentation of 4 spaces but found 2 indent 122:1 error Expected indentation of 4 spaces but found 2 indent 124:1 error Expected indentation of 8 spaces but found 4 indent 125:1 error Expected indentation of 12 spaces but found 6 indent 126:1 error Expected indentation of 8 spaces but found 4 indent 128:1 error Expected indentation of 8 spaces but found 4 indent 129:1 error Expected indentation of 12 spaces but found 6 indent 130:1 error Expected indentation of 16 spaces but found 8 indent 131:1 error Expected indentation of 20 spaces but found 10 indent 132:1 error Expected indentation of 20 spaces but found 10 indent 133:1 error Expected indentation of 20 spaces but found 10 indent 134:1 error Expected indentation of 20 spaces but found 10 indent 135:1 error Expected indentation of 20 spaces but found 10 indent 136:1 error Expected indentation of 20 spaces but found 10 indent 137:1 error Expected indentation of 20 spaces but found 10 indent 138:1 error Expected indentation of 20 spaces but found 10 indent 139:1 error Expected indentation of 20 spaces but found 10 indent 140:1 error Expected indentation of 24 spaces but found 12 indent 141:1 error Expected indentation of 24 spaces but found 12 indent 142:1 error Expected indentation of 24 spaces but found 12 indent 143:1 error Expected indentation of 20 spaces but found 10 indent 144:1 error Expected indentation of 16 spaces but found 8 indent 145:1 error Expected indentation of 16 spaces but found 8 indent 146:1 error Expected indentation of 20 spaces but found 10 indent 147:1 error Expected indentation of 20 spaces but found 10 indent 148:1 error Expected indentation of 20 spaces but found 10 indent 149:1 error Expected indentation of 20 spaces but found 10 indent 150:1 error Expected indentation of 16 spaces but found 8 indent 151:1 error Expected indentation of 12 spaces but found 6 indent 152:1 error Expected indentation of 8 spaces but found 4 indent 153:1 error Expected indentation of 4 spaces but found 2 indent 156:1 error '$' is not defined no-undef 157:1 error Expected indentation of 4 spaces but found 2 indent 158:1 error Expected indentation of 8 spaces but found 4 indent 159:1 error Expected indentation of 12 spaces but found 8 indent 159:36 error 'loris' is not defined no-undef 160:1 error Expected indentation of 8 spaces but found 4 indent 161:1 error Expected indentation of 4 spaces but found 2 indent 162:1 error Expected indentation of 4 spaces but found 2 indent 162:3 error 'ReactDOM' is not defined no-undef ? 121 problems (121 errors, 0 warnings) 107 errors and 0 warnings potentially fixable with the `--fix` option. ERROR in ./modules/dataquery/jsx/react.app.js Module Error (from ./node_modules/eslint-loader/index.js): /var/www/loris/modules/dataquery/jsx/react.app.js 19:1 error Expected indentation of 4 spaces but found 2 indent 20:1 error Expected indentation of 8 spaces but found 4 indent 21:1 error Expected indentation of 8 spaces but found 4 indent 23:1 error Expected indentation of 8 spaces but found 4 indent 24:1 error Expected indentation of 4 spaces but found 2 indent 26:1 error Expected indentation of 4 spaces but found 2 indent 28:1 error Expected indentation of 4 spaces but found 2 indent 30:1 error Expected indentation of 4 spaces but found 2 indent 33:1 error Expected indentation of 8 spaces but found 4 indent 34:1 error Expected indentation of 12 spaces but found 6 indent 35:1 error Expected indentation of 12 spaces but found 6 indent 36:1 error Expected indentation of 8 spaces but found 4 indent 37:1 error Expected indentation of 4 spaces but found 2 indent 39:1 error Expected indentation of 4 spaces but found 2 indent 42:1 error Expected indentation of 8 spaces but found 4 indent 43:1 error Expected indentation of 8 spaces but found 4 indent 44:1 error Expected indentation of 8 spaces but found 4 indent 46:1 error Expected indentation of 8 spaces but found 4 indent 47:1 error Expected indentation of 12 spaces but found 6 indent 48:1 error Expected indentation of 8 spaces but found 4 indent 49:1 error Expected indentation of 8 spaces but found 4 indent 50:1 error Expected indentation of 8 spaces but found 4 indent 51:1 error Expected indentation of 12 spaces but found 6 indent 52:1 error Expected indentation of 12 spaces but found 6 indent 53:1 error Expected indentation of 16 spaces but found 8 indent 54:1 error Expected indentation of 12 spaces but found 6 indent 55:1 error Expected indentation of 16 spaces but found 8 indent 56:1 error Expected indentation of 12 spaces but found 6 indent 57:1 error Expected indentation of 12 spaces but found 6 indent 58:1 error Expected indentation of 8 spaces but found 4 indent 59:1 error Expected indentation of 8 spaces but found 4 indent 60:1 error Expected indentation of 8 spaces but found 4 indent 61:1 error Expected indentation of 12 spaces but found 6 indent 62:1 error Expected indentation of 12 spaces but found 6 indent 63:1 error Expected indentation of 16 spaces but found 8 indent 64:1 error Expected indentation of 12 spaces but found 6 indent 65:1 error Expected indentation of 16 spaces but found 8 indent 66:1 error Expected indentation of 12 spaces but found 6 indent 67:1 error Expected indentation of 12 spaces but found 6 indent 68:1 error Expected indentation of 8 spaces but found 4 indent 69:1 error Expected indentation of 8 spaces but found 4 indent 70:1 error Expected indentation of 12 spaces but found 6 indent 71:1 error Expected indentation of 16 spaces but found 8 indent 72:1 error Expected indentation of 20 spaces but found 10 indent 73:1 error Expected indentation of 20 spaces but found 10 indent 74:1 error Expected indentation of 24 spaces but found 12 indent 75:1 error Expected indentation of 24 spaces but found 12 indent 76:1 error Expected indentation of 24 spaces but found 12 indent 77:1 error Expected indentation of 24 spaces but found 12 indent 78:1 error Expected indentation of 20 spaces but found 10 indent 79:1 error Expected indentation of 16 spaces but found 8 indent 80:1 error Expected indentation of 16 spaces but found 8 indent 81:1 error Expected indentation of 12 spaces but found 6 indent 82:1 error Expected indentation of 8 spaces but found 4 indent 83:1 error Expected indentation of 4 spaces but found 2 indent 87:1 error Expected indentation of 4 spaces but found 2 indent 88:1 error Expected indentation of 4 spaces but found 2 indent 91:1 error Expected indentation of 4 spaces but found 2 indent 92:1 error Expected indentation of 4 spaces but found 2 indent 100:1 error Expected indentation of 4 spaces but found 2 indent 101:1 error Expected indentation of 8 spaces but found 4 indent 103:1 error Expected indentation of 8 spaces but found 4 indent 104:1 error Expected indentation of 12 spaces but found 6 indent 105:1 error Expected indentation of 12 spaces but found 6 indent 106:1 error Expected indentation of 12 spaces but found 6 indent 107:1 error Expected indentation of 12 spaces but found 6 indent 108:1 error Expected indentation of 12 spaces but found 6 indent 109:1 error Expected indentation of 12 spaces but found 6 indent 110:1 error Expected indentation of 12 spaces but found 6 indent 111:1 error Expected indentation of 12 spaces but found 6 indent 112:1 error Expected indentation of 12 spaces but found 6 indent 113:1 error Expected indentation of 12 spaces but found 6 indent 114:1 error Expected indentation of 12 spaces but found 6 indent 115:1 error Expected indentation of 16 spaces but found 8 indent 116:1 error Expected indentation of 12 spaces but found 6 indent 117:1 error Expected indentation of 12 spaces but found 6 indent 118:1 error Expected indentation of 12 spaces but found 6 indent 119:1 error Expected indentation of 12 spaces but found 6 indent 120:1 error Expected indentation of 16 spaces but found 8 indent 121:1 error Expected indentation of 16 spaces but found 8 indent 122:1 error Expected indentation of 16 spaces but found 8 indent 123:1 error Expected indentation of 20 spaces but found 10 indent 124:1 error Expected indentation of 24 spaces but found 12 indent 125:1 error Expected indentation of 20 spaces but found 10 indent 126:1 error Expected indentation of 16 spaces but found 8 indent 127:1 error Expected indentation of 16 spaces but found 8 indent 128:1 error Expected indentation of 12 spaces but found 6 indent 129:1 error Expected indentation of 12 spaces but found 6 indent 130:1 error Expected indentation of 12 spaces but found 6 indent 131:1 error Expected indentation of 12 spaces but found 6 indent 132:1 error Expected indentation of 8 spaces but found 4 indent 133:1 error Expected indentation of 8 spaces but found 4 indent 134:1 error Expected indentation of 8 spaces but found 4 indent 135:1 error Expected indentation of 8 spaces but found 4 indent 136:1 error Expected indentation of 8 spaces but found 4 indent 137:1 error Expected indentation of 8 spaces but found 4 indent 138:1 error Expected indentation of 8 spaces but found 4 indent 139:1 error Expected indentation of 8 spaces but found 4 indent 140:1 error Expected indentation of 8 spaces but found 4 indent 141:1 error Expected indentation of 8 spaces but found 4 indent 142:1 error Expected indentation of 8 spaces but found 4 indent 143:1 error Expected indentation of 8 spaces but found 4 indent 144:1 error Expected indentation of 8 spaces but found 4 indent 145:1 error Expected indentation of 8 spaces but found 4 indent 146:1 error Expected indentation of 8 spaces but found 4 indent 147:1 error Expected indentation of 8 spaces but found 4 indent 148:1 error Expected indentation of 8 spaces but found 4 indent 149:1 error Expected indentation of 4 spaces but found 2 indent 151:1 error Expected indentation of 4 spaces but found 2 indent 155:1 error Expected indentation of 8 spaces but found 4 indent 156:1 error Expected indentation of 8 spaces but found 4 indent 157:1 error Expected indentation of 8 spaces but found 4 indent 158:1 error Expected indentation of 8 spaces but found 4 indent 159:1 error Expected indentation of 8 spaces but found 4 indent 159:5 error '$' is not defined no-undef 160:1 error Expected indentation of 12 spaces but found 6 indent 160:7 error '$' is not defined no-undef 161:1 error Expected indentation of 12 spaces but found 6 indent 162:1 error Expected indentation of 16 spaces but found 8 indent 163:1 error Expected indentation of 16 spaces but found 8 indent 164:1 error Expected indentation of 16 spaces but found 8 indent 165:1 error Expected indentation of 20 spaces but found 10 indent 166:1 error Expected indentation of 16 spaces but found 8 indent 167:1 error Expected indentation of 12 spaces but found 6 indent 168:1 error Expected indentation of 8 spaces but found 4 indent 170:1 error Expected indentation of 8 spaces but found 4 indent 171:1 error Expected indentation of 8 spaces but found 4 indent 172:1 error Expected indentation of 8 spaces but found 4 indent 173:1 error Expected indentation of 12 spaces but found 6 indent 174:1 error Expected indentation of 16 spaces but found 8 indent 175:1 error Expected indentation of 16 spaces but found 8 indent 176:1 error Expected indentation of 20 spaces but found 10 indent 176:11 error '$' is not defined no-undef 176:18 error 'loris' is not defined no-undef 177:1 error Expected indentation of 24 spaces but found 12 indent 178:1 error Expected indentation of 28 spaces but found 14 indent 179:1 error Expected indentation of 24 spaces but found 12 indent 180:1 error Expected indentation of 24 spaces but found 12 indent 181:1 error Expected indentation of 20 spaces but found 10 indent 182:1 error Expected indentation of 20 spaces but found 10 indent 184:1 error Expected indentation of 20 spaces but found 10 indent 185:1 error Expected indentation of 20 spaces but found 10 indent 186:1 error Expected indentation of 16 spaces but found 8 indent 187:1 error Expected indentation of 16 spaces but found 8 indent 188:1 error Expected indentation of 12 spaces but found 6 indent 189:1 error Expected indentation of 8 spaces but found 4 indent 191:1 error Expected indentation of 8 spaces but found 4 indent 191:9 error 'allDone' is assigned a value but never used no-unused-vars 191:47 error 'value' is defined but never used no-unused-vars 192:1 error Expected indentation of 12 spaces but found 6 indent 193:1 error Expected indentation of 8 spaces but found 4 indent 194:1 error Expected indentation of 8 spaces but found 4 indent 194:5 error '$' is not defined no-undef 195:1 error Expected indentation of 12 spaces but found 6 indent 196:1 error Expected indentation of 16 spaces but found 8 indent 197:1 error Expected indentation of 12 spaces but found 6 indent 198:1 error Expected indentation of 8 spaces but found 4 indent 199:1 error Expected indentation of 4 spaces but found 2 indent 201:1 error Expected indentation of 4 spaces but found 2 indent 204:1 error Expected indentation of 8 spaces but found 4 indent 205:1 error Expected indentation of 12 spaces but found 6 indent 206:1 error Expected indentation of 12 spaces but found 6 indent 207:1 error Expected indentation of 12 spaces but found 6 indent 208:1 error Expected indentation of 12 spaces but found 6 indent 209:1 error Expected indentation of 12 spaces but found 6 indent 210:1 error Expected indentation of 8 spaces but found 4 indent 211:1 error Expected indentation of 8 spaces but found 4 indent 212:1 error Expected indentation of 4 spaces but found 2 indent 214:1 error Expected indentation of 4 spaces but found 2 indent 217:1 error Expected indentation of 8 spaces but found 4 indent 218:1 error Expected indentation of 12 spaces but found 6 indent 219:1 error Expected indentation of 12 spaces but found 6 indent 220:1 error Expected indentation of 8 spaces but found 4 indent 221:1 error Expected indentation of 8 spaces but found 4 indent 222:1 error Expected indentation of 8 spaces but found 4 indent 223:1 error Expected indentation of 12 spaces but found 6 indent 224:1 error Expected indentation of 16 spaces but found 8 indent 225:1 error Expected indentation of 12 spaces but found 6 indent 226:1 error Expected indentation of 16 spaces but found 8 indent 227:1 error Expected indentation of 12 spaces but found 6 indent 228:1 error Expected indentation of 8 spaces but found 4 indent 229:1 error Expected indentation of 8 spaces but found 4 indent 230:1 error Expected indentation of 4 spaces but found 2 indent 232:1 error Expected indentation of 4 spaces but found 2 indent 235:1 error Expected indentation of 8 spaces but found 4 indent 237:1 error Expected indentation of 8 spaces but found 4 indent 237:5 error '$' is not defined no-undef 237:12 error 'loris' is not defined no-undef 238:1 error Expected indentation of 12 spaces but found 6 indent 239:1 error Expected indentation of 12 spaces but found 6 indent 240:1 error Expected indentation of 12 spaces but found 6 indent 241:1 error Expected indentation of 12 spaces but found 6 indent 242:1 error Expected indentation of 12 spaces but found 6 indent 243:1 error Expected indentation of 8 spaces but found 4 indent 244:1 error Expected indentation of 12 spaces but found 6 indent 245:1 error Expected indentation of 12 spaces but found 6 indent 246:1 error Expected indentation of 16 spaces but found 8 indent 247:1 error Expected indentation of 12 spaces but found 6 indent 248:1 error Expected indentation of 16 spaces but found 8 indent 249:1 error Expected indentation of 20 spaces but found 10 indent 250:1 error Expected indentation of 16 spaces but found 8 indent 251:1 error Expected indentation of 20 spaces but found 10 indent 252:1 error Expected indentation of 16 spaces but found 8 indent 253:1 error Expected indentation of 12 spaces but found 6 indent 254:1 error Expected indentation of 12 spaces but found 6 indent 254:7 error '$' is not defined no-undef 254:13 error 'loris' is not defined no-undef 255:1 error Expected indentation of 16 spaces but found 8 indent 256:1 error Expected indentation of 20 spaces but found 10 indent 258:1 error Expected indentation of 20 spaces but found 10 indent 259:1 error Expected indentation of 20 spaces but found 10 indent 260:1 error Expected indentation of 24 spaces but found 12 indent 261:1 error Expected indentation of 24 spaces but found 12 indent 262:1 error Expected indentation of 24 spaces but found 12 indent 263:1 error Expected indentation of 24 spaces but found 12 indent 264:1 error Expected indentation of 24 spaces but found 12 indent 265:1 error Expected indentation of 28 spaces but found 14 indent 266:1 error Expected indentation of 24 spaces but found 12 indent 267:1 error Expected indentation of 20 spaces but found 10 indent 268:1 error Expected indentation of 16 spaces but found 8 indent 269:1 error Expected indentation of 8 spaces but found 4 indent 270:1 error Expected indentation of 12 spaces but found 6 indent 271:1 error Expected indentation of 16 spaces but found 8 indent 272:1 error Expected indentation of 20 spaces but found 10 indent 273:1 error Expected indentation of 24 spaces but found 12 indent 274:1 error Expected indentation of 24 spaces but found 12 indent 275:1 error Expected indentation of 24 spaces but found 12 indent 276:1 error Expected indentation of 20 spaces but found 10 indent 277:1 error Expected indentation of 16 spaces but found 8 indent 277:11 error Missing semicolon semi 278:1 error Expected indentation of 12 spaces but found 6 indent 279:1 error Expected indentation of 8 spaces but found 4 indent 280:1 error Expected indentation of 4 spaces but found 2 indent 282:1 error Expected indentation of 4 spaces but found 2 indent 283:1 error Expected indentation of 8 spaces but found 4 indent 284:1 error Expected indentation of 12 spaces but found 6 indent 285:1 error Expected indentation of 12 spaces but found 6 indent 286:1 error Expected indentation of 12 spaces but found 6 indent 287:1 error Expected indentation of 8 spaces but found 4 indent 287:6 error Missing semicolon semi 288:1 error Expected indentation of 4 spaces but found 2 indent 290:1 error Expected indentation of 4 spaces but found 2 indent 293:1 error Expected indentation of 8 spaces but found 4 indent 294:1 error Expected indentation of 8 spaces but found 4 indent 295:1 error Expected indentation of 12 spaces but found 6 indent 295:25 error Missing semicolon semi 296:1 error Expected indentation of 8 spaces but found 4 indent 298:1 error Expected indentation of 8 spaces but found 4 indent 299:1 error Expected indentation of 8 spaces but found 4 indent 300:1 error Expected indentation of 8 spaces but found 4 indent 300:5 error '$' is not defined no-undef 301:1 error Expected indentation of 12 spaces but found 6 indent 301:12 error 'loris' is not defined no-undef 302:1 error Expected indentation of 12 spaces but found 6 indent 303:1 error Expected indentation of 16 spaces but found 8 indent 304:1 error Expected indentation of 12 spaces but found 6 indent 305:1 error Expected indentation of 12 spaces but found 6 indent 306:1 error Expected indentation of 12 spaces but found 6 indent 307:1 error Expected indentation of 12 spaces but found 6 indent 308:1 error Expected indentation of 8 spaces but found 4 indent 310:1 error Expected indentation of 8 spaces but found 4 indent 311:1 error Expected indentation of 8 spaces but found 4 indent 312:1 error Expected indentation of 12 spaces but found 6 indent 313:1 error Expected indentation of 16 spaces but found 8 indent 314:1 error Expected indentation of 16 spaces but found 8 indent 315:1 error Expected indentation of 12 spaces but found 6 indent 316:1 error Expected indentation of 8 spaces but found 4 indent 318:1 error Expected indentation of 8 spaces but found 4 indent 319:1 error Expected indentation of 8 spaces but found 4 indent 320:1 error Expected indentation of 8 spaces but found 4 indent 321:1 error Expected indentation of 8 spaces but found 6 indent 322:1 error Expected indentation of 8 spaces but found 6 indent 323:1 error Expected indentation of 12 spaces but found 8 indent 324:1 error Expected indentation of 12 spaces but found 8 indent 325:1 error Expected indentation of 8 spaces but found 6 indent 326:1 error Expected indentation of 8 spaces but found 6 indent 327:1 error Expected indentation of 12 spaces but found 8 indent 328:1 error Expected indentation of 12 spaces but found 8 indent 329:1 error Expected indentation of 8 spaces but found 6 indent 330:1 error Expected indentation of 12 spaces but found 8 indent 331:1 error Expected indentation of 12 spaces but found 8 indent 332:1 error Expected indentation of 8 spaces but found 6 indent 333:1 error Expected indentation of 12 spaces but found 8 indent 334:1 error Expected indentation of 12 spaces but found 8 indent 335:1 error Expected indentation of 8 spaces but found 6 indent 336:1 error Expected indentation of 12 spaces but found 8 indent 337:1 error Expected indentation of 12 spaces but found 8 indent 338:1 error Expected indentation of 8 spaces but found 6 indent 339:1 error Expected indentation of 12 spaces but found 8 indent 340:1 error Expected indentation of 12 spaces but found 8 indent 341:1 error Expected indentation of 8 spaces but found 6 indent 342:1 error Expected indentation of 12 spaces but found 8 indent 343:1 error Expected indentation of 8 spaces but found 4 indent 344:1 error Expected indentation of 8 spaces but found 4 indent 344:5 error '$' is not defined no-undef 345:1 error Expected indentation of 12 spaces but found 6 indent 345:12 error 'loris' is not defined no-undef 346:1 error Expected indentation of 12 spaces but found 6 indent 347:1 error Expected indentation of 16 spaces but found 8 indent 348:1 error Expected indentation of 20 spaces but found 10 indent 349:1 error Expected indentation of 20 spaces but found 10 indent 350:1 error Expected indentation of 16 spaces but found 8 indent 351:1 error Expected indentation of 16 spaces but found 8 indent 352:1 error Expected indentation of 16 spaces but found 8 indent 353:1 error Expected indentation of 20 spaces but found 10 indent 354:1 error Expected indentation of 24 spaces but found 12 indent 355:1 error Expected indentation of 20 spaces but found 10 indent 356:1 error Expected indentation of 20 spaces but found 10 indent 357:1 error Expected indentation of 20 spaces but found 10 indent 358:1 error Expected indentation of 24 spaces but found 12 indent 358:42 error Missing semicolon semi 359:1 error Expected indentation of 20 spaces but found 10 indent 360:1 error Expected indentation of 20 spaces but found 10 indent 361:1 error Expected indentation of 16 spaces but found 8 indent 362:1 error Expected indentation of 16 spaces but found 8 indent 363:1 error Expected indentation of 20 spaces but found 10 indent 364:1 error Expected indentation of 20 spaces but found 10 indent 365:1 error Expected indentation of 16 spaces but found 8 indent 366:1 error Expected indentation of 16 spaces but found 8 indent 367:1 error Expected indentation of 20 spaces but found 10 indent 368:1 error Expected indentation of 16 spaces but found 8 indent 369:1 error Expected indentation of 20 spaces but found 10 indent 370:1 error Expected indentation of 24 spaces but found 12 indent 371:1 error Expected indentation of 20 spaces but found 10 indent 372:1 error Expected indentation of 24 spaces but found 12 indent 373:1 error Expected indentation of 20 spaces but found 10 indent 374:1 error Expected indentation of 16 spaces but found 8 indent 375:1 error Expected indentation of 12 spaces but found 6 indent 376:1 error Expected indentation of 12 spaces but found 6 indent 377:1 error Expected indentation of 12 spaces but found 6 indent 378:1 error Expected indentation of 16 spaces but found 8 indent 379:1 error Expected indentation of 16 spaces but found 8 indent 380:1 error Expected indentation of 16 spaces but found 8 indent 381:1 error Expected indentation of 12 spaces but found 6 indent 382:1 error Expected indentation of 12 spaces but found 6 indent 383:1 error Expected indentation of 8 spaces but found 4 indent 385:1 error Expected indentation of 8 spaces but found 4 indent 386:1 error Expected indentation of 4 spaces but found 2 indent 388:1 error Expected indentation of 4 spaces but found 2 indent 391:1 error Expected indentation of 8 spaces but found 4 indent 392:1 error Expected indentation of 8 spaces but found 4 indent 393:1 error Expected indentation of 12 spaces but found 6 indent 394:1 error Expected indentation of 16 spaces but found 8 indent 395:1 error Expected indentation of 20 spaces but found 10 indent 395:43 error Missing semicolon semi 396:1 error Expected indentation of 16 spaces but found 8 indent 397:1 error Expected indentation of 16 spaces but found 8 indent 398:1 error Expected indentation of 12 spaces but found 6 indent 399:1 error Expected indentation of 16 spaces but found 8 indent 400:1 error Expected indentation of 12 spaces but found 6 indent 401:1 error Expected indentation of 8 spaces but found 4 indent 402:1 error Expected indentation of 8 spaces but found 4 indent 402:21 error 'getSessions' is not defined no-undef 403:1 error Expected indentation of 8 spaces but found 4 indent 404:1 error Expected indentation of 4 spaces but found 2 indent 406:1 error Expected indentation of 4 spaces but found 2 indent 409:1 error Expected indentation of 8 spaces but found 4 indent 410:1 error Expected indentation of 12 spaces but found 6 indent 411:1 error Expected indentation of 12 spaces but found 6 indent 412:1 error Expected indentation of 8 spaces but found 4 indent 413:1 error Expected indentation of 8 spaces but found 4 indent 414:1 error Expected indentation of 12 spaces but found 6 indent 415:1 error Expected indentation of 12 spaces but found 6 indent 416:1 error Expected indentation of 12 spaces but found 6 indent 418:1 error Expected indentation of 12 spaces but found 6 indent 419:1 error Expected indentation of 16 spaces but found 8 indent 420:1 error Expected indentation of 16 spaces but found 8 indent 421:1 error Expected indentation of 16 spaces but found 8 indent 422:1 error Expected indentation of 12 spaces but found 6 indent 423:1 error Expected indentation of 12 spaces but found 6 indent 424:1 error Expected indentation of 16 spaces but found 8 indent 425:1 error Expected indentation of 16 spaces but found 8 indent 426:1 error Expected indentation of 20 spaces but found 10 indent 427:1 error Expected indentation of 20 spaces but found 10 indent 428:1 error Expected indentation of 20 spaces but found 10 indent 429:1 error Expected indentation of 20 spaces but found 10 indent 430:1 error Expected indentation of 20 spaces but found 10 indent 431:1 error Expected indentation of 16 spaces but found 8 indent 432:1 error Expected indentation of 16 spaces but found 8 indent 433:1 error Expected indentation of 16 spaces but found 10 indent 434:1 error Expected indentation of 20 spaces but found 12 indent 435:1 error Expected indentation of 20 spaces but found 12 indent 436:1 error Expected indentation of 16 spaces but found 10 indent 437:1 error Expected indentation of 20 spaces but found 12 indent 438:1 error Expected indentation of 20 spaces but found 12 indent 439:1 error Expected indentation of 16 spaces but found 10 indent 440:1 error Expected indentation of 20 spaces but found 12 indent 441:1 error Expected indentation of 20 spaces but found 12 indent 442:1 error Expected indentation of 16 spaces but found 10 indent 443:1 error Expected indentation of 20 spaces but found 12 indent 444:1 error Expected indentation of 20 spaces but found 12 indent 445:1 error Expected indentation of 16 spaces but found 10 indent 446:1 error Expected indentation of 20 spaces but found 12 indent 447:1 error Expected indentation of 20 spaces but found 12 indent 448:1 error Expected indentation of 16 spaces but found 8 indent 449:1 error Expected indentation of 16 spaces but found 8 indent 450:1 error Expected indentation of 12 spaces but found 6 indent 452:1 error Expected indentation of 12 spaces but found 6 indent 453:1 error Expected indentation of 12 spaces but found 6 indent 454:1 error Expected indentation of 12 spaces but found 6 indent 455:1 error Expected indentation of 16 spaces but found 8 indent 456:1 error Expected indentation of 16 spaces but found 8 indent 457:1 error Expected indentation of 20 spaces but found 10 indent 458:1 error Expected indentation of 20 spaces but found 10 indent 459:1 error Expected indentation of 20 spaces but found 10 indent 460:1 error Expected indentation of 20 spaces but found 10 indent 461:1 error Expected indentation of 24 spaces but found 12 indent 462:1 error Expected indentation of 24 spaces but found 12 indent 463:1 error Expected indentation of 20 spaces but found 10 indent 464:1 error Expected indentation of 16 spaces but found 8 indent 465:1 error Expected indentation of 20 spaces but found 10 indent 466:1 error Expected indentation of 20 spaces but found 10 indent 467:1 error Expected indentation of 24 spaces but found 12 indent 468:1 error Expected indentation of 24 spaces but found 12 indent 469:1 error Expected indentation of 20 spaces but found 10 indent 470:1 error Expected indentation of 16 spaces but found 8 indent 471:1 error Expected indentation of 12 spaces but found 6 indent 472:1 error Expected indentation of 8 spaces but found 4 indent 473:1 error Expected indentation of 12 spaces but found 6 indent 474:1 error Expected indentation of 12 spaces but found 6 indent 475:1 error Expected indentation of 12 spaces but found 6 indent 476:1 error Expected indentation of 12 spaces but found 6 indent 477:1 error Expected indentation of 16 spaces but found 8 indent 478:1 error Expected indentation of 20 spaces but found 10 indent 479:1 error Expected indentation of 24 spaces but found 12 indent 480:1 error Expected indentation of 20 spaces but found 10 indent 481:1 error Expected indentation of 16 spaces but found 8 indent 482:1 error Expected indentation of 12 spaces but found 6 indent 483:1 error Expected indentation of 8 spaces but found 4 indent 484:1 error Expected indentation of 8 spaces but found 4 indent 485:1 error Expected indentation of 12 spaces but found 6 indent 486:1 error Expected indentation of 8 spaces but found 4 indent 487:1 error Expected indentation of 12 spaces but found 6 indent 488:1 error Expected indentation of 16 spaces but found 8 indent 489:1 error Expected indentation of 20 spaces but found 10 indent 490:1 error Expected indentation of 16 spaces but found 8 indent 491:1 error Expected indentation of 12 spaces but found 6 indent 492:1 error Expected indentation of 12 spaces but found 6 indent 493:1 error Expected indentation of 8 spaces but found 4 indent 494:1 error Expected indentation of 8 spaces but found 4 indent 495:1 error Expected indentation of 12 spaces but found 6 indent 496:1 error Expected indentation of 12 spaces but found 6 indent 497:1 error Expected indentation of 12 spaces but found 6 indent 498:1 error Expected indentation of 12 spaces but found 6 indent 499:1 error Expected indentation of 12 spaces but found 6 indent 500:1 error Expected indentation of 12 spaces but found 6 indent 501:1 error Expected indentation of 8 spaces but found 4 indent 502:1 error Expected indentation of 8 spaces but found 4 indent 503:1 error Expected indentation of 12 spaces but found 6 indent 503:7 error '$' is not defined no-undef 504:1 error Expected indentation of 16 spaces but found 8 indent 504:14 error 'loris' is not defined no-undef 505:1 error Expected indentation of 16 spaces but found 8 indent 506:1 error Expected indentation of 20 spaces but found 10 indent 507:1 error Expected indentation of 24 spaces but found 12 indent 508:1 error Expected indentation of 24 spaces but found 12 indent 509:1 error Expected indentation of 24 spaces but found 12 indent 510:1 error Expected indentation of 24 spaces but found 12 indent 511:1 error Expected indentation of 28 spaces but found 14 indent 512:1 error Expected indentation of 24 spaces but found 12 indent 512:15 error Missing semicolon semi 513:1 error Expected indentation of 20 spaces but found 10 indent 514:1 error Expected indentation of 16 spaces but found 8 indent 515:1 error Expected indentation of 16 spaces but found 8 indent 516:1 error Expected indentation of 16 spaces but found 8 indent 517:1 error Expected indentation of 12 spaces but found 6 indent 518:1 error Expected indentation of 8 spaces but found 4 indent 519:1 error Expected indentation of 4 spaces but found 2 indent 521:1 error Expected indentation of 4 spaces but found 2 indent 523:1 error Expected indentation of 8 spaces but found 4 indent 524:1 error Expected indentation of 12 spaces but found 6 indent 525:1 error Expected indentation of 12 spaces but found 6 indent 526:1 error Expected indentation of 16 spaces but found 8 indent 527:1 error Expected indentation of 16 spaces but found 8 indent 528:1 error Expected indentation of 16 spaces but found 8 indent 529:1 error Expected indentation of 16 spaces but found 8 indent 530:1 error Expected indentation of 20 spaces but found 10 indent 531:1 error Expected indentation of 16 spaces but found 8 indent 532:1 error Expected indentation of 20 spaces but found 10 indent 533:1 error Expected indentation of 16 spaces but found 8 indent 534:1 error Expected indentation of 12 spaces but found 6 indent 535:1 error Expected indentation of 16 spaces but found 8 indent 536:1 error Expected indentation of 16 spaces but found 8 indent 537:1 error Expected indentation of 16 spaces but found 8 indent 538:1 error Expected indentation of 20 spaces but found 10 indent 539:1 error Expected indentation of 20 spaces but found 10 indent 540:1 error Expected indentation of 20 spaces but found 10 indent 541:1 error Expected indentation of 16 spaces but found 8 indent 542:1 error Expected indentation of 20 spaces but found 10 indent 543:1 error Expected indentation of 20 spaces but found 10 indent 544:1 error Expected indentation of 16 spaces but found 8 indent 545:1 error Expected indentation of 12 spaces but found 6 indent 546:1 error Expected indentation of 12 spaces but found 6 indent 547:1 error Expected indentation of 8 spaces but found 4 indent 548:1 error Expected indentation of 4 spaces but found 2 indent 550:1 error Expected indentation of 4 spaces but found 2 indent 553:1 error Expected indentation of 8 spaces but found 4 indent 554:1 error Expected indentation of 12 spaces but found 6 indent 555:1 error Expected indentation of 16 spaces but found 8 indent 556:1 error Expected indentation of 12 spaces but found 6 indent 557:1 error Expected indentation of 16 spaces but found 8 indent 558:1 error Expected indentation of 16 spaces but found 8 indent 559:1 error Expected indentation of 16 spaces but found 8 indent 560:1 error Expected indentation of 16 spaces but found 8 indent 561:1 error Expected indentation of 16 spaces but found 8 indent 562:1 error Expected indentation of 16 spaces but found 8 indent 563:1 error Expected indentation of 16 spaces but found 8 indent 564:1 error Expected indentation of 20 spaces but found 10 indent 565:1 error Expected indentation of 16 spaces but found 8 indent 567:1 error Expected indentation of 16 spaces but found 8 indent 568:1 error Expected indentation of 16 spaces but found 8 indent 570:1 error Expected indentation of 16 spaces but found 8 indent 571:1 error Expected indentation of 20 spaces but found 10 indent 572:1 error Expected indentation of 20 spaces but found 10 indent 573:1 error Expected indentation of 16 spaces but found 8 indent 574:1 error Expected indentation of 12 spaces but found 6 indent 575:1 error Expected indentation of 16 spaces but found 8 indent 576:1 error Expected indentation of 16 spaces but found 8 indent 577:1 error Expected indentation of 20 spaces but found 10 indent 578:1 error Expected indentation of 20 spaces but found 10 indent 579:1 error Expected indentation of 24 spaces but found 12 indent 580:1 error Expected indentation of 20 spaces but found 10 indent 581:1 error Expected indentation of 24 spaces but found 12 indent 582:1 error Expected indentation of 20 spaces but found 10 indent 583:1 error Expected indentation of 16 spaces but found 8 indent 584:1 error Expected indentation of 16 spaces but found 8 indent 586:1 error Expected indentation of 16 spaces but found 8 indent 587:1 error Expected indentation of 16 spaces but found 8 indent 588:1 error Expected indentation of 16 spaces but found 8 indent 590:1 error Expected indentation of 16 spaces but found 8 indent 591:1 error Expected indentation of 20 spaces but found 10 indent 592:1 error Expected indentation of 20 spaces but found 10 indent 593:1 error Expected indentation of 20 spaces but found 10 indent 594:1 error Expected indentation of 16 spaces but found 8 indent 596:1 error Expected indentation of 16 spaces but found 8 indent 597:1 error Expected indentation of 20 spaces but found 10 indent 598:1 error Expected indentation of 20 spaces but found 10 indent 599:1 error Expected indentation of 16 spaces but found 8 indent 600:1 error Expected indentation of 12 spaces but found 6 indent 601:1 error Expected indentation of 16 spaces but found 8 indent 602:1 error Expected indentation of 16 spaces but found 8 indent 603:1 error Expected indentation of 20 spaces but found 10 indent 604:1 error Expected indentation of 16 spaces but found 8 indent 606:1 error Expected indentation of 16 spaces but found 8 indent 607:1 error Expected indentation of 16 spaces but found 8 indent 608:1 error Expected indentation of 20 spaces but found 10 indent 609:1 error Expected indentation of 24 spaces but found 12 indent 610:1 error Expected indentation of 20 spaces but found 10 indent 611:1 error Expected indentation of 20 spaces but found 10 indent 612:1 error Expected indentation of 20 spaces but found 10 indent 613:1 error Expected indentation of 16 spaces but found 8 indent 614:1 error Expected indentation of 16 spaces but found 8 indent 615:1 error Expected indentation of 16 spaces but found 8 indent 616:1 error Expected indentation of 20 spaces but found 10 indent 617:1 error Expected indentation of 20 spaces but found 10 indent 618:1 error Expected indentation of 16 spaces but found 8 indent 619:1 error Expected indentation of 12 spaces but found 6 indent 620:1 error Expected indentation of 12 spaces but found 6 indent 621:1 error Expected indentation of 16 spaces but found 8 indent 622:1 error Expected indentation of 16 spaces but found 8 indent 623:1 error Expected indentation of 12 spaces but found 6 indent 624:1 error Expected indentation of 8 spaces but found 4 indent 625:1 error Expected indentation of 4 spaces but found 2 indent 627:1 error Expected indentation of 4 spaces but found 2 indent 630:1 error Expected indentation of 8 spaces but found 4 indent 631:1 error Expected indentation of 12 spaces but found 6 indent 632:1 error Expected indentation of 12 spaces but found 6 indent 633:1 error Expected indentation of 8 spaces but found 4 indent 634:1 error Expected indentation of 12 spaces but found 6 indent 635:1 error Expected indentation of 12 spaces but found 6 indent 636:1 error Expected indentation of 8 spaces but found 4 indent 637:1 error Expected indentation of 4 spaces but found 2 indent 639:1 error Expected indentation of 4 spaces but found 2 indent 639:20 error 'sessions' is defined but never used no-unused-vars 642:1 error Expected indentation of 8 spaces but found 4 indent 643:1 error Expected indentation of 12 spaces but found 6 indent 644:1 error Expected indentation of 12 spaces but found 6 indent 645:1 error Expected indentation of 12 spaces but found 6 indent 646:1 error Expected indentation of 16 spaces but found 8 indent 647:1 error Expected indentation of 16 spaces but found 8 indent 648:1 error Expected indentation of 20 spaces but found 10 indent 649:1 error Expected indentation of 20 spaces but found 10 indent 650:1 error Expected indentation of 24 spaces but found 12 indent 651:1 error Expected indentation of 24 spaces but found 12 indent 652:1 error Expected indentation of 20 spaces but found 10 indent 653:1 error Expected indentation of 16 spaces but found 8 indent 654:1 error Expected indentation of 12 spaces but found 6 indent 656:1 error Expected indentation of 8 spaces but found 4 indent 657:1 error Expected indentation of 8 spaces but found 4 indent 658:1 error Expected indentation of 12 spaces but found 6 indent 659:1 error Expected indentation of 12 spaces but found 6 indent 660:1 error Expected indentation of 12 spaces but found 6 indent 661:1 error Expected indentation of 8 spaces but found 4 indent 663:1 error Expected indentation of 8 spaces but found 4 indent 664:1 error Expected indentation of 8 spaces but found 4 indent 665:1 error Expected indentation of 12 spaces but found 6 indent 666:1 error Expected indentation of 12 spaces but found 6 indent 668:1 error Expected indentation of 12 spaces but found 6 indent 669:1 error Expected indentation of 12 spaces but found 6 indent 670:1 error Expected indentation of 16 spaces but found 8 indent 672:1 error Expected indentation of 16 spaces but found 8 indent 673:1 error Expected indentation of 16 spaces but found 8 indent 674:1 error Expected indentation of 20 spaces but found 10 indent 675:1 error Expected indentation of 24 spaces but found 12 indent 676:1 error Expected indentation of 28 spaces but found 14 indent 677:1 error Expected indentation of 24 spaces but found 12 indent 678:1 error Expected indentation of 20 spaces but found 10 indent 679:1 error Expected indentation of 24 spaces but found 12 indent 680:1 error Expected indentation of 28 spaces but found 14 indent 682:1 error Expected indentation of 28 spaces but found 14 indent 683:1 error Expected indentation of 28 spaces but found 14 indent 684:1 error Expected indentation of 28 spaces but found 14 indent 685:1 error Expected indentation of 28 spaces but found 14 indent 686:1 error Expected indentation of 24 spaces but found 12 indent 687:1 error Expected indentation of 20 spaces but found 10 indent 688:1 error Expected indentation of 16 spaces but found 8 indent 690:1 error Expected indentation of 16 spaces but found 8 indent 691:1 error Expected indentation of 16 spaces but found 8 indent 692:1 error Expected indentation of 16 spaces but found 8 indent 693:1 error Expected indentation of 16 spaces but found 8 indent 694:1 error Expected indentation of 16 spaces but found 8 indent 694:9 error '$' is not defined no-undef 695:1 error Expected indentation of 20 spaces but found 10 indent 696:1 error Expected indentation of 20 spaces but found 10 indent 696:16 error 'loris' is not defined no-undef 697:1 error Expected indentation of 20 spaces but found 10 indent 698:1 error Expected indentation of 24 spaces but found 12 indent 699:1 error Expected indentation of 24 spaces but found 12 indent 700:1 error Expected indentation of 20 spaces but found 10 indent 701:1 error Expected indentation of 20 spaces but found 10 indent 702:1 error Expected indentation of 20 spaces but found 10 indent 703:1 error Expected indentation of 24 spaces but found 12 indent 704:1 error Expected indentation of 28 spaces but found 14 indent 705:1 error Expected indentation of 32 spaces but found 16 indent 706:1 error Expected indentation of 28 spaces but found 14 indent 707:1 error Expected indentation of 28 spaces but found 14 indent 708:1 error Expected indentation of 28 spaces but found 14 indent 709:1 error Expected indentation of 32 spaces but found 16 indent 720:1 error Expected indentation of 32 spaces but found 16 indent 721:1 error Expected indentation of 32 spaces but found 16 indent 722:1 error Expected indentation of 32 spaces but found 16 indent 723:1 error Expected indentation of 36 spaces but found 18 indent 723:47 error Missing semicolon semi 724:1 error Expected indentation of 32 spaces but found 16 indent 726:1 error Expected indentation of 32 spaces but found 16 indent 728:1 error Expected indentation of 28 spaces but found 14 indent 729:1 error Expected indentation of 28 spaces but found 14 indent 730:1 error Expected indentation of 24 spaces but found 12 indent 731:1 error Expected indentation of 24 spaces but found 12 indent 732:1 error Expected indentation of 24 spaces but found 12 indent 733:1 error Expected indentation of 20 spaces but found 10 indent 734:1 error Expected indentation of 16 spaces but found 8 indent 735:1 error Expected indentation of 12 spaces but found 6 indent 736:1 error Expected indentation of 8 spaces but found 4 indent 737:1 error Expected indentation of 4 spaces but found 2 indent 739:1 error Expected indentation of 4 spaces but found 2 indent 742:1 error Expected indentation of 8 spaces but found 4 indent 743:1 error Expected indentation of 8 spaces but found 4 indent 743:9 error 'sessions' is assigned a value but never used no-unused-vars 744:1 error Expected indentation of 8 spaces but found 4 indent 745:1 error Expected indentation of 8 spaces but found 4 indent 746:1 error Expected indentation of 8 spaces but found 4 indent 746:12 error 'j' is defined but never used no-unused-vars 747:1 error Expected indentation of 8 spaces but found 4 indent 748:1 error Expected indentation of 8 spaces but found 4 indent 749:1 error Expected indentation of 8 spaces but found 4 indent 750:1 error Expected indentation of 8 spaces but found 4 indent 751:1 error Expected indentation of 8 spaces but found 4 indent 752:1 error Expected indentation of 8 spaces but found 4 indent 754:1 error Expected indentation of 8 spaces but found 4 indent 755:1 error Expected indentation of 12 spaces but found 6 indent 757:1 error Expected indentation of 12 spaces but found 6 indent 758:1 error Expected indentation of 12 spaces but found 6 indent 759:1 error Expected indentation of 16 spaces but found 8 indent 760:1 error Expected indentation of 12 spaces but found 6 indent 762:1 error Expected indentation of 12 spaces but found 6 indent 763:1 error Expected indentation of 12 spaces but found 6 indent 764:1 error Expected indentation of 16 spaces but found 8 indent 765:1 error Expected indentation of 16 spaces but found 8 indent 766:1 error Expected indentation of 20 spaces but found 10 indent 767:1 error Expected indentation of 20 spaces but found 10 indent 768:1 error Expected indentation of 20 spaces but found 10 indent 769:1 error Expected indentation of 20 spaces but found 10 indent 770:1 error Expected indentation of 24 spaces but found 12 indent 771:1 error Expected indentation of 24 spaces but found 12 indent 771:20 error 'loris' is not defined no-undef 772:1 error Expected indentation of 24 spaces but found 12 indent 773:1 error Expected indentation of 28 spaces but found 14 indent 774:1 error Expected indentation of 32 spaces but found 16 indent 775:1 error Expected indentation of 28 spaces but found 14 indent 776:1 error Expected indentation of 24 spaces but found 12 indent 777:1 error Expected indentation of 24 spaces but found 12 indent 778:1 error Expected indentation of 20 spaces but found 10 indent 779:1 error Expected indentation of 24 spaces but found 12 indent 780:1 error Expected indentation of 24 spaces but found 12 indent 781:1 error Expected indentation of 20 spaces but found 10 indent 782:1 error Expected indentation of 16 spaces but found 8 indent 783:1 error Expected indentation of 16 spaces but found 8 indent 784:1 error Expected indentation of 16 spaces but found 8 indent 785:1 error Expected indentation of 12 spaces but found 6 indent 786:1 error Expected indentation of 8 spaces but found 4 indent 787:1 error Expected indentation of 12 spaces but found 6 indent 789:1 error Expected indentation of 12 spaces but found 6 indent 790:1 error Expected indentation of 16 spaces but found 8 indent 792:1 error Expected indentation of 12 spaces but found 6 indent 793:1 error Expected indentation of 12 spaces but found 6 indent 794:1 error Expected indentation of 16 spaces but found 8 indent 795:1 error Expected indentation of 16 spaces but found 8 indent 796:1 error Expected indentation of 16 spaces but found 8 indent 797:1 error Expected indentation of 20 spaces but found 10 indent 798:1 error Expected indentation of 16 spaces but found 8 indent 799:1 error Expected indentation of 16 spaces but found 8 indent 800:1 error Expected indentation of 16 spaces but found 8 indent 801:1 error Expected indentation of 20 spaces but found 10 indent 802:1 error Expected indentation of 16 spaces but found 8 indent 803:1 error Expected indentation of 12 spaces but found 6 indent 805:1 error Expected indentation of 12 spaces but found 6 indent 806:1 error Expected indentation of 12 spaces but found 6 indent 807:1 error Expected indentation of 12 spaces but found 6 indent 808:1 error Expected indentation of 16 spaces but found 8 indent 809:1 error Expected indentation of 20 spaces but found 10 indent 810:1 error Expected indentation of 20 spaces but found 10 indent 810:58 error Missing semicolon semi 811:1 error Expected indentation of 20 spaces but found 10 indent 812:1 error Expected indentation of 24 spaces but found 12 indent 812:53 error Missing semicolon semi 813:1 error Expected indentation of 20 spaces but found 10 indent 814:1 error Expected indentation of 16 spaces but found 8 indent 815:1 error Expected indentation of 12 spaces but found 6 indent 817:1 error Expected indentation of 12 spaces but found 6 indent 818:1 error Expected indentation of 12 spaces but found 6 indent 819:1 error Expected indentation of 16 spaces but found 8 indent 820:1 error Expected indentation of 16 spaces but found 8 indent 821:1 error Expected indentation of 20 spaces but found 10 indent 822:1 error Expected indentation of 20 spaces but found 10 indent 823:1 error Expected indentation of 20 spaces but found 10 indent 824:1 error Expected indentation of 24 spaces but found 12 indent 825:1 error Expected indentation of 20 spaces but found 10 indent 826:1 error Expected indentation of 24 spaces but found 12 indent 827:1 error Expected indentation of 24 spaces but found 12 indent 828:1 error Expected indentation of 24 spaces but found 12 indent 829:1 error Expected indentation of 28 spaces but found 14 indent 830:1 error Expected indentation of 32 spaces but found 16 indent 831:1 error Expected indentation of 32 spaces but found 16 indent 831:24 error 'loris' is not defined no-undef 832:1 error Expected indentation of 32 spaces but found 16 indent 833:1 error Expected indentation of 36 spaces but found 18 indent 834:1 error Expected indentation of 40 spaces but found 20 indent 835:1 error Expected indentation of 36 spaces but found 18 indent 836:1 error Expected indentation of 32 spaces but found 16 indent 837:1 error Expected indentation of 28 spaces but found 14 indent 838:1 error Expected indentation of 32 spaces but found 16 indent 839:1 error Expected indentation of 28 spaces but found 14 indent 840:1 error Expected indentation of 24 spaces but found 12 indent 841:1 error Expected indentation of 28 spaces but found 14 indent 842:1 error Expected indentation of 24 spaces but found 12 indent 843:1 error Expected indentation of 24 spaces but found 12 indent 844:1 error Expected indentation of 20 spaces but found 10 indent 845:1 error Expected indentation of 16 spaces but found 8 indent 846:1 error Expected indentation of 16 spaces but found 8 indent 847:1 error Expected indentation of 12 spaces but found 6 indent 848:1 error Expected indentation of 8 spaces but found 4 indent 849:1 error Expected indentation of 8 spaces but found 4 indent 850:1 error Expected indentation of 4 spaces but found 2 indent 852:1 error Expected indentation of 4 spaces but found 2 indent 854:1 error Expected indentation of 8 spaces but found 4 indent 855:1 error Expected indentation of 12 spaces but found 6 indent 856:1 error Expected indentation of 12 spaces but found 6 indent 857:1 error Expected indentation of 12 spaces but found 6 indent 858:1 error Expected indentation of 16 spaces but found 8 indent 859:1 error Expected indentation of 12 spaces but found 6 indent 860:1 error Expected indentation of 8 spaces but found 4 indent 861:1 error Expected indentation of 4 spaces but found 2 indent 863:1 error Expected indentation of 4 spaces but found 2 indent 865:1 error Expected indentation of 8 spaces but found 4 indent 866:1 error Expected indentation of 12 spaces but found 6 indent 867:1 error Expected indentation of 12 spaces but found 6 indent 868:1 error Expected indentation of 12 spaces but found 6 indent 869:1 error Expected indentation of 8 spaces but found 4 indent 870:1 error Expected indentation of 4 spaces but found 2 indent 872:1 error Expected indentation of 4 spaces but found 2 indent 874:1 error Expected indentation of 8 spaces but found 4 indent 875:1 error Expected indentation of 8 spaces but found 4 indent 876:1 error Expected indentation of 12 spaces but found 6 indent 877:1 error Expected indentation of 12 spaces but found 6 indent 878:1 error Expected indentation of 8 spaces but found 4 indent 879:1 error Expected indentation of 4 spaces but found 2 indent 881:1 error Expected indentation of 4 spaces but found 2 indent 883:1 error Expected indentation of 8 spaces but found 4 indent 884:1 error Expected indentation of 12 spaces but found 6 indent 884:46 error Missing semicolon semi 885:1 error Expected indentation of 8 spaces but found 4 indent 886:1 error Expected indentation of 8 spaces but found 4 indent 887:1 error Expected indentation of 4 spaces but found 2 indent 889:1 error Expected indentation of 4 spaces but found 2 indent 892:1 error Expected indentation of 8 spaces but found 4 indent 893:1 error Expected indentation of 8 spaces but found 4 indent 893:9 error 'tabsNav' is assigned a value but never used no-unused-vars 894:1 error Expected indentation of 8 spaces but found 4 indent 896:1 error Expected indentation of 8 spaces but found 4 indent 897:1 error Expected indentation of 8 spaces but found 4 indent 898:1 error Expected indentation of 12 spaces but found 6 indent 899:1 error Expected indentation of 12 spaces but found 6 indent 900:1 error Expected indentation of 12 spaces but found 6 indent 901:1 error Expected indentation of 12 spaces but found 6 indent 902:1 error Expected indentation of 12 spaces but found 6 indent 903:1 error Expected indentation of 8 spaces but found 4 indent 905:1 error Expected indentation of 8 spaces but found 4 indent 906:1 error Expected indentation of 8 spaces but found 4 indent 907:1 error Expected indentation of 12 spaces but found 6 indent 908:1 error Expected indentation of 12 spaces but found 6 indent 909:1 error Expected indentation of 12 spaces but found 6 indent 910:1 error Expected indentation of 12 spaces but found 6 indent 911:1 error Expected indentation of 12 spaces but found 6 indent 912:1 error Expected indentation of 12 spaces but found 6 indent 913:1 error Expected indentation of 12 spaces but found 6 indent 914:1 error Expected indentation of 12 spaces but found 6 indent 915:1 error Expected indentation of 12 spaces but found 6 indent 916:1 error Expected indentation of 8 spaces but found 4 indent 918:1 error Expected indentation of 8 spaces but found 4 indent 919:1 error Expected indentation of 8 spaces but found 4 indent 920:1 error Expected indentation of 12 spaces but found 8 indent 921:1 error Expected indentation of 12 spaces but found 8 indent 922:1 error Expected indentation of 12 spaces but found 8 indent 923:1 error Expected indentation of 12 spaces but found 8 indent 924:1 error Expected indentation of 12 spaces but found 8 indent 925:1 error Expected indentation of 12 spaces but found 8 indent 926:1 error Expected indentation of 12 spaces but found 8 indent 927:1 error Expected indentation of 12 spaces but found 8 indent 928:1 error Expected indentation of 8 spaces but found 6 indent 929:1 error Expected indentation of 8 spaces but found 4 indent 931:1 error Expected indentation of 8 spaces but found 4 indent 932:1 error Expected indentation of 8 spaces but found 4 indent 932:55 error Strings must use singlequote quotes 932:75 error Strings must use singlequote quotes 933:1 error Expected indentation of 8 spaces but found 4 indent 934:1 error Expected indentation of 12 spaces but found 6 indent 935:1 error Expected indentation of 12 spaces but found 6 indent 936:1 error Expected indentation of 12 spaces but found 6 indent 937:1 error Expected indentation of 12 spaces but found 6 indent 938:1 error Expected indentation of 12 spaces but found 6 indent 939:1 error Expected indentation of 12 spaces but found 6 indent 940:1 error Expected indentation of 12 spaces but found 6 indent 941:1 error Expected indentation of 12 spaces but found 6 indent 942:1 error Expected indentation of 12 spaces but found 6 indent 943:1 error Expected indentation of 12 spaces but found 6 indent 944:1 error Expected indentation of 12 spaces but found 6 indent 945:1 error Expected indentation of 12 spaces but found 6 indent 946:1 error Expected indentation of 12 spaces but found 6 indent 947:1 error Expected indentation of 12 spaces but found 6 indent 948:1 error Expected indentation of 12 spaces but found 6 indent 949:1 error Expected indentation of 8 spaces but found 4 indent 951:1 error Expected indentation of 8 spaces but found 4 indent 952:1 error Expected indentation of 8 spaces but found 4 indent 953:1 error Expected indentation of 12 spaces but found 6 indent 954:1 error Expected indentation of 12 spaces but found 6 indent 955:1 error Expected indentation of 12 spaces but found 6 indent 956:1 error Expected indentation of 12 spaces but found 6 indent 957:1 error Expected indentation of 12 spaces but found 6 indent 958:1 error Expected indentation of 12 spaces but found 6 indent 959:1 error Expected indentation of 8 spaces but found 4 indent 961:1 error Expected indentation of 8 spaces but found 4 indent 962:1 error Expected indentation of 8 spaces but found 4 indent 963:1 error Expected indentation of 12 spaces but found 6 indent 964:1 error Expected indentation of 12 spaces but found 6 indent 965:1 error Expected indentation of 12 spaces but found 6 indent 966:1 error Expected indentation of 12 spaces but found 6 indent 967:1 error Expected indentation of 12 spaces but found 6 indent 968:1 error Expected indentation of 12 spaces but found 6 indent 969:1 error Expected indentation of 12 spaces but found 6 indent 970:1 error Expected indentation of 12 spaces but found 6 indent 971:1 error Expected indentation of 8 spaces but found 4 indent 973:1 error Expected indentation of 8 spaces but found 4 indent 974:1 error Expected indentation of 8 spaces but found 4 indent 975:1 error Expected indentation of 12 spaces but found 6 indent 976:1 error Expected indentation of 16 spaces but found 8 indent 977:1 error Expected indentation of 20 spaces but found 10 indent 978:1 error Expected indentation of 24 spaces but found 12 indent 979:1 error Expected indentation of 20 spaces but found 10 indent 980:1 error Expected indentation of 20 spaces but found 10 indent 981:1 error Expected indentation of 16 spaces but found 8 indent 982:1 error Expected indentation of 12 spaces but found 6 indent 982:8 error Missing semicolon semi 983:1 error Expected indentation of 8 spaces but found 4 indent 985:1 error Expected indentation of 8 spaces but found 4 indent 986:1 error Expected indentation of 8 spaces but found 4 indent 987:1 error Expected indentation of 12 spaces but found 6 indent 988:1 error Expected indentation of 16 spaces but found 8 indent 989:1 error Expected indentation of 20 spaces but found 10 indent 990:1 error Expected indentation of 24 spaces but found 12 indent 991:1 error Expected indentation of 20 spaces but found 10 indent 992:1 error Expected indentation of 20 spaces but found 10 indent 993:1 error Expected indentation of 16 spaces but found 8 indent 994:1 error Expected indentation of 12 spaces but found 6 indent 994:8 error Missing semicolon semi 995:1 error Expected indentation of 8 spaces but found 4 indent 997:1 error Expected indentation of 8 spaces but found 4 indent 998:1 error Expected indentation of 8 spaces but found 4 indent 999:1 error Expected indentation of 12 spaces but found 6 indent 1000:1 error Expected indentation of 16 spaces but found 8 indent 1001:1 error Expected indentation of 20 spaces but found 10 indent 1002:1 error Expected indentation of 24 spaces but found 12 indent 1003:1 error Expected indentation of 20 spaces but found 10 indent 1004:1 error Expected indentation of 20 spaces but found 10 indent 1005:1 error Expected indentation of 24 spaces but found 12 indent 1006:1 error Expected indentation of 20 spaces but found 10 indent 1007:1 error Expected indentation of 20 spaces but found 10 indent 1008:1 error Expected indentation of 20 spaces but found 10 indent 1009:1 error Expected indentation of 16 spaces but found 8 indent 1010:1 error Expected indentation of 12 spaces but found 6 indent 1010:8 error Missing semicolon semi 1011:1 error Expected indentation of 8 spaces but found 4 indent 1013:1 error Expected indentation of 8 spaces but found 4 indent 1014:1 error Expected indentation of 8 spaces but found 4 indent 1016:1 error Expected indentation of 8 spaces but found 4 indent 1017:1 error Expected indentation of 8 spaces but found 4 indent 1021:1 error Expected indentation of 8 spaces but found 4 indent 1022:1 error Expected indentation of 12 spaces but found 6 indent 1023:1 error Expected indentation of 12 spaces but found 6 indent 1024:1 error Expected indentation of 16 spaces but found 8 indent 1025:1 error Expected indentation of 20 spaces but found 10 indent 1026:1 error Expected indentation of 20 spaces but found 10 indent 1027:1 error Expected indentation of 20 spaces but found 10 indent 1028:1 error Expected indentation of 16 spaces but found 8 indent 1029:1 error Expected indentation of 12 spaces but found 6 indent 1030:1 error Expected indentation of 8 spaces but found 4 indent 1031:1 error Expected indentation of 8 spaces but found 4 indent 1032:1 error Expected indentation of 12 spaces but found 6 indent 1033:1 error Expected indentation of 12 spaces but found 6 indent 1034:1 error Expected indentation of 16 spaces but found 8 indent 1035:1 error Expected indentation of 20 spaces but found 10 indent 1036:1 error Expected indentation of 24 spaces but found 12 indent 1037:1 error Expected indentation of 24 spaces but found 12 indent 1038:1 error Expected indentation of 24 spaces but found 12 indent 1039:1 error Expected indentation of 24 spaces but found 12 indent 1040:1 error Expected indentation of 24 spaces but found 12 indent 1041:1 error Expected indentation of 20 spaces but found 10 indent 1042:1 error Expected indentation of 20 spaces but found 10 indent 1043:1 error Expected indentation of 24 spaces but found 12 indent 1044:1 error Expected indentation of 24 spaces but found 12 indent 1045:1 error Expected indentation of 24 spaces but found 12 indent 1046:1 error Expected indentation of 24 spaces but found 12 indent 1047:1 error Expected indentation of 24 spaces but found 12 indent 1048:1 error Expected indentation of 24 spaces but found 12 indent 1049:1 error Expected indentation of 20 spaces but found 10 indent 1050:1 error Expected indentation of 16 spaces but found 8 indent 1051:1 error Expected indentation of 16 spaces but found 8 indent 1052:1 error Expected indentation of 20 spaces but found 10 indent 1053:1 error Expected indentation of 16 spaces but found 8 indent 1054:1 error Expected indentation of 12 spaces but found 6 indent 1055:1 error Expected indentation of 12 spaces but found 6 indent 1057:1 error Expected indentation of 8 spaces but found 4 indent 1058:1 error Expected indentation of 4 spaces but found 2 indent 1062:1 error Expected indentation of 4 spaces but found 2 indent 1063:1 error Expected indentation of 4 spaces but found 2 indent 1067:1 error Expected indentation of 4 spaces but found 2 indent 1068:1 error Expected indentation of 4 spaces but found 2 indent ? 957 problems (957 errors, 0 warnings) 931 errors and 0 warnings potentially fixable with the `--fix` option. ERROR in ./modules/dataquery/jsx/react.fieldselector.js Module Error (from ./node_modules/eslint-loader/index.js): /var/www/loris/modules/dataquery/jsx/react.fieldselector.js 10:8 error 'React' is defined but never used no-unused-vars 18:1 error Expected indentation of 4 spaces but found 2 indent 19:1 error Expected indentation of 8 spaces but found 4 indent 20:1 error Expected indentation of 4 spaces but found 2 indent 22:1 error Expected indentation of 4 spaces but found 2 indent 23:1 error Expected indentation of 8 spaces but found 4 indent 24:1 error Expected indentation of 12 spaces but found 6 indent 25:1 error Expected indentation of 8 spaces but found 4 indent 26:1 error Expected indentation of 12 spaces but found 6 indent 27:1 error Expected indentation of 8 spaces but found 4 indent 28:1 error Expected indentation of 8 spaces but found 4 indent 29:1 error Expected indentation of 12 spaces but found 6 indent 29:64 error Missing semicolon semi 30:1 error Expected indentation of 8 spaces but found 4 indent 31:1 error Expected indentation of 8 spaces but found 4 indent 32:1 error Expected indentation of 12 spaces but found 6 indent 33:1 error Expected indentation of 16 spaces but found 8 indent 34:1 error Expected indentation of 16 spaces but found 8 indent 35:1 error Expected indentation of 12 spaces but found 6 indent 36:1 error Expected indentation of 8 spaces but found 4 indent 37:1 error Expected indentation of 4 spaces but found 2 indent 44:1 error Expected indentation of 4 spaces but found 2 indent 45:1 error Expected indentation of 8 spaces but found 4 indent 46:1 error Expected indentation of 8 spaces but found 4 indent 47:1 error Expected indentation of 12 spaces but found 6 indent 48:1 error Expected indentation of 8 spaces but found 4 indent 49:1 error Expected indentation of 8 spaces but found 4 indent 50:1 error Expected indentation of 4 spaces but found 2 indent 52:1 error Expected indentation of 4 spaces but found 2 indent 53:1 error Expected indentation of 8 spaces but found 4 indent 53:14 error 'evt' is defined but never used no-unused-vars 54:1 error Expected indentation of 12 spaces but found 6 indent 55:1 error Expected indentation of 16 spaces but found 8 indent 56:1 error Expected indentation of 12 spaces but found 6 indent 57:1 error Expected indentation of 12 spaces but found 6 indent 58:1 error Expected indentation of 16 spaces but found 8 indent 59:1 error Expected indentation of 12 spaces but found 6 indent 60:1 error Expected indentation of 8 spaces but found 4 indent 61:1 error Expected indentation of 4 spaces but found 2 indent 63:1 error Expected indentation of 4 spaces but found 2 indent 64:1 error Expected indentation of 8 spaces but found 4 indent 65:1 error Expected indentation of 12 spaces but found 6 indent 65:7 error 'selectClosure' is assigned a value but never used no-unused-vars 66:1 error Expected indentation of 16 spaces but found 8 indent 67:1 error Expected indentation of 12 spaces but found 6 indent 68:1 error Expected indentation of 8 spaces but found 4 indent 68:10 error 'i' is not defined no-undef 68:17 error 'i' is not defined no-undef 68:46 error 'i' is not defined no-undef 69:1 error Expected indentation of 12 spaces but found 6 indent 70:1 error Expected indentation of 12 spaces but found 6 indent 70:28 error 'i' is not defined no-undef 71:1 error Expected indentation of 16 spaces but found 8 indent 72:1 error Expected indentation of 12 spaces but found 6 indent 73:1 error Expected indentation of 12 spaces but found 6 indent 74:1 error Expected indentation of 16 spaces but found 8 indent 74:31 error 'i' is not defined no-undef 75:1 error Expected indentation of 16 spaces but found 8 indent 75:32 error 'i' is not defined no-undef 76:1 error Expected indentation of 16 spaces but found 8 indent 76:33 error 'i' is not defined no-undef 77:1 error Expected indentation of 16 spaces but found 8 indent 78:1 error Expected indentation of 16 spaces but found 8 indent 78:62 error 'i' is not defined no-undef 79:1 error Expected indentation of 8 spaces but found 4 indent 80:1 error Expected indentation of 8 spaces but found 4 indent 81:1 error Expected indentation of 12 spaces but found 6 indent 82:1 error Expected indentation of 8 spaces but found 4 indent 83:1 error Expected indentation of 4 spaces but found 2 indent 90:1 error Expected indentation of 4 spaces but found 2 indent 91:1 error Expected indentation of 8 spaces but found 4 indent 92:1 error Expected indentation of 8 spaces but found 4 indent 93:1 error Expected indentation of 8 spaces but found 4 indent 94:1 error Expected indentation of 4 spaces but found 2 indent 96:1 error Expected indentation of 4 spaces but found 2 indent 98:1 error Expected indentation of 8 spaces but found 4 indent 99:1 error Expected indentation of 12 spaces but found 6 indent 100:1 error Expected indentation of 12 spaces but found 6 indent 101:1 error Expected indentation of 8 spaces but found 4 indent 102:1 error Expected indentation of 8 spaces but found 4 indent 103:1 error Expected indentation of 12 spaces but found 6 indent 104:1 error Expected indentation of 8 spaces but found 4 indent 105:1 error Expected indentation of 12 spaces but found 6 indent 106:1 error Expected indentation of 8 spaces but found 4 indent 107:1 error Expected indentation of 4 spaces but found 2 indent 109:1 error Expected indentation of 4 spaces but found 2 indent 112:1 error Expected indentation of 8 spaces but found 4 indent 113:1 error Expected indentation of 8 spaces but found 4 indent 114:1 error Expected indentation of 8 spaces but found 4 indent 115:1 error Expected indentation of 8 spaces but found 4 indent 117:1 error Expected indentation of 8 spaces but found 4 indent 118:1 error Expected indentation of 12 spaces but found 6 indent 119:1 error Expected indentation of 12 spaces but found 6 indent 120:1 error Expected indentation of 12 spaces but found 6 indent 121:1 error Expected indentation of 16 spaces but found 8 indent 122:1 error Expected indentation of 16 spaces but found 8 indent 123:1 error Expected indentation of 20 spaces but found 10 indent 124:1 error Expected indentation of 16 spaces but found 8 indent 125:1 error Expected indentation of 16 spaces but found 8 indent 126:1 error Expected indentation of 20 spaces but found 10 indent 127:1 error Expected indentation of 24 spaces but found 12 indent 128:1 error Expected indentation of 28 spaces but found 14 indent 129:1 error Expected indentation of 32 spaces but found 16 indent 130:1 error Expected indentation of 32 spaces but found 16 indent 131:1 error Expected indentation of 32 spaces but found 16 indent 132:1 error Expected indentation of 32 spaces but found 16 indent 133:1 error Expected indentation of 28 spaces but found 14 indent 134:1 error Expected indentation of 28 spaces but found 14 indent 135:1 error Expected indentation of 24 spaces but found 12 indent 136:1 error Expected indentation of 20 spaces but found 10 indent 137:1 error Expected indentation of 16 spaces but found 8 indent 138:1 error Expected indentation of 12 spaces but found 6 indent 139:1 error Expected indentation of 8 spaces but found 4 indent 141:1 error Expected indentation of 8 spaces but found 4 indent 142:1 error Expected indentation of 12 spaces but found 6 indent 143:1 error Expected indentation of 12 spaces but found 6 indent 143:117 error Missing semicolon semi 144:1 error Expected indentation of 8 spaces but found 4 indent 145:1 error Expected indentation of 8 spaces but found 4 indent 146:1 error Expected indentation of 8 spaces but found 4 indent 148:1 error Expected indentation of 8 spaces but found 4 indent 149:1 error Expected indentation of 12 spaces but found 6 indent 150:1 error Expected indentation of 16 spaces but found 8 indent 151:1 error Expected indentation of 20 spaces but found 10 indent 152:1 error Expected indentation of 20 spaces but found 10 indent 153:1 error Expected indentation of 16 spaces but found 8 indent 154:1 error Expected indentation of 16 spaces but found 8 indent 155:1 error Expected indentation of 20 spaces but found 10 indent 156:1 error Expected indentation of 16 spaces but found 8 indent 157:1 error Expected indentation of 12 spaces but found 6 indent 158:1 error Expected indentation of 8 spaces but found 4 indent 159:1 error Expected indentation of 4 spaces but found 2 indent 167:1 error Expected indentation of 4 spaces but found 2 indent 168:1 error Expected indentation of 8 spaces but found 4 indent 169:1 error Expected indentation of 8 spaces but found 4 indent 170:1 error Expected indentation of 8 spaces but found 4 indent 171:1 error Expected indentation of 4 spaces but found 2 indent 173:1 error Expected indentation of 4 spaces but found 2 indent 175:1 error Expected indentation of 8 spaces but found 4 indent 176:1 error Expected indentation of 4 spaces but found 2 indent 178:1 error Expected indentation of 4 spaces but found 2 indent 180:1 error Expected indentation of 8 spaces but found 4 indent 181:1 error Expected indentation of 8 spaces but found 4 indent 182:1 error Expected indentation of 8 spaces but found 4 indent 183:1 error Expected indentation of 8 spaces but found 4 indent 185:1 error Expected indentation of 8 spaces but found 4 indent 186:1 error Expected indentation of 8 spaces but found 4 indent 187:1 error Expected indentation of 8 spaces but found 4 indent 188:1 error Expected indentation of 8 spaces but found 4 indent 189:1 error Expected indentation of 12 spaces but found 6 indent 190:1 error Expected indentation of 8 spaces but found 4 indent 192:1 error Expected indentation of 8 spaces but found 4 indent 193:1 error Expected indentation of 8 spaces but found 4 indent 194:1 error Expected indentation of 12 spaces but found 6 indent 195:1 error Expected indentation of 12 spaces but found 6 indent 196:1 error Expected indentation of 12 spaces but found 6 indent 198:1 error Expected indentation of 12 spaces but found 6 indent 199:1 error Expected indentation of 16 spaces but found 8 indent 200:1 error Expected indentation of 12 spaces but found 6 indent 202:1 error Expected indentation of 12 spaces but found 6 indent 203:1 error Expected indentation of 12 spaces but found 6 indent 204:1 error Expected indentation of 12 spaces but found 6 indent 205:1 error Expected indentation of 16 spaces but found 8 indent 206:1 error Expected indentation of 12 spaces but found 6 indent 208:1 error Expected indentation of 12 spaces but found 6 indent 209:1 error Expected indentation of 12 spaces but found 6 indent 210:1 error Expected indentation of 12 spaces but found 6 indent 211:1 error Expected indentation of 16 spaces but found 8 indent 212:1 error Expected indentation of 12 spaces but found 6 indent 214:1 error Expected indentation of 12 spaces but found 6 indent 215:1 error Expected indentation of 12 spaces but found 6 indent 216:1 error Expected indentation of 16 spaces but found 8 indent 216:56 error Missing semicolon semi 217:1 error Expected indentation of 12 spaces but found 6 indent 218:1 error Expected indentation of 16 spaces but found 8 indent 218:28 error Missing semicolon semi 219:1 error Expected indentation of 12 spaces but found 6 indent 221:1 error Expected indentation of 12 spaces but found 6 indent 222:1 error Expected indentation of 16 spaces but found 29 indent 223:1 error Expected indentation of 16 spaces but found 29 indent 224:1 error Expected indentation of 16 spaces but found 29 indent 225:1 error Expected indentation of 16 spaces but found 29 indent 226:1 error Expected indentation of 16 spaces but found 29 indent 227:1 error Expected indentation of 16 spaces but found 29 indent 228:1 error Expected indentation of 16 spaces but found 29 indent 229:1 error Expected indentation of 16 spaces but found 29 indent 230:1 error Expected indentation of 16 spaces but found 29 indent 231:1 error Expected indentation of 16 spaces but found 29 indent 232:1 error Expected indentation of 12 spaces but found 6 indent 233:1 error Expected indentation of 12 spaces but found 6 indent 234:1 error Expected indentation of 16 spaces but found 8 indent 235:1 error Expected indentation of 12 spaces but found 6 indent 236:1 error Expected indentation of 8 spaces but found 4 indent 238:1 error Expected indentation of 8 spaces but found 4 indent 239:1 error Expected indentation of 12 spaces but found 6 indent 240:1 error Expected indentation of 16 spaces but found 8 indent 241:1 error Expected indentation of 16 spaces but found 8 indent 242:1 error Expected indentation of 12 spaces but found 6 indent 243:1 error Expected indentation of 8 spaces but found 4 indent 244:1 error Expected indentation of 4 spaces but found 2 indent 251:1 error Expected indentation of 4 spaces but found 2 indent 252:1 error Expected indentation of 8 spaces but found 4 indent 253:1 error Expected indentation of 8 spaces but found 4 indent 254:1 error Expected indentation of 8 spaces but found 4 indent 255:1 error Expected indentation of 12 spaces but found 6 indent 256:1 error Expected indentation of 8 spaces but found 4 indent 257:1 error Expected indentation of 8 spaces but found 4 indent 258:1 error Expected indentation of 12 spaces but found 6 indent 259:1 error Expected indentation of 12 spaces but found 6 indent 260:1 error Expected indentation of 12 spaces but found 6 indent 261:1 error Expected indentation of 12 spaces but found 6 indent 262:1 error Expected indentation of 12 spaces but found 6 indent 263:1 error Expected indentation of 8 spaces but found 4 indent 264:1 error Expected indentation of 8 spaces but found 4 indent 265:1 error Expected indentation of 8 spaces but found 4 indent 266:1 error Expected indentation of 8 spaces but found 4 indent 267:1 error Expected indentation of 8 spaces but found 4 indent 268:1 error Expected indentation of 8 spaces but found 4 indent 269:1 error Expected indentation of 8 spaces but found 4 indent 270:1 error Expected indentation of 8 spaces but found 4 indent 271:1 error Expected indentation of 4 spaces but found 2 indent 273:1 error Expected indentation of 4 spaces but found 2 indent 275:1 error Expected indentation of 8 spaces but found 4 indent 276:1 error Expected indentation of 4 spaces but found 2 indent 278:1 error Expected indentation of 4 spaces but found 2 indent 280:1 error Expected indentation of 8 spaces but found 4 indent 280:46 error Empty block statement no-empty 281:1 error Expected indentation of 8 spaces but found 4 indent 282:1 error Expected indentation of 12 spaces but found 6 indent 283:1 error Expected indentation of 12 spaces but found 6 indent 283:7 error '$' is not defined no-undef 283:13 error 'loris' is not defined no-undef 283:29 error Strings must use singlequote quotes 284:1 error Expected indentation of 16 spaces but found 8 indent 285:1 error Expected indentation of 16 spaces but found 8 indent 286:1 error Expected indentation of 16 spaces but found 8 indent 287:1 error Expected indentation of 20 spaces but found 10 indent 288:1 error Expected indentation of 16 spaces but found 8 indent 289:1 error Expected indentation of 12 spaces but found 6 indent 290:1 error Expected indentation of 8 spaces but found 4 indent 291:1 error Expected indentation of 8 spaces but found 4 indent 292:1 error Expected indentation of 12 spaces but found 6 indent 293:1 error Expected indentation of 12 spaces but found 6 indent 294:1 error Expected indentation of 8 spaces but found 4 indent 295:1 error Expected indentation of 4 spaces but found 2 indent 297:1 error Expected indentation of 4 spaces but found 2 indent 298:1 error Expected indentation of 8 spaces but found 4 indent 299:1 error Expected indentation of 12 spaces but found 6 indent 300:1 error Expected indentation of 8 spaces but found 4 indent 301:1 error Expected indentation of 4 spaces but found 2 indent 303:1 error Expected indentation of 4 spaces but found 2 indent 305:1 error Expected indentation of 8 spaces but found 4 indent 306:1 error Expected indentation of 8 spaces but found 4 indent 307:1 error Expected indentation of 12 spaces but found 6 indent 308:1 error Expected indentation of 12 spaces but found 6 indent 309:1 error Expected indentation of 12 spaces but found 6 indent 310:1 error Expected indentation of 16 spaces but found 8 indent 311:1 error Expected indentation of 12 spaces but found 6 indent 312:1 error Expected indentation of 16 spaces but found 8 indent 313:1 error Expected indentation of 16 spaces but found 8 indent 314:1 error Expected indentation of 12 spaces but found 6 indent 315:1 error Expected indentation of 8 spaces but found 4 indent 316:1 error Expected indentation of 4 spaces but found 2 indent 318:1 error Expected indentation of 4 spaces but found 2 indent 320:1 error Expected indentation of 8 spaces but found 4 indent 320:12 error 'index' is defined but never used no-unused-vars 321:1 error Expected indentation of 8 spaces but found 4 indent 322:1 error Expected indentation of 12 spaces but found 6 indent 323:1 error Expected indentation of 12 spaces but found 6 indent 323:7 error 'category' is not defined no-undef 324:1 error Expected indentation of 12 spaces but found 6 indent 324:37 error 'category' is not defined no-undef 324:76 error 'category' is not defined no-undef 325:1 error Expected indentation of 16 spaces but found 8 indent 325:9 error 'isFile' is not defined no-undef 325:45 error 'category' is not defined no-undef 326:1 error Expected indentation of 16 spaces but found 8 indent 326:45 error 'category' is not defined no-undef 326:55 error 'isFile' is not defined no-undef 327:1 error Expected indentation of 12 spaces but found 6 indent 328:1 error Expected indentation of 8 spaces but found 4 indent 329:1 error Expected indentation of 4 spaces but found 2 indent 331:1 error Expected indentation of 4 spaces but found 2 indent 332:1 error Expected indentation of 8 spaces but found 4 indent 333:1 error Expected indentation of 12 spaces but found 6 indent 334:1 error Expected indentation of 16 spaces but found 8 indent 335:1 error Expected indentation of 20 spaces but found 10 indent 336:1 error Expected indentation of 16 spaces but found 8 indent 337:1 error Expected indentation of 16 spaces but found 8 indent 338:1 error Expected indentation of 20 spaces but found 10 indent 339:1 error Expected indentation of 24 spaces but found 12 indent 340:1 error Expected indentation of 24 spaces but found 12 indent 341:1 error Expected indentation of 24 spaces but found 12 indent 342:1 error Expected indentation of 20 spaces but found 10 indent 343:1 error Expected indentation of 16 spaces but found 8 indent 344:1 error Expected indentation of 20 spaces but found 10 indent 345:1 error Expected indentation of 24 spaces but found 12 indent 346:1 error Expected indentation of 24 spaces but found 12 indent 347:1 error Expected indentation of 24 spaces but found 12 indent 348:1 error Expected indentation of 20 spaces but found 10 indent 349:1 error Expected indentation of 16 spaces but found 8 indent 350:1 error Expected indentation of 12 spaces but found 6 indent 351:1 error Expected indentation of 8 spaces but found 4 indent 352:1 error Expected indentation of 4 spaces but found 2 indent 354:1 error Expected indentation of 4 spaces but found 2 indent 355:1 error Expected indentation of 8 spaces but found 4 indent 356:1 error Expected indentation of 12 spaces but found 6 indent 357:1 error Expected indentation of 8 spaces but found 4 indent 358:1 error Expected indentation of 4 spaces but found 2 indent 360:1 error Expected indentation of 4 spaces but found 2 indent 362:1 error Expected indentation of 8 spaces but found 4 indent 363:1 error Expected indentation of 12 spaces but found 6 indent 364:1 error Expected indentation of 8 spaces but found 4 indent 365:1 error Expected indentation of 12 spaces but found 6 indent 366:1 error Expected indentation of 16 spaces but found 8 indent 367:1 error Expected indentation of 12 spaces but found 6 indent 368:1 error Expected indentation of 12 spaces but found 6 indent 369:1 error Expected indentation of 16 spaces but found 8 indent 372:1 error Expected indentation of 20 spaces but found 10 indent 373:1 error Expected indentation of 16 spaces but found 8 indent 374:1 error Expected indentation of 20 spaces but found 10 indent 375:1 error Expected indentation of 16 spaces but found 8 indent 376:1 error Expected indentation of 12 spaces but found 6 indent 377:1 error Expected indentation of 8 spaces but found 4 indent 379:1 error Expected indentation of 8 spaces but found 4 indent 380:1 error Expected indentation of 12 spaces but found 6 indent 381:1 error Expected indentation of 16 spaces but found 8 indent 382:1 error Expected indentation of 20 spaces but found 10 indent 383:1 error Expected indentation of 20 spaces but found 10 indent 384:1 error Expected indentation of 24 spaces but found 12 indent 385:1 error Expected indentation of 24 spaces but found 12 indent 386:1 error Expected indentation of 28 spaces but found 14 indent 387:1 error Expected indentation of 24 spaces but found 12 indent 388:1 error Expected indentation of 20 spaces but found 10 indent 389:1 error Expected indentation of 16 spaces but found 8 indent 390:1 error Expected indentation of 16 spaces but found 8 indent 391:1 error Expected indentation of 20 spaces but found 10 indent 392:1 error Expected indentation of 24 spaces but found 12 indent 393:1 error Expected indentation of 24 spaces but found 12 indent 394:1 error Expected indentation of 20 spaces but found 10 indent 395:1 error Expected indentation of 16 spaces but found 8 indent 396:1 error Expected indentation of 16 spaces but found 8 indent 397:1 error Expected indentation of 20 spaces but found 10 indent 398:1 error Expected indentation of 24 spaces but found 12 indent 399:1 error Expected indentation of 24 spaces but found 12 indent 400:1 error Expected indentation of 28 spaces but found 14 indent 401:1 error Expected indentation of 32 spaces but found 16 indent 402:1 error Expected indentation of 32 spaces but found 16 indent 403:1 error Expected indentation of 32 spaces but found 16 indent 404:1 error Expected indentation of 32 spaces but found 16 indent 405:1 error Expected indentation of 28 spaces but found 14 indent 406:1 error Expected indentation of 24 spaces but found 12 indent 407:1 error Expected indentation of 20 spaces but found 10 indent 408:1 error Expected indentation of 20 spaces but found 10 indent 409:1 error Expected indentation of 24 spaces but found 12 indent 410:1 error Expected indentation of 24 spaces but found 12 indent 411:1 error Expected indentation of 28 spaces but found 14 indent 412:1 error Expected indentation of 32 spaces but found 16 indent 413:1 error Expected indentation of 32 spaces but found 16 indent 414:1 error Expected indentation of 32 spaces but found 16 indent 415:1 error Expected indentation of 28 spaces but found 14 indent 416:1 error Expected indentation of 24 spaces but found 12 indent 417:1 error Expected indentation of 20 spaces but found 10 indent 418:1 error Expected indentation of 16 spaces but found 8 indent 419:1 error Expected indentation of 16 spaces but found 8 indent 420:1 error Expected indentation of 20 spaces but found 10 indent 421:1 error Expected indentation of 24 spaces but found 12 indent 422:1 error Expected indentation of 24 spaces but found 12 indent 423:1 error Expected indentation of 24 spaces but found 12 indent 424:1 error Expected indentation of 24 spaces but found 12 indent 425:1 error Expected indentation of 24 spaces but found 12 indent 426:1 error Expected indentation of 24 spaces but found 12 indent 427:1 error Expected indentation of 24 spaces but found 12 indent 428:1 error Expected indentation of 24 spaces but found 12 indent 429:1 error Expected indentation of 24 spaces but found 12 indent 430:1 error Expected indentation of 24 spaces but found 12 indent 431:1 error Expected indentation of 24 spaces but found 12 indent 432:1 error Expected indentation of 20 spaces but found 10 indent 433:1 error Expected indentation of 16 spaces but found 8 indent 434:1 error Expected indentation of 12 spaces but found 6 indent 435:1 error Expected indentation of 8 spaces but found 4 indent 436:1 error Expected indentation of 4 spaces but found 2 indent 440:1 error Expected indentation of 4 spaces but found 2 indent 450:1 error Expected indentation of 4 spaces but found 2 indent 451:1 error Expected indentation of 4 spaces but found 2 indent 452:1 error Expected indentation of 4 spaces but found 2 indent 453:1 error Expected indentation of 4 spaces but found 2 indent 454:1 error Expected indentation of 4 spaces but found 2 indent ? 388 problems (388 errors, 0 warnings) 366 errors and 0 warnings potentially fixable with the `--fix` option. ERROR in ./modules/dataquery/jsx/react.filterBuilder.js Module Error (from ./node_modules/eslint-loader/index.js): /var/www/loris/modules/dataquery/jsx/react.filterBuilder.js 9:8 error 'React' is defined but never used no-unused-vars 15:1 error Expected indentation of 4 spaces but found 2 indent 16:1 error Expected indentation of 8 spaces but found 4 indent 17:1 error Expected indentation of 8 spaces but found 4 indent 18:1 error Expected indentation of 4 spaces but found 2 indent 20:1 error Expected indentation of 4 spaces but found 2 indent 22:1 error Expected indentation of 8 spaces but found 4 indent 23:1 error Expected indentation of 4 spaces but found 2 indent 25:1 error Expected indentation of 4 spaces but found 2 indent 28:1 error Expected indentation of 8 spaces but found 4 indent 29:1 error Expected indentation of 12 spaces but found 6 indent 31:1 error Expected indentation of 8 spaces but found 4 indent 32:1 error Expected indentation of 8 spaces but found 4 indent 33:1 error Expected indentation of 12 spaces but found 6 indent 34:1 error Expected indentation of 12 spaces but found 6 indent 34:28 error Missing semicolon semi 35:1 error Expected indentation of 8 spaces but found 4 indent 36:1 error Expected indentation of 12 spaces but found 6 indent 37:1 error Expected indentation of 12 spaces but found 6 indent 37:27 error Missing semicolon semi 38:1 error Expected indentation of 8 spaces but found 4 indent 39:1 error Expected indentation of 8 spaces but found 4 indent 40:1 error Expected indentation of 12 spaces but found 6 indent 41:1 error Expected indentation of 16 spaces but found 8 indent 42:1 error Expected indentation of 16 spaces but found 8 indent 43:1 error Expected indentation of 12 spaces but found 6 indent 44:1 error Expected indentation of 8 spaces but found 4 indent 45:1 error Expected indentation of 4 spaces but found 2 indent 52:1 error Expected indentation of 4 spaces but found 2 indent 53:1 error Expected indentation of 8 spaces but found 4 indent 54:1 error Expected indentation of 8 spaces but found 4 indent 55:1 error Expected indentation of 12 spaces but found 6 indent 56:1 error Expected indentation of 16 spaces but found 8 indent 57:1 error Expected indentation of 16 spaces but found 8 indent 58:1 error Expected indentation of 16 spaces but found 8 indent 59:1 error Expected indentation of 16 spaces but found 8 indent 60:1 error Expected indentation of 16 spaces but found 8 indent 61:1 error Expected indentation of 16 spaces but found 8 indent 62:1 error Expected indentation of 16 spaces but found 8 indent 63:1 error Expected indentation of 16 spaces but found 8 indent 64:1 error Expected indentation of 12 spaces but found 6 indent 65:1 error Expected indentation of 12 spaces but found 6 indent 66:1 error Expected indentation of 8 spaces but found 4 indent 67:1 error Expected indentation of 8 spaces but found 4 indent 68:1 error Expected indentation of 8 spaces but found 4 indent 69:1 error Expected indentation of 8 spaces but found 4 indent 70:1 error Expected indentation of 8 spaces but found 4 indent 71:1 error Expected indentation of 8 spaces but found 4 indent 72:1 error Expected indentation of 8 spaces but found 4 indent 73:1 error Expected indentation of 4 spaces but found 2 indent 75:1 error Expected indentation of 4 spaces but found 2 indent 76:1 error Expected indentation of 8 spaces but found 4 indent 76:21 error 'loris' is not defined no-undef 77:1 error Expected indentation of 4 spaces but found 2 indent 79:1 error Expected indentation of 4 spaces but found 2 indent 81:1 error Expected indentation of 8 spaces but found 4 indent 82:1 error Expected indentation of 8 spaces but found 4 indent 83:1 error Expected indentation of 12 spaces but found 6 indent 84:1 error Expected indentation of 12 spaces but found 6 indent 84:7 error '$' is not defined no-undef 84:13 error 'loris' is not defined no-undef 85:1 error Expected indentation of 16 spaces but found 8 indent 86:1 error Expected indentation of 16 spaces but found 8 indent 87:1 error Expected indentation of 12 spaces but found 6 indent 88:1 error Expected indentation of 8 spaces but found 4 indent 89:1 error Expected indentation of 4 spaces but found 2 indent 91:1 error Expected indentation of 4 spaces but found 2 indent 93:1 error Expected indentation of 8 spaces but found 4 indent 94:1 error Expected indentation of 8 spaces but found 4 indent 95:1 error Expected indentation of 8 spaces but found 4 indent 96:1 error Expected indentation of 8 spaces but found 4 indent 97:1 error Expected indentation of 8 spaces but found 4 indent 98:1 error Expected indentation of 8 spaces but found 4 indent 99:1 error Expected indentation of 8 spaces but found 4 indent 100:1 error Expected indentation of 8 spaces but found 4 indent 101:1 error Expected indentation of 12 spaces but found 6 indent 102:1 error Expected indentation of 12 spaces but found 6 indent 103:1 error Expected indentation of 8 spaces but found 4 indent 104:1 error Expected indentation of 8 spaces but found 4 indent 105:1 error Expected indentation of 4 spaces but found 2 indent 107:1 error Expected indentation of 4 spaces but found 2 indent 109:1 error Expected indentation of 8 spaces but found 4 indent 110:1 error Expected indentation of 8 spaces but found 4 indent 111:1 error Expected indentation of 8 spaces but found 4 indent 112:1 error Expected indentation of 8 spaces but found 4 indent 113:1 error Expected indentation of 8 spaces but found 4 indent 114:1 error Expected indentation of 8 spaces but found 4 indent 115:1 error Expected indentation of 12 spaces but found 6 indent 116:1 error Expected indentation of 8 spaces but found 4 indent 117:1 error Expected indentation of 8 spaces but found 4 indent 118:1 error Expected indentation of 8 spaces but found 4 indent 119:1 error Expected indentation of 12 spaces but found 6 indent 120:1 error Expected indentation of 16 spaces but found 8 indent 121:1 error Expected indentation of 12 spaces but found 6 indent 122:1 error Expected indentation of 12 spaces but found 6 indent 123:1 error Expected indentation of 8 spaces but found 4 indent 124:1 error Expected indentation of 4 spaces but found 2 indent 126:1 error Expected indentation of 4 spaces but found 2 indent 127:1 error Expected indentation of 8 spaces but found 4 indent 128:1 error Expected indentation of 8 spaces but found 4 indent 129:1 error Expected indentation of 8 spaces but found 4 indent 131:1 error Expected indentation of 8 spaces but found 4 indent 133:1 error Expected indentation of 8 spaces but found 4 indent 134:1 error Expected indentation of 12 spaces but found 6 indent 135:1 error Expected indentation of 8 spaces but found 4 indent 136:1 error Expected indentation of 8 spaces but found 4 indent 137:1 error Expected indentation of 8 spaces but found 4 indent 138:1 error Expected indentation of 4 spaces but found 2 indent 140:1 error Expected indentation of 4 spaces but found 2 indent 142:1 error Expected indentation of 8 spaces but found 4 indent 143:1 error Expected indentation of 8 spaces but found 4 indent 144:1 error Expected indentation of 12 spaces but found 6 indent 145:1 error Expected indentation of 16 spaces but found 8 indent 146:1 error Expected indentation of 16 spaces but found 8 indent 147:1 error Expected indentation of 16 spaces but found 8 indent 148:1 error Expected indentation of 16 spaces but found 8 indent 149:1 error Expected indentation of 16 spaces but found 8 indent 150:1 error Expected indentation of 16 spaces but found 8 indent 151:1 error Expected indentation of 20 spaces but found 10 indent 152:1 error Expected indentation of 24 spaces but found 12 indent 153:1 error Expected indentation of 20 spaces but found 10 indent 154:1 error Expected indentation of 20 spaces but found 10 indent 155:1 error Expected indentation of 20 spaces but found 10 indent 156:1 error Expected indentation of 24 spaces but found 12 indent 157:1 error Expected indentation of 20 spaces but found 10 indent 158:1 error Expected indentation of 20 spaces but found 10 indent 159:1 error Expected indentation of 16 spaces but found 8 indent 160:1 error Expected indentation of 16 spaces but found 8 indent 161:1 error Expected indentation of 20 spaces but found 10 indent 162:1 error Expected indentation of 20 spaces but found 10 indent 163:1 error Expected indentation of 16 spaces but found 8 indent 164:1 error Expected indentation of 16 spaces but found 8 indent 165:1 error Expected indentation of 16 spaces but found 8 indent 166:1 error Expected indentation of 16 spaces but found 8 indent 167:1 error Expected indentation of 12 spaces but found 6 indent 168:1 error Expected indentation of 12 spaces but found 6 indent 169:1 error Expected indentation of 16 spaces but found 8 indent 169:9 error '$' is not defined no-undef 169:15 error 'loris' is not defined no-undef 170:1 error Expected indentation of 20 spaces but found 10 indent 171:1 error Expected indentation of 24 spaces but found 12 indent 172:1 error Expected indentation of 24 spaces but found 12 indent 173:1 error Expected indentation of 24 spaces but found 12 indent 174:1 error Expected indentation of 20 spaces but found 10 indent 175:1 error Expected indentation of 20 spaces but found 10 indent 176:1 error Expected indentation of 20 spaces but found 10 indent 177:1 error Expected indentation of 16 spaces but found 8 indent 178:1 error Expected indentation of 12 spaces but found 6 indent 179:1 error Expected indentation of 12 spaces but found 6 indent 180:1 error Expected indentation of 12 spaces but found 8 indent 181:1 error Expected indentation of 12 spaces but found 8 indent 182:1 error Expected indentation of 16 spaces but found 10 indent 183:1 error Expected indentation of 16 spaces but found 10 indent 184:1 error Expected indentation of 12 spaces but found 8 indent 185:1 error Expected indentation of 12 spaces but found 8 indent 186:1 error Expected indentation of 16 spaces but found 10 indent 187:1 error Expected indentation of 16 spaces but found 10 indent 188:1 error Expected indentation of 12 spaces but found 8 indent 189:1 error Expected indentation of 16 spaces but found 10 indent 190:1 error Expected indentation of 16 spaces but found 10 indent 191:1 error Expected indentation of 12 spaces but found 8 indent 192:1 error Expected indentation of 16 spaces but found 10 indent 193:1 error Expected indentation of 16 spaces but found 10 indent 194:1 error Expected indentation of 12 spaces but found 8 indent 195:1 error Expected indentation of 16 spaces but found 10 indent 196:1 error Expected indentation of 16 spaces but found 10 indent 197:1 error Expected indentation of 12 spaces but found 8 indent 198:1 error Expected indentation of 16 spaces but found 10 indent 199:1 error Expected indentation of 16 spaces but found 10 indent 200:1 error Expected indentation of 12 spaces but found 8 indent 201:1 error Expected indentation of 16 spaces but found 10 indent 202:1 error Expected indentation of 12 spaces but found 6 indent 203:1 error Expected indentation of 8 spaces but found 4 indent 204:1 error Expected indentation of 4 spaces but found 2 indent 206:1 error Expected indentation of 4 spaces but found 2 indent 208:1 error Expected indentation of 8 spaces but found 4 indent 209:1 error Expected indentation of 8 spaces but found 4 indent 211:1 error Expected indentation of 8 spaces but found 4 indent 212:1 error Expected indentation of 12 spaces but found 6 indent 213:1 error Expected indentation of 12 spaces but found 6 indent 214:1 error Expected indentation of 8 spaces but found 4 indent 215:1 error Expected indentation of 12 spaces but found 6 indent 216:1 error Expected indentation of 12 spaces but found 6 indent 217:1 error Expected indentation of 8 spaces but found 4 indent 218:1 error Expected indentation of 8 spaces but found 4 indent 219:1 error Expected indentation of 4 spaces but found 2 indent 221:1 error Expected indentation of 4 spaces but found 2 indent 224:1 error Expected indentation of 8 spaces but found 4 indent 225:1 error Expected indentation of 8 spaces but found 4 indent 226:1 error Expected indentation of 8 spaces but found 4 indent 227:1 error Expected indentation of 8 spaces but found 4 indent 228:1 error Expected indentation of 8 spaces but found 4 indent 229:1 error Expected indentation of 12 spaces but found 6 indent 230:1 error Expected indentation of 12 spaces but found 6 indent 231:1 error Expected indentation of 16 spaces but found 8 indent 232:1 error Expected indentation of 20 spaces but found 10 indent 233:1 error Expected indentation of 16 spaces but found 8 indent 234:1 error Expected indentation of 16 spaces but found 8 indent 235:1 error Expected indentation of 20 spaces but found 10 indent 236:1 error Expected indentation of 16 spaces but found 8 indent 237:1 error Expected indentation of 12 spaces but found 6 indent 238:1 error Expected indentation of 12 spaces but found 6 indent 239:1 error Expected indentation of 12 spaces but found 6 indent 240:1 error Expected indentation of 12 spaces but found 6 indent 241:1 error Expected indentation of 12 spaces but found 6 indent 242:1 error Expected indentation of 12 spaces but found 6 indent 243:1 error Expected indentation of 12 spaces but found 6 indent 244:1 error Expected indentation of 12 spaces but found 6 indent 245:1 error Expected indentation of 12 spaces but found 6 indent 247:1 error Expected indentation of 12 spaces but found 6 indent 248:1 error Expected indentation of 16 spaces but found 8 indent 249:1 error Expected indentation of 16 spaces but found 8 indent 249:53 error Strings must use singlequote quotes 250:1 error Expected indentation of 16 spaces but found 8 indent 250:35 error Missing semicolon semi 251:1 error Expected indentation of 16 spaces but found 8 indent 252:1 error Expected indentation of 20 spaces but found 10 indent 253:1 error Expected indentation of 24 spaces but found 12 indent 254:1 error Expected indentation of 28 spaces but found 14 indent 255:1 error Expected indentation of 24 spaces but found 12 indent 256:1 error Expected indentation of 20 spaces but found 10 indent 257:1 error Expected indentation of 16 spaces but found 8 indent 258:1 error Expected indentation of 16 spaces but found 8 indent 258:73 error Strings must use singlequote quotes 259:1 error Expected indentation of 16 spaces but found 8 indent 260:1 error Expected indentation of 20 spaces but found 10 indent 261:1 error Expected indentation of 24 spaces but found 12 indent 262:1 error Expected indentation of 24 spaces but found 12 indent 263:1 error Expected indentation of 20 spaces but found 10 indent 264:1 error Expected indentation of 16 spaces but found 8 indent 265:1 error Expected indentation of 16 spaces but found 8 indent 268:1 error Expected indentation of 16 spaces but found 8 indent 269:1 error Expected indentation of 20 spaces but found 10 indent 270:1 error Expected indentation of 20 spaces but found 10 indent 271:1 error Expected indentation of 20 spaces but found 10 indent 272:1 error Expected indentation of 20 spaces but found 12 indent 273:1 error Expected indentation of 24 spaces but found 14 indent 273:30 error 'enumToArray' is not defined no-undef 274:1 error Expected indentation of 24 spaces but found 14 indent 275:1 error Expected indentation of 28 spaces but found 16 indent 276:1 error Expected indentation of 32 spaces but found 18 indent 277:1 error Expected indentation of 36 spaces but found 20 indent 278:1 error Expected indentation of 32 spaces but found 18 indent 279:1 error Expected indentation of 28 spaces but found 16 indent 280:1 error Expected indentation of 24 spaces but found 14 indent 281:1 error Expected indentation of 24 spaces but found 14 indent 282:1 error Expected indentation of 24 spaces but found 14 indent 283:1 error Expected indentation of 28 spaces but found 16 indent 284:1 error Expected indentation of 32 spaces but found 18 indent 285:1 error Expected indentation of 32 spaces but found 18 indent 286:1 error Expected indentation of 28 spaces but found 16 indent 287:1 error Expected indentation of 24 spaces but found 14 indent 288:1 error Expected indentation of 24 spaces but found 14 indent 289:1 error Expected indentation of 20 spaces but found 12 indent 290:1 error Expected indentation of 24 spaces but found 14 indent 291:1 error Expected indentation of 28 spaces but found 16 indent 292:1 error Expected indentation of 32 spaces but found 23 indent 293:1 error Expected indentation of 32 spaces but found 23 indent 294:1 error Expected indentation of 32 spaces but found 23 indent 295:1 error Expected indentation of 28 spaces but found 16 indent 296:1 error Expected indentation of 24 spaces but found 14 indent 297:1 error Expected indentation of 24 spaces but found 14 indent 298:1 error Expected indentation of 20 spaces but found 10 indent 299:1 error Expected indentation of 16 spaces but found 8 indent 300:1 error Expected indentation of 16 spaces but found 8 indent 301:1 error Expected indentation of 20 spaces but found 10 indent 302:1 error Expected indentation of 20 spaces but found 10 indent 303:1 error Expected indentation of 20 spaces but found 10 indent 304:1 error Expected indentation of 24 spaces but found 12 indent 305:1 error Expected indentation of 28 spaces but found 14 indent 306:1 error Expected indentation of 32 spaces but found 16 indent 307:1 error Expected indentation of 28 spaces but found 14 indent 308:1 error Expected indentation of 24 spaces but found 12 indent 309:1 error Expected indentation of 20 spaces but found 10 indent 310:1 error Expected indentation of 20 spaces but found 10 indent 311:1 error Expected indentation of 24 spaces but found 12 indent 312:1 error Expected indentation of 28 spaces but found 14 indent 313:1 error Expected indentation of 28 spaces but found 14 indent 314:1 error Expected indentation of 24 spaces but found 12 indent 315:1 error Expected indentation of 20 spaces but found 10 indent 316:1 error Expected indentation of 16 spaces but found 8 indent 317:1 error Expected indentation of 12 spaces but found 6 indent 318:1 error Expected indentation of 12 spaces but found 6 indent 319:1 error Expected indentation of 16 spaces but found 8 indent 320:1 error Expected indentation of 20 spaces but found 10 indent 321:1 error Expected indentation of 24 spaces but found 12 indent 322:1 error Expected indentation of 20 spaces but found 10 indent 323:1 error Expected indentation of 20 spaces but found 10 indent 324:1 error Expected indentation of 24 spaces but found 12 indent 325:1 error Expected indentation of 28 spaces but found 14 indent 326:1 error Expected indentation of 28 spaces but found 14 indent 327:1 error Expected indentation of 24 spaces but found 12 indent 328:1 error Expected indentation of 24 spaces but found 12 indent 329:1 error Expected indentation of 24 spaces but found 12 indent 330:1 error Expected indentation of 24 spaces but found 12 indent 331:1 error Expected indentation of 20 spaces but found 10 indent 332:1 error Expected indentation of 16 spaces but found 8 indent 333:1 error Expected indentation of 12 spaces but found 6 indent 334:1 error Expected indentation of 8 spaces but found 4 indent 335:1 error Expected indentation of 12 spaces but found 6 indent 336:1 error Expected indentation of 12 spaces but found 6 indent 337:1 error Expected indentation of 16 spaces but found 8 indent 338:1 error Expected indentation of 20 spaces but found 10 indent 339:1 error Expected indentation of 16 spaces but found 8 indent 340:1 error Expected indentation of 12 spaces but found 6 indent 341:1 error Expected indentation of 12 spaces but found 6 indent 342:1 error Expected indentation of 16 spaces but found 8 indent 343:1 error Expected indentation of 20 spaces but found 10 indent 344:1 error Expected indentation of 20 spaces but found 10 indent 345:1 error Expected indentation of 16 spaces but found 8 indent 346:1 error Expected indentation of 12 spaces but found 6 indent 346:8 error Missing semicolon semi 347:1 error Expected indentation of 8 spaces but found 4 indent 348:1 error Expected indentation of 8 spaces but found 4 indent 349:1 error Expected indentation of 12 spaces but found 6 indent 350:1 error Expected indentation of 16 spaces but found 8 indent 351:1 error Expected indentation of 20 spaces but found 10 indent 352:1 error Expected indentation of 20 spaces but found 10 indent 353:1 error Expected indentation of 24 spaces but found 12 indent 354:1 error Expected indentation of 28 spaces but found 20 indent 355:1 error Expected indentation of 24 spaces but found 12 indent 356:1 error Expected indentation of 28 spaces but found 14 indent 357:1 error Expected indentation of 24 spaces but found 12 indent 358:1 error Expected indentation of 20 spaces but found 10 indent 359:1 error Expected indentation of 16 spaces but found 8 indent 360:1 error Expected indentation of 12 spaces but found 6 indent 361:1 error Expected indentation of 8 spaces but found 4 indent 362:1 error Expected indentation of 4 spaces but found 2 indent 369:1 error Expected indentation of 4 spaces but found 2 indent 370:1 error Expected indentation of 8 spaces but found 4 indent 371:1 error Expected indentation of 8 spaces but found 4 indent 372:1 error Expected indentation of 8 spaces but found 4 indent 373:1 error Expected indentation of 8 spaces but found 4 indent 374:1 error Expected indentation of 8 spaces but found 4 indent 375:1 error Expected indentation of 8 spaces but found 4 indent 376:1 error Expected indentation of 8 spaces but found 4 indent 377:1 error Expected indentation of 4 spaces but found 2 indent 379:1 error Expected indentation of 4 spaces but found 2 indent 382:1 error Expected indentation of 8 spaces but found 4 indent 383:1 error Expected indentation of 8 spaces but found 4 indent 385:1 error Expected indentation of 8 spaces but found 4 indent 386:1 error Expected indentation of 12 spaces but found 6 indent 387:1 error Expected indentation of 12 spaces but found 6 indent 388:1 error Expected indentation of 8 spaces but found 4 indent 389:1 error Expected indentation of 12 spaces but found 6 indent 390:1 error Expected indentation of 12 spaces but found 6 indent 391:1 error Expected indentation of 8 spaces but found 4 indent 392:1 error Expected indentation of 4 spaces but found 2 indent 394:1 error Expected indentation of 4 spaces but found 2 indent 396:1 error Expected indentation of 8 spaces but found 4 indent 397:1 error Expected indentation of 8 spaces but found 4 indent 399:1 error Expected indentation of 8 spaces but found 4 indent 400:1 error Expected indentation of 8 spaces but found 4 indent 400:21 error 'getSessions' is not defined no-undef 402:1 error Expected indentation of 8 spaces but found 4 indent 403:1 error Expected indentation of 12 spaces but found 6 indent 404:1 error Expected indentation of 12 spaces but found 6 indent 405:1 error Expected indentation of 8 spaces but found 4 indent 406:1 error Expected indentation of 12 spaces but found 6 indent 407:1 error Expected indentation of 12 spaces but found 6 indent 408:1 error Expected indentation of 8 spaces but found 4 indent 409:1 error Expected indentation of 4 spaces but found 2 indent 411:1 error Expected indentation of 4 spaces but found 2 indent 413:1 error Expected indentation of 8 spaces but found 4 indent 414:1 error Expected indentation of 12 spaces but found 6 indent 414:7 error 'sessions' is assigned a value but never used no-unused-vars 415:1 error Expected indentation of 12 spaces but found 6 indent 415:7 error 'session' is assigned a value but never used no-unused-vars 416:1 error Expected indentation of 8 spaces but found 4 indent 418:1 error Expected indentation of 8 spaces but found 4 indent 419:1 error Expected indentation of 8 spaces but found 4 indent 419:21 error 'getSessions' is not defined no-undef 420:1 error Expected indentation of 8 spaces but found 4 indent 421:1 error Expected indentation of 12 spaces but found 6 indent 422:1 error Expected indentation of 12 spaces but found 6 indent 423:1 error Expected indentation of 8 spaces but found 4 indent 424:1 error Expected indentation of 12 spaces but found 6 indent 425:1 error Expected indentation of 12 spaces but found 6 indent 425:37 error Missing semicolon semi 426:1 error Expected indentation of 8 spaces but found 4 indent 427:1 error Expected indentation of 4 spaces but found 2 indent 429:1 error Expected indentation of 4 spaces but found 2 indent 431:1 error Expected indentation of 8 spaces but found 4 indent 432:1 error Expected indentation of 12 spaces but found 6 indent 434:1 error Expected indentation of 8 spaces but found 4 indent 435:1 error Expected indentation of 8 spaces but found 4 indent 436:1 error Expected indentation of 12 spaces but found 6 indent 437:1 error Expected indentation of 16 spaces but found 8 indent 438:1 error Expected indentation of 12 spaces but found 6 indent 438:8 error Missing semicolon semi 439:1 error Expected indentation of 8 spaces but found 4 indent 440:1 error Expected indentation of 12 spaces but found 6 indent 441:1 error Expected indentation of 16 spaces but found 8 indent 442:1 error Expected indentation of 16 spaces but found 8 indent 443:1 error Expected indentation of 16 spaces but found 8 indent 444:1 error Expected indentation of 20 spaces but found 10 indent 445:1 error Expected indentation of 24 spaces but found 12 indent 446:1 error Expected indentation of 20 spaces but found 10 indent 447:1 error Expected indentation of 16 spaces but found 8 indent 448:1 error Expected indentation of 12 spaces but found 6 indent 448:8 error Missing semicolon semi 449:1 error Expected indentation of 8 spaces but found 4 indent 450:1 error Expected indentation of 8 spaces but found 4 indent 452:1 error Expected indentation of 8 spaces but found 4 indent 453:1 error Expected indentation of 12 spaces but found 6 indent 454:1 error Expected indentation of 12 spaces but found 6 indent 455:1 error Expected indentation of 8 spaces but found 4 indent 456:1 error Expected indentation of 12 spaces but found 6 indent 457:1 error Expected indentation of 12 spaces but found 6 indent 457:37 error Missing semicolon semi 458:1 error Expected indentation of 8 spaces but found 4 indent 459:1 error Expected indentation of 4 spaces but found 2 indent 461:1 error Expected indentation of 4 spaces but found 2 indent 464:1 error Expected indentation of 8 spaces but found 4 indent 465:1 error Expected indentation of 8 spaces but found 4 indent 467:1 error Expected indentation of 8 spaces but found 4 indent 468:1 error Expected indentation of 8 spaces but found 4 indent 468:21 error 'getSessions' is not defined no-undef 471:1 error Expected indentation of 8 spaces but found 4 indent 472:1 error Expected indentation of 12 spaces but found 6 indent 473:1 error Expected indentation of 12 spaces but found 6 indent 474:1 error Expected indentation of 8 spaces but found 4 indent 475:1 error Expected indentation of 12 spaces but found 6 indent 476:1 error Expected indentation of 12 spaces but found 6 indent 477:1 error Expected indentation of 8 spaces but found 4 indent 478:1 error Expected indentation of 4 spaces but found 2 indent 480:1 error Expected indentation of 4 spaces but found 2 indent 482:1 error Expected indentation of 8 spaces but found 4 indent 483:1 error Expected indentation of 12 spaces but found 6 indent 484:1 error Expected indentation of 16 spaces but found 8 indent 485:1 error Expected indentation of 16 spaces but found 8 indent 486:1 error Expected indentation of 12 spaces but found 6 indent 487:1 error Expected indentation of 8 spaces but found 4 indent 489:1 error Expected indentation of 8 spaces but found 4 indent 490:1 error Expected indentation of 8 spaces but found 4 indent 491:1 error Expected indentation of 12 spaces but found 6 indent 492:1 error Expected indentation of 16 spaces but found 8 indent 493:1 error Expected indentation of 20 spaces but found 10 indent 494:1 error Expected indentation of 24 spaces but found 12 indent 495:1 error Expected indentation of 28 spaces but found 24 indent 496:1 error Expected indentation of 28 spaces but found 24 indent 497:1 error Expected indentation of 28 spaces but found 24 indent 498:1 error Expected indentation of 28 spaces but found 24 indent 499:1 error Expected indentation of 28 spaces but found 24 indent 500:1 error Expected indentation of 28 spaces but found 24 indent 501:1 error Expected indentation of 24 spaces but found 12 indent 502:1 error Expected indentation of 20 spaces but found 10 indent 503:1 error Expected indentation of 16 spaces but found 8 indent 504:1 error Expected indentation of 12 spaces but found 6 indent 505:1 error Expected indentation of 16 spaces but found 8 indent 506:1 error Expected indentation of 20 spaces but found 10 indent 507:1 error Expected indentation of 24 spaces but found 12 indent 508:1 error Expected indentation of 28 spaces but found 25 indent 509:1 error Expected indentation of 28 spaces but found 25 indent 510:1 error Expected indentation of 28 spaces but found 25 indent 511:1 error Expected indentation of 28 spaces but found 25 indent 512:1 error Expected indentation of 28 spaces but found 25 indent 513:1 error Expected indentation of 28 spaces but found 25 indent 514:1 error Expected indentation of 24 spaces but found 12 indent 515:1 error Expected indentation of 20 spaces but found 10 indent 516:1 error Expected indentation of 16 spaces but found 8 indent 517:1 error Expected indentation of 12 spaces but found 6 indent 518:1 error Expected indentation of 8 spaces but found 4 indent 520:1 error Expected indentation of 8 spaces but found 4 indent 522:1 error Expected indentation of 8 spaces but found 4 indent 523:1 error Expected indentation of 12 spaces but found 6 indent 524:1 error Expected indentation of 12 spaces but found 6 indent 525:1 error Expected indentation of 16 spaces but found 8 indent 526:1 error Expected indentation of 20 spaces but found 10 indent 527:1 error Expected indentation of 20 spaces but found 10 indent 528:1 error Expected indentation of 16 spaces but found 8 indent 529:1 error Expected indentation of 20 spaces but found 10 indent 530:1 error Expected indentation of 16 spaces but found 8 indent 531:1 error Expected indentation of 12 spaces but found 6 indent 532:1 error Expected indentation of 8 spaces but found 4 indent 533:1 error Expected indentation of 8 spaces but found 4 indent 534:1 error Expected indentation of 12 spaces but found 6 indent 535:1 error Expected indentation of 16 spaces but found 8 indent 536:1 error Expected indentation of 20 spaces but found 10 indent 537:1 error Expected indentation of 24 spaces but found 12 indent 538:1 error Expected indentation of 28 spaces but found 14 indent 539:1 error Expected indentation of 32 spaces but found 16 indent 540:1 error Expected indentation of 28 spaces but found 14 indent 541:1 error Expected indentation of 28 spaces but found 14 indent 542:1 error Expected indentation of 32 spaces but found 16 indent 543:1 error Expected indentation of 32 spaces but found 16 indent 544:1 error Expected indentation of 36 spaces but found 24 indent 545:1 error Expected indentation of 32 spaces but found 16 indent 546:1 error Expected indentation of 36 spaces but found 18 indent 547:1 error Expected indentation of 32 spaces but found 16 indent 548:1 error Expected indentation of 32 spaces but found 16 indent 549:1 error Expected indentation of 36 spaces but found 24 indent 550:1 error Expected indentation of 32 spaces but found 16 indent 551:1 error Expected indentation of 36 spaces but found 18 indent 552:1 error Expected indentation of 32 spaces but found 16 indent 553:1 error Expected indentation of 28 spaces but found 14 indent 554:1 error Expected indentation of 24 spaces but found 12 indent 555:1 error Expected indentation of 24 spaces but found 12 indent 556:1 error Expected indentation of 28 spaces but found 14 indent 557:1 error Expected indentation of 24 spaces but found 12 indent 558:1 error Expected indentation of 20 spaces but found 10 indent 559:1 error Expected indentation of 16 spaces but found 8 indent 560:1 error Expected indentation of 12 spaces but found 6 indent 561:1 error Expected indentation of 8 spaces but found 4 indent 562:1 error Expected indentation of 4 spaces but found 2 indent 569:1 error Expected indentation of 4 spaces but found 2 indent 570:1 error Expected indentation of 8 spaces but found 4 indent 571:1 error Expected indentation of 8 spaces but found 4 indent 572:1 error Expected indentation of 4 spaces but found 2 indent 574:1 error Expected indentation of 4 spaces but found 2 indent 575:1 error Expected indentation of 8 spaces but found 4 indent 576:1 error Expected indentation of 12 spaces but found 6 indent 577:1 error Expected indentation of 16 spaces but found 8 indent 578:1 error Expected indentation of 16 spaces but found 8 indent 579:1 error Expected indentation of 20 spaces but found 10 indent 580:1 error Expected indentation of 24 spaces but found 12 indent 581:1 error Expected indentation of 28 spaces but found 25 indent 582:1 error Expected indentation of 28 spaces but found 25 indent 583:1 error Expected indentation of 28 spaces but found 25 indent 584:1 error Expected indentation of 24 spaces but found 12 indent 585:1 error Expected indentation of 20 spaces but found 10 indent 586:1 error Expected indentation of 16 spaces but found 8 indent 587:1 error Expected indentation of 12 spaces but found 6 indent 588:1 error Expected indentation of 8 spaces but found 4 indent 589:1 error Expected indentation of 4 spaces but found 2 indent 598:1 error Expected indentation of 4 spaces but found 2 indent 599:1 error Expected indentation of 4 spaces but found 2 indent 600:1 error Expected indentation of 4 spaces but found 2 indent 601:1 error Expected indentation of 4 spaces but found 2 indent ? 529 problems (529 errors, 0 warnings) 517 errors and 0 warnings potentially fixable with the `--fix` option. ERROR in ./modules/dataquery/jsx/react.paginator.js Module Error (from ./node_modules/eslint-loader/index.js): /var/www/loris/modules/dataquery/jsx/react.paginator.js 5:1 error Expected indentation of 4 spaces but found 2 indent 6:1 error Expected indentation of 8 spaces but found 4 indent 7:1 error Expected indentation of 8 spaces but found 4 indent 8:1 error Expected indentation of 12 spaces but found 6 indent 9:1 error Expected indentation of 12 spaces but found 6 indent 10:1 error Expected indentation of 8 spaces but found 4 indent 11:1 error Expected indentation of 8 spaces but found 4 indent 12:1 error Expected indentation of 4 spaces but found 2 indent 14:1 error Expected indentation of 4 spaces but found 2 indent 15:1 error Expected indentation of 8 spaces but found 4 indent 16:1 error Expected indentation of 8 spaces but found 4 indent 17:1 error Expected indentation of 12 spaces but found 6 indent 18:1 error Expected indentation of 12 spaces but found 6 indent 20:1 error Expected indentation of 12 spaces but found 6 indent 21:1 error Expected indentation of 16 spaces but found 8 indent 22:1 error Expected indentation of 12 spaces but found 6 indent 23:1 error Expected indentation of 8 spaces but found 4 indent 24:1 error Expected indentation of 4 spaces but found 2 indent 26:1 error Expected indentation of 4 spaces but found 2 indent 27:1 error Expected indentation of 8 spaces but found 4 indent 28:1 error Expected indentation of 8 spaces but found 4 indent 29:1 error Expected indentation of 8 spaces but found 4 indent 30:1 error Expected indentation of 8 spaces but found 4 indent 31:1 error Expected indentation of 8 spaces but found 4 indent 32:1 error Expected indentation of 8 spaces but found 4 indent 34:1 error Expected indentation of 8 spaces but found 4 indent 35:1 error Expected indentation of 12 spaces but found 6 indent 36:1 error Expected indentation of 8 spaces but found 4 indent 38:1 error Expected indentation of 8 spaces but found 4 indent 39:1 error Expected indentation of 12 spaces but found 6 indent 40:1 error Expected indentation of 12 spaces but found 6 indent 41:1 error Expected indentation of 16 spaces but found 8 indent 42:1 error Expected indentation of 16 spaces but found 8 indent 42:33 error Missing semicolon semi 43:1 error Expected indentation of 12 spaces but found 6 indent 45:1 error Expected indentation of 8 spaces but found 4 indent 48:1 error Expected indentation of 8 spaces but found 4 indent 49:1 error Expected indentation of 12 spaces but found 6 indent 50:1 error Expected indentation of 8 spaces but found 4 indent 51:1 error Expected indentation of 8 spaces but found 4 indent 52:1 error Expected indentation of 12 spaces but found 6 indent 53:1 error Expected indentation of 12 spaces but found 6 indent 54:1 error Expected indentation of 16 spaces but found 8 indent 55:1 error Expected indentation of 12 spaces but found 6 indent 56:1 error Expected indentation of 12 spaces but found 6 indent 57:1 error Expected indentation of 8 spaces but found 4 indent 58:1 error Expected indentation of 8 spaces but found 4 indent 59:1 error Expected indentation of 12 spaces but found 6 indent 60:1 error Expected indentation of 8 spaces but found 4 indent 61:1 error Expected indentation of 8 spaces but found 4 indent 62:1 error Expected indentation of 12 spaces but found 6 indent 63:1 error Expected indentation of 16 spaces but found 8 indent 64:1 error Expected indentation of 12 spaces but found 6 indent 65:1 error Expected indentation of 8 spaces but found 4 indent 66:1 error Expected indentation of 4 spaces but found 2 indent 69:1 error Expected indentation of 4 spaces but found 2 indent ? 56 problems (56 errors, 0 warnings) 56 errors and 0 warnings potentially fixable with the `--fix` option. ERROR in ./modules/dataquery/jsx/react.sidebar.js Module Error (from ./node_modules/eslint-loader/index.js): /var/www/loris/modules/dataquery/jsx/react.sidebar.js 1:8 error 'React' is defined but never used no-unused-vars 5:1 error Expected indentation of 4 spaces but found 2 indent 6:1 error Expected indentation of 8 spaces but found 4 indent 7:1 error Expected indentation of 8 spaces but found 4 indent 8:1 error Expected indentation of 12 spaces but found 6 indent 9:1 error Expected indentation of 8 spaces but found 4 indent 10:1 error Expected indentation of 8 spaces but found 4 indent 11:1 error Expected indentation of 8 spaces but found 4 indent 12:1 error Expected indentation of 8 spaces but found 4 indent 13:1 error Expected indentation of 4 spaces but found 2 indent 15:1 error Expected indentation of 4 spaces but found 2 indent 16:1 error Expected indentation of 8 spaces but found 4 indent 17:1 error Expected indentation of 4 spaces but found 2 indent 19:1 error Expected indentation of 4 spaces but found 2 indent 20:1 error Expected indentation of 8 spaces but found 4 indent 21:1 error Expected indentation of 4 spaces but found 2 indent 23:1 error Expected indentation of 4 spaces but found 2 indent 24:1 error Expected indentation of 8 spaces but found 4 indent 25:1 error Expected indentation of 4 spaces but found 2 indent 27:1 error Expected indentation of 4 spaces but found 2 indent 28:1 error Expected indentation of 8 spaces but found 4 indent 29:1 error Expected indentation of 12 spaces but found 6 indent 30:1 error Expected indentation of 8 spaces but found 4 indent 31:1 error Expected indentation of 8 spaces but found 4 indent 32:1 error Expected indentation of 12 spaces but found 6 indent 33:1 error Expected indentation of 16 spaces but found 8 indent 34:1 error Expected indentation of 16 spaces but found 8 indent 35:1 error Expected indentation of 12 spaces but found 6 indent 36:1 error Expected indentation of 8 spaces but found 4 indent 37:1 error Expected indentation of 4 spaces but found 2 indent 41:1 error Expected indentation of 4 spaces but found 2 indent 42:1 error Expected indentation of 8 spaces but found 4 indent 43:1 error Expected indentation of 8 spaces but found 4 indent 45:1 error Expected indentation of 4 spaces but found 2 indent 47:1 error Expected indentation of 4 spaces but found 2 indent 48:1 error Expected indentation of 8 spaces but found 4 indent 51:1 error Expected indentation of 12 spaces but found 6 indent 52:1 error Expected indentation of 8 spaces but found 4 indent 54:1 error Expected indentation of 8 spaces but found 4 indent 54:9 error 'fieldDiv' is assigned a value but never used no-unused-vars 55:1 error Expected indentation of 8 spaces but found 4 indent 56:1 error Expected indentation of 8 spaces but found 4 indent 57:1 error Expected indentation of 12 spaces but found 6 indent 58:1 error Expected indentation of 16 spaces but found 8 indent 59:1 error Expected indentation of 16 spaces but found 8 indent 60:1 error Expected indentation of 20 spaces but found 10 indent 61:1 error Expected indentation of 24 spaces but found 12 indent 62:1 error Expected indentation of 24 spaces but found 12 indent 63:1 error Expected indentation of 20 spaces but found 10 indent 64:1 error Expected indentation of 16 spaces but found 8 indent 65:1 error Expected indentation of 12 spaces but found 6 indent 66:1 error Expected indentation of 8 spaces but found 4 indent 67:1 error Expected indentation of 8 spaces but found 4 indent 68:1 error Expected indentation of 12 spaces but found 6 indent 69:1 error Expected indentation of 16 spaces but found 8 indent 70:1 error Expected indentation of 20 spaces but found 10 indent 71:1 error Expected indentation of 16 spaces but found 8 indent 72:1 error Expected indentation of 16 spaces but found 8 indent 73:1 error Expected indentation of 12 spaces but found 6 indent 74:1 error Expected indentation of 4 spaces but found 2 indent 77:1 error Expected indentation of 4 spaces but found 2 indent 78:1 error Expected indentation of 4 spaces but found 2 indent 82:1 error Expected indentation of 4 spaces but found 2 indent 83:1 error Expected indentation of 4 spaces but found 2 indent 90:1 error Expected indentation of 4 spaces but found 2 indent 91:1 error Expected indentation of 4 spaces but found 2 indent ? 66 problems (66 errors, 0 warnings) 64 errors and 0 warnings potentially fixable with the `--fix` option. ERROR in ./modules/dataquery/jsx/react.tabs.js Module Error (from ./node_modules/eslint-loader/index.js): /var/www/loris/modules/dataquery/jsx/react.tabs.js 10:8 error 'React' is defined but never used no-unused-vars 18:1 error Expected indentation of 4 spaces but found 2 indent 19:1 error Expected indentation of 8 spaces but found 4 indent 20:1 error Expected indentation of 8 spaces but found 4 indent 22:1 error Expected indentation of 4 spaces but found 2 indent 24:1 error Expected indentation of 4 spaces but found 2 indent 25:1 error Expected indentation of 8 spaces but found 4 indent 26:1 error Expected indentation of 12 spaces but found 6 indent 27:1 error Expected indentation of 16 spaces but found 8 indent 29:1 error Expected indentation of 16 spaces but found 8 indent 30:1 error Expected indentation of 16 spaces but found 8 indent 31:1 error Expected indentation of 20 spaces but found 10 indent 32:1 error Expected indentation of 20 spaces but found 10 indent 33:1 error Expected indentation of 20 spaces but found 10 indent 34:1 error Expected indentation of 16 spaces but found 8 indent 35:1 error Expected indentation of 12 spaces but found 6 indent 36:1 error Expected indentation of 8 spaces but found 4 indent 37:1 error Expected indentation of 4 spaces but found 2 indent 44:1 error Expected indentation of 4 spaces but found 2 indent 45:1 error Expected indentation of 8 spaces but found 4 indent 46:1 error Expected indentation of 8 spaces but found 4 indent 47:1 error Expected indentation of 4 spaces but found 2 indent 49:1 error Expected indentation of 4 spaces but found 2 indent 50:1 error Expected indentation of 8 spaces but found 4 indent 51:1 error Expected indentation of 8 spaces but found 4 indent 52:1 error Expected indentation of 12 spaces but found 6 indent 52:29 error Missing semicolon semi 53:1 error Expected indentation of 8 spaces but found 4 indent 54:1 error Expected indentation of 8 spaces but found 4 indent 55:1 error Expected indentation of 12 spaces but found 6 indent 56:1 error Expected indentation of 16 spaces but found 8 indent 57:1 error Expected indentation of 20 spaces but found 10 indent 58:1 error Expected indentation of 16 spaces but found 8 indent 59:1 error Expected indentation of 12 spaces but found 6 indent 60:1 error Expected indentation of 8 spaces but found 4 indent 61:1 error Expected indentation of 8 spaces but found 4 indent 62:1 error Expected indentation of 12 spaces but found 6 indent 63:1 error Expected indentation of 16 spaces but found 8 indent 64:1 error Expected indentation of 16 spaces but found 8 indent 65:1 error Expected indentation of 12 spaces but found 6 indent 66:1 error Expected indentation of 8 spaces but found 4 indent 67:1 error Expected indentation of 4 spaces but found 2 indent 74:1 error Expected indentation of 4 spaces but found 2 indent 75:1 error Expected indentation of 8 spaces but found 4 indent 76:1 error Expected indentation of 8 spaces but found 4 indent 77:1 error Expected indentation of 4 spaces but found 2 indent 79:1 error Expected indentation of 4 spaces but found 2 indent 80:1 error Expected indentation of 8 spaces but found 4 indent 81:1 error Expected indentation of 12 spaces but found 6 indent 82:1 error Expected indentation of 16 spaces but found 8 indent 83:1 error Expected indentation of 16 spaces but found 8 indent 84:1 error Expected indentation of 16 spaces but found 8 indent 85:1 error Expected indentation of 16 spaces but found 8 indent 86:1 error Expected indentation of 12 spaces but found 6 indent 87:1 error Expected indentation of 16 spaces but found 8 indent 88:1 error Expected indentation of 16 spaces but found 8 indent 89:1 error Expected indentation of 16 spaces but found 8 indent 90:1 error Expected indentation of 20 spaces but found 10 indent 91:1 error Expected indentation of 20 spaces but found 10 indent 92:1 error Expected indentation of 20 spaces but found 10 indent 93:1 error Expected indentation of 20 spaces but found 10 indent 94:1 error Expected indentation of 20 spaces but found 10 indent 95:1 error Expected indentation of 20 spaces but found 10 indent 96:1 error Expected indentation of 20 spaces but found 10 indent 97:1 error Expected indentation of 20 spaces but found 10 indent 98:1 error Expected indentation of 20 spaces but found 10 indent 99:1 error Expected indentation of 20 spaces but found 10 indent 100:1 error Expected indentation of 20 spaces but found 10 indent 101:1 error Expected indentation of 20 spaces but found 10 indent 102:1 error Expected indentation of 16 spaces but found 8 indent 103:1 error Expected indentation of 12 spaces but found 6 indent 104:1 error Expected indentation of 8 spaces but found 4 indent 105:1 error Expected indentation of 4 spaces but found 2 indent 112:1 error Expected indentation of 4 spaces but found 2 indent 113:1 error Expected indentation of 8 spaces but found 4 indent 114:1 error Expected indentation of 8 spaces but found 4 indent 115:1 error Expected indentation of 4 spaces but found 2 indent 117:1 error Expected indentation of 4 spaces but found 2 indent 118:1 error Expected indentation of 8 spaces but found 4 indent 119:1 error Expected indentation of 12 spaces but found 6 indent 120:1 error Expected indentation of 16 spaces but found 8 indent 121:1 error Expected indentation of 16 spaces but found 8 indent 122:1 error Expected indentation of 16 spaces but found 8 indent 123:1 error Expected indentation of 12 spaces but found 6 indent 124:1 error Expected indentation of 16 spaces but found 8 indent 125:1 error Expected indentation of 20 spaces but found 10 indent 126:1 error Expected indentation of 20 spaces but found 10 indent 127:1 error Expected indentation of 20 spaces but found 10 indent 128:1 error Expected indentation of 20 spaces but found 10 indent 129:1 error Expected indentation of 20 spaces but found 10 indent 130:1 error Expected indentation of 20 spaces but found 10 indent 131:1 error Expected indentation of 16 spaces but found 8 indent 132:1 error Expected indentation of 12 spaces but found 6 indent 133:1 error Expected indentation of 8 spaces but found 4 indent 134:1 error Expected indentation of 4 spaces but found 2 indent 141:1 error Expected indentation of 4 spaces but found 2 indent 142:1 error Expected indentation of 8 spaces but found 4 indent 143:1 error Expected indentation of 8 spaces but found 4 indent 144:1 error Expected indentation of 4 spaces but found 2 indent 146:1 error Expected indentation of 4 spaces but found 2 indent 147:1 error Expected indentation of 8 spaces but found 4 indent 148:1 error Expected indentation of 12 spaces but found 6 indent 149:1 error Expected indentation of 16 spaces but found 8 indent 150:1 error Expected indentation of 20 spaces but found 23 indent 151:1 error Expected indentation of 20 spaces but found 23 indent 152:1 error Expected indentation of 20 spaces but found 23 indent 153:1 error Expected indentation of 20 spaces but found 23 indent 154:1 error Expected indentation of 16 spaces but found 8 indent 155:1 error Expected indentation of 12 spaces but found 6 indent 156:1 error Expected indentation of 8 spaces but found 4 indent 157:1 error Expected indentation of 4 spaces but found 2 indent 164:1 error Expected indentation of 4 spaces but found 2 indent 165:1 error Expected indentation of 8 spaces but found 4 indent 166:1 error Expected indentation of 8 spaces but found 4 indent 167:1 error Expected indentation of 12 spaces but found 6 indent 168:1 error Expected indentation of 8 spaces but found 4 indent 169:1 error Expected indentation of 8 spaces but found 4 indent 170:1 error Expected indentation of 8 spaces but found 4 indent 171:1 error Expected indentation of 8 spaces but found 4 indent 172:1 error Expected indentation of 8 spaces but found 4 indent 173:1 error Expected indentation of 8 spaces but found 4 indent 174:1 error Expected indentation of 4 spaces but found 2 indent 176:1 error Expected indentation of 4 spaces but found 2 indent 177:1 error Expected indentation of 8 spaces but found 4 indent 178:1 error Expected indentation of 4 spaces but found 2 indent 180:1 error Expected indentation of 4 spaces but found 2 indent 182:1 error Expected indentation of 8 spaces but found 4 indent 183:1 error Expected indentation of 4 spaces but found 2 indent 185:1 error Expected indentation of 4 spaces but found 2 indent 188:1 error Expected indentation of 8 spaces but found 4 indent 189:1 error Expected indentation of 12 spaces but found 6 indent 191:1 error Expected indentation of 8 spaces but found 4 indent 192:1 error Expected indentation of 12 spaces but found 6 indent 193:1 error Expected indentation of 8 spaces but found 4 indent 195:1 error Expected indentation of 8 spaces but found 4 indent 197:1 error Expected indentation of 8 spaces but found 4 indent 198:1 error Expected indentation of 8 spaces but found 4 indent 199:1 error Expected indentation of 8 spaces but found 4 indent 200:1 error Expected indentation of 8 spaces but found 4 indent 201:1 error Expected indentation of 4 spaces but found 2 indent 203:1 error Expected indentation of 4 spaces but found 2 indent 206:1 error Expected indentation of 8 spaces but found 4 indent 207:1 error Expected indentation of 12 spaces but found 6 indent 208:1 error Expected indentation of 12 spaces but found 6 indent 210:1 error Expected indentation of 8 spaces but found 4 indent 211:1 error Expected indentation of 12 spaces but found 6 indent 212:1 error Expected indentation of 8 spaces but found 4 indent 215:1 error Expected indentation of 8 spaces but found 4 indent 217:1 error Expected indentation of 8 spaces but found 4 indent 218:1 error Expected indentation of 8 spaces but found 4 indent 219:1 error Expected indentation of 8 spaces but found 4 indent 220:1 error Expected indentation of 8 spaces but found 4 indent 221:1 error Expected indentation of 8 spaces but found 4 indent 222:1 error Expected indentation of 8 spaces but found 4 indent 223:1 error Expected indentation of 8 spaces but found 4 indent 224:1 error Expected indentation of 8 spaces but found 4 indent 225:1 error Expected indentation of 8 spaces but found 4 indent 226:1 error Expected indentation of 4 spaces but found 2 indent 228:1 error Expected indentation of 4 spaces but found 2 indent 231:1 error Expected indentation of 8 spaces but found 4 indent 231:9 error 'zip' is assigned a value but never used no-unused-vars 231:19 error 'JSZip' is not defined no-undef 232:1 error Expected indentation of 12 spaces but found 6 indent 232:7 error 'i' is assigned a value but never used no-unused-vars 233:1 error Expected indentation of 12 spaces but found 6 indent 234:1 error Expected indentation of 12 spaces but found 6 indent 234:7 error 'CompleteMask' is assigned a value but never used no-unused-vars 235:1 error Expected indentation of 12 spaces but found 6 indent 236:1 error Expected indentation of 12 spaces but found 6 indent 237:1 error Expected indentation of 12 spaces but found 6 indent 237:7 error 'multiLinkHandler' is assigned a value but never used no-unused-vars 238:1 error Expected indentation of 16 spaces but found 8 indent 239:1 error Expected indentation of 20 spaces but found 10 indent 240:1 error Expected indentation of 24 spaces but found 12 indent 241:1 error Expected indentation of 24 spaces but found 12 indent 243:1 error Expected indentation of 20 spaces but found 10 indent 244:1 error Expected indentation of 20 spaces but found 10 indent 246:1 error Expected indentation of 20 spaces but found 10 indent 247:1 error Expected indentation of 20 spaces but found 10 indent 248:1 error Expected indentation of 20 spaces but found 10 indent 249:1 error Expected indentation of 20 spaces but found 10 indent 251:1 error Expected indentation of 20 spaces but found 10 indent 252:1 error Expected indentation of 16 spaces but found 8 indent 253:1 error Expected indentation of 12 spaces but found 6 indent 255:1 error Expected indentation of 8 spaces but found 4 indent 256:1 error Expected indentation of 8 spaces but found 4 indent 257:1 error Expected indentation of 8 spaces but found 4 indent 259:1 error Expected indentation of 8 spaces but found 4 indent 260:1 error Expected indentation of 12 spaces but found 6 indent 260:31 error 'loris' is not defined no-undef 261:1 error Expected indentation of 12 spaces but found 6 indent 262:1 error Expected indentation of 16 spaces but found 8 indent 263:1 error Expected indentation of 20 spaces but found 10 indent 264:1 error Expected indentation of 20 spaces but found 10 indent 265:1 error Expected indentation of 20 spaces but found 10 indent 266:1 error Expected indentation of 20 spaces but found 10 indent 267:1 error Expected indentation of 20 spaces but found 10 indent 268:1 error Expected indentation of 16 spaces but found 8 indent 269:1 error Expected indentation of 20 spaces but found 10 indent 270:1 error Expected indentation of 20 spaces but found 10 indent 271:1 error Expected indentation of 20 spaces but found 10 indent 272:1 error Expected indentation of 20 spaces but found 10 indent 273:1 error Expected indentation of 20 spaces but found 10 indent 274:1 error Expected indentation of 20 spaces but found 10 indent 274:11 error Unnecessary semicolon no-extra-semi 275:1 error Expected indentation of 20 spaces but found 10 indent 277:1 error Expected indentation of 20 spaces but found 10 indent 278:1 error Expected indentation of 20 spaces but found 10 indent 279:1 error Expected indentation of 20 spaces but found 10 indent 280:1 error Expected indentation of 20 spaces but found 10 indent 281:1 error Expected indentation of 20 spaces but found 10 indent 282:1 error Expected indentation of 20 spaces but found 10 indent 284:1 error Expected indentation of 16 spaces but found 8 indent 285:1 error Expected indentation of 20 spaces but found 10 indent 286:1 error Expected indentation of 20 spaces but found 10 indent 287:1 error Expected indentation of 16 spaces but found 8 indent 288:1 error Expected indentation of 20 spaces but found 10 indent 289:1 error Expected indentation of 24 spaces but found 12 indent 289:13 error '$' is not defined no-undef 290:1 error Expected indentation of 20 spaces but found 10 indent 292:1 error Expected indentation of 20 spaces but found 10 indent 293:1 error Expected indentation of 24 spaces but found 12 indent 294:1 error Expected indentation of 24 spaces but found 12 indent 296:1 error Expected indentation of 24 spaces but found 12 indent 296:29 error '$' is not defined no-undef 297:1 error Expected indentation of 24 spaces but found 12 indent 298:1 error Expected indentation of 28 spaces but found 14 indent 299:1 error Expected indentation of 28 spaces but found 14 indent 300:1 error Expected indentation of 28 spaces but found 14 indent 301:1 error Expected indentation of 28 spaces but found 14 indent 302:1 error Expected indentation of 28 spaces but found 14 indent 303:1 error Expected indentation of 24 spaces but found 12 indent 304:1 error Expected indentation of 20 spaces but found 10 indent 305:1 error Expected indentation of 20 spaces but found 10 indent 306:1 error Expected indentation of 20 spaces but found 10 indent 307:1 error Expected indentation of 20 spaces but found 10 indent 309:1 error Expected indentation of 16 spaces but found 8 indent 310:1 error Expected indentation of 20 spaces but found 10 indent 311:1 error Expected indentation of 20 spaces but found 10 indent 312:1 error Expected indentation of 16 spaces but found 8 indent 314:1 error Expected indentation of 12 spaces but found 6 indent 316:1 error Expected indentation of 12 spaces but found 6 indent 316:57 error 'loris' is not defined no-undef 317:1 error Expected indentation of 8 spaces but found 4 indent 318:1 error Expected indentation of 4 spaces but found 2 indent 320:1 error Expected indentation of 4 spaces but found 2 indent 321:1 error Expected indentation of 8 spaces but found 4 indent 321:9 error 'downloadData' is defined but never used no-unused-vars 322:1 error Expected indentation of 8 spaces but found 4 indent 323:1 error Expected indentation of 12 spaces but found 6 indent 324:1 error Expected indentation of 16 spaces but found 8 indent 325:1 error Expected indentation of 20 spaces but found 10 indent 326:1 error Expected indentation of 20 spaces but found 10 indent 327:1 error Expected indentation of 16 spaces but found 8 indent 328:1 error Expected indentation of 16 spaces but found 8 indent 329:1 error Expected indentation of 16 spaces but found 8 indent 330:1 error Expected indentation of 20 spaces but found 10 indent 331:1 error Expected indentation of 16 spaces but found 8 indent 332:1 error Expected indentation of 12 spaces but found 6 indent 333:1 error Expected indentation of 8 spaces but found 4 indent 334:1 error Expected indentation of 8 spaces but found 4 indent 335:1 error Expected indentation of 8 spaces but found 4 indent 336:1 error Expected indentation of 12 spaces but found 6 indent 337:1 error Expected indentation of 16 spaces but found 8 indent 338:1 error Expected indentation of 12 spaces but found 6 indent 339:1 error Expected indentation of 12 spaces but found 6 indent 340:1 error Expected indentation of 12 spaces but found 6 indent 341:1 error Expected indentation of 16 spaces but found 8 indent 342:1 error Expected indentation of 20 spaces but found 10 indent 343:1 error Expected indentation of 24 spaces but found 12 indent 344:1 error Expected indentation of 20 spaces but found 10 indent 345:1 error Expected indentation of 16 spaces but found 8 indent 346:1 error Expected indentation of 12 spaces but found 6 indent 347:1 error Expected indentation of 16 spaces but found 8 indent 348:1 error Expected indentation of 20 spaces but found 10 indent 349:1 error Expected indentation of 24 spaces but found 12 indent 350:1 error Expected indentation of 24 spaces but found 12 indent 351:1 error Expected indentation of 24 spaces but found 12 indent 352:1 error Expected indentation of 20 spaces but found 10 indent 353:1 error Expected indentation of 16 spaces but found 8 indent 354:1 error Expected indentation of 12 spaces but found 6 indent 356:1 error Expected indentation of 8 spaces but found 4 indent 357:1 error Expected indentation of 8 spaces but found 4 indent 358:1 error Expected indentation of 12 spaces but found 6 indent 359:1 error Expected indentation of 16 spaces but found 8 indent 360:1 error Expected indentation of 16 spaces but found 8 indent 361:1 error Expected indentation of 16 spaces but found 8 indent 362:1 error Expected indentation of 12 spaces but found 6 indent 363:1 error Expected indentation of 16 spaces but found 8 indent 364:1 error Expected indentation of 16 spaces but found 8 indent 365:1 error Expected indentation of 16 spaces but found 8 indent 366:1 error Expected indentation of 16 spaces but found 8 indent 367:1 error Expected indentation of 20 spaces but found 10 indent 368:1 error Expected indentation of 20 spaces but found 10 indent 369:1 error Expected indentation of 24 spaces but found 12 indent 370:1 error Expected indentation of 28 spaces but found 14 indent 371:1 error Expected indentation of 32 spaces but found 16 indent 372:1 error Expected indentation of 32 spaces but found 16 indent 373:1 error Expected indentation of 28 spaces but found 14 indent 374:1 error Expected indentation of 28 spaces but found 14 indent 375:1 error Expected indentation of 32 spaces but found 16 indent 376:1 error Expected indentation of 36 spaces but found 18 indent 377:1 error Expected indentation of 40 spaces but found 20 indent 378:1 error Expected indentation of 36 spaces but found 18 indent 379:1 error Expected indentation of 32 spaces but found 16 indent 380:1 error Expected indentation of 32 spaces but found 16 indent 381:1 error Expected indentation of 36 spaces but found 18 indent 382:1 error Expected indentation of 40 spaces but found 20 indent 383:1 error Expected indentation of 36 spaces but found 18 indent 384:1 error Expected indentation of 32 spaces but found 16 indent 385:1 error Expected indentation of 28 spaces but found 14 indent 386:1 error Expected indentation of 24 spaces but found 12 indent 387:1 error Expected indentation of 20 spaces but found 10 indent 388:1 error Expected indentation of 16 spaces but found 8 indent 389:1 error Expected indentation of 16 spaces but found 8 indent 390:1 error Expected indentation of 20 spaces but found 10 indent 391:1 error Expected indentation of 20 spaces but found 10 indent 392:1 error Expected indentation of 20 spaces but found 10 indent 393:1 error Expected indentation of 20 spaces but found 10 indent 394:1 error Expected indentation of 16 spaces but found 8 indent 395:1 error Expected indentation of 12 spaces but found 6 indent 396:1 error Expected indentation of 8 spaces but found 4 indent 397:1 error Expected indentation of 4 spaces but found 2 indent 400:1 error Expected indentation of 4 spaces but found 2 indent 409:1 error Expected indentation of 4 spaces but found 2 indent 410:1 error Expected indentation of 8 spaces but found 4 indent 411:1 error Expected indentation of 8 spaces but found 4 indent 412:1 error Expected indentation of 8 spaces but found 4 indent 413:1 error Expected indentation of 8 spaces but found 4 indent 414:1 error Expected indentation of 8 spaces but found 4 indent 415:1 error Expected indentation of 4 spaces but found 2 indent 417:1 error Expected indentation of 4 spaces but found 2 indent 418:1 error Expected indentation of 8 spaces but found 4 indent 419:1 error Expected indentation of 12 spaces but found 6 indent 419:15 error 'jStat' is not defined no-undef 420:1 error Expected indentation of 12 spaces but found 6 indent 421:1 error Expected indentation of 12 spaces but found 6 indent 422:1 error Expected indentation of 12 spaces but found 6 indent 422:7 error 'interim' is assigned a value but never used no-unused-vars 423:1 error Expected indentation of 12 spaces but found 6 indent 424:1 error Expected indentation of 12 spaces but found 6 indent 425:1 error Expected indentation of 12 spaces but found 6 indent 426:1 error Expected indentation of 12 spaces but found 6 indent 427:1 error Expected indentation of 12 spaces but found 6 indent 429:1 error Expected indentation of 8 spaces but found 4 indent 430:1 error Expected indentation of 12 spaces but found 6 indent 431:1 error Expected indentation of 12 spaces but found 6 indent 432:1 error Expected indentation of 12 spaces but found 6 indent 433:1 error Expected indentation of 12 spaces but found 6 indent 434:1 error Expected indentation of 8 spaces but found 4 indent 436:1 error Expected indentation of 8 spaces but found 4 indent 438:1 error Expected indentation of 8 spaces but found 4 indent 439:1 error Expected indentation of 4 spaces but found 2 indent 441:1 error Expected indentation of 4 spaces but found 2 indent 442:1 error Expected indentation of 8 spaces but found 4 indent 444:1 error Expected indentation of 8 spaces but found 4 indent 445:1 error Expected indentation of 12 spaces but found 6 indent 446:1 error Expected indentation of 16 spaces but found 8 indent 447:1 error Expected indentation of 20 spaces but found 10 indent 448:1 error Expected indentation of 16 spaces but found 8 indent 449:1 error Expected indentation of 12 spaces but found 6 indent 450:1 error Expected indentation of 12 spaces but found 6 indent 451:1 error Expected indentation of 16 spaces but found 8 indent 452:1 error Expected indentation of 20 spaces but found 10 indent 453:1 error Expected indentation of 16 spaces but found 8 indent 454:1 error Expected indentation of 12 spaces but found 6 indent 455:1 error Expected indentation of 8 spaces but found 4 indent 456:1 error Expected indentation of 8 spaces but found 4 indent 457:1 error Expected indentation of 4 spaces but found 2 indent 459:1 error Expected indentation of 4 spaces but found 2 indent 460:1 error Expected indentation of 8 spaces but found 4 indent 461:1 error Expected indentation of 12 spaces but found 6 indent 462:1 error Expected indentation of 12 spaces but found 6 indent 463:1 error Expected indentation of 12 spaces but found 6 indent 464:1 error Expected indentation of 12 spaces but found 6 indent 465:1 error Expected indentation of 12 spaces but found 6 indent 466:1 error Expected indentation of 12 spaces but found 6 indent 467:1 error Expected indentation of 12 spaces but found 6 indent 468:1 error Expected indentation of 12 spaces but found 6 indent 469:1 error Expected indentation of 12 spaces but found 6 indent 470:1 error Expected indentation of 12 spaces but found 6 indent 471:1 error Expected indentation of 12 spaces but found 6 indent 472:1 error Expected indentation of 12 spaces but found 6 indent 473:1 error Expected indentation of 12 spaces but found 6 indent 474:1 error Expected indentation of 12 spaces but found 6 indent 475:1 error Expected indentation of 12 spaces but found 6 indent 476:1 error Expected indentation of 12 spaces but found 6 indent 477:1 error Expected indentation of 12 spaces but found 6 indent 477:7 error 'label' is assigned a value but never used no-unused-vars 478:1 error Expected indentation of 12 spaces but found 6 indent 479:1 error Expected indentation of 16 spaces but found 8 indent 480:1 error Expected indentation of 12 spaces but found 6 indent 481:1 error Expected indentation of 12 spaces but found 6 indent 483:1 error Expected indentation of 8 spaces but found 4 indent 484:1 error Expected indentation of 12 spaces but found 6 indent 485:1 error Expected indentation of 12 spaces but found 6 indent 486:1 error Expected indentation of 12 spaces but found 6 indent 487:1 error Expected indentation of 12 spaces but found 6 indent 488:1 error Expected indentation of 16 spaces but found 8 indent 489:1 error Expected indentation of 16 spaces but found 8 indent 490:1 error Expected indentation of 20 spaces but found 10 indent 491:1 error Expected indentation of 16 spaces but found 8 indent 492:1 error Expected indentation of 16 spaces but found 8 indent 493:1 error Expected indentation of 12 spaces but found 6 indent 494:1 error Expected indentation of 8 spaces but found 4 indent 496:1 error Expected indentation of 8 spaces but found 4 indent 497:1 error Expected indentation of 12 spaces but found 6 indent 498:1 error Expected indentation of 12 spaces but found 6 indent 499:1 error Expected indentation of 12 spaces but found 6 indent 500:1 error Expected indentation of 12 spaces but found 6 indent 501:1 error Expected indentation of 12 spaces but found 6 indent 502:1 error Expected indentation of 12 spaces but found 6 indent 504:1 error Expected indentation of 12 spaces but found 6 indent 504:7 error '$' is not defined no-undef 506:1 error Expected indentation of 16 spaces but found 8 indent 507:1 error Expected indentation of 16 spaces but found 8 indent 508:1 error Expected indentation of 16 spaces but found 8 indent 509:1 error Expected indentation of 12 spaces but found 6 indent 510:1 error Expected indentation of 12 spaces but found 8 indent 511:1 error Expected indentation of 16 spaces but found 10 indent 512:1 error Expected indentation of 16 spaces but found 10 indent 512:17 error 'jStat' is not defined no-undef 513:1 error Expected indentation of 16 spaces but found 10 indent 514:1 error Expected indentation of 12 spaces but found 8 indent 515:1 error Expected indentation of 8 spaces but found 4 indent 516:1 error Expected indentation of 12 spaces but found 6 indent 517:1 error Expected indentation of 12 spaces but found 6 indent 518:1 error Expected indentation of 12 spaces but found 6 indent 519:1 error Expected indentation of 12 spaces but found 6 indent 521:1 error Expected indentation of 12 spaces but found 6 indent 522:1 error Expected indentation of 16 spaces but found 8 indent 523:1 error Expected indentation of 20 spaces but found 10 indent 523:43 error Strings must use singlequote quotes 523:98 error Strings must use singlequote quotes 524:1 error Expected indentation of 20 spaces but found 10 indent 525:1 error Expected indentation of 24 spaces but found 12 indent 526:1 error Expected indentation of 24 spaces but found 12 indent 527:1 error Expected indentation of 24 spaces but found 12 indent 528:1 error Expected indentation of 24 spaces but found 12 indent 529:1 error Expected indentation of 20 spaces but found 10 indent 530:1 error Expected indentation of 20 spaces but found 10 indent 531:1 error Expected indentation of 20 spaces but found 10 indent 532:1 error Expected indentation of 20 spaces but found 10 indent 533:1 error Expected indentation of 20 spaces but found 10 indent 534:1 error Expected indentation of 20 spaces but found 10 indent 535:1 error Expected indentation of 24 spaces but found 12 indent 536:1 error Expected indentation of 24 spaces but found 12 indent 537:1 error Expected indentation of 24 spaces but found 12 indent 537:19 error 'jStat' is not defined no-undef 538:1 error Expected indentation of 24 spaces but found 12 indent 539:1 error Expected indentation of 20 spaces but found 10 indent 540:1 error Expected indentation of 20 spaces but found 10 indent 541:1 error Expected indentation of 16 spaces but found 8 indent 542:1 error Expected indentation of 12 spaces but found 6 indent 543:1 error Expected indentation of 12 spaces but found 6 indent 543:7 error '$' is not defined no-undef 544:1 error Expected indentation of 8 spaces but found 4 indent 546:1 error Expected indentation of 8 spaces but found 4 indent 546:5 error '$' is not defined no-undef 547:1 error Expected indentation of 8 spaces but found 4 indent 547:5 error '$' is not defined no-undef 547:52 error 'jStat' is not defined no-undef 547:101 error 'jStat' is not defined no-undef 548:1 error Expected indentation of 4 spaces but found 2 indent 550:1 error Expected indentation of 4 spaces but found 2 indent 551:1 error Expected indentation of 8 spaces but found 4 indent 552:1 error Expected indentation of 16 spaces but found 8 indent 552:9 error Unexpected console statement no-console 553:1 error Expected indentation of 16 spaces but found 8 indent 554:1 error Expected indentation of 20 spaces but found 10 indent 555:1 error Expected indentation of 24 spaces but found 12 indent 556:1 error Expected indentation of 20 spaces but found 10 indent 557:1 error Expected indentation of 16 spaces but found 8 indent 558:1 error Expected indentation of 12 spaces but found 6 indent 559:1 error Expected indentation of 12 spaces but found 6 indent 560:1 error Expected indentation of 16 spaces but found 8 indent 561:1 error Expected indentation of 16 spaces but found 8 indent 562:1 error Expected indentation of 12 spaces but found 6 indent 563:1 error Expected indentation of 8 spaces but found 4 indent 564:1 error Expected indentation of 12 spaces but found 6 indent 565:1 error Expected indentation of 16 spaces but found 8 indent 567:1 error Expected indentation of 16 spaces but found 8 indent 569:1 error Expected indentation of 16 spaces but found 8 indent 570:1 error Expected indentation of 16 spaces but found 8 indent 571:1 error Expected indentation of 20 spaces but found 10 indent 572:1 error Expected indentation of 24 spaces but found 12 indent 573:1 error Expected indentation of 24 spaces but found 12 indent 574:1 error Expected indentation of 20 spaces but found 10 indent 575:1 error Expected indentation of 16 spaces but found 8 indent 577:1 error Expected indentation of 16 spaces but found 8 indent 579:1 error Expected indentation of 16 spaces but found 8 indent 580:1 error Expected indentation of 16 spaces but found 8 indent 581:1 error Expected indentation of 20 spaces but found 10 indent 582:1 error Expected indentation of 24 spaces but found 12 indent 583:1 error Expected indentation of 24 spaces but found 12 indent 584:1 error Expected indentation of 20 spaces but found 10 indent 585:1 error Expected indentation of 16 spaces but found 8 indent 587:1 error Expected indentation of 16 spaces but found 8 indent 589:1 error Expected indentation of 16 spaces but found 8 indent 590:1 error Expected indentation of 16 spaces but found 8 indent 591:1 error Expected indentation of 20 spaces but found 10 indent 592:1 error Expected indentation of 24 spaces but found 12 indent 593:1 error Expected indentation of 24 spaces but found 12 indent 594:1 error Expected indentation of 20 spaces but found 10 indent 595:1 error Expected indentation of 16 spaces but found 8 indent 596:1 error Expected indentation of 16 spaces but found 8 indent 597:1 error Expected indentation of 16 spaces but found 8 indent 598:1 error Expected indentation of 16 spaces but found 8 indent 599:1 error Expected indentation of 16 spaces but found 8 indent 600:1 error Expected indentation of 20 spaces but found 10 indent 601:1 error Expected indentation of 24 spaces but found 10 indent 602:1 error Expected indentation of 28 spaces but found 12 indent 603:1 error Expected indentation of 28 spaces but found 12 indent 604:1 error Expected indentation of 24 spaces but found 10 indent 605:1 error Expected indentation of 20 spaces but found 10 indent 606:1 error Expected indentation of 20 spaces but found 10 indent 607:1 error Expected indentation of 20 spaces but found 10 indent 608:1 error Expected indentation of 16 spaces but found 8 indent 609:1 error Expected indentation of 12 spaces but found 6 indent 610:1 error Expected indentation of 8 spaces but found 4 indent 611:1 error Expected indentation of 4 spaces but found 2 indent 618:1 error Expected indentation of 4 spaces but found 2 indent 619:1 error Expected indentation of 8 spaces but found 4 indent 620:1 error Expected indentation of 8 spaces but found 4 indent 621:1 error Expected indentation of 12 spaces but found 6 indent 622:1 error Expected indentation of 8 spaces but found 4 indent 623:1 error Expected indentation of 4 spaces but found 2 indent 625:1 error Expected indentation of 4 spaces but found 2 indent 626:1 error Expected indentation of 8 spaces but found 4 indent 627:1 error Expected indentation of 12 spaces but found 6 indent 628:1 error Expected indentation of 8 spaces but found 4 indent 629:1 error Expected indentation of 8 spaces but found 4 indent 630:1 error Expected indentation of 8 spaces but found 4 indent 631:1 error Expected indentation of 8 spaces but found 4 indent 632:1 error Expected indentation of 8 spaces but found 4 indent 633:1 error Expected indentation of 8 spaces but found 4 indent 634:1 error Expected indentation of 12 spaces but found 6 indent 634:11 error 'content' is assigned a value but never used no-unused-vars 635:1 error Expected indentation of 12 spaces but found 6 indent 636:1 error Expected indentation of 8 spaces but found 4 indent 637:1 error Expected indentation of 12 spaces but found 6 indent 637:19 error 'jStat' is not defined no-undef 638:1 error Expected indentation of 16 spaces but found 8 indent 639:1 error Expected indentation of 16 spaces but found 8 indent 640:1 error Expected indentation of 16 spaces but found 8 indent 641:1 error Expected indentation of 16 spaces but found 8 indent 642:1 error Expected indentation of 16 spaces but found 8 indent 643:1 error Expected indentation of 16 spaces but found 8 indent 644:1 error Expected indentation of 16 spaces but found 8 indent 645:1 error Expected indentation of 16 spaces but found 8 indent 648:1 error Expected indentation of 12 spaces but found 6 indent 649:1 error Expected indentation of 16 spaces but found 8 indent 650:1 error Expected indentation of 20 spaces but found 10 indent 651:1 error Expected indentation of 20 spaces but found 10 indent 652:1 error Expected indentation of 20 spaces but found 10 indent 653:1 error Expected indentation of 20 spaces but found 10 indent 654:1 error Expected indentation of 20 spaces but found 10 indent 655:1 error Expected indentation of 20 spaces but found 10 indent 656:1 error Expected indentation of 20 spaces but found 10 indent 657:1 error Expected indentation of 20 spaces but found 10 indent 658:1 error Expected indentation of 20 spaces but found 10 indent 659:1 error Expected indentation of 20 spaces but found 10 indent 660:1 error Expected indentation of 16 spaces but found 8 indent 661:1 error Expected indentation of 12 spaces but found 6 indent 663:1 error Expected indentation of 12 spaces but found 6 indent 664:1 error Expected indentation of 16 spaces but found 8 indent 665:1 error Expected indentation of 20 spaces but found 10 indent 666:1 error Expected indentation of 24 spaces but found 10 indent 667:1 error Expected indentation of 28 spaces but found 12 indent 668:1 error Expected indentation of 28 spaces but found 12 indent 669:1 error Expected indentation of 28 spaces but found 12 indent 670:1 error Expected indentation of 28 spaces but found 12 indent 671:1 error Expected indentation of 28 spaces but found 12 indent 672:1 error Expected indentation of 28 spaces but found 12 indent 673:1 error Expected indentation of 28 spaces but found 12 indent 674:1 error Expected indentation of 28 spaces but found 12 indent 675:1 error Expected indentation of 28 spaces but found 12 indent 676:1 error Expected indentation of 28 spaces but found 12 indent 677:1 error Expected indentation of 24 spaces but found 10 indent 678:1 error Expected indentation of 20 spaces but found 10 indent 679:1 error Expected indentation of 20 spaces but found 10 indent 680:1 error Expected indentation of 24 spaces but found 10 indent 681:1 error Expected indentation of 20 spaces but found 10 indent 682:1 error Expected indentation of 16 spaces but found 8 indent 683:1 error Expected indentation of 12 spaces but found 6 indent 685:1 error Expected indentation of 12 spaces but found 6 indent 686:1 error Expected indentation of 16 spaces but found 8 indent 687:1 error Expected indentation of 20 spaces but found 10 indent 688:1 error Expected indentation of 20 spaces but found 10 indent 690:1 error Expected indentation of 20 spaces but found 10 indent 691:1 error Expected indentation of 24 spaces but found 12 indent 692:1 error Expected indentation of 24 spaces but found 12 indent 693:1 error Expected indentation of 20 spaces but found 10 indent 694:1 error Expected indentation of 16 spaces but found 8 indent 695:1 error Expected indentation of 12 spaces but found 6 indent 696:1 error Expected indentation of 8 spaces but found 4 indent 697:1 error Expected indentation of 8 spaces but found 4 indent 698:1 error Expected indentation of 12 spaces but found 6 indent 699:1 error Expected indentation of 16 spaces but found 8 indent 700:1 error Expected indentation of 12 spaces but found 6 indent 701:1 error Expected indentation of 8 spaces but found 4 indent 702:1 error Expected indentation of 4 spaces but found 2 indent 705:1 error Expected indentation of 4 spaces but found 2 indent 708:1 error Expected indentation of 4 spaces but found 2 indent 716:1 error Expected indentation of 4 spaces but found 2 indent 717:1 error Expected indentation of 8 spaces but found 4 indent 718:1 error Expected indentation of 8 spaces but found 4 indent 719:1 error Expected indentation of 12 spaces but found 6 indent 720:1 error Expected indentation of 12 spaces but found 6 indent 721:1 error Expected indentation of 8 spaces but found 4 indent 722:1 error Expected indentation of 8 spaces but found 4 indent 723:1 error Expected indentation of 8 spaces but found 4 indent 724:1 error Expected indentation of 8 spaces but found 4 indent 725:1 error Expected indentation of 8 spaces but found 4 indent 726:1 error Expected indentation of 4 spaces but found 2 indent 728:1 error Expected indentation of 4 spaces but found 2 indent 729:1 error Expected indentation of 8 spaces but found 4 indent 730:1 error Expected indentation of 4 spaces but found 2 indent 732:1 error Expected indentation of 4 spaces but found 2 indent 733:1 error Expected indentation of 8 spaces but found 4 indent 734:1 error Expected indentation of 4 spaces but found 2 indent 736:1 error Expected indentation of 4 spaces but found 2 indent 739:1 error Expected indentation of 8 spaces but found 4 indent 740:1 error Expected indentation of 12 spaces but found 6 indent 741:1 error Expected indentation of 8 spaces but found 4 indent 742:1 error Expected indentation of 4 spaces but found 2 indent 744:1 error Expected indentation of 4 spaces but found 2 indent 745:1 error Expected indentation of 8 spaces but found 4 indent 746:1 error Expected indentation of 12 spaces but found 6 indent 747:1 error Expected indentation of 8 spaces but found 4 indent 748:1 error Expected indentation of 4 spaces but found 2 indent 750:1 error Expected indentation of 4 spaces but found 2 indent 751:1 error Expected indentation of 8 spaces but found 4 indent 752:1 error Expected indentation of 12 spaces but found 6 indent 753:1 error Expected indentation of 16 spaces but found 8 indent 754:1 error Expected indentation of 20 spaces but found 10 indent 755:1 error Expected indentation of 24 spaces but found 12 indent 756:1 error Expected indentation of 28 spaces but found 14 indent 757:1 error Expected indentation of 28 spaces but found 14 indent 758:1 error Expected indentation of 24 spaces but found 12 indent 759:1 error Expected indentation of 24 spaces but found 12 indent 760:1 error Expected indentation of 28 spaces but found 14 indent 761:1 error Expected indentation of 28 spaces but found 14 indent 763:1 error Expected indentation of 28 spaces but found 14 indent 764:1 error Expected indentation of 28 spaces but found 14 indent 766:1 error Expected indentation of 24 spaces but found 12 indent 767:1 error Expected indentation of 24 spaces but found 12 indent 768:1 error Expected indentation of 28 spaces but found 14 indent 769:1 error Expected indentation of 28 spaces but found 14 indent 770:1 error Expected indentation of 24 spaces but found 12 indent 771:1 error Expected indentation of 20 spaces but found 10 indent 772:1 error Expected indentation of 16 spaces but found 8 indent 773:1 error Expected indentation of 12 spaces but found 6 indent 774:1 error Expected indentation of 8 spaces but found 4 indent 775:1 error Expected indentation of 4 spaces but found 2 indent 783:1 error Expected indentation of 4 spaces but found 2 indent 784:1 error Expected indentation of 8 spaces but found 4 indent 785:1 error Expected indentation of 8 spaces but found 4 indent 786:1 error Expected indentation of 4 spaces but found 2 indent 788:1 error Expected indentation of 4 spaces but found 2 indent 789:1 error Expected indentation of 8 spaces but found 4 indent 790:1 error Expected indentation of 12 spaces but found 6 indent 791:1 error Expected indentation of 8 spaces but found 4 indent 792:1 error Expected indentation of 12 spaces but found 6 indent 793:1 error Expected indentation of 16 spaces but found 8 indent 793:50 error 'key' is defined but never used no-unused-vars 794:1 error Expected indentation of 20 spaces but found 10 indent 795:1 error Expected indentation of 24 spaces but found 12 indent 796:1 error Expected indentation of 20 spaces but found 10 indent 796:13 error Missing semicolon semi 797:1 error Expected indentation of 16 spaces but found 8 indent 798:1 error Expected indentation of 12 spaces but found 6 indent 799:1 error Expected indentation of 16 spaces but found 8 indent 799:23 error Missing semicolon semi 800:1 error Expected indentation of 12 spaces but found 6 indent 801:1 error Expected indentation of 12 spaces but found 6 indent 802:1 error Expected indentation of 16 spaces but found 8 indent 803:1 error Expected indentation of 20 spaces but found 10 indent 804:1 error Expected indentation of 20 spaces but found 10 indent 805:1 error Expected indentation of 24 spaces but found 12 indent 806:1 error Expected indentation of 20 spaces but found 10 indent 807:1 error Expected indentation of 16 spaces but found 8 indent 808:1 error Expected indentation of 12 spaces but found 6 indent 808:8 error Missing semicolon semi 809:1 error Expected indentation of 8 spaces but found 4 indent 810:1 error Expected indentation of 12 spaces but found 6 indent 811:1 error Expected indentation of 12 spaces but found 6 indent 812:1 error Expected indentation of 16 spaces but found 8 indent 813:1 error Expected indentation of 16 spaces but found 8 indent 814:1 error Expected indentation of 16 spaces but found 10 indent 815:1 error Expected indentation of 20 spaces but found 12 indent 816:1 error Expected indentation of 20 spaces but found 12 indent 817:1 error Expected indentation of 16 spaces but found 10 indent 818:1 error Expected indentation of 20 spaces but found 12 indent 819:1 error Expected indentation of 20 spaces but found 12 indent 820:1 error Expected indentation of 16 spaces but found 10 indent 821:1 error Expected indentation of 20 spaces but found 12 indent 822:1 error Expected indentation of 20 spaces but found 12 indent 823:1 error Expected indentation of 16 spaces but found 10 indent 824:1 error Expected indentation of 20 spaces but found 12 indent 825:1 error Expected indentation of 20 spaces but found 12 indent 826:1 error Expected indentation of 16 spaces but found 10 indent 827:1 error Expected indentation of 20 spaces but found 12 indent 828:1 error Expected indentation of 20 spaces but found 12 indent 829:1 error Expected indentation of 16 spaces but found 8 indent 830:1 error Expected indentation of 16 spaces but found 8 indent 831:1 error Expected indentation of 20 spaces but found 10 indent 832:1 error Expected indentation of 16 spaces but found 8 indent 832:10 error Missing semicolon semi 833:1 error Expected indentation of 12 spaces but found 6 indent 834:1 error Expected indentation of 16 spaces but found 8 indent 835:1 error Expected indentation of 20 spaces but found 10 indent 836:1 error Expected indentation of 16 spaces but found 8 indent 836:10 error Missing semicolon semi 837:1 error Expected indentation of 12 spaces but found 6 indent 838:1 error Expected indentation of 8 spaces but found 4 indent 839:1 error Expected indentation of 8 spaces but found 4 indent 840:1 error Expected indentation of 12 spaces but found 6 indent 841:1 error Expected indentation of 8 spaces but found 4 indent 842:1 error Expected indentation of 4 spaces but found 2 indent 850:1 error Expected indentation of 4 spaces but found 2 indent 851:1 error Expected indentation of 8 spaces but found 4 indent 852:1 error Expected indentation of 8 spaces but found 4 indent 853:1 error Expected indentation of 4 spaces but found 2 indent 855:1 error Expected indentation of 4 spaces but found 2 indent 856:1 error Expected indentation of 8 spaces but found 4 indent 857:1 error Expected indentation of 8 spaces but found 4 indent 858:1 error Expected indentation of 8 spaces but found 4 indent 859:1 error Expected indentation of 12 spaces but found 6 indent 860:1 error Expected indentation of 16 spaces but found 8 indent 861:1 error Expected indentation of 12 spaces but found 6 indent 862:1 error Expected indentation of 8 spaces but found 4 indent 863:1 error Expected indentation of 12 spaces but found 6 indent 864:1 error Expected indentation of 16 spaces but found 8 indent 865:1 error Expected indentation of 20 spaces but found 10 indent 865:25 error Strings must use singlequote quotes 866:1 error Expected indentation of 24 spaces but found 12 indent 867:1 error Expected indentation of 20 spaces but found 10 indent 868:1 error Expected indentation of 24 spaces but found 12 indent 869:1 error Expected indentation of 20 spaces but found 10 indent 870:1 error Expected indentation of 16 spaces but found 8 indent 871:1 error Expected indentation of 12 spaces but found 6 indent 872:1 error Expected indentation of 8 spaces but found 4 indent 874:1 error Expected indentation of 8 spaces but found 4 indent 875:1 error Expected indentation of 12 spaces but found 6 indent 876:1 error Expected indentation of 8 spaces but found 4 indent 878:1 error Expected indentation of 8 spaces but found 4 indent 879:1 error Expected indentation of 12 spaces but found 6 indent 880:1 error Expected indentation of 16 spaces but found 8 indent 881:1 error Expected indentation of 12 spaces but found 6 indent 882:1 error Expected indentation of 16 spaces but found 8 indent 883:1 error Expected indentation of 20 spaces but found 10 indent 884:1 error Expected indentation of 24 spaces but found 12 indent 884:42 error Missing semicolon semi 885:1 error Expected indentation of 20 spaces but found 10 indent 886:1 error Expected indentation of 24 spaces but found 12 indent 886:41 error Missing semicolon semi 887:1 error Expected indentation of 20 spaces but found 10 indent 888:1 error Expected indentation of 20 spaces but found 10 indent 889:1 error Expected indentation of 24 spaces but found 12 indent 890:1 error Expected indentation of 28 spaces but found 14 indent 891:1 error Expected indentation of 32 spaces but found 16 indent 892:1 error Expected indentation of 32 spaces but found 16 indent 893:1 error Expected indentation of 28 spaces but found 14 indent 894:1 error Expected indentation of 24 spaces but found 12 indent 895:1 error Expected indentation of 20 spaces but found 10 indent 896:1 error Expected indentation of 16 spaces but found 8 indent 897:1 error Expected indentation of 20 spaces but found 10 indent 898:1 error Expected indentation of 16 spaces but found 8 indent 899:1 error Expected indentation of 12 spaces but found 6 indent 900:1 error Expected indentation of 16 spaces but found 8 indent 901:1 error Expected indentation of 20 spaces but found 10 indent 902:1 error Expected indentation of 16 spaces but found 8 indent 903:1 error Expected indentation of 20 spaces but found 10 indent 904:1 error Expected indentation of 20 spaces but found 10 indent 905:1 error Expected indentation of 24 spaces but found 12 indent 906:1 error Expected indentation of 28 spaces but found 14 indent 907:1 error Expected indentation of 32 spaces but found 16 indent 908:1 error Expected indentation of 32 spaces but found 16 indent 909:1 error Expected indentation of 28 spaces but found 14 indent 910:1 error Expected indentation of 24 spaces but found 12 indent 911:1 error Expected indentation of 20 spaces but found 10 indent 912:1 error Expected indentation of 16 spaces but found 8 indent 913:1 error Expected indentation of 12 spaces but found 6 indent 914:1 error Expected indentation of 12 spaces but found 6 indent 915:1 error Expected indentation of 16 spaces but found 8 indent 916:1 error Expected indentation of 20 spaces but found 10 indent 917:1 error Expected indentation of 24 spaces but found 12 indent 918:1 error Expected indentation of 28 spaces but found 14 indent 919:1 error Expected indentation of 28 spaces but found 14 indent 920:1 error Expected indentation of 32 spaces but found 16 indent 921:1 error Expected indentation of 28 spaces but found 14 indent 922:1 error Expected indentation of 24 spaces but found 12 indent 923:1 error Expected indentation of 20 spaces but found 10 indent 924:1 error Expected indentation of 16 spaces but found 8 indent 925:1 error Expected indentation of 12 spaces but found 6 indent 926:1 error Expected indentation of 8 spaces but found 4 indent 927:1 error Expected indentation of 8 spaces but found 4 indent 928:1 error Expected indentation of 12 spaces but found 6 indent 929:1 error Expected indentation of 8 spaces but found 4 indent 930:1 error Expected indentation of 8 spaces but found 4 indent 931:1 error Expected indentation of 12 spaces but found 6 indent 932:1 error Expected indentation of 16 spaces but found 8 indent 933:1 error Expected indentation of 16 spaces but found 8 indent 934:1 error Expected indentation of 20 spaces but found 10 indent 935:1 error Expected indentation of 16 spaces but found 8 indent 936:1 error Expected indentation of 16 spaces but found 8 indent 937:1 error Expected indentation of 12 spaces but found 6 indent 938:1 error Expected indentation of 8 spaces but found 4 indent 939:1 error Expected indentation of 4 spaces but found 2 indent 942:1 error Expected indentation of 4 spaces but found 2 indent 943:1 error Expected indentation of 4 spaces but found 2 indent 946:1 error Expected indentation of 4 spaces but found 2 indent 947:1 error Expected indentation of 4 spaces but found 2 indent 948:1 error Expected indentation of 8 spaces but found 4 indent 949:1 error Expected indentation of 4 spaces but found 2 indent 956:1 error Expected indentation of 4 spaces but found 2 indent 957:1 error Expected indentation of 8 spaces but found 4 indent 958:1 error Expected indentation of 8 spaces but found 4 indent 959:1 error Expected indentation of 12 spaces but found 6 indent 960:1 error Expected indentation of 12 spaces but found 6 indent 961:1 error Expected indentation of 12 spaces but found 6 indent 962:1 error Expected indentation of 8 spaces but found 4 indent 963:1 error Expected indentation of 8 spaces but found 4 indent 964:1 error Expected indentation of 8 spaces but found 4 indent 965:1 error Expected indentation of 8 spaces but found 4 indent 966:1 error Expected indentation of 4 spaces but found 2 indent 968:1 error Expected indentation of 4 spaces but found 2 indent 969:1 error Expected indentation of 8 spaces but found 4 indent 970:1 error Expected indentation of 4 spaces but found 2 indent 972:1 error Expected indentation of 4 spaces but found 2 indent 973:1 error Expected indentation of 8 spaces but found 4 indent 974:1 error Expected indentation of 4 spaces but found 2 indent 976:1 error Expected indentation of 4 spaces but found 2 indent 977:1 error Expected indentation of 8 spaces but found 4 indent 978:1 error Expected indentation of 12 spaces but found 6 indent 979:1 error Expected indentation of 8 spaces but found 4 indent 980:1 error Expected indentation of 8 spaces but found 4 indent 981:1 error Expected indentation of 4 spaces but found 2 indent 983:1 error Expected indentation of 4 spaces but found 2 indent 984:1 error Expected indentation of 8 spaces but found 4 indent 985:1 error Expected indentation of 8 spaces but found 4 indent 986:1 error Expected indentation of 12 spaces but found 6 indent 987:1 error Expected indentation of 16 spaces but found 8 indent 988:1 error Expected indentation of 16 spaces but found 8 indent 989:1 error Expected indentation of 16 spaces but found 8 indent 990:1 error Expected indentation of 20 spaces but found 10 indent 991:1 error Expected indentation of 16 spaces but found 8 indent 992:1 error Expected indentation of 16 spaces but found 8 indent 993:1 error Expected indentation of 20 spaces but found 10 indent 994:1 error Expected indentation of 16 spaces but found 8 indent 995:1 error Expected indentation of 12 spaces but found 6 indent 996:1 error Expected indentation of 8 spaces but found 4 indent 997:1 error Expected indentation of 12 spaces but found 6 indent 998:1 error Expected indentation of 16 spaces but found 8 indent 999:1 error Expected indentation of 20 spaces but found 10 indent 1000:1 error Expected indentation of 16 spaces but found 8 indent 1001:1 error Expected indentation of 12 spaces but found 6 indent 1002:1 error Expected indentation of 8 spaces but found 4 indent 1004:1 error Expected indentation of 8 spaces but found 4 indent 1005:1 error Expected indentation of 8 spaces but found 4 indent 1006:1 error Expected indentation of 12 spaces but found 6 indent 1008:1 error Expected indentation of 8 spaces but found 4 indent 1009:1 error Expected indentation of 8 spaces but found 4 indent 1010:1 error Expected indentation of 12 spaces but found 6 indent 1011:1 error Expected indentation of 16 spaces but found 8 indent 1012:1 error Expected indentation of 16 spaces but found 8 indent 1013:1 error Expected indentation of 16 spaces but found 8 indent 1014:1 error Expected indentation of 20 spaces but found 10 indent 1015:1 error Expected indentation of 24 spaces but found 10 indent 1016:1 error Expected indentation of 28 spaces but found 12 indent 1017:1 error Expected indentation of 28 spaces but found 12 indent 1018:1 error Expected indentation of 28 spaces but found 12 indent 1019:1 error Expected indentation of 24 spaces but found 10 indent 1020:1 error Expected indentation of 20 spaces but found 10 indent 1021:1 error Expected indentation of 20 spaces but found 10 indent 1022:1 error Expected indentation of 24 spaces but found 10 indent 1023:1 error Expected indentation of 20 spaces but found 10 indent 1024:1 error Expected indentation of 16 spaces but found 8 indent 1025:1 error Expected indentation of 16 spaces but found 8 indent 1026:1 error Expected indentation of 12 spaces but found 6 indent 1027:1 error Expected indentation of 8 spaces but found 4 indent 1028:1 error Expected indentation of 8 spaces but found 4 indent 1029:1 error Expected indentation of 12 spaces but found 6 indent 1030:1 error Expected indentation of 16 spaces but found 8 indent 1031:1 error Expected indentation of 12 spaces but found 6 indent 1032:1 error Expected indentation of 8 spaces but found 4 indent 1033:1 error Expected indentation of 4 spaces but found 2 indent 1036:1 error Expected indentation of 4 spaces but found 2 indent 1037:1 error Expected indentation of 4 spaces but found 2 indent 1038:1 error Expected indentation of 4 spaces but found 2 indent 1039:1 error Expected indentation of 4 spaces but found 2 indent 1042:1 error Expected indentation of 4 spaces but found 2 indent 1043:1 error Expected indentation of 4 spaces but found 2 indent 1044:1 error Expected indentation of 4 spaces but found 2 indent 1045:1 error Expected indentation of 4 spaces but found 2 indent 1062:1 error Expected indentation of 4 spaces but found 2 indent 1063:1 error Expected indentation of 4 spaces but found 2 indent 1064:1 error Expected indentation of 4 spaces but found 2 indent 1065:1 error Expected indentation of 4 spaces but found 2 indent 1066:1 error Expected indentation of 4 spaces but found 2 indent 1067:1 error Expected indentation of 4 spaces but found 2 indent 1068:1 error Expected indentation of 4 spaces but found 2 indent 1069:1 error Expected indentation of 4 spaces but found 2 indent 1070:1 error Expected indentation of 4 spaces but found 2 indent 1071:1 error Expected indentation of 4 spaces but found 2 indent 1072:1 error Expected indentation of 4 spaces but found 2 indent 1073:1 error Expected indentation of 4 spaces but found 2 indent ? 908 problems (908 errors, 0 warnings) 882 errors and 0 warnings potentially fixable with the `--fix` option. ERROR in ./modules/dicom_archive/jsx/dicom_archive.js Module Error (from ./node_modules/eslint-loader/index.js): /var/www/loris/modules/dicom_archive/jsx/dicom_archive.js 1:8 error 'React' is defined but never used no-unused-vars 4:8 error 'Loader' is defined but never used no-unused-vars 5:8 error 'FilterableDataTable' is defined but never used no-unused-vars 21:1 error Expected indentation of 4 spaces but found 2 indent 22:1 error Expected indentation of 8 spaces but found 4 indent 24:1 error Expected indentation of 8 spaces but found 4 indent 25:1 error Expected indentation of 12 spaces but found 6 indent 26:1 error Expected indentation of 12 spaces but found 6 indent 27:1 error Expected indentation of 12 spaces but found 6 indent 28:1 error Expected indentation of 8 spaces but found 4 indent 30:1 error Expected indentation of 8 spaces but found 4 indent 31:1 error Expected indentation of 8 spaces but found 4 indent 32:1 error Expected indentation of 4 spaces but found 2 indent 34:1 error Expected indentation of 4 spaces but found 2 indent 35:1 error Expected indentation of 8 spaces but found 4 indent 36:1 error Expected indentation of 12 spaces but found 6 indent 37:1 error Expected indentation of 4 spaces but found 2 indent 39:1 error Expected indentation of 4 spaces but found 2 indent 44:1 error Expected indentation of 4 spaces but found 2 indent 45:1 error Expected indentation of 8 spaces but found 4 indent 46:1 error Expected indentation of 12 spaces but found 6 indent 47:1 error Expected indentation of 12 spaces but found 6 indent 48:1 error Expected indentation of 12 spaces but found 6 indent 49:1 error Expected indentation of 16 spaces but found 8 indent 50:1 error Expected indentation of 16 spaces but found 8 indent 50:9 error Unexpected console statement no-console 51:1 error Expected indentation of 12 spaces but found 6 indent 52:1 error Expected indentation of 4 spaces but found 2 indent 54:1 error Expected indentation of 4 spaces but found 2 indent 63:1 error Expected indentation of 4 spaces but found 2 indent 64:1 error Expected indentation of 8 spaces but found 4 indent 65:1 error Expected indentation of 8 spaces but found 4 indent 66:1 error Expected indentation of 8 spaces but found 6 indent 67:1 error Expected indentation of 12 spaces but found 8 indent 69:1 error Expected indentation of 12 spaces but found 8 indent 71:1 error Expected indentation of 14 spaces but found 12 indent 72:1 error Expected indentation of 18 spaces but found 14 indent 74:1 error Expected indentation of 18 spaces but found 14 indent 75:1 error Expected indentation of 14 spaces but found 12 indent 77:1 error Expected indentation of 8 spaces but found 6 indent 78:1 error Expected indentation of 12 spaces but found 6 indent 79:1 error Expected indentation of 8 spaces but found 6 indent 80:1 error Expected indentation of 12 spaces but found 8 indent 80:29 error 'loris' is not defined no-undef 82:1 error Expected indentation of 12 spaces but found 8 indent 83:1 error Expected indentation of 8 spaces but found 6 indent 84:1 error Expected indentation of 12 spaces but found 6 indent 85:1 error Expected indentation of 8 spaces but found 6 indent 86:1 error Expected indentation of 12 spaces but found 8 indent 87:1 error Expected indentation of 16 spaces but found 10 indent 88:1 error Expected indentation of 12 spaces but found 8 indent 89:1 error Expected indentation of 16 spaces but found 10 indent 89:24 error 'loris' is not defined no-undef 91:1 error Expected indentation of 16 spaces but found 10 indent 92:1 error Expected indentation of 12 spaces but found 8 indent 93:1 error Expected indentation of 12 spaces but found 6 indent 94:1 error Expected indentation of 8 spaces but found 6 indent 95:1 error Expected indentation of 8 spaces but found 6 indent 96:1 error Expected indentation of 12 spaces but found 8 indent 97:1 error Expected indentation of 12 spaces but found 6 indent 98:1 error Expected indentation of 8 spaces but found 4 indent 100:1 error Expected indentation of 8 spaces but found 4 indent 101:1 error Expected indentation of 4 spaces but found 2 indent 103:1 error Expected indentation of 4 spaces but found 2 indent 106:1 error Expected indentation of 8 spaces but found 4 indent 107:1 error Expected indentation of 12 spaces but found 6 indent 108:1 error Expected indentation of 8 spaces but found 4 indent 110:1 error Expected indentation of 8 spaces but found 4 indent 111:1 error Expected indentation of 8 spaces but found 4 indent 112:1 error Expected indentation of 12 spaces but found 6 indent 113:1 error Expected indentation of 8 spaces but found 4 indent 115:1 error Expected indentation of 8 spaces but found 4 indent 119:1 error Expected indentation of 8 spaces but found 4 indent 120:1 error Expected indentation of 8 spaces but found 4 indent 121:1 error Expected indentation of 12 spaces but found 6 indent 122:1 error Expected indentation of 16 spaces but found 8 indent 123:1 error Expected indentation of 16 spaces but found 8 indent 124:1 error Expected indentation of 12 spaces but found 6 indent 125:1 error Expected indentation of 12 spaces but found 6 indent 126:1 error Expected indentation of 16 spaces but found 8 indent 127:1 error Expected indentation of 16 spaces but found 8 indent 128:1 error Expected indentation of 12 spaces but found 6 indent 129:1 error Expected indentation of 12 spaces but found 6 indent 130:1 error Expected indentation of 16 spaces but found 8 indent 131:1 error Expected indentation of 16 spaces but found 8 indent 132:1 error Expected indentation of 12 spaces but found 6 indent 133:1 error Expected indentation of 12 spaces but found 6 indent 134:1 error Expected indentation of 16 spaces but found 8 indent 135:1 error Expected indentation of 16 spaces but found 8 indent 136:1 error Expected indentation of 12 spaces but found 6 indent 137:1 error Expected indentation of 12 spaces but found 6 indent 138:1 error Expected indentation of 16 spaces but found 8 indent 139:1 error Expected indentation of 16 spaces but found 8 indent 140:1 error Expected indentation of 12 spaces but found 6 indent 141:1 error Expected indentation of 12 spaces but found 6 indent 142:1 error Expected indentation of 16 spaces but found 8 indent 143:1 error Expected indentation of 16 spaces but found 8 indent 144:1 error Expected indentation of 12 spaces but found 6 indent 145:1 error Expected indentation of 12 spaces but found 6 indent 146:1 error Expected indentation of 12 spaces but found 6 indent 147:1 error Expected indentation of 12 spaces but found 6 indent 148:1 error Expected indentation of 16 spaces but found 8 indent 149:1 error Expected indentation of 16 spaces but found 8 indent 150:1 error Expected indentation of 12 spaces but found 6 indent 151:1 error Expected indentation of 12 spaces but found 6 indent 152:1 error Expected indentation of 16 spaces but found 8 indent 153:1 error Expected indentation of 16 spaces but found 8 indent 154:1 error Expected indentation of 16 spaces but found 8 indent 155:1 error Expected indentation of 12 spaces but found 6 indent 156:1 error Expected indentation of 12 spaces but found 6 indent 157:1 error Expected indentation of 12 spaces but found 6 indent 158:1 error Expected indentation of 8 spaces but found 4 indent 160:1 error Expected indentation of 8 spaces but found 4 indent 161:1 error Expected indentation of 12 spaces but found 6 indent 162:1 error Expected indentation of 16 spaces but found 8 indent 163:1 error Expected indentation of 16 spaces but found 8 indent 164:1 error Expected indentation of 16 spaces but found 8 indent 165:1 error Expected indentation of 16 spaces but found 8 indent 166:1 error Expected indentation of 16 spaces but found 8 indent 167:1 error Expected indentation of 12 spaces but found 6 indent 168:1 error Expected indentation of 8 spaces but found 4 indent 169:1 error Expected indentation of 4 spaces but found 2 indent 173:1 error Expected indentation of 4 spaces but found 2 indent 177:1 error Expected indentation of 4 spaces but found 2 indent 177:3 error 'ReactDOM' is not defined no-undef 178:1 error Expected indentation of 8 spaces but found 4 indent 178:28 error 'loris' is not defined no-undef 179:1 error Expected indentation of 8 spaces but found 4 indent 180:1 error Expected indentation of 4 spaces but found 2 indent ? 129 problems (129 errors, 0 warnings) 121 errors and 0 warnings potentially fixable with the `--fix` option. ERROR in ./modules/document_repository/jsx/docIndex.js Module Error (from ./node_modules/eslint-loader/index.js): /var/www/loris/modules/document_repository/jsx/docIndex.js 1:9 error 'Tabs' is defined but never used no-unused-vars 1:15 error 'TabPane' is defined but never used no-unused-vars 2:8 error 'DocUploadForm' is defined but never used no-unused-vars 3:8 error 'DocCategoryForm' is defined but never used no-unused-vars 4:8 error 'ParentTree' is defined but never used no-unused-vars 5:8 error 'ChildTree' is defined but never used no-unused-vars 6:8 error 'Loader' is defined but never used no-unused-vars 7:8 error 'FilterableDataTable' is defined but never used no-unused-vars 8:8 error 'NullFilterableDataTable' is defined but never used no-unused-vars 10:7 error 'DocIndex' is defined but never used no-unused-vars 10:24 error 'React' is not defined no-undef 11:1 error Expected indentation of 4 spaces but found 2 indent 12:1 error Expected indentation of 8 spaces but found 4 indent 13:1 error Expected indentation of 8 spaces but found 4 indent 14:1 error Expected indentation of 12 spaces but found 6 indent 15:1 error Expected indentation of 12 spaces but found 6 indent 16:1 error Expected indentation of 12 spaces but found 6 indent 17:1 error Expected indentation of 12 spaces but found 6 indent 18:1 error Expected indentation of 12 spaces but found 6 indent 19:1 error Expected indentation of 12 spaces but found 6 indent 20:1 error Expected indentation of 12 spaces but found 6 indent 21:1 error Expected indentation of 12 spaces but found 6 indent 22:1 error Expected indentation of 8 spaces but found 4 indent 23:1 error Expected indentation of 8 spaces but found 4 indent 24:1 error Expected indentation of 8 spaces but found 4 indent 25:1 error Expected indentation of 8 spaces but found 4 indent 26:1 error Expected indentation of 8 spaces but found 4 indent 27:1 error Expected indentation of 8 spaces but found 4 indent 28:1 error Expected indentation of 8 spaces but found 4 indent 29:1 error Expected indentation of 8 spaces but found 4 indent 30:1 error Expected indentation of 4 spaces but found 2 indent 32:1 error Expected indentation of 4 spaces but found 2 indent 33:1 error Expected indentation of 8 spaces but found 4 indent 34:1 error Expected indentation of 12 spaces but found 6 indent 35:1 error Expected indentation of 4 spaces but found 2 indent 37:1 error Expected indentation of 4 spaces but found 2 indent 38:1 error Expected indentation of 8 spaces but found 4 indent 39:1 error Expected indentation of 8 spaces but found 4 indent 40:1 error Expected indentation of 8 spaces but found 4 indent 41:1 error Expected indentation of 12 spaces but found 6 indent 42:1 error Expected indentation of 12 spaces but found 6 indent 43:1 error Expected indentation of 8 spaces but found 4 indent 44:1 error Expected indentation of 8 spaces but found 4 indent 45:1 error Expected indentation of 4 spaces but found 2 indent 47:1 error Expected indentation of 4 spaces but found 2 indent 48:1 error Expected indentation of 4 spaces but found 2 indent 49:1 error Expected indentation of 8 spaces but found 4 indent 49:18 error 'loris' is not defined no-undef 50:1 error Expected indentation of 12 spaces but found 6 indent 51:1 error Expected indentation of 12 spaces but found 6 indent 52:1 error Expected indentation of 16 spaces but found 8 indent 53:1 error Expected indentation of 16 spaces but found 8 indent 54:1 error Expected indentation of 16 spaces but found 8 indent 55:1 error Expected indentation of 16 spaces but found 8 indent 56:1 error Expected indentation of 20 spaces but found 10 indent 57:1 error Expected indentation of 16 spaces but found 8 indent 58:1 error Expected indentation of 16 spaces but found 8 indent 59:1 error Expected indentation of 16 spaces but found 8 indent 60:1 error Expected indentation of 20 spaces but found 10 indent 61:1 error Expected indentation of 16 spaces but found 8 indent 62:1 error Expected indentation of 16 spaces but found 8 indent 63:1 error Expected indentation of 20 spaces but found 10 indent 64:1 error Expected indentation of 16 spaces but found 8 indent 65:1 error Expected indentation of 16 spaces but found 8 indent 66:1 error Expected indentation of 20 spaces but found 10 indent 67:1 error Expected indentation of 20 spaces but found 10 indent 68:1 error Expected indentation of 20 spaces but found 10 indent 69:1 error Expected indentation of 16 spaces but found 8 indent 70:1 error Expected indentation of 12 spaces but found 6 indent 71:1 error Expected indentation of 4 spaces but found 2 indent 73:1 error Expected indentation of 4 spaces but found 2 indent 74:1 error Expected indentation of 8 spaces but found 4 indent 75:1 error Expected indentation of 12 spaces but found 6 indent 76:1 error Expected indentation of 12 spaces but found 6 indent 77:1 error Expected indentation of 16 spaces but found 8 indent 78:1 error Expected indentation of 12 spaces but found 6 indent 79:1 error Expected indentation of 16 spaces but found 8 indent 80:1 error Expected indentation of 12 spaces but found 6 indent 81:1 error Expected indentation of 12 spaces but found 6 indent 82:1 error Expected indentation of 12 spaces but found 6 indent 82:15 error 'error' is defined but never used no-unused-vars 83:1 error Expected indentation of 16 spaces but found 8 indent 84:1 error Expected indentation of 12 spaces but found 6 indent 85:1 error Expected indentation of 4 spaces but found 2 indent 87:1 error Expected indentation of 4 spaces but found 2 indent 88:1 error Expected indentation of 8 spaces but found 4 indent 89:1 error Expected indentation of 4 spaces but found 2 indent 91:1 error Expected indentation of 4 spaces but found 2 indent 92:1 error Expected indentation of 8 spaces but found 4 indent 93:1 error Expected indentation of 4 spaces but found 2 indent 95:1 error Expected indentation of 4 spaces but found 2 indent 102:1 error Expected indentation of 4 spaces but found 2 indent 103:1 error Expected indentation of 8 spaces but found 4 indent 104:1 error Expected indentation of 8 spaces but found 4 indent 105:1 error Expected indentation of 8 spaces but found 6 indent 106:1 error Expected indentation of 12 spaces but found 8 indent 106:9 error Unexpected lexical declaration in case block no-case-declarations 106:27 error 'loris' is not defined no-undef 107:1 error Expected indentation of 12 spaces but found 8 indent 108:1 error Expected indentation of 12 spaces but found 8 indent 109:1 error Expected indentation of 8 spaces but found 6 indent 110:1 error Expected indentation of 12 spaces but found 8 indent 110:9 error Unexpected lexical declaration in case block no-case-declarations 110:23 error 'loris' is not defined no-undef 111:1 error Expected indentation of 12 spaces but found 8 indent 112:1 error Expected indentation of 12 spaces but found 8 indent 113:1 error Expected indentation of 8 spaces but found 6 indent 114:1 error Expected indentation of 12 spaces but found 8 indent 114:9 error Unexpected lexical declaration in case block no-case-declarations 115:1 error Expected indentation of 12 spaces but found 8 indent 115:9 error Move function declaration to function body root no-inner-declarations 115:9 error Unexpected lexical declaration in case block no-case-declarations 116:1 error Expected indentation of 16 spaces but found 10 indent 116:11 error 'swal' is not defined no-undef 117:1 error Expected indentation of 20 spaces but found 12 indent 118:1 error Expected indentation of 20 spaces but found 12 indent 119:1 error Expected indentation of 20 spaces but found 12 indent 120:1 error Expected indentation of 20 spaces but found 12 indent 121:1 error Expected indentation of 20 spaces but found 12 indent 122:1 error Expected indentation of 20 spaces but found 12 indent 123:1 error Expected indentation of 20 spaces but found 12 indent 124:1 error Expected indentation of 16 spaces but found 10 indent 125:1 error Expected indentation of 16 spaces but found 10 indent 126:1 error Expected indentation of 20 spaces but found 12 indent 126:29 error 'loris' is not defined no-undef 127:1 error Expected indentation of 20 spaces but found 14 indent 128:1 error Expected indentation of 24 spaces but found 14 indent 129:1 error Expected indentation of 24 spaces but found 14 indent 130:1 error Expected indentation of 24 spaces but found 14 indent 131:1 error Expected indentation of 20 spaces but found 14 indent 132:1 error Expected indentation of 24 spaces but found 16 indent 133:1 error Expected indentation of 28 spaces but found 18 indent 134:1 error Expected indentation of 28 spaces but found 18 indent 134:19 error 'swal' is not defined no-undef 135:1 error Expected indentation of 24 spaces but found 16 indent 136:1 error Expected indentation of 16 spaces but found 10 indent 137:1 error Expected indentation of 16 spaces but found 10 indent 138:1 error Expected indentation of 12 spaces but found 8 indent 139:1 error Expected indentation of 12 spaces but found 8 indent 140:1 error Expected indentation of 12 spaces but found 8 indent 141:1 error Expected indentation of 8 spaces but found 4 indent 142:1 error Expected indentation of 8 spaces but found 4 indent 143:1 error Expected indentation of 4 spaces but found 2 indent 145:1 error Expected indentation of 4 spaces but found 2 indent 148:1 error Expected indentation of 8 spaces but found 4 indent 149:1 error Expected indentation of 12 spaces but found 6 indent 150:1 error Expected indentation of 8 spaces but found 4 indent 152:1 error Expected indentation of 8 spaces but found 4 indent 153:1 error Expected indentation of 8 spaces but found 4 indent 154:1 error Expected indentation of 12 spaces but found 6 indent 155:1 error Expected indentation of 8 spaces but found 4 indent 156:1 error Expected indentation of 8 spaces but found 4 indent 157:1 error Expected indentation of 8 spaces but found 4 indent 158:1 error Expected indentation of 12 spaces but found 6 indent 159:1 error Expected indentation of 16 spaces but found 8 indent 160:1 error Expected indentation of 16 spaces but found 8 indent 161:1 error Expected indentation of 12 spaces but found 6 indent 162:1 error Expected indentation of 12 spaces but found 6 indent 163:1 error Expected indentation of 16 spaces but found 8 indent 164:1 error Expected indentation of 16 spaces but found 8 indent 165:1 error Expected indentation of 12 spaces but found 6 indent 166:1 error Expected indentation of 12 spaces but found 6 indent 167:1 error Expected indentation of 16 spaces but found 8 indent 168:1 error Expected indentation of 16 spaces but found 8 indent 169:1 error Expected indentation of 16 spaces but found 8 indent 170:1 error Expected indentation of 12 spaces but found 6 indent 171:1 error Expected indentation of 12 spaces but found 6 indent 172:1 error Expected indentation of 12 spaces but found 6 indent 173:1 error Expected indentation of 16 spaces but found 8 indent 174:1 error Expected indentation of 16 spaces but found 8 indent 175:1 error Expected indentation of 12 spaces but found 8 indent 176:1 error Expected indentation of 12 spaces but found 6 indent 177:1 error Expected indentation of 16 spaces but found 8 indent 178:1 error Expected indentation of 16 spaces but found 8 indent 179:1 error Expected indentation of 16 spaces but found 8 indent 180:1 error Expected indentation of 12 spaces but found 6 indent 181:1 error Expected indentation of 12 spaces but found 6 indent 182:1 error Expected indentation of 16 spaces but found 8 indent 183:1 error Expected indentation of 16 spaces but found 8 indent 184:1 error Expected indentation of 12 spaces but found 6 indent 185:1 error Expected indentation of 12 spaces but found 6 indent 186:1 error Expected indentation of 12 spaces but found 6 indent 187:1 error Expected indentation of 12 spaces but found 6 indent 188:1 error Expected indentation of 12 spaces but found 6 indent 189:1 error Expected indentation of 12 spaces but found 6 indent 190:1 error Expected indentation of 12 spaces but found 6 indent 191:1 error Expected indentation of 8 spaces but found 4 indent 193:1 error Expected indentation of 8 spaces but found 4 indent 194:1 error Expected indentation of 12 spaces but found 6 indent 195:1 error Expected indentation of 12 spaces but found 6 indent 196:1 error Expected indentation of 12 spaces but found 6 indent 197:1 error Expected indentation of 8 spaces but found 4 indent 198:1 error Expected indentation of 8 spaces but found 4 indent 200:1 error Expected indentation of 16 spaces but found 6 indent 201:1 error Expected indentation of 20 spaces but found 8 indent 202:1 error Expected indentation of 24 spaces but found 10 indent 203:1 error Expected indentation of 28 spaces but found 12 indent 204:1 error Expected indentation of 28 spaces but found 12 indent 205:1 error Expected indentation of 28 spaces but found 12 indent 206:1 error Expected indentation of 28 spaces but found 12 indent 207:1 error Expected indentation of 28 spaces but found 12 indent 208:1 error Expected indentation of 28 spaces but found 12 indent 209:1 error Expected indentation of 24 spaces but found 10 indent 210:1 error Expected indentation of 24 spaces but found 10 indent 211:1 error Expected indentation of 28 spaces but found 12 indent 212:1 error Expected indentation of 28 spaces but found 12 indent 213:1 error Expected indentation of 28 spaces but found 12 indent 214:1 error Expected indentation of 28 spaces but found 12 indent 215:1 error Expected indentation of 28 spaces but found 12 indent 216:1 error Expected indentation of 32 spaces but found 14 indent 217:1 error Expected indentation of 36 spaces but found 16 indent 218:1 error Expected indentation of 36 spaces but found 16 indent 219:1 error Expected indentation of 32 spaces but found 14 indent 220:1 error Expected indentation of 28 spaces but found 12 indent 221:1 error Expected indentation of 24 spaces but found 10 indent 222:1 error Expected indentation of 28 spaces but found 12 indent 223:1 error Expected indentation of 32 spaces but found 14 indent 224:1 error Expected indentation of 36 spaces but found 16 indent 225:1 error Expected indentation of 36 spaces but found 16 indent 226:1 error Expected indentation of 32 spaces but found 14 indent 227:1 error Expected indentation of 28 spaces but found 12 indent 228:1 error Expected indentation of 24 spaces but found 10 indent 229:1 error Expected indentation of 20 spaces but found 8 indent 230:1 error Expected indentation of 16 spaces but found 6 indent 231:1 error Expected indentation of 12 spaces but found 4 indent 232:1 error Expected indentation of 16 spaces but found 6 indent 233:1 error Expected indentation of 20 spaces but found 8 indent 234:1 error Expected indentation of 24 spaces but found 10 indent 235:1 error Expected indentation of 24 spaces but found 10 indent 236:1 error Expected indentation of 24 spaces but found 10 indent 237:1 error Expected indentation of 24 spaces but found 10 indent 238:1 error Expected indentation of 24 spaces but found 10 indent 239:1 error Expected indentation of 24 spaces but found 10 indent 240:1 error Expected indentation of 20 spaces but found 8 indent 241:1 error Expected indentation of 20 spaces but found 8 indent 242:1 error Expected indentation of 24 spaces but found 10 indent 243:1 error Expected indentation of 24 spaces but found 10 indent 244:1 error Expected indentation of 24 spaces but found 10 indent 245:1 error Expected indentation of 24 spaces but found 10 indent 246:1 error Expected indentation of 24 spaces but found 10 indent 247:1 error Expected indentation of 24 spaces but found 10 indent 248:1 error Expected indentation of 28 spaces but found 10 indent 249:1 error Expected indentation of 32 spaces but found 12 indent 250:1 error Expected indentation of 32 spaces but found 12 indent 251:1 error Expected indentation of 28 spaces but found 10 indent 252:1 error Expected indentation of 20 spaces but found 8 indent 253:1 error Expected indentation of 24 spaces but found 8 indent 254:1 error Expected indentation of 28 spaces but found 10 indent 255:1 error Expected indentation of 32 spaces but found 12 indent 256:1 error Expected indentation of 32 spaces but found 12 indent 257:1 error Expected indentation of 28 spaces but found 10 indent 258:1 error Expected indentation of 24 spaces but found 8 indent 259:1 error Expected indentation of 20 spaces but found 8 indent 260:1 error Expected indentation of 16 spaces but found 6 indent 261:1 error Expected indentation of 12 spaces but found 4 indent 263:1 error Expected indentation of 8 spaces but found 4 indent 264:1 error Expected indentation of 12 spaces but found 6 indent 265:1 error Expected indentation of 16 spaces but found 8 indent 266:1 error Expected indentation of 20 spaces but found 10 indent 267:1 error Expected indentation of 16 spaces but found 8 indent 268:1 error Expected indentation of 16 spaces but found 8 indent 269:1 error Expected indentation of 20 spaces but found 10 indent 270:1 error Expected indentation of 24 spaces but found 12 indent 270:25 error 'loris' is not defined no-undef 271:1 error Expected indentation of 24 spaces but found 12 indent 271:24 error 'loris' is not defined no-undef 272:1 error Expected indentation of 24 spaces but found 12 indent 273:1 error Expected indentation of 24 spaces but found 12 indent 274:1 error Expected indentation of 24 spaces but found 12 indent 275:1 error Expected indentation of 20 spaces but found 10 indent 276:1 error Expected indentation of 16 spaces but found 8 indent 277:1 error Expected indentation of 16 spaces but found 8 indent 278:1 error Expected indentation of 20 spaces but found 10 indent 279:1 error Expected indentation of 24 spaces but found 12 indent 279:25 error 'loris' is not defined no-undef 280:1 error Expected indentation of 24 spaces but found 12 indent 280:24 error 'loris' is not defined no-undef 281:1 error Expected indentation of 24 spaces but found 12 indent 282:1 error Expected indentation of 24 spaces but found 12 indent 283:1 error Expected indentation of 20 spaces but found 10 indent 284:1 error Expected indentation of 16 spaces but found 8 indent 285:1 error Expected indentation of 12 spaces but found 6 indent 286:1 error Expected indentation of 8 spaces but found 4 indent 287:1 error Expected indentation of 4 spaces but found 2 indent 291:1 error Expected indentation of 4 spaces but found 2 indent 291:3 error 'ReactDOM' is not defined no-undef 292:1 error Expected indentation of 8 spaces but found 4 indent 293:1 error Expected indentation of 12 spaces but found 4 indent 294:1 error Expected indentation of 16 spaces but found 6 indent 294:19 error 'loris' is not defined no-undef 295:1 error Expected indentation of 16 spaces but found 6 indent 295:22 error 'loris' is not defined no-undef 296:1 error Expected indentation of 12 spaces but found 4 indent 297:1 error Expected indentation of 8 spaces but found 4 indent 298:1 error Expected indentation of 8 spaces but found 4 indent 299:1 error Expected indentation of 4 spaces but found 2 indent ? 296 problems (296 errors, 0 warnings) 266 errors and 0 warnings potentially fixable with the `--fix` option. ERROR in ./modules/document_repository/jsx/editFormIndex.js Module Error (from ./node_modules/eslint-loader/index.js): /var/www/loris/modules/document_repository/jsx/editFormIndex.js 3:8 error 'DocEditForm' is defined but never used no-unused-vars 8:1 error Expected indentation of 4 spaces but found 2 indent 9:1 error Expected indentation of 8 spaces but found 3 indent 10:1 error Expected indentation of 12 spaces but found 6 indent 11:1 error Expected indentation of 16 spaces but found 8 indent 12:1 error Expected indentation of 20 spaces but found 10 indent 13:1 error Expected indentation of 24 spaces but found 12 indent 13:25 error 'loris' is not defined no-undef 14:1 error Expected indentation of 24 spaces but found 12 indent 14:24 error 'loris' is not defined no-undef 15:1 error Expected indentation of 20 spaces but found 10 indent 16:1 error Expected indentation of 16 spaces but found 8 indent 17:1 error Expected indentation of 12 spaces but found 6 indent 18:1 error Expected indentation of 8 spaces but found 4 indent 19:1 error Expected indentation of 8 spaces but found 4 indent 20:1 error Expected indentation of 4 spaces but found 2 indent ? 16 problems (16 errors, 0 warnings) 13 errors and 0 warnings potentially fixable with the `--fix` option. ERROR in ./modules/examiner/jsx/examinerIndex.js Module Error (from ./node_modules/eslint-loader/index.js): /var/www/loris/modules/examiner/jsx/examinerIndex.js 1:8 error 'React' is defined but never used no-unused-vars 5:8 error 'Modal' is defined but never used no-unused-vars 6:8 error 'Loader' is defined but never used no-unused-vars 7:8 error 'FilterableDataTable' is defined but never used no-unused-vars 22:1 error Expected indentation of 4 spaces but found 2 indent 23:1 error Expected indentation of 8 spaces but found 4 indent 25:1 error Expected indentation of 8 spaces but found 4 indent 26:1 error Expected indentation of 12 spaces but found 6 indent 27:1 error Expected indentation of 12 spaces but found 6 indent 28:1 error Expected indentation of 12 spaces but found 6 indent 29:1 error Expected indentation of 12 spaces but found 6 indent 30:1 error Expected indentation of 16 spaces but found 8 indent 31:1 error Expected indentation of 16 spaces but found 8 indent 32:1 error Expected indentation of 16 spaces but found 8 indent 33:1 error Expected indentation of 12 spaces but found 6 indent 34:1 error Expected indentation of 12 spaces but found 6 indent 35:1 error Expected indentation of 8 spaces but found 4 indent 37:1 error Expected indentation of 8 spaces but found 4 indent 38:1 error Expected indentation of 8 spaces but found 4 indent 39:1 error Expected indentation of 8 spaces but found 4 indent 40:1 error Expected indentation of 8 spaces but found 4 indent 41:1 error Expected indentation of 8 spaces but found 4 indent 42:1 error Expected indentation of 8 spaces but found 4 indent 43:1 error Expected indentation of 8 spaces but found 4 indent 44:1 error Expected indentation of 4 spaces but found 2 indent 46:1 error Expected indentation of 4 spaces but found 2 indent 47:1 error Expected indentation of 8 spaces but found 4 indent 48:1 error Expected indentation of 12 spaces but found 6 indent 49:1 error Expected indentation of 4 spaces but found 2 indent 51:1 error Expected indentation of 4 spaces but found 2 indent 58:1 error Expected indentation of 4 spaces but found 2 indent 59:1 error Expected indentation of 8 spaces but found 4 indent 60:1 error Expected indentation of 12 spaces but found 6 indent 61:1 error Expected indentation of 12 spaces but found 6 indent 62:1 error Expected indentation of 12 spaces but found 6 indent 63:1 error Expected indentation of 16 spaces but found 8 indent 64:1 error Expected indentation of 16 spaces but found 8 indent 64:9 error Unexpected console statement no-console 65:1 error Expected indentation of 12 spaces but found 6 indent 66:1 error Expected indentation of 4 spaces but found 2 indent 68:1 error Expected indentation of 4 spaces but found 2 indent 74:1 error Expected indentation of 4 spaces but found 2 indent 75:1 error Expected indentation of 8 spaces but found 4 indent 76:1 error Expected indentation of 8 spaces but found 4 indent 77:1 error Expected indentation of 8 spaces but found 4 indent 78:1 error Expected indentation of 12 spaces but found 6 indent 79:1 error Expected indentation of 8 spaces but found 4 indent 80:1 error Expected indentation of 4 spaces but found 2 indent 82:1 error Expected indentation of 4 spaces but found 2 indent 87:1 error Expected indentation of 4 spaces but found 2 indent 87:16 error 'e' is defined but never used no-unused-vars 88:1 error Expected indentation of 8 spaces but found 4 indent 89:1 error Expected indentation of 8 spaces but found 4 indent 90:1 error Expected indentation of 8 spaces but found 4 indent 91:1 error Expected indentation of 12 spaces but found 6 indent 92:1 error Expected indentation of 16 spaces but found 8 indent 93:1 error Expected indentation of 12 spaces but found 6 indent 94:1 error Expected indentation of 8 spaces but found 4 indent 95:1 error Expected indentation of 8 spaces but found 4 indent 97:1 error Expected indentation of 8 spaces but found 4 indent 98:1 error Expected indentation of 12 spaces but found 6 indent 99:1 error Expected indentation of 12 spaces but found 6 indent 100:1 error Expected indentation of 12 spaces but found 6 indent 101:1 error Expected indentation of 12 spaces but found 6 indent 102:1 error Expected indentation of 8 spaces but found 4 indent 103:1 error Expected indentation of 12 spaces but found 4 indent 104:1 error Expected indentation of 16 spaces but found 6 indent 105:1 error Expected indentation of 20 spaces but found 8 indent 106:1 error Expected indentation of 24 spaces but found 10 indent 107:1 error Expected indentation of 28 spaces but found 12 indent 108:1 error Expected indentation of 28 spaces but found 12 indent 109:1 error Expected indentation of 24 spaces but found 10 indent 110:1 error Expected indentation of 20 spaces but found 8 indent 111:1 error Expected indentation of 16 spaces but found 6 indent 112:1 error Expected indentation of 20 spaces but found 8 indent 113:1 error Expected indentation of 24 spaces but found 10 indent 114:1 error Expected indentation of 20 spaces but found 8 indent 115:1 error Expected indentation of 16 spaces but found 6 indent 116:1 error Expected indentation of 12 spaces but found 4 indent 117:1 error Expected indentation of 12 spaces but found 4 indent 118:1 error Expected indentation of 16 spaces but found 6 indent 118:7 error Unexpected console statement no-console 119:1 error Expected indentation of 12 spaces but found 4 indent 120:1 error Expected indentation of 4 spaces but found 2 indent 122:1 error Expected indentation of 4 spaces but found 2 indent 131:1 error Expected indentation of 4 spaces but found 2 indent 132:1 error Expected indentation of 8 spaces but found 4 indent 134:1 error Expected indentation of 8 spaces but found 4 indent 135:1 error Expected indentation of 8 spaces but found 6 indent 136:1 error Expected indentation of 12 spaces but found 8 indent 136:9 error Unexpected lexical declaration in case block no-case-declarations 136:21 error 'loris' is not defined no-undef 138:1 error Expected indentation of 12 spaces but found 8 indent 139:1 error Expected indentation of 12 spaces but found 8 indent 140:1 error Expected indentation of 8 spaces but found 6 indent 141:1 error Expected indentation of 12 spaces but found 8 indent 142:1 error Expected indentation of 16 spaces but found 10 indent 143:1 error Expected indentation of 12 spaces but found 8 indent 144:1 error Expected indentation of 16 spaces but found 10 indent 145:1 error Expected indentation of 12 spaces but found 8 indent 146:1 error Expected indentation of 12 spaces but found 8 indent 147:1 error Expected indentation of 8 spaces but found 6 indent 148:1 error Expected indentation of 12 spaces but found 8 indent 149:1 error Expected indentation of 16 spaces but found 10 indent 150:1 error Expected indentation of 12 spaces but found 8 indent 151:1 error Expected indentation of 12 spaces but found 8 indent 152:1 error Expected indentation of 8 spaces but found 4 indent 153:1 error Expected indentation of 8 spaces but found 4 indent 154:1 error Expected indentation of 4 spaces but found 2 indent 156:1 error Expected indentation of 4 spaces but found 2 indent 157:1 error Expected indentation of 8 spaces but found 4 indent 158:1 error Expected indentation of 4 spaces but found 2 indent 160:1 error Expected indentation of 4 spaces but found 2 indent 161:1 error Expected indentation of 8 spaces but found 4 indent 162:1 error Expected indentation of 12 spaces but found 6 indent 163:1 error Expected indentation of 12 spaces but found 6 indent 164:1 error Expected indentation of 8 spaces but found 4 indent 165:1 error Expected indentation of 4 spaces but found 2 indent 167:1 error Expected indentation of 4 spaces but found 2 indent 168:1 error Expected indentation of 8 spaces but found 4 indent 169:1 error Expected indentation of 12 spaces but found 6 indent 170:1 error Expected indentation of 16 spaces but found 8 indent 171:1 error Expected indentation of 16 spaces but found 8 indent 172:1 error Expected indentation of 16 spaces but found 8 indent 173:1 error Expected indentation of 12 spaces but found 6 indent 174:1 error Expected indentation of 16 spaces but found 8 indent 175:1 error Expected indentation of 20 spaces but found 10 indent 176:1 error Expected indentation of 20 spaces but found 10 indent 177:1 error Expected indentation of 20 spaces but found 10 indent 178:1 error Expected indentation of 20 spaces but found 10 indent 179:1 error Expected indentation of 20 spaces but found 10 indent 180:1 error Expected indentation of 16 spaces but found 8 indent 181:1 error Expected indentation of 20 spaces but found 10 indent 182:1 error Expected indentation of 24 spaces but found 12 indent 183:1 error Expected indentation of 24 spaces but found 12 indent 184:1 error Expected indentation of 24 spaces but found 12 indent 185:1 error Expected indentation of 24 spaces but found 12 indent 186:1 error Expected indentation of 24 spaces but found 12 indent 187:1 error Expected indentation of 20 spaces but found 10 indent 188:1 error Expected indentation of 20 spaces but found 10 indent 189:1 error Expected indentation of 24 spaces but found 12 indent 190:1 error Expected indentation of 24 spaces but found 12 indent 191:1 error Expected indentation of 24 spaces but found 12 indent 192:1 error Expected indentation of 24 spaces but found 12 indent 193:1 error Expected indentation of 24 spaces but found 12 indent 194:1 error Expected indentation of 24 spaces but found 12 indent 195:1 error Expected indentation of 20 spaces but found 10 indent 196:1 error Expected indentation of 20 spaces but found 10 indent 197:1 error Expected indentation of 24 spaces but found 12 indent 198:1 error Expected indentation of 24 spaces but found 12 indent 199:1 error Expected indentation of 24 spaces but found 12 indent 200:1 error Expected indentation of 24 spaces but found 12 indent 201:1 error Expected indentation of 24 spaces but found 12 indent 202:1 error Expected indentation of 20 spaces but found 10 indent 203:1 error Expected indentation of 20 spaces but found 10 indent 204:1 error Expected indentation of 24 spaces but found 12 indent 205:1 error Expected indentation of 24 spaces but found 12 indent 206:1 error Expected indentation of 28 spaces but found 14 indent 207:1 error Expected indentation of 32 spaces but found 16 indent 208:1 error Expected indentation of 28 spaces but found 14 indent 209:1 error Expected indentation of 24 spaces but found 12 indent 210:1 error Expected indentation of 24 spaces but found 12 indent 211:1 error Expected indentation of 24 spaces but found 12 indent 212:1 error Expected indentation of 20 spaces but found 10 indent 213:1 error Expected indentation of 16 spaces but found 8 indent 214:1 error Expected indentation of 12 spaces but found 6 indent 215:1 error Expected indentation of 8 spaces but found 4 indent 216:1 error Expected indentation of 4 spaces but found 2 indent 218:1 error Expected indentation of 4 spaces but found 2 indent 221:1 error Expected indentation of 8 spaces but found 4 indent 222:1 error Expected indentation of 12 spaces but found 6 indent 223:1 error Expected indentation of 8 spaces but found 4 indent 225:1 error Expected indentation of 8 spaces but found 4 indent 226:1 error Expected indentation of 8 spaces but found 4 indent 227:1 error Expected indentation of 12 spaces but found 6 indent 228:1 error Expected indentation of 8 spaces but found 4 indent 230:1 error Expected indentation of 8 spaces but found 3 indent 234:1 error Expected indentation of 8 spaces but found 4 indent 235:1 error Expected indentation of 8 spaces but found 4 indent 236:1 error Expected indentation of 12 spaces but found 6 indent 237:1 error Expected indentation of 16 spaces but found 8 indent 238:1 error Expected indentation of 16 spaces but found 8 indent 239:1 error Expected indentation of 12 spaces but found 6 indent 240:1 error Expected indentation of 12 spaces but found 6 indent 241:1 error Expected indentation of 12 spaces but found 6 indent 242:1 error Expected indentation of 16 spaces but found 8 indent 243:1 error Expected indentation of 16 spaces but found 8 indent 244:1 error Expected indentation of 16 spaces but found 8 indent 245:1 error Expected indentation of 12 spaces but found 6 indent 246:1 error Expected indentation of 12 spaces but found 6 indent 247:1 error Expected indentation of 16 spaces but found 8 indent 248:1 error Expected indentation of 16 spaces but found 8 indent 249:1 error Expected indentation of 16 spaces but found 8 indent 250:1 error Expected indentation of 12 spaces but found 6 indent 251:1 error Expected indentation of 12 spaces but found 6 indent 252:1 error Expected indentation of 8 spaces but found 4 indent 253:1 error Expected indentation of 8 spaces but found 4 indent 254:1 error Expected indentation of 12 spaces but found 6 indent 255:1 error Expected indentation of 8 spaces but found 4 indent 257:1 error Expected indentation of 8 spaces but found 4 indent 258:1 error Expected indentation of 12 spaces but found 6 indent 259:1 error Expected indentation of 16 spaces but found 8 indent 260:1 error Expected indentation of 16 spaces but found 8 indent 261:1 error Expected indentation of 20 spaces but found 10 indent 262:1 error Expected indentation of 20 spaces but found 10 indent 263:1 error Expected indentation of 20 spaces but found 10 indent 264:1 error Expected indentation of 20 spaces but found 10 indent 265:1 error Expected indentation of 20 spaces but found 10 indent 266:1 error Expected indentation of 20 spaces but found 10 indent 267:1 error Expected indentation of 16 spaces but found 8 indent 268:1 error Expected indentation of 12 spaces but found 6 indent 269:1 error Expected indentation of 8 spaces but found 4 indent 270:1 error Expected indentation of 4 spaces but found 2 indent 274:1 error Expected indentation of 4 spaces but found 2 indent 275:1 error Expected indentation of 4 spaces but found 2 indent 279:1 error Expected indentation of 4 spaces but found 2 indent 279:3 error 'ReactDOM' is not defined no-undef 280:1 error Expected indentation of 8 spaces but found 4 indent 281:1 error Expected indentation of 12 spaces but found 6 indent 281:19 error 'loris' is not defined no-undef 282:1 error Expected indentation of 12 spaces but found 6 indent 282:21 error 'loris' is not defined no-undef 283:1 error Expected indentation of 12 spaces but found 6 indent 283:22 error 'loris' is not defined no-undef 284:1 error Expected indentation of 8 spaces but found 4 indent 285:1 error Expected indentation of 8 spaces but found 4 indent 286:1 error Expected indentation of 4 spaces but found 2 indent ? 227 problems (227 errors, 0 warnings) 214 errors and 0 warnings potentially fixable with the `--fix` option. ERROR in ./modules/genomic_browser/jsx/FileUploadModal.js Module Error (from ./node_modules/eslint-loader/index.js): /var/www/loris/modules/genomic_browser/jsx/FileUploadModal.js 9:1 error Expected indentation of 4 spaces but found 2 indent 10:1 error Expected indentation of 8 spaces but found 4 indent 11:1 error Expected indentation of 8 spaces but found 4 indent 12:1 error Expected indentation of 12 spaces but found 6 indent 13:1 error Expected indentation of 12 spaces but found 6 indent 14:1 error Expected indentation of 12 spaces but found 6 indent 15:1 error Expected indentation of 8 spaces but found 4 indent 16:1 error Expected indentation of 8 spaces but found 4 indent 17:1 error Expected indentation of 8 spaces but found 4 indent 18:1 error Expected indentation of 8 spaces but found 4 indent 19:1 error Expected indentation of 4 spaces but found 2 indent 21:1 error Expected indentation of 4 spaces but found 2 indent 22:1 error Expected indentation of 8 spaces but found 4 indent 25:1 error Expected indentation of 4 spaces but found 2 indent 27:1 error Expected indentation of 4 spaces but found 2 indent 29:1 error Expected indentation of 8 spaces but found 4 indent 30:1 error Expected indentation of 8 spaces but found 4 indent 31:1 error Expected indentation of 12 spaces but found 6 indent 32:1 error Expected indentation of 16 spaces but found 8 indent 32:33 error 'currentValue' is defined but never used no-unused-vars 32:47 error 'currentIndex' is defined but never used no-unused-vars 32:61 error 'array' is defined but never used no-unused-vars 33:1 error Expected indentation of 20 spaces but found 10 indent 34:1 error Expected indentation of 16 spaces but found 8 indent 35:1 error Expected indentation of 8 spaces but found 4 indent 36:1 error Expected indentation of 4 spaces but found 2 indent 38:1 error Expected indentation of 4 spaces but found 2 indent 39:1 error Expected indentation of 8 spaces but found 4 indent 39:5 error '$' is not defined no-undef 40:1 error Expected indentation of 8 spaces but found 4 indent 40:5 error '$' is not defined no-undef 41:1 error Expected indentation of 4 spaces but found 2 indent 43:1 error Expected indentation of 4 spaces but found 2 indent 44:1 error Expected indentation of 8 spaces but found 4 indent 45:1 error Expected indentation of 8 spaces but found 4 indent 46:1 error Expected indentation of 8 spaces but found 4 indent 48:1 error Expected indentation of 8 spaces but found 4 indent 49:1 error Expected indentation of 8 spaces but found 4 indent 50:1 error Expected indentation of 8 spaces but found 4 indent 51:1 error Expected indentation of 12 spaces but found 6 indent 51:7 error Unexpected console statement no-console 52:1 error Expected indentation of 8 spaces but found 4 indent 53:1 error Expected indentation of 8 spaces but found 4 indent 54:1 error Expected indentation of 12 spaces but found 6 indent 55:1 error Expected indentation of 12 spaces but found 6 indent 56:1 error Expected indentation of 16 spaces but found 8 indent 57:1 error Expected indentation of 16 spaces but found 10 indent 58:1 error Expected indentation of 20 spaces but found 12 indent 59:1 error Expected indentation of 16 spaces but found 10 indent 60:1 error Expected indentation of 20 spaces but found 12 indent 61:1 error Expected indentation of 16 spaces but found 10 indent 62:1 error Expected indentation of 20 spaces but found 12 indent 63:1 error Expected indentation of 16 spaces but found 10 indent 65:1 error Expected indentation of 20 spaces but found 12 indent 65:13 error Unexpected lexical declaration in case block no-case-declarations 66:1 error Expected indentation of 20 spaces but found 12 indent 66:13 error Unexpected lexical declaration in case block no-case-declarations 67:1 error Expected indentation of 20 spaces but found 12 indent 68:1 error Expected indentation of 20 spaces but found 12 indent 69:1 error Expected indentation of 20 spaces but found 12 indent 70:1 error Expected indentation of 24 spaces but found 14 indent 71:1 error Expected indentation of 20 spaces but found 12 indent 73:1 error Expected indentation of 20 spaces but found 12 indent 74:1 error Expected indentation of 20 spaces but found 12 indent 75:1 error Expected indentation of 16 spaces but found 10 indent 76:1 error Expected indentation of 20 spaces but found 12 indent 77:1 error Expected indentation of 20 spaces but found 12 indent 78:1 error Expected indentation of 16 spaces but found 10 indent 79:1 error Expected indentation of 20 spaces but found 12 indent 80:1 error Expected indentation of 16 spaces but found 8 indent 81:1 error Expected indentation of 12 spaces but found 6 indent 82:1 error Expected indentation of 16 spaces but found 8 indent 82:9 error Unexpected console statement no-console 83:1 error Expected indentation of 16 spaces but found 8 indent 84:1 error Expected indentation of 16 spaces but found 8 indent 85:1 error Expected indentation of 16 spaces but found 8 indent 86:1 error Expected indentation of 12 spaces but found 6 indent 87:1 error Expected indentation of 8 spaces but found 4 indent 88:1 error Expected indentation of 8 spaces but found 4 indent 89:1 error Expected indentation of 8 spaces but found 4 indent 90:1 error Expected indentation of 8 spaces but found 4 indent 91:1 error Expected indentation of 4 spaces but found 2 indent 93:1 error Expected indentation of 4 spaces but found 2 indent 94:1 error Expected indentation of 8 spaces but found 4 indent 96:1 error Expected indentation of 8 spaces but found 4 indent 97:1 error Expected indentation of 12 spaces but found 6 indent 98:1 error Expected indentation of 8 spaces but found 4 indent 99:1 error Expected indentation of 12 spaces but found 6 indent 100:1 error Expected indentation of 16 spaces but found 8 indent 101:1 error Expected indentation of 12 spaces but found 6 indent 103:1 error Expected indentation of 12 spaces but found 6 indent 104:1 error Expected indentation of 8 spaces but found 4 indent 105:1 error Expected indentation of 8 spaces but found 4 indent 123:1 error Expected indentation of 4 spaces but found 2 indent 126:1 error Expected indentation of 4 spaces but found 2 indent 132:1 error Expected indentation of 4 spaces but found 2 indent 133:1 error Expected indentation of 8 spaces but found 4 indent 134:1 error Expected indentation of 8 spaces but found 4 indent 135:1 error Expected indentation of 12 spaces but found 6 indent 136:1 error Expected indentation of 12 spaces but found 6 indent 137:1 error Expected indentation of 12 spaces but found 6 indent 138:1 error Expected indentation of 8 spaces but found 4 indent 139:1 error Expected indentation of 8 spaces but found 4 indent 140:1 error Expected indentation of 8 spaces but found 4 indent 141:1 error Expected indentation of 4 spaces but found 2 indent 143:1 error Expected indentation of 4 spaces but found 2 indent 144:1 error Expected indentation of 8 spaces but found 4 indent 145:1 error Expected indentation of 8 spaces but found 4 indent 146:1 error Expected indentation of 4 spaces but found 2 indent 148:1 error Expected indentation of 4 spaces but found 2 indent 149:1 error Expected indentation of 8 spaces but found 4 indent 150:1 error Expected indentation of 12 spaces but found 6 indent 151:1 error Expected indentation of 8 spaces but found 4 indent 152:1 error Expected indentation of 4 spaces but found 2 indent 154:1 error Expected indentation of 4 spaces but found 2 indent 154:23 error 'prevProps' is defined but never used no-unused-vars 154:34 error 'prevState' is defined but never used no-unused-vars 155:1 error Expected indentation of 8 spaces but found 4 indent 156:1 error Expected indentation of 4 spaces but found 2 indent 158:1 error Expected indentation of 4 spaces but found 2 indent 159:1 error Expected indentation of 8 spaces but found 4 indent 160:1 error Expected indentation of 8 spaces but found 4 indent 162:1 error Expected indentation of 8 spaces but found 4 indent 164:1 error Expected indentation of 8 spaces but found 4 indent 165:1 error Expected indentation of 8 spaces but found 6 indent 166:1 error Expected indentation of 12 spaces but found 8 indent 167:1 error Expected indentation of 12 spaces but found 8 indent 168:1 error Expected indentation of 12 spaces but found 8 indent 169:1 error Expected indentation of 16 spaces but found 10 indent 170:1 error Expected indentation of 12 spaces but found 8 indent 171:1 error Expected indentation of 12 spaces but found 8 indent 172:1 error Expected indentation of 12 spaces but found 8 indent 173:1 error Expected indentation of 12 spaces but found 8 indent 174:1 error Expected indentation of 8 spaces but found 6 indent 175:1 error Expected indentation of 12 spaces but found 8 indent 176:1 error Expected indentation of 12 spaces but found 8 indent 177:1 error Expected indentation of 12 spaces but found 8 indent 178:1 error Expected indentation of 12 spaces but found 8 indent 179:1 error Expected indentation of 8 spaces but found 6 indent 181:1 error Expected indentation of 8 spaces but found 4 indent 183:1 error Expected indentation of 8 spaces but found 4 indent 184:1 error Expected indentation of 12 spaces but found 6 indent 185:1 error Expected indentation of 16 spaces but found 10 indent 186:1 error Expected indentation of 20 spaces but found 14 indent 187:1 error Expected indentation of 20 spaces but found 14 indent 188:1 error Expected indentation of 16 spaces but found 10 indent 189:1 error Expected indentation of 12 spaces but found 6 indent 190:1 error Expected indentation of 8 spaces but found 4 indent 191:1 error Expected indentation of 4 spaces but found 2 indent 194:1 error Expected indentation of 4 spaces but found 2 indent 197:1 error Expected indentation of 4 spaces but found 2 indent 201:1 error Expected indentation of 4 spaces but found 2 indent 202:1 error Expected indentation of 8 spaces but found 4 indent 203:1 error Expected indentation of 8 spaces but found 4 indent 204:1 error Expected indentation of 12 spaces but found 6 indent 205:1 error Expected indentation of 8 spaces but found 4 indent 206:1 error Expected indentation of 8 spaces but found 4 indent 207:1 error Expected indentation of 4 spaces but found 2 indent 209:1 error Expected indentation of 4 spaces but found 2 indent 210:1 error Expected indentation of 8 spaces but found 4 indent 211:1 error Expected indentation of 4 spaces but found 2 indent 213:1 error Expected indentation of 4 spaces but found 2 indent 214:1 error Expected indentation of 8 spaces but found 4 indent 215:1 error Expected indentation of 8 spaces but found 4 indent 216:1 error Expected indentation of 8 spaces but found 4 indent 217:1 error Expected indentation of 12 spaces but found 6 indent 218:1 error Expected indentation of 16 spaces but found 8 indent 219:1 error Expected indentation of 16 spaces but found 10 indent 220:1 error Expected indentation of 20 spaces but found 12 indent 221:1 error Expected indentation of 16 spaces but found 10 indent 222:1 error Expected indentation of 20 spaces but found 12 indent 223:1 error Expected indentation of 16 spaces but found 10 indent 224:1 error Expected indentation of 20 spaces but found 12 indent 225:1 error Expected indentation of 16 spaces but found 10 indent 226:1 error Expected indentation of 20 spaces but found 12 indent 227:1 error Expected indentation of 20 spaces but found 12 indent 228:1 error Expected indentation of 16 spaces but found 10 indent 229:1 error Expected indentation of 20 spaces but found 12 indent 229:13 error Unexpected lexical declaration in case block no-case-declarations 230:1 error Expected indentation of 20 spaces but found 12 indent 231:1 error Expected indentation of 20 spaces but found 12 indent 232:1 error Expected indentation of 16 spaces but found 10 indent 233:1 error Expected indentation of 20 spaces but found 12 indent 234:1 error Expected indentation of 16 spaces but found 8 indent 235:1 error Expected indentation of 12 spaces but found 6 indent 236:1 error Expected indentation of 16 spaces but found 8 indent 236:9 error Unexpected console statement no-console 237:1 error Expected indentation of 12 spaces but found 6 indent 238:1 error Expected indentation of 8 spaces but found 4 indent 239:1 error Expected indentation of 8 spaces but found 4 indent 240:1 error Expected indentation of 8 spaces but found 4 indent 241:1 error Expected indentation of 8 spaces but found 4 indent 242:1 error Expected indentation of 4 spaces but found 2 indent 244:1 error Expected indentation of 4 spaces but found 2 indent 245:1 error Expected indentation of 8 spaces but found 4 indent 246:1 error Expected indentation of 12 spaces but found 6 indent 247:1 error Expected indentation of 8 spaces but found 4 indent 249:1 error Expected indentation of 8 spaces but found 4 indent 259:1 error Expected indentation of 4 spaces but found 2 indent 262:1 error Expected indentation of 4 spaces but found 2 indent 263:1 error Expected indentation of 4 spaces but found 2 indent 264:1 error Expected indentation of 4 spaces but found 2 indent 267:1 error Expected indentation of 4 spaces but found 2 indent 268:1 error Expected indentation of 4 spaces but found 2 indent 269:1 error Expected indentation of 4 spaces but found 2 indent 273:1 error Expected indentation of 4 spaces but found 2 indent 274:1 error Expected indentation of 8 spaces but found 4 indent 275:1 error Expected indentation of 8 spaces but found 4 indent 277:1 error Expected indentation of 8 spaces but found 4 indent 278:1 error Expected indentation of 4 spaces but found 2 indent 280:1 error Expected indentation of 4 spaces but found 2 indent 281:1 error Expected indentation of 8 spaces but found 4 indent 282:1 error Expected indentation of 12 spaces but found 6 indent 283:1 error Expected indentation of 16 spaces but found 10 indent 284:1 error Expected indentation of 16 spaces but found 10 indent 285:1 error Expected indentation of 20 spaces but found 14 indent 286:1 error Expected indentation of 16 spaces but found 10 indent 287:1 error Expected indentation of 12 spaces but found 6 indent 288:1 error Expected indentation of 8 spaces but found 4 indent 289:1 error Expected indentation of 4 spaces but found 2 indent 292:1 error Expected indentation of 4 spaces but found 2 indent 293:1 error Expected indentation of 4 spaces but found 2 indent 297:1 error Expected indentation of 4 spaces but found 2 indent 298:1 error Expected indentation of 8 spaces but found 4 indent 299:1 error Expected indentation of 8 spaces but found 4 indent 301:1 error Expected indentation of 8 spaces but found 4 indent 302:1 error Expected indentation of 4 spaces but found 2 indent 303:1 error Expected indentation of 4 spaces but found 2 indent 304:1 error Expected indentation of 8 spaces but found 4 indent 305:1 error Expected indentation of 12 spaces but found 6 indent 306:1 error Expected indentation of 16 spaces but found 10 indent 307:1 error Expected indentation of 16 spaces but found 10 indent 308:1 error Expected indentation of 20 spaces but found 14 indent 309:1 error Expected indentation of 16 spaces but found 10 indent 310:1 error Expected indentation of 12 spaces but found 6 indent 311:1 error Expected indentation of 8 spaces but found 4 indent 312:1 error Expected indentation of 4 spaces but found 2 indent 315:1 error Expected indentation of 4 spaces but found 2 indent 316:1 error Expected indentation of 4 spaces but found 2 indent 320:1 error Expected indentation of 4 spaces but found 2 indent 321:1 error Expected indentation of 8 spaces but found 4 indent 322:1 error Expected indentation of 8 spaces but found 4 indent 323:1 error Expected indentation of 12 spaces but found 6 indent 324:1 error Expected indentation of 8 spaces but found 4 indent 325:1 error Expected indentation of 4 spaces but found 2 indent 327:1 error Expected indentation of 4 spaces but found 2 indent 329:1 error Expected indentation of 8 spaces but found 4 indent 330:1 error Expected indentation of 12 spaces but found 6 indent 331:1 error Expected indentation of 16 spaces but found 10 indent 332:1 error Expected indentation of 16 spaces but found 10 indent 333:1 error Expected indentation of 20 spaces but found 14 indent 335:1 error Expected indentation of 20 spaces but found 14 indent 336:1 error Expected indentation of 16 spaces but found 10 indent 337:1 error Expected indentation of 12 spaces but found 6 indent 338:1 error Expected indentation of 8 spaces but found 4 indent 339:1 error Expected indentation of 4 spaces but found 2 indent 342:1 error Expected indentation of 4 spaces but found 2 indent 346:1 error Expected indentation of 4 spaces but found 2 indent 347:1 error Expected indentation of 8 spaces but found 4 indent 348:1 error Expected indentation of 8 spaces but found 4 indent 350:1 error Expected indentation of 8 spaces but found 4 indent 351:1 error Expected indentation of 4 spaces but found 2 indent 353:1 error Expected indentation of 4 spaces but found 2 indent 354:1 error Expected indentation of 8 spaces but found 4 indent 355:1 error Expected indentation of 12 spaces but found 6 indent 356:1 error Expected indentation of 16 spaces but found 10 indent 357:1 error Expected indentation of 16 spaces but found 10 indent 358:1 error Expected indentation of 20 spaces but found 14 indent 359:1 error Expected indentation of 24 spaces but found 18 indent 360:1 error Expected indentation of 20 spaces but found 14 indent 361:1 error Expected indentation of 16 spaces but found 10 indent 362:1 error Expected indentation of 12 spaces but found 6 indent 363:1 error Expected indentation of 8 spaces but found 4 indent 364:1 error Expected indentation of 4 spaces but found 2 indent 367:1 error Expected indentation of 4 spaces but found 2 indent 368:1 error Expected indentation of 4 spaces but found 2 indent 381:1 error Expected indentation of 4 spaces but found 2 indent 382:1 error Expected indentation of 4 spaces but found 2 indent 383:1 error Expected indentation of 4 spaces but found 2 indent 384:1 error Expected indentation of 4 spaces but found 2 indent 385:1 error Expected indentation of 4 spaces but found 2 indent 386:1 error Expected indentation of 4 spaces but found 2 indent 387:1 error Expected indentation of 4 spaces but found 2 indent 388:1 error Expected indentation of 4 spaces but found 2 indent ? 284 problems (284 errors, 0 warnings) 271 errors and 0 warnings potentially fixable with the `--fix` option. ERROR in ./modules/genomic_browser/jsx/profileColumnFormatter.js Module Error (from ./node_modules/eslint-loader/index.js): /var/www/loris/modules/genomic_browser/jsx/profileColumnFormatter.js 10:1 error Expected indentation of 4 spaces but found 2 indent 11:1 error Expected indentation of 4 spaces but found 2 indent 11:7 error 'loris' is not defined no-undef 12:1 error Expected indentation of 8 spaces but found 4 indent 13:1 error Expected indentation of 4 spaces but found 2 indent 15:1 error Expected indentation of 4 spaces but found 2 indent 16:1 error Expected indentation of 4 spaces but found 2 indent 17:1 error Expected indentation of 4 spaces but found 2 indent 18:1 error Expected indentation of 8 spaces but found 4 indent 19:1 error Expected indentation of 4 spaces but found 2 indent 21:1 error Expected indentation of 4 spaces but found 2 indent 22:1 error Expected indentation of 4 spaces but found 2 indent 24:1 error Expected indentation of 8 spaces but found 6 indent 24:19 error 'loris' is not defined no-undef 25:1 error Expected indentation of 8 spaces but found 6 indent 26:1 error Expected indentation of 12 spaces but found 8 indent 27:1 error Expected indentation of 8 spaces but found 6 indent 28:1 error Expected indentation of 8 spaces but found 6 indent 31:1 error Expected indentation of 8 spaces but found 6 indent 32:1 error Expected indentation of 12 spaces but found 8 indent 32:14 error 'loris' is not defined no-undef 33:1 error Expected indentation of 8 spaces but found 6 indent 34:1 error Expected indentation of 8 spaces but found 6 indent 36:1 error Expected indentation of 8 spaces but found 6 indent 37:1 error Expected indentation of 12 spaces but found 8 indent 38:1 error Expected indentation of 16 spaces but found 10 indent 39:1 error Expected indentation of 20 spaces but found 12 indent 39:34 error 'loris' is not defined no-undef 40:1 error Expected indentation of 24 spaces but found 14 indent 41:1 error Expected indentation of 24 spaces but found 14 indent 42:1 error Expected indentation of 20 spaces but found 12 indent 43:1 error Expected indentation of 16 spaces but found 10 indent 44:1 error Expected indentation of 12 spaces but found 8 indent 45:1 error Expected indentation of 8 spaces but found 6 indent 46:1 error Expected indentation of 12 spaces but found 8 indent 47:1 error Expected indentation of 16 spaces but found 10 indent 48:1 error Expected indentation of 12 spaces but found 8 indent 49:1 error Expected indentation of 8 spaces but found 6 indent 50:1 error Expected indentation of 8 spaces but found 6 indent 54:1 error Expected indentation of 8 spaces but found 6 indent 55:1 error Expected indentation of 12 spaces but found 8 indent 56:1 error Expected indentation of 16 spaces but found 10 indent 57:1 error Expected indentation of 20 spaces but found 12 indent 58:1 error Expected indentation of 24 spaces but found 14 indent 59:1 error Expected indentation of 24 spaces but found 14 indent 59:24 error 'loris' is not defined no-undef 60:1 error Expected indentation of 28 spaces but found 16 indent 61:1 error Expected indentation of 24 spaces but found 14 indent 62:1 error Expected indentation of 20 spaces but found 12 indent 63:1 error Expected indentation of 24 spaces but found 14 indent 64:1 error Expected indentation of 20 spaces but found 12 indent 65:1 error Expected indentation of 16 spaces but found 10 indent 66:1 error Expected indentation of 12 spaces but found 8 indent 67:1 error Expected indentation of 8 spaces but found 6 indent 68:1 error Expected indentation of 12 spaces but found 8 indent 69:1 error Expected indentation of 16 spaces but found 10 indent 70:1 error Expected indentation of 12 spaces but found 8 indent 71:1 error Expected indentation of 8 spaces but found 6 indent 72:1 error Expected indentation of 8 spaces but found 6 indent 74:1 error Expected indentation of 8 spaces but found 6 indent 75:1 error Expected indentation of 12 spaces but found 7 indent 76:1 error Expected indentation of 8 spaces but found 5 indent 77:1 error Expected indentation of 4 spaces but found 2 indent 78:1 error Expected indentation of 4 spaces but found 2 indent ? 64 problems (64 errors, 0 warnings) 59 errors and 0 warnings potentially fixable with the `--fix` option. ERROR in ./modules/help_editor/jsx/help_editor.js Module Error (from ./node_modules/eslint-loader/index.js): /var/www/loris/modules/help_editor/jsx/help_editor.js 1:8 error 'FilterableDataTable' is defined but never used no-unused-vars 2:8 error 'Loader' is defined but never used no-unused-vars 17:26 error 'React' is not defined no-undef 18:1 error Expected indentation of 4 spaces but found 2 indent 19:1 error Expected indentation of 8 spaces but found 4 indent 21:1 error Expected indentation of 8 spaces but found 4 indent 22:1 error Expected indentation of 12 spaces but found 6 indent 23:1 error Expected indentation of 12 spaces but found 6 indent 24:1 error Expected indentation of 12 spaces but found 6 indent 25:1 error Expected indentation of 12 spaces but found 6 indent 26:1 error Expected indentation of 8 spaces but found 4 indent 28:1 error Expected indentation of 8 spaces but found 4 indent 29:1 error Expected indentation of 8 spaces but found 4 indent 30:1 error Expected indentation of 4 spaces but found 2 indent 32:1 error Expected indentation of 4 spaces but found 2 indent 33:1 error Expected indentation of 8 spaces but found 4 indent 34:1 error Expected indentation of 12 spaces but found 6 indent 34:53 error Unnecessary semicolon no-extra-semi 35:1 error Expected indentation of 4 spaces but found 2 indent 37:1 error Expected indentation of 4 spaces but found 2 indent 42:1 error Expected indentation of 4 spaces but found 2 indent 43:1 error Expected indentation of 8 spaces but found 4 indent 44:1 error Expected indentation of 12 spaces but found 6 indent 45:1 error Expected indentation of 12 spaces but found 6 indent 46:1 error Expected indentation of 12 spaces but found 6 indent 47:1 error Expected indentation of 16 spaces but found 8 indent 48:1 error Expected indentation of 16 spaces but found 8 indent 48:9 error Unexpected console statement no-console 49:1 error Expected indentation of 12 spaces but found 6 indent 50:1 error Expected indentation of 4 spaces but found 2 indent 52:1 error Expected indentation of 4 spaces but found 1 indent 61:1 error Expected indentation of 4 spaces but found 2 indent 62:1 error Expected indentation of 8 spaces but found 4 indent 63:1 error Expected indentation of 8 spaces but found 4 indent 64:1 error Expected indentation of 8 spaces but found 4 indent 65:1 error Expected indentation of 8 spaces but found 4 indent 66:1 error Expected indentation of 12 spaces but found 6 indent 66:13 error 'loris' is not defined no-undef 68:1 error Expected indentation of 12 spaces but found 6 indent 69:1 error Expected indentation of 12 spaces but found 6 indent 70:1 error Expected indentation of 8 spaces but found 4 indent 71:1 error Expected indentation of 12 spaces but found 6 indent 71:13 error 'loris' is not defined no-undef 73:1 error Expected indentation of 12 spaces but found 6 indent 74:1 error Expected indentation of 8 spaces but found 4 indent 76:1 error Expected indentation of 8 spaces but found 4 indent 77:1 error Expected indentation of 4 spaces but found 2 indent 79:1 error Expected indentation of 4 spaces but found 2 indent 82:1 error Expected indentation of 8 spaces but found 4 indent 83:1 error Expected indentation of 12 spaces but found 6 indent 84:1 error Expected indentation of 8 spaces but found 4 indent 86:1 error Expected indentation of 8 spaces but found 4 indent 87:1 error Expected indentation of 8 spaces but found 4 indent 88:1 error Expected indentation of 12 spaces but found 6 indent 89:1 error Expected indentation of 8 spaces but found 4 indent 91:1 error Expected indentation of 8 spaces but found 4 indent 92:1 error Expected indentation of 8 spaces but found 4 indent 96:1 error Expected indentation of 8 spaces but found 4 indent 97:1 error Expected indentation of 12 spaces but found 6 indent 98:1 error Expected indentation of 12 spaces but found 6 indent 99:1 error Expected indentation of 16 spaces but found 8 indent 100:1 error Expected indentation of 16 spaces but found 8 indent 101:1 error Expected indentation of 12 spaces but found 6 indent 102:1 error Expected indentation of 12 spaces but found 6 indent 103:1 error Expected indentation of 12 spaces but found 6 indent 104:1 error Expected indentation of 12 spaces but found 6 indent 105:1 error Expected indentation of 12 spaces but found 6 indent 106:1 error Expected indentation of 16 spaces but found 8 indent 107:1 error Expected indentation of 16 spaces but found 8 indent 108:1 error Expected indentation of 12 spaces but found 6 indent 109:1 error Expected indentation of 8 spaces but found 4 indent 111:1 error Expected indentation of 8 spaces but found 4 indent 112:1 error Expected indentation of 12 spaces but found 6 indent 113:1 error Expected indentation of 16 spaces but found 8 indent 114:1 error Expected indentation of 16 spaces but found 8 indent 115:1 error Expected indentation of 16 spaces but found 8 indent 116:1 error Expected indentation of 16 spaces but found 8 indent 117:1 error Expected indentation of 12 spaces but found 6 indent 118:1 error Expected indentation of 8 spaces but found 4 indent 119:1 error Expected indentation of 4 spaces but found 2 indent 123:1 error Expected indentation of 4 spaces but found 2 indent 127:1 error Expected indentation of 4 spaces but found 2 indent 127:3 error 'ReactDOM' is not defined no-undef 128:1 error Expected indentation of 8 spaces but found 4 indent 129:1 error Expected indentation of 12 spaces but found 6 indent 130:1 error Expected indentation of 12 spaces but found 6 indent 130:16 error 'loris' is not defined no-undef 131:1 error Expected indentation of 8 spaces but found 4 indent 132:1 error Expected indentation of 8 spaces but found 4 indent 133:1 error Expected indentation of 4 spaces but found 2 indent ? 90 problems (90 errors, 0 warnings) 82 errors and 0 warnings potentially fixable with the `--fix` option. ERROR in ./modules/imaging_browser/jsx/ImagePanel.js Module Error (from ./node_modules/eslint-loader/index.js): /var/www/loris/modules/imaging_browser/jsx/ImagePanel.js 11:1 error Expected indentation of 4 spaces but found 2 indent 12:1 error Expected indentation of 8 spaces but found 4 indent 13:1 error Expected indentation of 4 spaces but found 2 indent 15:1 error Expected indentation of 4 spaces but found 2 indent 16:1 error Expected indentation of 8 spaces but found 4 indent 16:5 error '$' is not defined no-undef 17:1 error Expected indentation of 4 spaces but found 2 indent 19:1 error Expected indentation of 4 spaces but found 2 indent 20:1 error Expected indentation of 8 spaces but found 4 indent 21:1 error Expected indentation of 8 spaces but found 4 indent 22:1 error Expected indentation of 12 spaces but found 6 indent 23:1 error Expected indentation of 16 spaces but found 25 indent 24:1 error Expected indentation of 12 spaces but found 22 indent 25:1 error Expected indentation of 8 spaces but found 4 indent 26:1 error Expected indentation of 12 spaces but found 6 indent 27:1 error Expected indentation of 16 spaces but found 25 indent 28:1 error Expected indentation of 12 spaces but found 22 indent 29:1 error Expected indentation of 8 spaces but found 4 indent 31:1 error Expected indentation of 8 spaces but found 4 indent 32:1 error Expected indentation of 8 spaces but found 4 indent 33:1 error Expected indentation of 12 spaces but found 6 indent 34:1 error Expected indentation of 16 spaces but found 20 indent 35:1 error Expected indentation of 12 spaces but found 14 indent 36:1 error Expected indentation of 8 spaces but found 4 indent 37:1 error Expected indentation of 12 spaces but found 6 indent 38:1 error Expected indentation of 16 spaces but found 20 indent 39:1 error Expected indentation of 12 spaces but found 14 indent 40:1 error Expected indentation of 8 spaces but found 4 indent 41:1 error Expected indentation of 8 spaces but found 4 indent 42:1 error Expected indentation of 12 spaces but found 6 indent 43:1 error Expected indentation of 16 spaces but found 8 indent 44:1 error Expected indentation of 20 spaces but found 10 indent 45:1 error Expected indentation of 24 spaces but found 12 indent 46:1 error Expected indentation of 24 spaces but found 12 indent 47:1 error Expected indentation of 24 spaces but found 12 indent 48:1 error Expected indentation of 24 spaces but found 12 indent 50:1 error Expected indentation of 20 spaces but found 10 indent 51:1 error Expected indentation of 20 spaces but found 10 indent 52:1 error Expected indentation of 16 spaces but found 8 indent 53:1 error Expected indentation of 12 spaces but found 6 indent 54:1 error Expected indentation of 8 spaces but found 4 indent 55:1 error Expected indentation of 8 spaces but found 4 indent 57:1 error Expected indentation of 12 spaces but found 6 indent 58:1 error Expected indentation of 16 spaces but found 8 indent 59:1 error Expected indentation of 20 spaces but found 15 indent 60:1 error Expected indentation of 16 spaces but found 8 indent 61:1 error Expected indentation of 20 spaces but found 10 indent 62:1 error Expected indentation of 16 spaces but found 8 indent 63:1 error Expected indentation of 16 spaces but found 8 indent 64:1 error Expected indentation of 16 spaces but found 8 indent 65:1 error Expected indentation of 16 spaces but found 8 indent 66:1 error Expected indentation of 12 spaces but found 6 indent 67:1 error Expected indentation of 8 spaces but found 4 indent 68:1 error Expected indentation of 4 spaces but found 2 indent 72:1 error Expected indentation of 4 spaces but found 2 indent 73:1 error Expected indentation of 4 spaces but found 2 indent 74:1 error Expected indentation of 4 spaces but found 2 indent 75:1 error Expected indentation of 4 spaces but found 2 indent 76:1 error Expected indentation of 4 spaces but found 2 indent 77:1 error Expected indentation of 4 spaces but found 2 indent 81:1 error Expected indentation of 4 spaces but found 2 indent 82:1 error Expected indentation of 8 spaces but found 4 indent 83:1 error Expected indentation of 4 spaces but found 2 indent 85:1 error Expected indentation of 4 spaces but found 2 indent 86:1 error Expected indentation of 8 spaces but found 4 indent 86:5 error '$' is not defined no-undef 86:7 error 'ReactDOM' is not defined no-undef 87:1 error Expected indentation of 4 spaces but found 2 indent 89:1 error Expected indentation of 4 spaces but found 2 indent 91:1 error Expected indentation of 8 spaces but found 4 indent 91:5 error '$' is not defined no-undef 91:7 error 'ReactDOM' is not defined no-undef 92:1 error Expected indentation of 12 spaces but found 6 indent 93:1 error Expected indentation of 8 spaces but found 4 indent 94:1 error Expected indentation of 4 spaces but found 2 indent 96:1 error Expected indentation of 4 spaces but found 2 indent 97:1 error Expected indentation of 8 spaces but found 4 indent 98:1 error Expected indentation of 12 spaces but found 6 indent 99:1 error Expected indentation of 16 spaces but found 15 indent 100:1 error Expected indentation of 16 spaces but found 8 indent 101:1 error Expected indentation of 20 spaces but found 8 indent 102:1 error Expected indentation of 24 spaces but found 10 indent 103:1 error Expected indentation of 24 spaces but found 10 indent 104:1 error Expected indentation of 28 spaces but found 12 indent 106:1 error Expected indentation of 28 spaces but found 12 indent 108:1 error Expected indentation of 28 spaces but found 12 indent 110:1 error Expected indentation of 24 spaces but found 10 indent 111:1 error Expected indentation of 24 spaces but found 10 indent 112:1 error Expected indentation of 24 spaces but found 10 indent 113:1 error Expected indentation of 28 spaces but found 12 indent 114:1 error Expected indentation of 24 spaces but found 10 indent 115:1 error Expected indentation of 20 spaces but found 8 indent 116:1 error Expected indentation of 20 spaces but found 8 indent 117:1 error Expected indentation of 24 spaces but found 10 indent 118:1 error Expected indentation of 24 spaces but found 10 indent 119:1 error Expected indentation of 28 spaces but found 12 indent 120:1 error Expected indentation of 24 spaces but found 10 indent 122:1 error Expected indentation of 24 spaces but found 10 indent 123:1 error Expected indentation of 24 spaces but found 10 indent 124:1 error Expected indentation of 28 spaces but found 12 indent 125:1 error Expected indentation of 24 spaces but found 10 indent 127:1 error Expected indentation of 24 spaces but found 10 indent 128:1 error Expected indentation of 24 spaces but found 10 indent 129:1 error Expected indentation of 28 spaces but found 12 indent 130:1 error Expected indentation of 24 spaces but found 10 indent 131:1 error Expected indentation of 20 spaces but found 8 indent 132:1 error Expected indentation of 20 spaces but found 8 indent 133:1 error Expected indentation of 24 spaces but found 10 indent 134:1 error Expected indentation of 24 spaces but found 10 indent 135:1 error Expected indentation of 28 spaces but found 12 indent 136:1 error Expected indentation of 24 spaces but found 10 indent 138:1 error Expected indentation of 24 spaces but found 10 indent 139:1 error Expected indentation of 24 spaces but found 10 indent 140:1 error Expected indentation of 28 spaces but found 12 indent 141:1 error Expected indentation of 24 spaces but found 10 indent 143:1 error Expected indentation of 24 spaces but found 10 indent 144:1 error Expected indentation of 24 spaces but found 10 indent 145:1 error Expected indentation of 28 spaces but found 12 indent 146:1 error Expected indentation of 24 spaces but found 10 indent 147:1 error Expected indentation of 20 spaces but found 8 indent 148:1 error Expected indentation of 20 spaces but found 8 indent 149:1 error Expected indentation of 24 spaces but found 10 indent 150:1 error Expected indentation of 24 spaces but found 10 indent 151:1 error Expected indentation of 28 spaces but found 12 indent 152:1 error Expected indentation of 24 spaces but found 10 indent 154:1 error Expected indentation of 24 spaces but found 10 indent 155:1 error Expected indentation of 24 spaces but found 10 indent 156:1 error Expected indentation of 28 spaces but found 12 indent 157:1 error Expected indentation of 24 spaces but found 10 indent 159:1 error Expected indentation of 24 spaces but found 10 indent 160:1 error Expected indentation of 24 spaces but found 10 indent 161:1 error Expected indentation of 28 spaces but found 12 indent 162:1 error Expected indentation of 24 spaces but found 10 indent 163:1 error Expected indentation of 20 spaces but found 8 indent 164:1 error Expected indentation of 20 spaces but found 8 indent 165:1 error Expected indentation of 24 spaces but found 10 indent 166:1 error Expected indentation of 24 spaces but found 10 indent 167:1 error Expected indentation of 28 spaces but found 12 indent 168:1 error Expected indentation of 24 spaces but found 10 indent 170:1 error Expected indentation of 24 spaces but found 10 indent 171:1 error Expected indentation of 24 spaces but found 10 indent 172:1 error Expected indentation of 28 spaces but found 12 indent 173:1 error Expected indentation of 24 spaces but found 10 indent 175:1 error Expected indentation of 24 spaces but found 10 indent 176:1 error Expected indentation of 24 spaces but found 10 indent 177:1 error Expected indentation of 28 spaces but found 12 indent 178:1 error Expected indentation of 24 spaces but found 10 indent 179:1 error Expected indentation of 20 spaces but found 8 indent 180:1 error Expected indentation of 20 spaces but found 8 indent 181:1 error Expected indentation of 24 spaces but found 10 indent 183:1 error Expected indentation of 24 spaces but found 10 indent 184:1 error Expected indentation of 24 spaces but found 10 indent 185:1 error Expected indentation of 28 spaces but found 12 indent 186:1 error Expected indentation of 24 spaces but found 10 indent 188:1 error Expected indentation of 24 spaces but found 10 indent 190:1 error Expected indentation of 24 spaces but found 10 indent 191:1 error Expected indentation of 24 spaces but found 10 indent 192:1 error Expected indentation of 28 spaces but found 12 indent 193:1 error Expected indentation of 24 spaces but found 10 indent 195:1 error Expected indentation of 24 spaces but found 10 indent 197:1 error Expected indentation of 24 spaces but found 10 indent 198:1 error Expected indentation of 24 spaces but found 10 indent 199:1 error Expected indentation of 28 spaces but found 12 indent 200:1 error Expected indentation of 24 spaces but found 10 indent 201:1 error Expected indentation of 20 spaces but found 8 indent 202:1 error Expected indentation of 20 spaces but found 8 indent 203:1 error Expected indentation of 24 spaces but found 10 indent 205:1 error Expected indentation of 24 spaces but found 10 indent 206:1 error Expected indentation of 24 spaces but found 10 indent 207:1 error Expected indentation of 28 spaces but found 12 indent 208:1 error Expected indentation of 24 spaces but found 10 indent 209:1 error Expected indentation of 24 spaces but found 10 indent 211:1 error Expected indentation of 24 spaces but found 10 indent 212:1 error Expected indentation of 24 spaces but found 10 indent 213:1 error Expected indentation of 28 spaces but found 12 indent 214:1 error Expected indentation of 24 spaces but found 10 indent 215:1 error Expected indentation of 24 spaces but found 10 indent 216:1 error Expected indentation of 20 spaces but found 8 indent 217:1 error Expected indentation of 16 spaces but found 8 indent 218:1 error Expected indentation of 12 spaces but found 6 indent 219:1 error Expected indentation of 8 spaces but found 4 indent 220:1 error Expected indentation of 4 spaces but found 2 indent 223:1 error Expected indentation of 4 spaces but found 2 indent 227:1 error Expected indentation of 4 spaces but found 2 indent 228:1 error Expected indentation of 8 spaces but found 4 indent 229:1 error Expected indentation of 4 spaces but found 2 indent 231:1 error Expected indentation of 4 spaces but found 2 indent 232:1 error Expected indentation of 8 spaces but found 4 indent 233:1 error Expected indentation of 8 spaces but found 4 indent 234:1 error Expected indentation of 12 spaces but found 6 indent 235:1 error Expected indentation of 16 spaces but found 8 indent 236:1 error Expected indentation of 12 spaces but found 6 indent 237:1 error Expected indentation of 8 spaces but found 4 indent 238:1 error Expected indentation of 8 spaces but found 4 indent 239:1 error Expected indentation of 8 spaces but found 4 indent 240:1 error Expected indentation of 12 spaces but found 6 indent 241:1 error Expected indentation of 12 spaces but found 6 indent 242:1 error Expected indentation of 16 spaces but found 8 indent 243:1 error Expected indentation of 20 spaces but found 10 indent 244:1 error Expected indentation of 24 spaces but found 12 indent 245:1 error Expected indentation of 28 spaces but found 20 indent 246:1 error Expected indentation of 28 spaces but found 20 indent 247:1 error Expected indentation of 24 spaces but found 12 indent 248:1 error Expected indentation of 20 spaces but found 10 indent 249:1 error Expected indentation of 16 spaces but found 8 indent 250:1 error Expected indentation of 12 spaces but found 6 indent 251:1 error Expected indentation of 12 spaces but found 6 indent 252:1 error Expected indentation of 16 spaces but found 8 indent 256:1 error Expected indentation of 16 spaces but found 8 indent 257:1 error Expected indentation of 20 spaces but found 10 indent 258:1 error Expected indentation of 16 spaces but found 8 indent 259:1 error Expected indentation of 12 spaces but found 6 indent 260:1 error Expected indentation of 8 spaces but found 4 indent 261:1 error Expected indentation of 12 spaces but found 6 indent 262:1 error Expected indentation of 16 spaces but found 8 indent 263:1 error Expected indentation of 20 spaces but found 10 indent 264:1 error Expected indentation of 16 spaces but found 8 indent 265:1 error Expected indentation of 12 spaces but found 6 indent 266:1 error Expected indentation of 8 spaces but found 4 indent 267:1 error Expected indentation of 8 spaces but found 4 indent 268:1 error Expected indentation of 12 spaces but found 6 indent 269:1 error Expected indentation of 16 spaces but found 8 indent 270:1 error Expected indentation of 16 spaces but found 8 indent 271:1 error Expected indentation of 12 spaces but found 6 indent 272:1 error Expected indentation of 8 spaces but found 4 indent 273:1 error Expected indentation of 4 spaces but found 2 indent 276:1 error Expected indentation of 4 spaces but found 2 indent 277:1 error Expected indentation of 4 spaces but found 2 indent 278:1 error Expected indentation of 4 spaces but found 2 indent 279:1 error Expected indentation of 4 spaces but found 2 indent 280:1 error Expected indentation of 4 spaces but found 2 indent 281:1 error Expected indentation of 4 spaces but found 2 indent 282:1 error Expected indentation of 4 spaces but found 2 indent 286:1 error Expected indentation of 4 spaces but found 2 indent 287:1 error Expected indentation of 8 spaces but found 4 indent 288:1 error Expected indentation of 4 spaces but found 2 indent 290:1 error Expected indentation of 4 spaces but found 2 indent 291:1 error Expected indentation of 8 spaces but found 4 indent 292:1 error Expected indentation of 8 spaces but found 4 indent 293:1 error Expected indentation of 12 spaces but found 6 indent 294:1 error Expected indentation of 16 spaces but found 8 indent 295:1 error Expected indentation of 12 spaces but found 6 indent 296:1 error Expected indentation of 8 spaces but found 4 indent 297:1 error Expected indentation of 8 spaces but found 4 indent 298:1 error Expected indentation of 12 spaces but found 6 indent 299:1 error Expected indentation of 16 spaces but found 8 indent 300:1 error Expected indentation of 16 spaces but found 8 indent 301:1 error Expected indentation of 12 spaces but found 6 indent 302:1 error Expected indentation of 8 spaces but found 4 indent 303:1 error Expected indentation of 4 spaces but found 2 indent 306:1 error Expected indentation of 4 spaces but found 2 indent 307:1 error Expected indentation of 4 spaces but found 2 indent 311:1 error Expected indentation of 4 spaces but found 2 indent 312:1 error Expected indentation of 8 spaces but found 4 indent 313:1 error Expected indentation of 4 spaces but found 2 indent 315:1 error Expected indentation of 4 spaces but found 2 indent 316:1 error Expected indentation of 8 spaces but found 4 indent 317:1 error Expected indentation of 8 spaces but found 4 indent 318:1 error Expected indentation of 12 spaces but found 6 indent 321:1 error Expected indentation of 20 spaces but found 27 indent 322:1 error Expected indentation of 16 spaces but found 25 indent 323:1 error Expected indentation of 12 spaces but found 22 indent 324:1 error Expected indentation of 8 spaces but found 4 indent 325:1 error Expected indentation of 12 spaces but found 6 indent 326:1 error Expected indentation of 8 spaces but found 4 indent 328:1 error Expected indentation of 8 spaces but found 4 indent 329:1 error Expected indentation of 12 spaces but found 6 indent 330:1 error Expected indentation of 16 spaces but found 8 indent 331:1 error Expected indentation of 16 spaces but found 8 indent 332:1 error Expected indentation of 16 spaces but found 8 indent 333:1 error Expected indentation of 16 spaces but found 8 indent 334:1 error Expected indentation of 16 spaces but found 8 indent 335:1 error Expected indentation of 16 spaces but found 8 indent 336:1 error Expected indentation of 12 spaces but found 6 indent 337:1 error Expected indentation of 8 spaces but found 4 indent 338:1 error Expected indentation of 4 spaces but found 2 indent 341:1 error Expected indentation of 4 spaces but found 2 indent 342:1 error Expected indentation of 4 spaces but found 2 indent 343:1 error Expected indentation of 4 spaces but found 2 indent 347:1 error Expected indentation of 4 spaces but found 2 indent 348:1 error Expected indentation of 8 spaces but found 4 indent 349:1 error Expected indentation of 4 spaces but found 2 indent 351:1 error Expected indentation of 4 spaces but found 2 indent 352:1 error Expected indentation of 8 spaces but found 4 indent 353:1 error Expected indentation of 12 spaces but found 6 indent 354:1 error Expected indentation of 16 spaces but found 8 indent 355:1 error Expected indentation of 16 spaces but found 8 indent 356:1 error Expected indentation of 16 spaces but found 8 indent 357:1 error Expected indentation of 16 spaces but found 8 indent 358:1 error Expected indentation of 16 spaces but found 8 indent 359:1 error Expected indentation of 16 spaces but found 8 indent 360:1 error Expected indentation of 12 spaces but found 6 indent 361:1 error Expected indentation of 8 spaces but found 4 indent 362:1 error Expected indentation of 4 spaces but found 2 indent 365:1 error Expected indentation of 4 spaces but found 2 indent 366:1 error Expected indentation of 4 spaces but found 2 indent 367:1 error Expected indentation of 4 spaces but found 2 indent 371:1 error Expected indentation of 4 spaces but found 2 indent 372:1 error Expected indentation of 8 spaces but found 4 indent 373:1 error Expected indentation of 4 spaces but found 2 indent 375:1 error Expected indentation of 4 spaces but found 2 indent 377:1 error Expected indentation of 8 spaces but found 4 indent 378:1 error Expected indentation of 8 spaces but found 4 indent 379:1 error Expected indentation of 12 spaces but found 6 indent 382:1 error Expected indentation of 8 spaces but found 4 indent 384:1 error Expected indentation of 8 spaces but found 4 indent 385:1 error Expected indentation of 12 spaces but found 6 indent 386:1 error Expected indentation of 16 spaces but found 8 indent 387:1 error Expected indentation of 16 spaces but found 8 indent 388:1 error Expected indentation of 16 spaces but found 8 indent 389:1 error Expected indentation of 16 spaces but found 8 indent 390:1 error Expected indentation of 16 spaces but found 8 indent 391:1 error Expected indentation of 20 spaces but found 10 indent 392:1 error Expected indentation of 24 spaces but found 12 indent 393:1 error Expected indentation of 24 spaces but found 12 indent 394:1 error Expected indentation of 24 spaces but found 12 indent 395:1 error Expected indentation of 20 spaces but found 10 indent 396:1 error Expected indentation of 16 spaces but found 8 indent 397:1 error Expected indentation of 16 spaces but found 8 indent 398:1 error Expected indentation of 16 spaces but found 8 indent 399:1 error Expected indentation of 12 spaces but found 6 indent 400:1 error Expected indentation of 8 spaces but found 4 indent 401:1 error Expected indentation of 4 spaces but found 2 indent 404:1 error Expected indentation of 4 spaces but found 2 indent 405:1 error Expected indentation of 4 spaces but found 2 indent 406:1 error Expected indentation of 4 spaces but found 2 indent 407:1 error Expected indentation of 4 spaces but found 2 indent 411:1 error Expected indentation of 4 spaces but found 2 indent 412:1 error Expected indentation of 8 spaces but found 4 indent 413:1 error Expected indentation of 4 spaces but found 2 indent 415:1 error Expected indentation of 4 spaces but found 2 indent 416:1 error Expected indentation of 8 spaces but found 4 indent 417:1 error Expected indentation of 12 spaces but found 6 indent 418:1 error Expected indentation of 16 spaces but found 8 indent 419:1 error Expected indentation of 16 spaces but found 8 indent 420:1 error Expected indentation of 16 spaces but found 8 indent 421:1 error Expected indentation of 16 spaces but found 8 indent 422:1 error Expected indentation of 12 spaces but found 6 indent 423:1 error Expected indentation of 8 spaces but found 4 indent 424:1 error Expected indentation of 4 spaces but found 2 indent 427:1 error Expected indentation of 4 spaces but found 2 indent 428:1 error Expected indentation of 4 spaces but found 2 indent 432:1 error Expected indentation of 4 spaces but found 2 indent 433:1 error Expected indentation of 8 spaces but found 4 indent 434:1 error Expected indentation of 4 spaces but found 2 indent 436:1 error Expected indentation of 4 spaces but found 2 indent 437:1 error Expected indentation of 8 spaces but found 4 indent 438:1 error Expected indentation of 12 spaces but found 6 indent 439:1 error Expected indentation of 16 spaces but found 8 indent 440:1 error Expected indentation of 20 spaces but found 10 indent 441:1 error Expected indentation of 20 spaces but found 10 indent 442:1 error Expected indentation of 20 spaces but found 10 indent 443:1 error Expected indentation of 20 spaces but found 10 indent 444:1 error Expected indentation of 16 spaces but found 8 indent 445:1 error Expected indentation of 16 spaces but found 8 indent 446:1 error Expected indentation of 20 spaces but found 10 indent 447:1 error Expected indentation of 20 spaces but found 10 indent 448:1 error Expected indentation of 20 spaces but found 10 indent 449:1 error Expected indentation of 16 spaces but found 8 indent 450:1 error Expected indentation of 16 spaces but found 8 indent 451:1 error Expected indentation of 20 spaces but found 10 indent 452:1 error Expected indentation of 20 spaces but found 10 indent 453:1 error Expected indentation of 20 spaces but found 10 indent 454:1 error Expected indentation of 20 spaces but found 10 indent 455:1 error Expected indentation of 16 spaces but found 8 indent 456:1 error Expected indentation of 16 spaces but found 8 indent 457:1 error Expected indentation of 20 spaces but found 10 indent 458:1 error Expected indentation of 20 spaces but found 10 indent 459:1 error Expected indentation of 16 spaces but found 8 indent 460:1 error Expected indentation of 12 spaces but found 6 indent 461:1 error Expected indentation of 8 spaces but found 4 indent 462:1 error Expected indentation of 4 spaces but found 2 indent 465:1 error Expected indentation of 4 spaces but found 2 indent 466:1 error Expected indentation of 4 spaces but found 2 indent 467:1 error Expected indentation of 4 spaces but found 2 indent 468:1 error Expected indentation of 4 spaces but found 2 indent 469:1 error Expected indentation of 4 spaces but found 2 indent 470:1 error Expected indentation of 4 spaces but found 2 indent 471:1 error Expected indentation of 4 spaces but found 2 indent 472:1 error Expected indentation of 4 spaces but found 2 indent 476:1 error Expected indentation of 4 spaces but found 2 indent 477:1 error Expected indentation of 8 spaces but found 4 indent 478:1 error Expected indentation of 4 spaces but found 2 indent 480:1 error Expected indentation of 4 spaces but found 2 indent 481:1 error Expected indentation of 8 spaces but found 4 indent 482:1 error Expected indentation of 12 spaces but found 6 indent 483:1 error Expected indentation of 8 spaces but found 4 indent 484:1 error Expected indentation of 8 spaces but found 4 indent 485:1 error Expected indentation of 12 spaces but found 6 indent 486:1 error Expected indentation of 8 spaces but found 4 indent 487:1 error Expected indentation of 8 spaces but found 4 indent 488:1 error Expected indentation of 12 spaces but found 6 indent 490:1 error Expected indentation of 12 spaces but found 9 indent 491:1 error Expected indentation of 16 spaces but found 8 indent 492:1 error Expected indentation of 16 spaces but found 8 indent 493:1 error Expected indentation of 12 spaces but found 6 indent 494:1 error Expected indentation of 8 spaces but found 4 indent 495:1 error Expected indentation of 4 spaces but found 2 indent 498:1 error Expected indentation of 4 spaces but found 2 indent 499:1 error Expected indentation of 4 spaces but found 2 indent 500:1 error Expected indentation of 4 spaces but found 2 indent 504:1 error Expected indentation of 4 spaces but found 2 indent 505:1 error Expected indentation of 8 spaces but found 4 indent 506:1 error Expected indentation of 8 spaces but found 4 indent 507:1 error Expected indentation of 4 spaces but found 2 indent 509:1 error Expected indentation of 4 spaces but found 2 indent 510:1 error Expected indentation of 8 spaces but found 4 indent 511:1 error Expected indentation of 8 spaces but found 4 indent 512:1 error Expected indentation of 12 spaces but found 6 indent 514:1 error Expected indentation of 12 spaces but found 6 indent 515:1 error Expected indentation of 12 spaces but found 6 indent 517:1 error Expected indentation of 8 spaces but found 4 indent 518:1 error Expected indentation of 4 spaces but found 2 indent 520:1 error Expected indentation of 4 spaces but found 2 indent 521:1 error Expected indentation of 8 spaces but found 4 indent 522:1 error Expected indentation of 12 spaces but found 6 indent 523:1 error Expected indentation of 8 spaces but found 4 indent 524:1 error Expected indentation of 8 spaces but found 4 indent 525:1 error Expected indentation of 12 spaces but found 6 indent 526:1 error Expected indentation of 16 spaces but found 9 indent 527:1 error Expected indentation of 16 spaces but found 9 indent 528:1 error Expected indentation of 12 spaces but found 6 indent 529:1 error Expected indentation of 16 spaces but found 8 indent 530:1 error Expected indentation of 20 spaces but found 12 indent 531:1 error Expected indentation of 20 spaces but found 12 indent 532:1 error Expected indentation of 16 spaces but found 8 indent 533:1 error Expected indentation of 12 spaces but found 6 indent 534:1 error Expected indentation of 8 spaces but found 4 indent 535:1 error Expected indentation of 4 spaces but found 2 indent 538:1 error Expected indentation of 4 spaces but found 2 indent 539:1 error Expected indentation of 4 spaces but found 2 indent 543:1 error Expected indentation of 4 spaces but found 2 indent 544:1 error Expected indentation of 8 spaces but found 4 indent 545:1 error Expected indentation of 8 spaces but found 4 indent 546:1 error Expected indentation of 4 spaces but found 2 indent 548:1 error Expected indentation of 4 spaces but found 2 indent 549:1 error Expected indentation of 8 spaces but found 4 indent 550:1 error Expected indentation of 8 spaces but found 4 indent 551:1 error Expected indentation of 12 spaces but found 6 indent 553:1 error Expected indentation of 12 spaces but found 6 indent 554:1 error Expected indentation of 12 spaces but found 6 indent 555:1 error Expected indentation of 8 spaces but found 4 indent 556:1 error Expected indentation of 4 spaces but found 2 indent 558:1 error Expected indentation of 4 spaces but found 2 indent 559:1 error Expected indentation of 8 spaces but found 4 indent 560:1 error Expected indentation of 12 spaces but found 6 indent 561:1 error Expected indentation of 8 spaces but found 4 indent 562:1 error Expected indentation of 8 spaces but found 4 indent 563:1 error Expected indentation of 12 spaces but found 6 indent 564:1 error Expected indentation of 16 spaces but found 9 indent 565:1 error Expected indentation of 16 spaces but found 9 indent 566:1 error Expected indentation of 12 spaces but found 6 indent 567:1 error Expected indentation of 16 spaces but found 8 indent 568:1 error Expected indentation of 20 spaces but found 12 indent 569:1 error Expected indentation of 20 spaces but found 12 indent 570:1 error Expected indentation of 16 spaces but found 8 indent 571:1 error Expected indentation of 12 spaces but found 6 indent 572:1 error Expected indentation of 8 spaces but found 4 indent 573:1 error Expected indentation of 4 spaces but found 2 indent 576:1 error Expected indentation of 4 spaces but found 2 indent 577:1 error Expected indentation of 4 spaces but found 2 indent 578:1 error Expected indentation of 4 spaces but found 2 indent 582:1 error Expected indentation of 4 spaces but found 2 indent 583:1 error Expected indentation of 8 spaces but found 4 indent 584:1 error Expected indentation of 4 spaces but found 2 indent 586:1 error Expected indentation of 4 spaces but found 2 indent 587:1 error Expected indentation of 8 spaces but found 4 indent 588:1 error Expected indentation of 12 spaces but found 6 indent 589:1 error Expected indentation of 16 spaces but found 8 indent 590:1 error Expected indentation of 20 spaces but found 31 indent 591:1 error Expected indentation of 16 spaces but found 8 indent 592:1 error Expected indentation of 16 spaces but found 8 indent 593:1 error Expected indentation of 20 spaces but found 24 indent 594:1 error Expected indentation of 20 spaces but found 24 indent 595:1 error Expected indentation of 16 spaces but found 8 indent 596:1 error Expected indentation of 16 spaces but found 8 indent 597:1 error Expected indentation of 20 spaces but found 24 indent 598:1 error Expected indentation of 20 spaces but found 24 indent 599:1 error Expected indentation of 16 spaces but found 8 indent 600:1 error Expected indentation of 16 spaces but found 8 indent 601:1 error Expected indentation of 20 spaces but found 24 indent 602:1 error Expected indentation of 20 spaces but found 24 indent 603:1 error Expected indentation of 16 spaces but found 8 indent 604:1 error Expected indentation of 16 spaces but found 8 indent 605:1 error Expected indentation of 20 spaces but found 24 indent 606:1 error Expected indentation of 20 spaces but found 24 indent 607:1 error Expected indentation of 16 spaces but found 8 indent 608:1 error Expected indentation of 16 spaces but found 8 indent 609:1 error Expected indentation of 20 spaces but found 32 indent 610:1 error Expected indentation of 20 spaces but found 32 indent 611:1 error Expected indentation of 16 spaces but found 8 indent 612:1 error Expected indentation of 12 spaces but found 6 indent 613:1 error Expected indentation of 8 spaces but found 4 indent 614:1 error Expected indentation of 4 spaces but found 2 indent 617:1 error Expected indentation of 4 spaces but found 2 indent 618:1 error Expected indentation of 4 spaces but found 2 indent 619:1 error Expected indentation of 4 spaces but found 2 indent 620:1 error Expected indentation of 4 spaces but found 2 indent 621:1 error Expected indentation of 4 spaces but found 2 indent 622:1 error Expected indentation of 4 spaces but found 2 indent 623:1 error Expected indentation of 4 spaces but found 2 indent 627:1 error Expected indentation of 4 spaces but found 2 indent 628:1 error Expected indentation of 8 spaces but found 4 indent 629:1 error Expected indentation of 8 spaces but found 4 indent 630:1 error Expected indentation of 4 spaces but found 2 indent 633:1 error Expected indentation of 4 spaces but found 2 indent 634:1 error Expected indentation of 8 spaces but found 4 indent 635:1 error Expected indentation of 8 spaces but found 4 indent 637:1 error Expected indentation of 8 spaces but found 6 indent 638:1 error Expected indentation of 4 spaces but found 2 indent 640:1 error Expected indentation of 4 spaces but found 2 indent 641:1 error Expected indentation of 8 spaces but found 4 indent 642:1 error Expected indentation of 12 spaces but found 6 indent 643:1 error Expected indentation of 16 spaces but found 8 indent 644:1 error Expected indentation of 20 spaces but found 10 indent 645:1 error Expected indentation of 24 spaces but found 12 indent 646:1 error Expected indentation of 28 spaces but found 14 indent 647:1 error Expected indentation of 32 spaces but found 19 indent 648:1 error Expected indentation of 24 spaces but found 12 indent 649:1 error Expected indentation of 20 spaces but found 10 indent 650:1 error Expected indentation of 20 spaces but found 10 indent 651:1 error Expected indentation of 24 spaces but found 12 indent 652:1 error Expected indentation of 28 spaces but found 14 indent 653:1 error Expected indentation of 28 spaces but found 14 indent 654:1 error Expected indentation of 28 spaces but found 14 indent 655:1 error Expected indentation of 28 spaces but found 14 indent 656:1 error Expected indentation of 28 spaces but found 14 indent 657:1 error Expected indentation of 28 spaces but found 14 indent 658:1 error Expected indentation of 28 spaces but found 14 indent 659:1 error Expected indentation of 28 spaces but found 14 indent 660:1 error Expected indentation of 24 spaces but found 12 indent 661:1 error Expected indentation of 20 spaces but found 10 indent 662:1 error Expected indentation of 16 spaces but found 8 indent 663:1 error Expected indentation of 16 spaces but found 8 indent 664:1 error Expected indentation of 20 spaces but found 10 indent 665:1 error Expected indentation of 20 spaces but found 10 indent 666:1 error Expected indentation of 20 spaces but found 10 indent 667:1 error Expected indentation of 20 spaces but found 10 indent 668:1 error Expected indentation of 20 spaces but found 10 indent 669:1 error Expected indentation of 20 spaces but found 10 indent 670:1 error Expected indentation of 20 spaces but found 10 indent 671:1 error Expected indentation of 16 spaces but found 8 indent 672:1 error Expected indentation of 16 spaces but found 8 indent 673:1 error Expected indentation of 20 spaces but found 10 indent 674:1 error Expected indentation of 12 spaces but found 6 indent 675:1 error Expected indentation of 8 spaces but found 4 indent 676:1 error Expected indentation of 4 spaces but found 2 indent 679:1 error Expected indentation of 4 spaces but found 2 indent 680:1 error Expected indentation of 4 spaces but found 2 indent 681:1 error Expected indentation of 4 spaces but found 2 indent 682:1 error Expected indentation of 4 spaces but found 2 indent 683:1 error Expected indentation of 4 spaces but found 2 indent 684:1 error Expected indentation of 4 spaces but found 2 indent 685:1 error Expected indentation of 4 spaces but found 2 indent 686:1 error Expected indentation of 4 spaces but found 2 indent 687:1 error Expected indentation of 4 spaces but found 2 indent 688:1 error Expected indentation of 4 spaces but found 2 indent 689:1 error Expected indentation of 4 spaces but found 2 indent 690:1 error Expected indentation of 4 spaces but found 2 indent 691:1 error Expected indentation of 4 spaces but found 2 indent 692:1 error Expected indentation of 4 spaces but found 2 indent 693:1 error Expected indentation of 4 spaces but found 2 indent 694:1 error Expected indentation of 4 spaces but found 2 indent 698:1 error Expected indentation of 4 spaces but found 2 indent 699:1 error Expected indentation of 8 spaces but found 4 indent 700:1 error Expected indentation of 8 spaces but found 4 indent 701:1 error Expected indentation of 12 spaces but found 6 indent 702:1 error Expected indentation of 12 spaces but found 6 indent 703:1 error Expected indentation of 8 spaces but found 4 indent 704:1 error Expected indentation of 8 spaces but found 4 indent 705:1 error Expected indentation of 8 spaces but found 4 indent 706:1 error Expected indentation of 4 spaces but found 2 indent 708:1 error Expected indentation of 4 spaces but found 2 indent 708:14 error 'e' is defined but never used no-unused-vars 709:1 error Expected indentation of 8 spaces but found 4 indent 710:1 error Expected indentation of 12 spaces but found 6 indent 711:1 error Expected indentation of 8 spaces but found 4 indent 712:1 error Expected indentation of 4 spaces but found 2 indent 714:1 error Expected indentation of 4 spaces but found 2 indent 714:17 error 'e' is defined but never used no-unused-vars 715:1 error Expected indentation of 8 spaces but found 4 indent 716:1 error Expected indentation of 12 spaces but found 6 indent 717:1 error Expected indentation of 8 spaces but found 4 indent 718:1 error Expected indentation of 4 spaces but found 2 indent 720:1 error Expected indentation of 4 spaces but found 2 indent 721:1 error Expected indentation of 8 spaces but found 4 indent 722:1 error Expected indentation of 12 spaces but found 6 indent 723:1 error Expected indentation of 16 spaces but found 8 indent 724:1 error Expected indentation of 20 spaces but found 10 indent 725:1 error Expected indentation of 24 spaces but found 12 indent 726:1 error Expected indentation of 24 spaces but found 12 indent 727:1 error Expected indentation of 24 spaces but found 12 indent 728:1 error Expected indentation of 24 spaces but found 12 indent 729:1 error Expected indentation of 24 spaces but found 12 indent 730:1 error Expected indentation of 24 spaces but found 12 indent 731:1 error Expected indentation of 24 spaces but found 12 indent 732:1 error Expected indentation of 20 spaces but found 10 indent 733:1 error Expected indentation of 20 spaces but found 10 indent 734:1 error Expected indentation of 24 spaces but found 12 indent 735:1 error Expected indentation of 28 spaces but found 14 indent 737:1 error Expected indentation of 28 spaces but found 14 indent 738:1 error Expected indentation of 28 spaces but found 14 indent 739:1 error Expected indentation of 28 spaces but found 14 indent 740:1 error Expected indentation of 28 spaces but found 14 indent 742:1 error Expected indentation of 28 spaces but found 14 indent 744:1 error Expected indentation of 28 spaces but found 14 indent 745:1 error Expected indentation of 28 spaces but found 14 indent 746:1 error Expected indentation of 28 spaces but found 14 indent 747:1 error Expected indentation of 28 spaces but found 14 indent 748:1 error Expected indentation of 28 spaces but found 14 indent 749:1 error Expected indentation of 28 spaces but found 14 indent 751:1 error Expected indentation of 28 spaces but found 14 indent 752:1 error Expected indentation of 28 spaces but found 14 indent 753:1 error Expected indentation of 28 spaces but found 14 indent 754:1 error Expected indentation of 28 spaces but found 14 indent 755:1 error Expected indentation of 28 spaces but found 14 indent 756:1 error Expected indentation of 28 spaces but found 14 indent 757:1 error Expected indentation of 24 spaces but found 12 indent 758:1 error Expected indentation of 16 spaces but found 8 indent 759:1 error Expected indentation of 12 spaces but found 6 indent 760:1 error Expected indentation of 8 spaces but found 4 indent 761:1 error Expected indentation of 4 spaces but found 2 indent 764:1 error Expected indentation of 4 spaces but found 2 indent 765:1 error Expected indentation of 4 spaces but found 2 indent 766:1 error Expected indentation of 4 spaces but found 2 indent 767:1 error Expected indentation of 4 spaces but found 2 indent 768:1 error Expected indentation of 4 spaces but found 2 indent 769:1 error Expected indentation of 4 spaces but found 2 indent 770:1 error Expected indentation of 4 spaces but found 2 indent 771:1 error Expected indentation of 4 spaces but found 2 indent 772:1 error Expected indentation of 4 spaces but found 2 indent 773:1 error Expected indentation of 4 spaces but found 2 indent 774:1 error Expected indentation of 4 spaces but found 2 indent 775:1 error Expected indentation of 4 spaces but found 2 indent 776:1 error Expected indentation of 4 spaces but found 2 indent 777:1 error Expected indentation of 4 spaces but found 2 indent 778:1 error Expected indentation of 4 spaces but found 2 indent 779:1 error Expected indentation of 4 spaces but found 2 indent 780:1 error Expected indentation of 4 spaces but found 2 indent 802:1 error Expected indentation of 4 spaces but found 2 indent 803:1 error Expected indentation of 4 spaces but found 2 indent 804:1 error Expected indentation of 4 spaces but found 2 indent 805:1 error Expected indentation of 4 spaces but found 2 indent 806:1 error Expected indentation of 4 spaces but found 2 indent 807:1 error Expected indentation of 4 spaces but found 2 indent 808:1 error Expected indentation of 4 spaces but found 2 indent 809:1 error Expected indentation of 4 spaces but found 2 indent 810:1 error Expected indentation of 4 spaces but found 2 indent 811:1 error Expected indentation of 4 spaces but found 2 indent 812:1 error Expected indentation of 4 spaces but found 2 indent 813:1 error Expected indentation of 4 spaces but found 2 indent 814:1 error Expected indentation of 4 spaces but found 2 indent 815:1 error Expected indentation of 4 spaces but found 2 indent 816:1 error Expected indentation of 4 spaces but found 2 indent ? 654 problems (654 errors, 0 warnings) 647 errors and 0 warnings potentially fixable with the `--fix` option. ERROR in ./modules/imaging_browser/jsx/imagingBrowserIndex.js Module Error (from ./node_modules/eslint-loader/index.js): /var/www/loris/modules/imaging_browser/jsx/imagingBrowserIndex.js 1:8 error 'React' is defined but never used no-unused-vars 3:8 error 'Loader' is defined but never used no-unused-vars 4:8 error 'FilterableDataTable' is defined but never used no-unused-vars 7:1 error Expected indentation of 4 spaces but found 2 indent 8:1 error Expected indentation of 8 spaces but found 4 indent 10:1 error Expected indentation of 8 spaces but found 4 indent 11:1 error Expected indentation of 12 spaces but found 6 indent 12:1 error Expected indentation of 12 spaces but found 6 indent 13:1 error Expected indentation of 12 spaces but found 6 indent 14:1 error Expected indentation of 8 spaces but found 4 indent 16:1 error Expected indentation of 8 spaces but found 4 indent 17:1 error Expected indentation of 4 spaces but found 2 indent 19:1 error Expected indentation of 4 spaces but found 2 indent 20:1 error Expected indentation of 8 spaces but found 4 indent 21:1 error Expected indentation of 12 spaces but found 6 indent 22:1 error Expected indentation of 4 spaces but found 2 indent 24:1 error Expected indentation of 4 spaces but found 2 indent 29:1 error Expected indentation of 4 spaces but found 2 indent 30:1 error Expected indentation of 8 spaces but found 4 indent 31:1 error Expected indentation of 12 spaces but found 6 indent 32:1 error Expected indentation of 12 spaces but found 6 indent 33:1 error Expected indentation of 12 spaces but found 6 indent 34:1 error Expected indentation of 16 spaces but found 8 indent 35:1 error Expected indentation of 16 spaces but found 8 indent 35:9 error Unexpected console statement no-console 36:1 error Expected indentation of 12 spaces but found 6 indent 37:1 error Expected indentation of 4 spaces but found 2 indent 39:1 error Expected indentation of 4 spaces but found 2 indent 48:1 error Expected indentation of 4 spaces but found 2 indent 50:1 error Expected indentation of 8 spaces but found 4 indent 51:1 error Expected indentation of 8 spaces but found 4 indent 52:1 error Expected indentation of 8 spaces but found 4 indent 53:1 error Expected indentation of 8 spaces but found 6 indent 54:1 error Expected indentation of 12 spaces but found 8 indent 55:1 error Expected indentation of 16 spaces but found 10 indent 56:1 error Expected indentation of 20 spaces but found 12 indent 57:1 error Expected indentation of 16 spaces but found 10 indent 58:1 error Expected indentation of 12 spaces but found 8 indent 59:1 error Expected indentation of 12 spaces but found 8 indent 60:1 error Expected indentation of 8 spaces but found 6 indent 61:1 error Expected indentation of 12 spaces but found 8 indent 61:9 error Unexpected lexical declaration in case block no-case-declarations 62:1 error Expected indentation of 12 spaces but found 8 indent 62:9 error Unexpected lexical declaration in case block no-case-declarations 63:1 error Expected indentation of 12 spaces but found 8 indent 64:1 error Expected indentation of 16 spaces but found 10 indent 64:43 error 'loris' is not defined no-undef 68:1 error Expected indentation of 20 spaces but found 12 indent 69:1 error Expected indentation of 16 spaces but found 10 indent 70:1 error Expected indentation of 16 spaces but found 10 indent 71:1 error Expected indentation of 12 spaces but found 8 indent 72:1 error Expected indentation of 12 spaces but found 8 indent 72:48 error 'loris' is not defined no-undef 77:1 error Expected indentation of 12 spaces but found 8 indent 79:1 error Expected indentation of 12 spaces but found 8 indent 80:1 error Expected indentation of 12 spaces but found 8 indent 80:43 error 'loris' is not defined no-undef 85:1 error Expected indentation of 12 spaces but found 8 indent 86:1 error Expected indentation of 12 spaces but found 8 indent 87:1 error Expected indentation of 12 spaces but found 8 indent 88:1 error Expected indentation of 8 spaces but found 4 indent 90:1 error Expected indentation of 8 spaces but found 4 indent 91:1 error Expected indentation of 4 spaces but found 2 indent 93:1 error Expected indentation of 4 spaces but found 2 indent 96:1 error Expected indentation of 8 spaces but found 4 indent 97:1 error Expected indentation of 12 spaces but found 6 indent 98:1 error Expected indentation of 8 spaces but found 4 indent 100:1 error Expected indentation of 8 spaces but found 4 indent 101:1 error Expected indentation of 8 spaces but found 4 indent 102:1 error Expected indentation of 12 spaces but found 6 indent 103:1 error Expected indentation of 8 spaces but found 4 indent 105:1 error Expected indentation of 8 spaces but found 4 indent 109:1 error Expected indentation of 8 spaces but found 4 indent 110:1 error Expected indentation of 8 spaces but found 4 indent 111:1 error Expected indentation of 8 spaces but found 4 indent 112:1 error Expected indentation of 12 spaces but found 6 indent 113:1 error Expected indentation of 16 spaces but found 8 indent 114:1 error Expected indentation of 16 spaces but found 8 indent 115:1 error Expected indentation of 16 spaces but found 8 indent 116:1 error Expected indentation of 12 spaces but found 6 indent 117:1 error Expected indentation of 12 spaces but found 6 indent 118:1 error Expected indentation of 16 spaces but found 8 indent 119:1 error Expected indentation of 16 spaces but found 8 indent 120:1 error Expected indentation of 12 spaces but found 6 indent 121:1 error Expected indentation of 12 spaces but found 6 indent 122:1 error Expected indentation of 16 spaces but found 8 indent 123:1 error Expected indentation of 16 spaces but found 8 indent 124:1 error Expected indentation of 12 spaces but found 6 indent 125:1 error Expected indentation of 12 spaces but found 6 indent 126:1 error Expected indentation of 16 spaces but found 8 indent 127:1 error Expected indentation of 16 spaces but found 8 indent 128:1 error Expected indentation of 16 spaces but found 8 indent 129:1 error Expected indentation of 12 spaces but found 6 indent 130:1 error Expected indentation of 12 spaces but found 6 indent 131:1 error Expected indentation of 16 spaces but found 8 indent 132:1 error Expected indentation of 16 spaces but found 8 indent 133:1 error Expected indentation of 12 spaces but found 6 indent 134:1 error Expected indentation of 12 spaces but found 6 indent 135:1 error Expected indentation of 16 spaces but found 8 indent 136:1 error Expected indentation of 16 spaces but found 8 indent 137:1 error Expected indentation of 16 spaces but found 8 indent 138:1 error Expected indentation of 12 spaces but found 6 indent 139:1 error Expected indentation of 12 spaces but found 6 indent 140:1 error Expected indentation of 12 spaces but found 6 indent 141:1 error Expected indentation of 12 spaces but found 6 indent 142:1 error Expected indentation of 12 spaces but found 6 indent 143:1 error Expected indentation of 12 spaces but found 6 indent 144:1 error Expected indentation of 12 spaces but found 6 indent 145:1 error Expected indentation of 12 spaces but found 6 indent 146:1 error Expected indentation of 16 spaces but found 8 indent 147:1 error Expected indentation of 16 spaces but found 8 indent 148:1 error Expected indentation of 16 spaces but found 8 indent 149:1 error Expected indentation of 12 spaces but found 6 indent 150:1 error Expected indentation of 12 spaces but found 6 indent 151:1 error Expected indentation of 16 spaces but found 8 indent 152:1 error Expected indentation of 16 spaces but found 8 indent 153:1 error Expected indentation of 16 spaces but found 8 indent 154:1 error Expected indentation of 12 spaces but found 6 indent 155:1 error Expected indentation of 8 spaces but found 4 indent 156:1 error Expected indentation of 8 spaces but found 4 indent 160:1 error Expected indentation of 8 spaces but found 4 indent 161:1 error Expected indentation of 12 spaces but found 6 indent 162:1 error Expected indentation of 12 spaces but found 6 indent 163:1 error Expected indentation of 8 spaces but found 4 indent 165:1 error Expected indentation of 8 spaces but found 4 indent 166:1 error Expected indentation of 12 spaces but found 6 indent 167:1 error Expected indentation of 16 spaces but found 8 indent 168:1 error Expected indentation of 16 spaces but found 8 indent 169:1 error Expected indentation of 16 spaces but found 8 indent 170:1 error Expected indentation of 16 spaces but found 8 indent 171:1 error Expected indentation of 12 spaces but found 6 indent 173:1 error Expected indentation of 8 spaces but found 4 indent 174:1 error Expected indentation of 4 spaces but found 2 indent 178:1 error Expected indentation of 4 spaces but found 2 indent 182:1 error Expected indentation of 4 spaces but found 2 indent 182:3 error 'ReactDOM' is not defined no-undef 183:1 error Expected indentation of 8 spaces but found 4 indent 184:1 error Expected indentation of 12 spaces but found 6 indent 184:19 error 'loris' is not defined no-undef 185:1 error Expected indentation of 8 spaces but found 4 indent 186:1 error Expected indentation of 8 spaces but found 4 indent 187:1 error Expected indentation of 4 spaces but found 2 indent ? 142 problems (142 errors, 0 warnings) 131 errors and 0 warnings potentially fixable with the `--fix` option. ERROR in ./modules/imaging_uploader/jsx/index.js Module Error (from ./node_modules/eslint-loader/index.js): /var/www/loris/modules/imaging_uploader/jsx/index.js 3:8 error 'ImagingUploader' is defined but never used no-unused-vars 8:1 error '$' is not defined no-undef 9:1 error Expected indentation of 4 spaces but found 2 indent 10:1 error Expected indentation of 8 spaces but found 4 indent 11:1 error Expected indentation of 12 spaces but found 6 indent 12:1 error Expected indentation of 16 spaces but found 8 indent 13:1 error Expected indentation of 16 spaces but found 8 indent 13:18 error 'loris' is not defined no-undef 14:1 error Expected indentation of 12 spaces but found 6 indent 15:1 error Expected indentation of 8 spaces but found 4 indent 16:1 error Expected indentation of 4 spaces but found 2 indent 18:1 error Expected indentation of 4 spaces but found 2 indent ? 12 problems (12 errors, 0 warnings) 9 errors and 0 warnings potentially fixable with the `--fix` option. ERROR in ./modules/instrument_builder/jsx/react.instrument_builder.js Module Error (from ./node_modules/eslint-loader/index.js): /var/www/loris/modules/instrument_builder/jsx/react.instrument_builder.js 3:9 error 'Tabs' is defined but never used no-unused-vars 3:15 error 'TabPane' is defined but never used no-unused-vars 17:1 error Expected indentation of 4 spaces but found 2 indent 18:1 error Expected indentation of 8 spaces but found 4 indent 19:1 error Expected indentation of 8 spaces but found 4 indent 20:1 error Expected indentation of 12 spaces but found 6 indent 21:1 error Expected indentation of 12 spaces but found 6 indent 22:1 error Expected indentation of 12 spaces but found 6 indent 23:1 error Expected indentation of 12 spaces but found 6 indent 24:1 error Expected indentation of 12 spaces but found 6 indent 25:1 error Expected indentation of 8 spaces but found 4 indent 26:1 error Expected indentation of 8 spaces but found 4 indent 27:1 error Expected indentation of 8 spaces but found 4 indent 28:1 error Expected indentation of 8 spaces but found 4 indent 29:1 error Expected indentation of 8 spaces but found 4 indent 30:1 error Expected indentation of 4 spaces but found 2 indent 32:1 error Expected indentation of 4 spaces but found 2 indent 33:1 error Expected indentation of 4 spaces but found 2 indent 34:1 error Expected indentation of 8 spaces but found 4 indent 35:1 error Expected indentation of 8 spaces but found 4 indent 36:1 error Expected indentation of 12 spaces but found 6 indent 37:1 error Expected indentation of 12 spaces but found 6 indent 38:1 error Expected indentation of 12 spaces but found 6 indent 39:1 error Expected indentation of 8 spaces but found 4 indent 40:1 error Expected indentation of 8 spaces but found 4 indent 41:1 error Expected indentation of 12 spaces but found 6 indent 42:1 error Expected indentation of 8 spaces but found 4 indent 43:1 error Expected indentation of 4 spaces but found 2 indent 44:1 error Expected indentation of 4 spaces but found 2 indent 45:1 error Expected indentation of 4 spaces but found 2 indent 46:1 error Expected indentation of 8 spaces but found 4 indent 47:1 error Expected indentation of 12 spaces but found 6 indent 48:1 error Expected indentation of 12 spaces but found 6 indent 49:1 error Expected indentation of 8 spaces but found 4 indent 50:1 error Expected indentation of 4 spaces but found 2 indent 51:1 error Expected indentation of 4 spaces but found 2 indent 52:1 error Expected indentation of 4 spaces but found 2 indent 53:1 error Expected indentation of 8 spaces but found 4 indent 54:1 error Expected indentation of 12 spaces but found 6 indent 55:1 error Expected indentation of 12 spaces but found 6 indent 56:1 error Expected indentation of 8 spaces but found 4 indent 57:1 error Expected indentation of 4 spaces but found 2 indent 58:1 error Expected indentation of 4 spaces but found 2 indent 59:1 error Expected indentation of 4 spaces but found 2 indent 61:1 error Expected indentation of 8 spaces but found 4 indent 62:1 error Expected indentation of 12 spaces but found 6 indent 63:1 error Expected indentation of 12 spaces but found 6 indent 64:1 error Expected indentation of 8 spaces but found 4 indent 65:1 error Expected indentation of 8 spaces but found 4 indent 66:1 error Expected indentation of 4 spaces but found 2 indent 67:1 error Expected indentation of 4 spaces but found 2 indent 68:1 error Expected indentation of 4 spaces but found 2 indent 69:1 error Expected indentation of 8 spaces but found 4 indent 70:1 error Expected indentation of 12 spaces but found 6 indent 71:1 error Expected indentation of 12 spaces but found 6 indent 72:1 error Expected indentation of 12 spaces but found 6 indent 73:1 error Expected indentation of 8 spaces but found 4 indent 74:1 error Expected indentation of 8 spaces but found 4 indent 75:1 error Expected indentation of 8 spaces but found 4 indent 76:1 error Expected indentation of 8 spaces but found 6 indent 77:1 error Expected indentation of 12 spaces but found 8 indent 78:1 error Expected indentation of 16 spaces but found 10 indent 79:1 error Expected indentation of 16 spaces but found 10 indent 80:1 error Expected indentation of 16 spaces but found 10 indent 81:1 error Expected indentation of 16 spaces but found 10 indent 82:1 error Expected indentation of 12 spaces but found 8 indent 83:1 error Expected indentation of 12 spaces but found 8 indent 84:1 error Expected indentation of 8 spaces but found 6 indent 85:1 error Expected indentation of 12 spaces but found 8 indent 86:1 error Expected indentation of 16 spaces but found 10 indent 87:1 error Expected indentation of 16 spaces but found 10 indent 88:1 error Expected indentation of 16 spaces but found 10 indent 89:1 error Expected indentation of 16 spaces but found 10 indent 90:1 error Expected indentation of 12 spaces but found 8 indent 91:1 error Expected indentation of 12 spaces but found 8 indent 92:1 error Expected indentation of 8 spaces but found 6 indent 93:1 error Expected indentation of 12 spaces but found 8 indent 94:1 error Expected indentation of 16 spaces but found 10 indent 95:1 error Expected indentation of 16 spaces but found 10 indent 96:1 error Expected indentation of 16 spaces but found 10 indent 97:1 error Expected indentation of 16 spaces but found 10 indent 98:1 error Expected indentation of 12 spaces but found 8 indent 99:1 error Expected indentation of 12 spaces but found 8 indent 100:1 error Expected indentation of 8 spaces but found 6 indent 101:1 error Expected indentation of 12 spaces but found 8 indent 102:1 error Expected indentation of 8 spaces but found 4 indent 103:1 error Expected indentation of 8 spaces but found 4 indent 104:1 error Expected indentation of 12 spaces but found 6 indent 105:1 error Expected indentation of 16 spaces but found 8 indent 106:1 error Expected indentation of 20 spaces but found 10 indent 107:1 error Expected indentation of 24 spaces but found 12 indent 108:1 error Expected indentation of 28 spaces but found 14 indent 109:1 error Expected indentation of 24 spaces but found 12 indent 110:1 error Expected indentation of 24 spaces but found 12 indent 111:1 error Expected indentation of 24 spaces but found 12 indent 112:1 error Expected indentation of 20 spaces but found 10 indent 113:1 error Expected indentation of 20 spaces but found 10 indent 114:1 error Expected indentation of 24 spaces but found 12 indent 115:1 error Expected indentation of 24 spaces but found 12 indent 116:1 error Expected indentation of 24 spaces but found 12 indent 117:1 error Expected indentation of 20 spaces but found 10 indent 118:1 error Expected indentation of 20 spaces but found 10 indent 119:1 error Expected indentation of 24 spaces but found 12 indent 120:1 error Expected indentation of 24 spaces but found 12 indent 121:1 error Expected indentation of 24 spaces but found 12 indent 122:1 error Expected indentation of 24 spaces but found 12 indent 123:1 error Expected indentation of 24 spaces but found 12 indent 124:1 error Expected indentation of 20 spaces but found 10 indent 125:1 error Expected indentation of 16 spaces but found 8 indent 126:1 error Expected indentation of 12 spaces but found 6 indent 127:1 error Expected indentation of 8 spaces but found 4 indent 128:1 error Expected indentation of 4 spaces but found 2 indent 131:1 error Expected indentation of 4 spaces but found 2 indent 138:1 error Expected indentation of 4 spaces but found 2 indent 139:1 error Expected indentation of 8 spaces but found 4 indent 140:1 error Expected indentation of 8 spaces but found 4 indent 141:1 error Expected indentation of 12 spaces but found 6 indent 142:1 error Expected indentation of 12 spaces but found 6 indent 143:1 error Expected indentation of 8 spaces but found 4 indent 144:1 error Expected indentation of 8 spaces but found 4 indent 145:1 error Expected indentation of 8 spaces but found 4 indent 146:1 error Expected indentation of 8 spaces but found 4 indent 147:1 error Expected indentation of 4 spaces but found 2 indent 149:1 error Expected indentation of 4 spaces but found 2 indent 150:1 error Expected indentation of 4 spaces but found 2 indent 151:1 error Expected indentation of 4 spaces but found 2 indent 152:1 error Expected indentation of 8 spaces but found 4 indent 153:1 error Expected indentation of 12 spaces but found 6 indent 154:1 error Expected indentation of 12 spaces but found 6 indent 155:1 error Expected indentation of 8 spaces but found 4 indent 156:1 error Expected indentation of 4 spaces but found 2 indent 157:1 error Expected indentation of 4 spaces but found 2 indent 158:1 error Expected indentation of 4 spaces but found 2 indent 159:1 error Expected indentation of 8 spaces but found 4 indent 160:1 error Expected indentation of 8 spaces but found 4 indent 161:1 error Expected indentation of 12 spaces but found 6 indent 162:1 error Expected indentation of 8 spaces but found 4 indent 163:1 error Expected indentation of 4 spaces but found 2 indent 164:1 error Expected indentation of 4 spaces but found 2 indent 165:1 error Expected indentation of 4 spaces but found 2 indent 166:1 error Expected indentation of 8 spaces but found 4 indent 167:1 error Expected indentation of 8 spaces but found 4 indent 168:1 error Expected indentation of 12 spaces but found 6 indent 169:1 error Expected indentation of 8 spaces but found 4 indent 170:1 error Expected indentation of 4 spaces but found 2 indent 171:1 error Expected indentation of 4 spaces but found 2 indent 172:1 error Expected indentation of 4 spaces but found 2 indent 173:1 error Expected indentation of 8 spaces but found 4 indent 174:1 error Expected indentation of 8 spaces but found 4 indent 175:1 error Expected indentation of 12 spaces but found 6 indent 176:1 error Expected indentation of 16 spaces but found 8 indent 177:1 error Expected indentation of 20 spaces but found 10 indent 178:1 error Expected indentation of 24 spaces but found 12 indent 179:1 error Expected indentation of 24 spaces but found 12 indent 180:1 error Expected indentation of 28 spaces but found 14 indent 181:1 error Expected indentation of 32 spaces but found 21 indent 182:1 error Expected indentation of 32 spaces but found 21 indent 183:1 error Expected indentation of 32 spaces but found 21 indent 184:1 error Expected indentation of 28 spaces but found 14 indent 185:1 error Expected indentation of 24 spaces but found 12 indent 186:1 error Expected indentation of 20 spaces but found 10 indent 187:1 error Expected indentation of 20 spaces but found 10 indent 188:1 error Expected indentation of 24 spaces but found 12 indent 189:1 error Expected indentation of 24 spaces but found 12 indent 190:1 error Expected indentation of 28 spaces but found 14 indent 191:1 error Expected indentation of 32 spaces but found 21 indent 192:1 error Expected indentation of 32 spaces but found 21 indent 193:1 error Expected indentation of 32 spaces but found 21 indent 194:1 error Expected indentation of 28 spaces but found 14 indent 195:1 error Expected indentation of 24 spaces but found 12 indent 196:1 error Expected indentation of 20 spaces but found 10 indent 197:1 error Expected indentation of 20 spaces but found 10 indent 198:1 error Expected indentation of 24 spaces but found 12 indent 199:1 error Expected indentation of 28 spaces but found 14 indent 200:1 error Expected indentation of 32 spaces but found 21 indent 201:1 error Expected indentation of 32 spaces but found 21 indent 202:1 error Expected indentation of 28 spaces but found 14 indent 203:1 error Expected indentation of 24 spaces but found 12 indent 204:1 error Expected indentation of 20 spaces but found 10 indent 205:1 error Expected indentation of 16 spaces but found 8 indent 206:1 error Expected indentation of 12 spaces but found 6 indent 207:1 error Expected indentation of 8 spaces but found 4 indent 208:1 error Expected indentation of 4 spaces but found 2 indent 211:1 error Expected indentation of 4 spaces but found 2 indent 219:1 error Expected indentation of 4 spaces but found 2 indent 220:1 error Expected indentation of 8 spaces but found 4 indent 221:1 error Expected indentation of 8 spaces but found 4 indent 222:1 error Expected indentation of 8 spaces but found 4 indent 223:1 error Expected indentation of 8 spaces but found 4 indent 224:1 error Expected indentation of 8 spaces but found 4 indent 225:1 error Expected indentation of 8 spaces but found 4 indent 226:1 error Expected indentation of 8 spaces but found 4 indent 227:1 error Expected indentation of 8 spaces but found 4 indent 228:1 error Expected indentation of 8 spaces but found 4 indent 229:1 error Expected indentation of 4 spaces but found 2 indent 230:1 error Expected indentation of 4 spaces but found 2 indent 231:1 error Expected indentation of 4 spaces but found 2 indent 232:1 error Expected indentation of 8 spaces but found 4 indent 233:1 error Expected indentation of 12 spaces but found 6 indent 234:1 error Expected indentation of 12 spaces but found 6 indent 235:1 error Expected indentation of 12 spaces but found 6 indent 236:1 error Expected indentation of 12 spaces but found 6 indent 237:1 error Expected indentation of 12 spaces but found 6 indent 238:1 error Expected indentation of 12 spaces but found 6 indent 239:1 error Expected indentation of 12 spaces but found 6 indent 240:1 error Expected indentation of 8 spaces but found 4 indent 241:1 error Expected indentation of 8 spaces but found 4 indent 242:1 error Expected indentation of 4 spaces but found 2 indent 243:1 error Expected indentation of 4 spaces but found 2 indent 244:1 error Expected indentation of 4 spaces but found 2 indent 245:1 error Expected indentation of 8 spaces but found 4 indent 246:1 error Expected indentation of 12 spaces but found 6 indent 247:1 error Expected indentation of 8 spaces but found 4 indent 249:1 error Expected indentation of 8 spaces but found 4 indent 249:12 error '$' is not defined no-undef 250:1 error Expected indentation of 4 spaces but found 2 indent 251:1 error Expected indentation of 4 spaces but found 2 indent 252:1 error Expected indentation of 4 spaces but found 2 indent 253:1 error Expected indentation of 8 spaces but found 4 indent 254:1 error Expected indentation of 8 spaces but found 4 indent 255:1 error Expected indentation of 8 spaces but found 4 indent 256:1 error Expected indentation of 8 spaces but found 4 indent 257:1 error Expected indentation of 4 spaces but found 2 indent 258:1 error Expected indentation of 4 spaces but found 2 indent 259:1 error Expected indentation of 4 spaces but found 2 indent 259:11 error 'e' is defined but never used no-unused-vars 260:1 error Expected indentation of 8 spaces but found 4 indent 261:1 error Expected indentation of 8 spaces but found 4 indent 263:1 error Expected indentation of 8 spaces but found 4 indent 264:1 error Expected indentation of 8 spaces but found 4 indent 265:1 error Expected indentation of 8 spaces but found 4 indent 266:1 error Expected indentation of 8 spaces but found 4 indent 267:1 error Expected indentation of 8 spaces but found 4 indent 268:1 error Expected indentation of 8 spaces but found 4 indent 269:1 error Expected indentation of 8 spaces but found 4 indent 270:1 error Expected indentation of 8 spaces but found 4 indent 271:1 error Expected indentation of 12 spaces but found 6 indent 272:1 error Expected indentation of 8 spaces but found 4 indent 273:1 error Expected indentation of 4 spaces but found 2 indent 274:1 error Expected indentation of 4 spaces but found 2 indent 275:1 error Expected indentation of 4 spaces but found 2 indent 276:1 error Expected indentation of 8 spaces but found 4 indent 277:1 error Expected indentation of 8 spaces but found 4 indent 279:1 error Expected indentation of 8 spaces but found 4 indent 280:1 error Expected indentation of 8 spaces but found 4 indent 281:1 error Expected indentation of 8 spaces but found 4 indent 282:1 error Expected indentation of 8 spaces but found 4 indent 283:1 error Expected indentation of 8 spaces but found 4 indent 283:26 error '$' is not defined no-undef 284:1 error Expected indentation of 8 spaces but found 4 indent 285:1 error Expected indentation of 8 spaces but found 4 indent 287:1 error Expected indentation of 8 spaces but found 4 indent 288:1 error Expected indentation of 12 spaces but found 6 indent 289:1 error Expected indentation of 12 spaces but found 6 indent 290:1 error Expected indentation of 8 spaces but found 4 indent 291:1 error Expected indentation of 12 spaces but found 6 indent 292:1 error Expected indentation of 12 spaces but found 6 indent 293:1 error Expected indentation of 8 spaces but found 4 indent 294:1 error Expected indentation of 4 spaces but found 2 indent 295:1 error Expected indentation of 4 spaces but found 2 indent 296:1 error Expected indentation of 4 spaces but found 2 indent 297:1 error Expected indentation of 8 spaces but found 4 indent 298:1 error Expected indentation of 12 spaces but found 6 indent 299:1 error Expected indentation of 12 spaces but found 6 indent 300:1 error Expected indentation of 12 spaces but found 6 indent 301:1 error Expected indentation of 16 spaces but found 8 indent 302:1 error Expected indentation of 16 spaces but found 8 indent 303:1 error Expected indentation of 20 spaces but found 10 indent 304:1 error Expected indentation of 24 spaces but found 14 indent 305:1 error Expected indentation of 24 spaces but found 14 indent 306:1 error Expected indentation of 24 spaces but found 14 indent 307:1 error Expected indentation of 24 spaces but found 14 indent 308:1 error Expected indentation of 20 spaces but found 10 indent 309:1 error Expected indentation of 24 spaces but found 12 indent 310:1 error Expected indentation of 28 spaces but found 14 indent 311:1 error Expected indentation of 32 spaces but found 16 indent 312:1 error Expected indentation of 32 spaces but found 16 indent 313:1 error Expected indentation of 28 spaces but found 14 indent 314:1 error Expected indentation of 24 spaces but found 12 indent 315:1 error Expected indentation of 20 spaces but found 10 indent 316:1 error Expected indentation of 16 spaces but found 8 indent 317:1 error Expected indentation of 12 spaces but found 6 indent 318:1 error Expected indentation of 16 spaces but found 8 indent 319:1 error Expected indentation of 16 spaces but found 8 indent 320:1 error Expected indentation of 20 spaces but found 10 indent 321:1 error Expected indentation of 24 spaces but found 14 indent 322:1 error Expected indentation of 24 spaces but found 14 indent 323:1 error Expected indentation of 24 spaces but found 14 indent 324:1 error Expected indentation of 24 spaces but found 14 indent 325:1 error Expected indentation of 24 spaces but found 12 indent 326:1 error Expected indentation of 28 spaces but found 14 indent 327:1 error Expected indentation of 24 spaces but found 12 indent 328:1 error Expected indentation of 24 spaces but found 12 indent 329:1 error Expected indentation of 28 spaces but found 14 indent 330:1 error Expected indentation of 24 spaces but found 12 indent 331:1 error Expected indentation of 24 spaces but found 12 indent 332:1 error Expected indentation of 28 spaces but found 14 indent 334:1 error Expected indentation of 28 spaces but found 14 indent 335:1 error Expected indentation of 28 spaces but found 14 indent 337:1 error Expected indentation of 28 spaces but found 14 indent 338:1 error Expected indentation of 24 spaces but found 12 indent 339:1 error Expected indentation of 20 spaces but found 10 indent 340:1 error Expected indentation of 16 spaces but found 8 indent 341:1 error Expected indentation of 12 spaces but found 6 indent 342:1 error Expected indentation of 12 spaces but found 6 indent 343:1 error Expected indentation of 8 spaces but found 4 indent 344:1 error Expected indentation of 4 spaces but found 2 indent 346:1 error Expected indentation of 4 spaces but found 2 indent 347:1 error Expected indentation of 4 spaces but found 2 indent 349:1 error Expected indentation of 8 spaces but found 4 indent 350:1 error Expected indentation of 12 spaces but found 6 indent 351:1 error Expected indentation of 8 spaces but found 4 indent 353:1 error Expected indentation of 8 spaces but found 4 indent 355:1 error Expected indentation of 8 spaces but found 4 indent 356:1 error Expected indentation of 12 spaces but found 6 indent 357:1 error Expected indentation of 16 spaces but found 8 indent 358:1 error Expected indentation of 20 spaces but found 8 indent 359:1 error Expected indentation of 24 spaces but found 10 indent 360:1 error Expected indentation of 24 spaces but found 10 indent 361:1 error Expected indentation of 24 spaces but found 10 indent 362:1 error Expected indentation of 20 spaces but found 8 indent 363:1 error Expected indentation of 16 spaces but found 8 indent 364:1 error Expected indentation of 16 spaces but found 8 indent 365:1 error Expected indentation of 20 spaces but found 8 indent 366:1 error Expected indentation of 16 spaces but found 8 indent 367:1 error Expected indentation of 12 spaces but found 6 indent 368:1 error Expected indentation of 8 spaces but found 4 indent 369:1 error Expected indentation of 4 spaces but found 2 indent 372:1 error Expected indentation of 4 spaces but found 2 indent 373:1 error Expected indentation of 4 spaces but found 2 indent 374:1 error Expected indentation of 4 spaces but found 2 indent 375:1 error Expected indentation of 4 spaces but found 2 indent 382:1 error Expected indentation of 4 spaces but found 2 indent 383:1 error Expected indentation of 8 spaces but found 4 indent 384:1 error Expected indentation of 8 spaces but found 4 indent 385:1 error Expected indentation of 12 spaces but found 6 indent 386:1 error Expected indentation of 12 spaces but found 6 indent 387:1 error Expected indentation of 16 spaces but found 8 indent 388:1 error Expected indentation of 16 spaces but found 8 indent 389:1 error Expected indentation of 16 spaces but found 8 indent 390:1 error Expected indentation of 16 spaces but found 8 indent 391:1 error Expected indentation of 16 spaces but found 8 indent 392:1 error Expected indentation of 12 spaces but found 6 indent 393:1 error Expected indentation of 12 spaces but found 6 indent 394:1 error Expected indentation of 12 spaces but found 6 indent 395:1 error Expected indentation of 12 spaces but found 6 indent 396:1 error Expected indentation of 12 spaces but found 6 indent 397:1 error Expected indentation of 12 spaces but found 6 indent 398:1 error Expected indentation of 12 spaces but found 6 indent 399:1 error Expected indentation of 12 spaces but found 6 indent 400:1 error Expected indentation of 12 spaces but found 6 indent 401:1 error Expected indentation of 12 spaces but found 6 indent 402:1 error Expected indentation of 8 spaces but found 4 indent 403:1 error Expected indentation of 8 spaces but found 4 indent 404:1 error Expected indentation of 8 spaces but found 4 indent 405:1 error Expected indentation of 8 spaces but found 4 indent 406:1 error Expected indentation of 8 spaces but found 4 indent 407:1 error Expected indentation of 8 spaces but found 4 indent 408:1 error Expected indentation of 8 spaces but found 4 indent 409:1 error Expected indentation of 8 spaces but found 4 indent 410:1 error Expected indentation of 4 spaces but found 2 indent 411:1 error Expected indentation of 4 spaces but found 2 indent 412:1 error Expected indentation of 4 spaces but found 2 indent 413:1 error Expected indentation of 4 spaces but found 2 indent 415:1 error Expected indentation of 8 spaces but found 4 indent 416:1 error Expected indentation of 8 spaces but found 4 indent 417:1 error Expected indentation of 8 spaces but found 4 indent 418:1 error Expected indentation of 12 spaces but found 6 indent 419:1 error Expected indentation of 8 spaces but found 4 indent 421:1 error Expected indentation of 8 spaces but found 4 indent 422:1 error Expected indentation of 12 spaces but found 6 indent 423:1 error Expected indentation of 12 spaces but found 6 indent 424:1 error Expected indentation of 8 spaces but found 4 indent 425:1 error Expected indentation of 4 spaces but found 2 indent 426:1 error Expected indentation of 4 spaces but found 2 indent 427:1 error Expected indentation of 4 spaces but found 2 indent 428:1 error Expected indentation of 4 spaces but found 2 indent 429:1 error Expected indentation of 4 spaces but found 2 indent 433:1 error Expected indentation of 8 spaces but found 4 indent 434:1 error Expected indentation of 12 spaces but found 6 indent 435:1 error Expected indentation of 12 spaces but found 6 indent 436:1 error Expected indentation of 12 spaces but found 6 indent 437:1 error Expected indentation of 12 spaces but found 6 indent 438:1 error Expected indentation of 12 spaces but found 6 indent 439:1 error Expected indentation of 12 spaces but found 6 indent 440:1 error Expected indentation of 16 spaces but found 8 indent 441:1 error Expected indentation of 16 spaces but found 8 indent 442:1 error Expected indentation of 16 spaces but found 8 indent 443:1 error Expected indentation of 12 spaces but found 6 indent 444:1 error Expected indentation of 8 spaces but found 4 indent 445:1 error Expected indentation of 4 spaces but found 2 indent 446:1 error Expected indentation of 4 spaces but found 2 indent 447:1 error Expected indentation of 4 spaces but found 2 indent 451:1 error Expected indentation of 8 spaces but found 4 indent 452:1 error Expected indentation of 12 spaces but found 6 indent 453:1 error Expected indentation of 12 spaces but found 6 indent 454:1 error Expected indentation of 12 spaces but found 6 indent 455:1 error Expected indentation of 12 spaces but found 6 indent 456:1 error Expected indentation of 12 spaces but found 6 indent 457:1 error Expected indentation of 16 spaces but found 8 indent 458:1 error Expected indentation of 12 spaces but found 6 indent 459:1 error Expected indentation of 8 spaces but found 4 indent 460:1 error Expected indentation of 4 spaces but found 2 indent 461:1 error Expected indentation of 4 spaces but found 2 indent 462:1 error Expected indentation of 4 spaces but found 2 indent 463:1 error Expected indentation of 8 spaces but found 4 indent 464:1 error Expected indentation of 12 spaces but found 6 indent 465:1 error Expected indentation of 12 spaces but found 6 indent 466:1 error Expected indentation of 8 spaces but found 4 indent 467:1 error Expected indentation of 8 spaces but found 4 indent 468:1 error Expected indentation of 8 spaces but found 4 indent 469:1 error Expected indentation of 8 spaces but found 4 indent 470:1 error Expected indentation of 8 spaces but found 4 indent 471:1 error Expected indentation of 12 spaces but found 6 indent 472:1 error Expected indentation of 12 spaces but found 6 indent 473:1 error Expected indentation of 12 spaces but found 6 indent 474:1 error Expected indentation of 12 spaces but found 6 indent 475:1 error Expected indentation of 12 spaces but found 6 indent 476:1 error Expected indentation of 12 spaces but found 6 indent 477:1 error Expected indentation of 16 spaces but found 8 indent 478:1 error Expected indentation of 16 spaces but found 8 indent 479:1 error Expected indentation of 12 spaces but found 6 indent 480:1 error Expected indentation of 12 spaces but found 6 indent 481:1 error Expected indentation of 16 spaces but found 8 indent 482:1 error Expected indentation of 16 spaces but found 8 indent 483:1 error Expected indentation of 16 spaces but found 8 indent 484:1 error Expected indentation of 12 spaces but found 6 indent 485:1 error Expected indentation of 8 spaces but found 4 indent 486:1 error Expected indentation of 8 spaces but found 4 indent 487:1 error Expected indentation of 4 spaces but found 2 indent 488:1 error Expected indentation of 4 spaces but found 2 indent 489:1 error Expected indentation of 4 spaces but found 2 indent 490:1 error Expected indentation of 8 spaces but found 4 indent 491:1 error Expected indentation of 12 spaces but found 6 indent 492:1 error Expected indentation of 12 spaces but found 6 indent 493:1 error Expected indentation of 8 spaces but found 4 indent 494:1 error Expected indentation of 8 spaces but found 4 indent 495:1 error Expected indentation of 8 spaces but found 4 indent 496:1 error Expected indentation of 8 spaces but found 4 indent 497:1 error Expected indentation of 8 spaces but found 4 indent 498:1 error Expected indentation of 12 spaces but found 6 indent 499:1 error Expected indentation of 12 spaces but found 6 indent 500:1 error Expected indentation of 12 spaces but found 6 indent 501:1 error Expected indentation of 16 spaces but found 8 indent 502:1 error Expected indentation of 16 spaces but found 8 indent 503:1 error Expected indentation of 12 spaces but found 6 indent 504:1 error Expected indentation of 12 spaces but found 6 indent 505:1 error Expected indentation of 12 spaces but found 6 indent 506:1 error Expected indentation of 16 spaces but found 8 indent 507:1 error Expected indentation of 16 spaces but found 8 indent 508:1 error Expected indentation of 12 spaces but found 6 indent 509:1 error Expected indentation of 8 spaces but found 4 indent 510:1 error Expected indentation of 8 spaces but found 4 indent 511:1 error Expected indentation of 4 spaces but found 2 indent 512:1 error Expected indentation of 4 spaces but found 2 indent 513:1 error Expected indentation of 4 spaces but found 2 indent 517:1 error Expected indentation of 8 spaces but found 4 indent 518:1 error Expected indentation of 12 spaces but found 6 indent 519:1 error Expected indentation of 12 spaces but found 6 indent 520:1 error Expected indentation of 12 spaces but found 6 indent 521:1 error Expected indentation of 12 spaces but found 6 indent 522:1 error Expected indentation of 16 spaces but found 8 indent 523:1 error Expected indentation of 16 spaces but found 8 indent 524:1 error Expected indentation of 16 spaces but found 8 indent 525:1 error Expected indentation of 16 spaces but found 8 indent 526:1 error Expected indentation of 12 spaces but found 6 indent 527:1 error Expected indentation of 12 spaces but found 6 indent 528:1 error Expected indentation of 16 spaces but found 8 indent 529:1 error Expected indentation of 16 spaces but found 8 indent 530:1 error Expected indentation of 12 spaces but found 6 indent 531:1 error Expected indentation of 8 spaces but found 4 indent 532:1 error Expected indentation of 4 spaces but found 2 indent 533:1 error Expected indentation of 4 spaces but found 2 indent 534:1 error Expected indentation of 4 spaces but found 2 indent 535:1 error Expected indentation of 8 spaces but found 4 indent 536:1 error Expected indentation of 12 spaces but found 6 indent 537:1 error Expected indentation of 8 spaces but found 4 indent 538:1 error Expected indentation of 4 spaces but found 2 indent 539:1 error Expected indentation of 4 spaces but found 2 indent 540:1 error Expected indentation of 4 spaces but found 2 indent 541:1 error Expected indentation of 8 spaces but found 4 indent 542:1 error Expected indentation of 8 spaces but found 4 indent 543:1 error Expected indentation of 8 spaces but found 4 indent 544:1 error Expected indentation of 12 spaces but found 6 indent 545:1 error Expected indentation of 16 spaces but found 8 indent 546:1 error Expected indentation of 20 spaces but found 10 indent 547:1 error Expected indentation of 16 spaces but found 8 indent 548:1 error Expected indentation of 12 spaces but found 6 indent 549:1 error Expected indentation of 8 spaces but found 4 indent 551:1 error Expected indentation of 8 spaces but found 4 indent 552:1 error Expected indentation of 12 spaces but found 6 indent 553:1 error Expected indentation of 16 spaces but found 8 indent 554:1 error Expected indentation of 20 spaces but found 10 indent 555:1 error Expected indentation of 20 spaces but found 10 indent 556:1 error Expected indentation of 24 spaces but found 12 indent 557:1 error Expected indentation of 28 spaces but found 14 indent 558:1 error Expected indentation of 32 spaces but found 16 indent 559:1 error Expected indentation of 32 spaces but found 16 indent 560:1 error Expected indentation of 28 spaces but found 14 indent 561:1 error Expected indentation of 28 spaces but found 14 indent 562:1 error Expected indentation of 32 spaces but found 16 indent 563:1 error Expected indentation of 28 spaces but found 14 indent 564:1 error Expected indentation of 24 spaces but found 12 indent 565:1 error Expected indentation of 20 spaces but found 10 indent 566:1 error Expected indentation of 16 spaces but found 8 indent 567:1 error Expected indentation of 16 spaces but found 8 indent 568:1 error Expected indentation of 20 spaces but found 10 indent 569:1 error Expected indentation of 20 spaces but found 10 indent 570:1 error Expected indentation of 20 spaces but found 10 indent 571:1 error Expected indentation of 20 spaces but found 10 indent 572:1 error Expected indentation of 20 spaces but found 10 indent 573:1 error Expected indentation of 16 spaces but found 8 indent 574:1 error Expected indentation of 16 spaces but found 8 indent 575:1 error Expected indentation of 20 spaces but found 10 indent 576:1 error Expected indentation of 16 spaces but found 8 indent 577:1 error Expected indentation of 12 spaces but found 6 indent 578:1 error Expected indentation of 8 spaces but found 4 indent 579:1 error Expected indentation of 4 spaces but found 2 indent 588:1 error Expected indentation of 4 spaces but found 2 indent 589:1 error Expected indentation of 8 spaces but found 4 indent 590:1 error Expected indentation of 8 spaces but found 4 indent 592:1 error Expected indentation of 8 spaces but found 4 indent 593:1 error Expected indentation of 8 spaces but found 4 indent 594:1 error Expected indentation of 8 spaces but found 4 indent 595:1 error Expected indentation of 4 spaces but found 2 indent 597:1 error Expected indentation of 4 spaces but found 2 indent 598:1 error Expected indentation of 4 spaces but found 2 indent 601:1 error Expected indentation of 8 spaces but found 4 indent 602:1 error Expected indentation of 4 spaces but found 2 indent 603:1 error Expected indentation of 4 spaces but found 2 indent 604:1 error Expected indentation of 4 spaces but found 2 indent 606:1 error Expected indentation of 8 spaces but found 4 indent 607:1 error Expected indentation of 8 spaces but found 4 indent 608:1 error Expected indentation of 8 spaces but found 4 indent 609:1 error Expected indentation of 8 spaces but found 4 indent 610:1 error Expected indentation of 8 spaces but found 4 indent 611:1 error Expected indentation of 4 spaces but found 2 indent 612:1 error Expected indentation of 4 spaces but found 2 indent 613:1 error Expected indentation of 4 spaces but found 2 indent 614:1 error Expected indentation of 8 spaces but found 4 indent 615:1 error Expected indentation of 8 spaces but found 4 indent 616:1 error Expected indentation of 12 spaces but found 6 indent 617:1 error Expected indentation of 16 spaces but found 8 indent 618:1 error Expected indentation of 16 spaces but found 8 indent 619:1 error Expected indentation of 16 spaces but found 8 indent 620:1 error Expected indentation of 16 spaces but found 8 indent 621:1 error Expected indentation of 12 spaces but found 6 indent 622:1 error Expected indentation of 8 spaces but found 4 indent 623:1 error Expected indentation of 8 spaces but found 4 indent 624:1 error Expected indentation of 12 spaces but found 6 indent 625:1 error Expected indentation of 16 spaces but found 8 indent 626:1 error Expected indentation of 16 spaces but found 8 indent 627:1 error Expected indentation of 16 spaces but found 8 indent 628:1 error Expected indentation of 12 spaces but found 6 indent 629:1 error Expected indentation of 8 spaces but found 4 indent 630:1 error Expected indentation of 8 spaces but found 4 indent 631:1 error Expected indentation of 12 spaces but found 6 indent 632:1 error Expected indentation of 16 spaces but found 8 indent 633:1 error Expected indentation of 16 spaces but found 8 indent 634:1 error Expected indentation of 16 spaces but found 8 indent 635:1 error Expected indentation of 16 spaces but found 8 indent 636:1 error Expected indentation of 12 spaces but found 6 indent 637:1 error Expected indentation of 8 spaces but found 4 indent 639:1 error Expected indentation of 8 spaces but found 4 indent 640:1 error Expected indentation of 12 spaces but found 6 indent 641:1 error Expected indentation of 16 spaces but found 8 indent 642:1 error Expected indentation of 16 spaces but found 8 indent 643:1 error Expected indentation of 12 spaces but found 6 indent 644:1 error Expected indentation of 12 spaces but found 6 indent 645:1 error Expected indentation of 16 spaces but found 8 indent 646:1 error Expected indentation of 16 spaces but found 8 indent 647:1 error Expected indentation of 12 spaces but found 6 indent 648:1 error Expected indentation of 12 spaces but found 6 indent 649:1 error Expected indentation of 16 spaces but found 8 indent 650:1 error Expected indentation of 16 spaces but found 8 indent 651:1 error Expected indentation of 12 spaces but found 6 indent 652:1 error Expected indentation of 8 spaces but found 4 indent 654:1 error Expected indentation of 8 spaces but found 4 indent 655:1 error Expected indentation of 12 spaces but found 6 indent 656:1 error Expected indentation of 16 spaces but found 8 indent 657:1 error Expected indentation of 20 spaces but found 10 indent 658:1 error Expected indentation of 16 spaces but found 8 indent 659:1 error Expected indentation of 12 spaces but found 6 indent 660:1 error Expected indentation of 8 spaces but found 4 indent 661:1 error Expected indentation of 4 spaces but found 2 indent ? 585 problems (585 errors, 0 warnings) 580 errors and 0 warnings potentially fixable with the `--fix` option. ERROR in ./modules/instrument_builder/jsx/react.questions.js Module Error (from ./node_modules/eslint-loader/index.js): /var/www/loris/modules/instrument_builder/jsx/react.questions.js 12:8 error 'React' is defined but never used no-unused-vars 23:1 error Expected indentation of 4 spaces but found 2 indent 24:1 error Expected indentation of 8 spaces but found 4 indent 25:1 error Expected indentation of 8 spaces but found 4 indent 27:1 error Expected indentation of 8 spaces but found 4 indent 28:1 error Expected indentation of 4 spaces but found 2 indent 30:1 error Expected indentation of 4 spaces but found 2 indent 31:1 error Expected indentation of 8 spaces but found 4 indent 32:1 error Expected indentation of 8 spaces but found 4 indent 33:1 error Expected indentation of 8 spaces but found 4 indent 34:1 error Expected indentation of 8 spaces but found 6 indent 35:1 error Expected indentation of 12 spaces but found 8 indent 36:1 error Expected indentation of 12 spaces but found 8 indent 37:1 error Expected indentation of 8 spaces but found 6 indent 38:1 error Expected indentation of 12 spaces but found 8 indent 39:1 error Expected indentation of 12 spaces but found 8 indent 40:1 error Expected indentation of 8 spaces but found 6 indent 41:1 error Expected indentation of 12 spaces but found 8 indent 43:1 error Expected indentation of 12 spaces but found 8 indent 44:1 error Expected indentation of 8 spaces but found 6 indent 45:1 error Expected indentation of 12 spaces but found 8 indent 46:1 error Expected indentation of 16 spaces but found 10 indent 47:1 error Expected indentation of 12 spaces but found 8 indent 48:1 error Expected indentation of 16 spaces but found 10 indent 49:1 error Expected indentation of 12 spaces but found 8 indent 50:1 error Expected indentation of 12 spaces but found 8 indent 51:1 error Expected indentation of 8 spaces but found 6 indent 52:1 error Expected indentation of 12 spaces but found 8 indent 53:1 error Expected indentation of 16 spaces but found 10 indent 54:1 error Expected indentation of 20 spaces but found 39 indent 55:1 error Expected indentation of 20 spaces but found 39 indent 56:1 error Expected indentation of 20 spaces but found 39 indent 57:1 error Expected indentation of 12 spaces but found 8 indent 58:1 error Expected indentation of 16 spaces but found 10 indent 59:1 error Expected indentation of 20 spaces but found 39 indent 60:1 error Expected indentation of 20 spaces but found 39 indent 61:1 error Expected indentation of 12 spaces but found 8 indent 62:1 error Expected indentation of 12 spaces but found 8 indent 63:1 error Expected indentation of 8 spaces but found 6 indent 64:1 error Expected indentation of 12 spaces but found 8 indent 65:1 error Expected indentation of 16 spaces but found 10 indent 66:1 error Expected indentation of 16 spaces but found 10 indent 67:1 error Expected indentation of 16 spaces but found 10 indent 68:1 error Expected indentation of 12 spaces but found 8 indent 69:1 error Expected indentation of 12 spaces but found 8 indent 70:1 error Expected indentation of 8 spaces but found 6 indent 71:1 error Expected indentation of 12 spaces but found 8 indent 72:1 error Expected indentation of 16 spaces but found 10 indent 73:1 error Expected indentation of 16 spaces but found 10 indent 74:1 error Expected indentation of 16 spaces but found 10 indent 75:1 error Expected indentation of 12 spaces but found 8 indent 76:1 error Expected indentation of 12 spaces but found 8 indent 77:1 error Expected indentation of 8 spaces but found 6 indent 78:1 error Expected indentation of 12 spaces but found 8 indent 79:1 error Expected indentation of 8 spaces but found 4 indent 80:1 error Expected indentation of 8 spaces but found 4 indent 81:1 error Expected indentation of 12 spaces but found 6 indent 82:1 error Expected indentation of 8 spaces but found 4 indent 83:1 error Expected indentation of 4 spaces but found 2 indent 90:1 error Expected indentation of 4 spaces but found 2 indent 91:1 error Expected indentation of 8 spaces but found 4 indent 92:1 error Expected indentation of 8 spaces but found 4 indent 94:1 error Expected indentation of 8 spaces but found 4 indent 95:1 error Expected indentation of 8 spaces but found 4 indent 96:1 error Expected indentation of 4 spaces but found 2 indent 98:1 error Expected indentation of 4 spaces but found 2 indent 99:1 error Expected indentation of 8 spaces but found 4 indent 100:1 error Expected indentation of 4 spaces but found 2 indent 102:1 error Expected indentation of 4 spaces but found 2 indent 103:1 error Expected indentation of 8 spaces but found 4 indent 104:1 error Expected indentation of 8 spaces but found 4 indent 105:1 error Expected indentation of 8 spaces but found 4 indent 106:1 error Expected indentation of 12 spaces but found 6 indent 107:1 error Expected indentation of 12 spaces but found 6 indent 108:1 error Expected indentation of 12 spaces but found 6 indent 109:1 error Expected indentation of 8 spaces but found 4 indent 110:1 error Expected indentation of 8 spaces but found 4 indent 111:1 error Expected indentation of 12 spaces but found 6 indent 112:1 error Expected indentation of 16 spaces but found 8 indent 113:1 error Expected indentation of 16 spaces but found 8 indent 114:1 error Expected indentation of 20 spaces but found 10 indent 115:1 error Expected indentation of 24 spaces but found 12 indent 116:1 error Expected indentation of 24 spaces but found 12 indent 117:1 error Expected indentation of 24 spaces but found 12 indent 118:1 error Expected indentation of 24 spaces but found 12 indent 119:1 error Expected indentation of 20 spaces but found 10 indent 120:1 error Expected indentation of 20 spaces but found 10 indent 121:1 error Expected indentation of 16 spaces but found 8 indent 122:1 error Expected indentation of 12 spaces but found 6 indent 123:1 error Expected indentation of 8 spaces but found 4 indent 124:1 error Expected indentation of 4 spaces but found 2 indent 127:1 error Expected indentation of 4 spaces but found 2 indent 130:1 error Expected indentation of 4 spaces but found 2 indent 137:1 error Expected indentation of 4 spaces but found 2 indent 138:1 error Expected indentation of 8 spaces but found 4 indent 139:1 error Expected indentation of 8 spaces but found 4 indent 141:1 error Expected indentation of 8 spaces but found 4 indent 142:1 error Expected indentation of 8 spaces but found 4 indent 143:1 error Expected indentation of 4 spaces but found 2 indent 144:1 error Expected indentation of 4 spaces but found 2 indent 145:1 error Expected indentation of 4 spaces but found 2 indent 147:1 error Expected indentation of 8 spaces but found 4 indent 148:1 error Expected indentation of 8 spaces but found 4 indent 149:1 error Expected indentation of 4 spaces but found 2 indent 150:1 error Expected indentation of 4 spaces but found 2 indent 151:1 error Expected indentation of 4 spaces but found 2 indent 152:1 error Expected indentation of 8 spaces but found 4 indent 153:1 error Expected indentation of 8 spaces but found 4 indent 154:1 error Expected indentation of 8 spaces but found 4 indent 155:1 error Expected indentation of 12 spaces but found 6 indent 156:1 error Expected indentation of 12 spaces but found 6 indent 157:1 error Expected indentation of 12 spaces but found 6 indent 158:1 error Expected indentation of 8 spaces but found 4 indent 159:1 error Expected indentation of 8 spaces but found 4 indent 160:1 error Expected indentation of 12 spaces but found 6 indent 161:1 error Expected indentation of 16 spaces but found 8 indent 162:1 error Expected indentation of 20 spaces but found 10 indent 163:1 error Expected indentation of 20 spaces but found 10 indent 164:1 error Expected indentation of 24 spaces but found 12 indent 165:1 error Expected indentation of 28 spaces but found 14 indent 166:1 error Expected indentation of 28 spaces but found 14 indent 167:1 error Expected indentation of 28 spaces but found 14 indent 168:1 error Expected indentation of 24 spaces but found 12 indent 169:1 error Expected indentation of 24 spaces but found 12 indent 170:1 error Expected indentation of 20 spaces but found 10 indent 171:1 error Expected indentation of 16 spaces but found 8 indent 172:1 error Expected indentation of 16 spaces but found 8 indent 173:1 error Expected indentation of 20 spaces but found 10 indent 174:1 error Expected indentation of 20 spaces but found 10 indent 175:1 error Expected indentation of 16 spaces but found 8 indent 176:1 error Expected indentation of 12 spaces but found 6 indent 177:1 error Expected indentation of 8 spaces but found 4 indent 178:1 error Expected indentation of 4 spaces but found 2 indent 185:1 error Expected indentation of 4 spaces but found 2 indent 186:1 error Expected indentation of 8 spaces but found 4 indent 187:1 error Expected indentation of 8 spaces but found 4 indent 188:1 error Expected indentation of 12 spaces but found 6 indent 189:1 error Expected indentation of 8 spaces but found 4 indent 190:1 error Expected indentation of 8 spaces but found 4 indent 191:1 error Expected indentation of 8 spaces but found 4 indent 192:1 error Expected indentation of 8 spaces but found 4 indent 193:1 error Expected indentation of 4 spaces but found 2 indent 194:1 error Expected indentation of 4 spaces but found 2 indent 195:1 error Expected indentation of 8 spaces but found 4 indent 196:1 error Expected indentation of 12 spaces but found 6 indent 197:1 error Expected indentation of 8 spaces but found 4 indent 198:1 error Expected indentation of 4 spaces but found 2 indent 199:1 error Expected indentation of 4 spaces but found 2 indent 200:1 error Expected indentation of 4 spaces but found 2 indent 201:1 error Expected indentation of 8 spaces but found 4 indent 203:1 error Expected indentation of 8 spaces but found 4 indent 204:1 error Expected indentation of 8 spaces but found 4 indent 205:1 error Expected indentation of 12 spaces but found 6 indent 206:1 error Expected indentation of 12 spaces but found 6 indent 207:1 error Expected indentation of 12 spaces but found 6 indent 208:1 error Expected indentation of 16 spaces but found 8 indent 209:1 error Expected indentation of 12 spaces but found 6 indent 210:1 error Expected indentation of 12 spaces but found 6 indent 211:1 error Expected indentation of 8 spaces but found 4 indent 213:1 error Expected indentation of 8 spaces but found 4 indent 214:1 error Expected indentation of 8 spaces but found 4 indent 215:1 error Expected indentation of 12 spaces but found 6 indent 216:1 error Expected indentation of 12 spaces but found 6 indent 217:1 error Expected indentation of 12 spaces but found 6 indent 218:1 error Expected indentation of 16 spaces but found 8 indent 219:1 error Expected indentation of 12 spaces but found 6 indent 220:1 error Expected indentation of 8 spaces but found 4 indent 222:1 error Expected indentation of 8 spaces but found 4 indent 223:1 error Expected indentation of 8 spaces but found 4 indent 224:1 error Expected indentation of 8 spaces but found 4 indent 225:1 error Expected indentation of 8 spaces but found 4 indent 226:1 error Expected indentation of 8 spaces but found 4 indent 228:1 error Expected indentation of 8 spaces but found 4 indent 229:1 error Expected indentation of 8 spaces but found 4 indent 230:1 error Expected indentation of 4 spaces but found 2 indent 231:1 error Expected indentation of 4 spaces but found 2 indent 232:1 error Expected indentation of 4 spaces but found 2 indent 233:1 error Expected indentation of 8 spaces but found 4 indent 234:1 error Expected indentation of 8 spaces but found 4 indent 235:1 error Expected indentation of 8 spaces but found 4 indent 236:1 error Expected indentation of 4 spaces but found 2 indent 237:1 error Expected indentation of 4 spaces but found 2 indent 238:1 error Expected indentation of 4 spaces but found 2 indent 239:1 error Expected indentation of 8 spaces but found 4 indent 240:1 error Expected indentation of 8 spaces but found 4 indent 241:1 error Expected indentation of 8 spaces but found 4 indent 242:1 error Expected indentation of 8 spaces but found 4 indent 244:1 error Expected indentation of 8 spaces but found 4 indent 245:1 error Expected indentation of 8 spaces but found 4 indent 246:1 error Expected indentation of 12 spaces but found 6 indent 247:1 error Expected indentation of 8 spaces but found 4 indent 249:1 error Expected indentation of 8 spaces but found 4 indent 250:1 error Expected indentation of 8 spaces but found 4 indent 251:1 error Expected indentation of 12 spaces but found 6 indent 252:1 error Expected indentation of 16 spaces but found 8 indent 253:1 error Expected indentation of 12 spaces but found 6 indent 254:1 error Expected indentation of 12 spaces but found 6 indent 255:1 error Expected indentation of 8 spaces but found 4 indent 257:1 error Expected indentation of 8 spaces but found 4 indent 258:1 error Expected indentation of 12 spaces but found 6 indent 259:1 error Expected indentation of 16 spaces but found 8 indent 260:1 error Expected indentation of 20 spaces but found 10 indent 261:1 error Expected indentation of 20 spaces but found 10 indent 262:1 error Expected indentation of 16 spaces but found 8 indent 263:1 error Expected indentation of 16 spaces but found 8 indent 264:1 error Expected indentation of 20 spaces but found 10 indent 265:1 error Expected indentation of 20 spaces but found 10 indent 266:1 error Expected indentation of 24 spaces but found 12 indent 267:1 error Expected indentation of 28 spaces but found 14 indent 268:1 error Expected indentation of 28 spaces but found 14 indent 269:1 error Expected indentation of 28 spaces but found 14 indent 270:1 error Expected indentation of 28 spaces but found 14 indent 271:1 error Expected indentation of 28 spaces but found 14 indent 272:1 error Expected indentation of 24 spaces but found 12 indent 273:1 error Expected indentation of 20 spaces but found 10 indent 274:1 error Expected indentation of 20 spaces but found 10 indent 275:1 error Expected indentation of 24 spaces but found 12 indent 276:1 error Expected indentation of 24 spaces but found 12 indent 277:1 error Expected indentation of 24 spaces but found 12 indent 278:1 error Expected indentation of 24 spaces but found 12 indent 279:1 error Expected indentation of 20 spaces but found 10 indent 280:1 error Expected indentation of 20 spaces but found 10 indent 281:1 error Expected indentation of 24 spaces but found 12 indent 282:1 error Expected indentation of 24 spaces but found 12 indent 283:1 error Expected indentation of 24 spaces but found 12 indent 284:1 error Expected indentation of 24 spaces but found 12 indent 285:1 error Expected indentation of 20 spaces but found 10 indent 286:1 error Expected indentation of 20 spaces but found 10 indent 287:1 error Expected indentation of 24 spaces but found 12 indent 288:1 error Expected indentation of 20 spaces but found 10 indent 289:1 error Expected indentation of 16 spaces but found 8 indent 290:1 error Expected indentation of 16 spaces but found 8 indent 291:1 error Expected indentation of 20 spaces but found 10 indent 292:1 error Expected indentation of 20 spaces but found 10 indent 293:1 error Expected indentation of 24 spaces but found 12 indent 294:1 error Expected indentation of 28 spaces but found 14 indent 295:1 error Expected indentation of 32 spaces but found 16 indent 296:1 error Expected indentation of 28 spaces but found 14 indent 297:1 error Expected indentation of 24 spaces but found 12 indent 298:1 error Expected indentation of 20 spaces but found 10 indent 299:1 error Expected indentation of 16 spaces but found 8 indent 300:1 error Expected indentation of 12 spaces but found 6 indent 301:1 error Expected indentation of 8 spaces but found 4 indent 302:1 error Expected indentation of 4 spaces but found 2 indent 309:1 error Expected indentation of 4 spaces but found 2 indent 310:1 error Expected indentation of 8 spaces but found 4 indent 311:1 error Expected indentation of 8 spaces but found 4 indent 312:1 error Expected indentation of 12 spaces but found 6 indent 313:1 error Expected indentation of 16 spaces but found 8 indent 314:1 error Expected indentation of 16 spaces but found 8 indent 315:1 error Expected indentation of 16 spaces but found 8 indent 316:1 error Expected indentation of 12 spaces but found 6 indent 317:1 error Expected indentation of 8 spaces but found 4 indent 318:1 error Expected indentation of 8 spaces but found 4 indent 319:1 error Expected indentation of 4 spaces but found 2 indent 321:1 error Expected indentation of 4 spaces but found 2 indent 322:1 error Expected indentation of 8 spaces but found 4 indent 323:1 error Expected indentation of 4 spaces but found 2 indent 325:1 error Expected indentation of 4 spaces but found 2 indent 326:1 error Expected indentation of 8 spaces but found 4 indent 327:1 error Expected indentation of 8 spaces but found 4 indent 328:1 error Expected indentation of 12 spaces but found 6 indent 329:1 error Expected indentation of 8 spaces but found 4 indent 330:1 error Expected indentation of 12 spaces but found 6 indent 331:1 error Expected indentation of 8 spaces but found 4 indent 332:1 error Expected indentation of 12 spaces but found 6 indent 333:1 error Expected indentation of 8 spaces but found 4 indent 334:1 error Expected indentation of 8 spaces but found 4 indent 335:1 error Expected indentation of 4 spaces but found 2 indent 336:1 error Expected indentation of 4 spaces but found 2 indent 337:1 error Expected indentation of 4 spaces but found 2 indent 339:1 error Expected indentation of 8 spaces but found 4 indent 340:1 error Expected indentation of 8 spaces but found 4 indent 342:1 error Expected indentation of 8 spaces but found 4 indent 343:1 error Expected indentation of 8 spaces but found 4 indent 345:1 error Expected indentation of 8 spaces but found 4 indent 347:1 error Expected indentation of 8 spaces but found 4 indent 348:1 error Expected indentation of 12 spaces but found 6 indent 349:1 error Expected indentation of 12 spaces but found 6 indent 350:1 error Expected indentation of 16 spaces but found 8 indent 351:1 error Expected indentation of 12 spaces but found 6 indent 352:1 error Expected indentation of 12 spaces but found 6 indent 353:1 error Expected indentation of 8 spaces but found 4 indent 355:1 error Expected indentation of 8 spaces but found 4 indent 356:1 error Expected indentation of 12 spaces but found 6 indent 357:1 error Expected indentation of 16 spaces but found 8 indent 358:1 error Expected indentation of 20 spaces but found 10 indent 359:1 error Expected indentation of 20 spaces but found 10 indent 360:1 error Expected indentation of 16 spaces but found 8 indent 361:1 error Expected indentation of 16 spaces but found 8 indent 362:1 error Expected indentation of 20 spaces but found 10 indent 363:1 error Expected indentation of 20 spaces but found 10 indent 364:1 error Expected indentation of 24 spaces but found 12 indent 365:1 error Expected indentation of 28 spaces but found 14 indent 366:1 error Expected indentation of 28 spaces but found 14 indent 367:1 error Expected indentation of 28 spaces but found 14 indent 368:1 error Expected indentation of 28 spaces but found 14 indent 369:1 error Expected indentation of 28 spaces but found 14 indent 370:1 error Expected indentation of 28 spaces but found 14 indent 371:1 error Expected indentation of 28 spaces but found 14 indent 372:1 error Expected indentation of 24 spaces but found 12 indent 373:1 error Expected indentation of 24 spaces but found 12 indent 374:1 error Expected indentation of 20 spaces but found 10 indent 375:1 error Expected indentation of 20 spaces but found 10 indent 376:1 error Expected indentation of 20 spaces but found 10 indent 377:1 error Expected indentation of 24 spaces but found 12 indent 378:1 error Expected indentation of 28 spaces but found 14 indent 379:1 error Expected indentation of 28 spaces but found 14 indent 380:1 error Expected indentation of 28 spaces but found 14 indent 381:1 error Expected indentation of 28 spaces but found 14 indent 382:1 error Expected indentation of 28 spaces but found 14 indent 383:1 error Expected indentation of 28 spaces but found 14 indent 384:1 error Expected indentation of 28 spaces but found 14 indent 385:1 error Expected indentation of 24 spaces but found 12 indent 386:1 error Expected indentation of 20 spaces but found 10 indent 387:1 error Expected indentation of 16 spaces but found 8 indent 388:1 error Expected indentation of 16 spaces but found 8 indent 389:1 error Expected indentation of 20 spaces but found 10 indent 390:1 error Expected indentation of 20 spaces but found 10 indent 391:1 error Expected indentation of 24 spaces but found 12 indent 392:1 error Expected indentation of 28 spaces but found 14 indent 393:1 error Expected indentation of 28 spaces but found 14 indent 394:1 error Expected indentation of 28 spaces but found 14 indent 395:1 error Expected indentation of 28 spaces but found 14 indent 396:1 error Expected indentation of 32 spaces but found 16 indent 397:1 error Expected indentation of 36 spaces but found 18 indent 398:1 error Expected indentation of 40 spaces but found 20 indent 399:1 error Expected indentation of 36 spaces but found 18 indent 400:1 error Expected indentation of 32 spaces but found 16 indent 401:1 error Expected indentation of 28 spaces but found 14 indent 402:1 error Expected indentation of 24 spaces but found 12 indent 403:1 error Expected indentation of 20 spaces but found 10 indent 404:1 error Expected indentation of 16 spaces but found 8 indent 405:1 error Expected indentation of 12 spaces but found 6 indent 406:1 error Expected indentation of 8 spaces but found 4 indent 407:1 error Expected indentation of 4 spaces but found 2 indent 414:1 error Expected indentation of 4 spaces but found 2 indent 415:1 error Expected indentation of 8 spaces but found 4 indent 416:1 error Expected indentation of 8 spaces but found 4 indent 418:1 error Expected indentation of 8 spaces but found 4 indent 419:1 error Expected indentation of 8 spaces but found 4 indent 420:1 error Expected indentation of 4 spaces but found 2 indent 422:1 error Expected indentation of 4 spaces but found 2 indent 423:1 error Expected indentation of 4 spaces but found 2 indent 424:1 error Expected indentation of 4 spaces but found 2 indent 425:1 error Expected indentation of 8 spaces but found 4 indent 427:1 error Expected indentation of 8 spaces but found 4 indent 428:1 error Expected indentation of 12 spaces but found 6 indent 429:1 error Expected indentation of 8 spaces but found 4 indent 430:1 error Expected indentation of 12 spaces but found 6 indent 431:1 error Expected indentation of 8 spaces but found 4 indent 432:1 error Expected indentation of 8 spaces but found 4 indent 433:1 error Expected indentation of 4 spaces but found 2 indent 434:1 error Expected indentation of 4 spaces but found 2 indent 435:1 error Expected indentation of 4 spaces but found 2 indent 436:1 error Expected indentation of 8 spaces but found 4 indent 437:1 error Expected indentation of 8 spaces but found 4 indent 440:1 error Expected indentation of 8 spaces but found 4 indent 441:1 error Expected indentation of 12 spaces but found 6 indent 442:1 error Expected indentation of 12 spaces but found 6 indent 443:1 error Expected indentation of 8 spaces but found 4 indent 445:1 error Expected indentation of 8 spaces but found 4 indent 446:1 error Expected indentation of 12 spaces but found 6 indent 447:1 error Expected indentation of 16 spaces but found 8 indent 448:1 error Expected indentation of 20 spaces but found 10 indent 449:1 error Expected indentation of 20 spaces but found 10 indent 450:1 error Expected indentation of 16 spaces but found 8 indent 451:1 error Expected indentation of 16 spaces but found 8 indent 452:1 error Expected indentation of 20 spaces but found 10 indent 453:1 error Expected indentation of 20 spaces but found 10 indent 454:1 error Expected indentation of 24 spaces but found 12 indent 455:1 error Expected indentation of 28 spaces but found 14 indent 456:1 error Expected indentation of 28 spaces but found 14 indent 457:1 error Expected indentation of 28 spaces but found 14 indent 458:1 error Expected indentation of 28 spaces but found 14 indent 459:1 error Expected indentation of 28 spaces but found 14 indent 460:1 error Expected indentation of 24 spaces but found 12 indent 461:1 error Expected indentation of 20 spaces but found 10 indent 462:1 error Expected indentation of 20 spaces but found 10 indent 463:1 error Expected indentation of 20 spaces but found 10 indent 464:1 error Expected indentation of 24 spaces but found 12 indent 465:1 error Expected indentation of 28 spaces but found 14 indent 466:1 error Expected indentation of 28 spaces but found 14 indent 467:1 error Expected indentation of 28 spaces but found 14 indent 468:1 error Expected indentation of 28 spaces but found 14 indent 469:1 error Expected indentation of 28 spaces but found 14 indent 470:1 error Expected indentation of 24 spaces but found 12 indent 471:1 error Expected indentation of 20 spaces but found 10 indent 472:1 error Expected indentation of 20 spaces but found 10 indent 473:1 error Expected indentation of 24 spaces but found 12 indent 474:1 error Expected indentation of 20 spaces but found 10 indent 475:1 error Expected indentation of 16 spaces but found 8 indent 476:1 error Expected indentation of 12 spaces but found 6 indent 477:1 error Expected indentation of 8 spaces but found 4 indent 478:1 error Expected indentation of 4 spaces but found 2 indent 486:1 error Expected indentation of 4 spaces but found 2 indent 487:1 error Expected indentation of 8 spaces but found 4 indent 488:1 error Expected indentation of 8 spaces but found 4 indent 490:1 error Expected indentation of 8 spaces but found 4 indent 491:1 error Expected indentation of 8 spaces but found 4 indent 492:1 error Expected indentation of 4 spaces but found 2 indent 494:1 error Expected indentation of 4 spaces but found 2 indent 495:1 error Expected indentation of 8 spaces but found 4 indent 496:1 error Expected indentation of 12 spaces but found 6 indent 497:1 error Expected indentation of 16 spaces but found 8 indent 498:1 error Expected indentation of 16 spaces but found 8 indent 499:1 error Expected indentation of 12 spaces but found 6 indent 500:1 error Expected indentation of 8 spaces but found 4 indent 501:1 error Expected indentation of 8 spaces but found 4 indent 502:1 error Expected indentation of 8 spaces but found 4 indent 503:1 error Expected indentation of 8 spaces but found 4 indent 504:1 error Expected indentation of 8 spaces but found 4 indent 505:1 error Expected indentation of 8 spaces but found 6 indent 506:1 error Expected indentation of 12 spaces but found 8 indent 508:1 error Expected indentation of 8 spaces but found 6 indent 509:1 error Expected indentation of 12 spaces but found 8 indent 510:1 error Expected indentation of 16 spaces but found 10 indent 511:1 error Expected indentation of 12 spaces but found 8 indent 512:1 error Expected indentation of 12 spaces but found 8 indent 513:1 error Expected indentation of 8 spaces but found 6 indent 514:1 error Expected indentation of 12 spaces but found 8 indent 516:1 error Expected indentation of 8 spaces but found 6 indent 517:1 error Expected indentation of 12 spaces but found 8 indent 518:1 error Expected indentation of 16 spaces but found 10 indent 519:1 error Expected indentation of 16 spaces but found 10 indent 520:1 error Expected indentation of 12 spaces but found 8 indent 521:1 error Expected indentation of 12 spaces but found 8 indent 522:1 error Expected indentation of 8 spaces but found 6 indent 523:1 error Expected indentation of 12 spaces but found 8 indent 524:1 error Expected indentation of 16 spaces but found 10 indent 525:1 error Expected indentation of 16 spaces but found 10 indent 526:1 error Expected indentation of 12 spaces but found 8 indent 527:1 error Expected indentation of 12 spaces but found 8 indent 528:1 error Expected indentation of 8 spaces but found 6 indent 529:1 error Expected indentation of 12 spaces but found 8 indent 530:1 error Expected indentation of 16 spaces but found 10 indent 531:1 error Expected indentation of 16 spaces but found 10 indent 532:1 error Expected indentation of 12 spaces but found 8 indent 533:1 error Expected indentation of 12 spaces but found 8 indent 534:1 error Expected indentation of 8 spaces but found 6 indent 535:1 error Expected indentation of 12 spaces but found 8 indent 536:1 error Expected indentation of 8 spaces but found 4 indent 537:1 error Expected indentation of 8 spaces but found 4 indent 538:1 error Expected indentation of 4 spaces but found 2 indent 540:1 error Expected indentation of 4 spaces but found 2 indent 541:1 error Expected indentation of 8 spaces but found 4 indent 542:1 error Expected indentation of 12 spaces but found 8 indent 543:1 error Expected indentation of 16 spaces but found 12 indent 544:1 error Expected indentation of 16 spaces but found 12 indent 545:1 error Expected indentation of 20 spaces but found 16 indent 546:1 error Expected indentation of 24 spaces but found 20 indent 547:1 error Expected indentation of 28 spaces but found 24 indent 548:1 error Expected indentation of 28 spaces but found 24 indent 549:1 error Expected indentation of 24 spaces but found 20 indent 550:1 error Expected indentation of 24 spaces but found 20 indent 551:1 error Expected indentation of 28 spaces but found 24 indent 552:1 error Expected indentation of 32 spaces but found 28 indent 553:1 error Expected indentation of 28 spaces but found 24 indent 554:1 error Expected indentation of 28 spaces but found 24 indent 555:1 error Expected indentation of 32 spaces but found 28 indent 556:1 error Expected indentation of 28 spaces but found 24 indent 557:1 error Expected indentation of 28 spaces but found 24 indent 558:1 error Expected indentation of 32 spaces but found 28 indent 559:1 error Expected indentation of 28 spaces but found 24 indent 560:1 error Expected indentation of 28 spaces but found 24 indent 561:1 error Expected indentation of 32 spaces but found 28 indent 562:1 error Expected indentation of 28 spaces but found 24 indent 563:1 error Expected indentation of 28 spaces but found 24 indent 564:1 error Expected indentation of 28 spaces but found 24 indent 565:1 error Expected indentation of 32 spaces but found 28 indent 566:1 error Expected indentation of 28 spaces but found 24 indent 567:1 error Expected indentation of 28 spaces but found 24 indent 568:1 error Expected indentation of 32 spaces but found 28 indent 569:1 error Expected indentation of 28 spaces but found 24 indent 570:1 error Expected indentation of 28 spaces but found 24 indent 571:1 error Expected indentation of 32 spaces but found 28 indent 572:1 error Expected indentation of 28 spaces but found 24 indent 573:1 error Expected indentation of 28 spaces but found 24 indent 574:1 error Expected indentation of 32 spaces but found 28 indent 575:1 error Expected indentation of 28 spaces but found 24 indent 576:1 error Expected indentation of 28 spaces but found 24 indent 577:1 error Expected indentation of 32 spaces but found 28 indent 578:1 error Expected indentation of 28 spaces but found 24 indent 579:1 error Expected indentation of 28 spaces but found 24 indent 580:1 error Expected indentation of 32 spaces but found 28 indent 581:1 error Expected indentation of 28 spaces but found 24 indent 582:1 error Expected indentation of 28 spaces but found 24 indent 583:1 error Expected indentation of 32 spaces but found 28 indent 584:1 error Expected indentation of 28 spaces but found 24 indent 585:1 error Expected indentation of 28 spaces but found 24 indent 586:1 error Expected indentation of 28 spaces but found 24 indent 587:1 error Expected indentation of 32 spaces but found 28 indent 588:1 error Expected indentation of 28 spaces but found 24 indent 589:1 error Expected indentation of 28 spaces but found 24 indent 590:1 error Expected indentation of 32 spaces but found 28 indent 591:1 error Expected indentation of 28 spaces but found 24 indent 592:1 error Expected indentation of 28 spaces but found 24 indent 593:1 error Expected indentation of 32 spaces but found 28 indent 594:1 error Expected indentation of 28 spaces but found 24 indent 595:1 error Expected indentation of 24 spaces but found 20 indent 596:1 error Expected indentation of 20 spaces but found 16 indent 597:1 error Expected indentation of 16 spaces but found 12 indent 598:1 error Expected indentation of 12 spaces but found 8 indent 599:1 error Expected indentation of 8 spaces but found 4 indent 600:1 error Expected indentation of 4 spaces but found 2 indent 608:1 error Expected indentation of 4 spaces but found 2 indent 609:1 error Expected indentation of 8 spaces but found 4 indent 610:1 error Expected indentation of 8 spaces but found 4 indent 611:1 error Expected indentation of 12 spaces but found 6 indent 612:1 error Expected indentation of 12 spaces but found 6 indent 613:1 error Expected indentation of 16 spaces but found 8 indent 614:1 error Expected indentation of 16 spaces but found 8 indent 615:1 error Expected indentation of 16 spaces but found 8 indent 616:1 error Expected indentation of 16 spaces but found 8 indent 617:1 error Expected indentation of 12 spaces but found 6 indent 618:1 error Expected indentation of 8 spaces but found 4 indent 619:1 error Expected indentation of 12 spaces but found 6 indent 620:1 error Expected indentation of 16 spaces but found 8 indent 621:1 error Expected indentation of 16 spaces but found 8 indent 622:1 error Expected indentation of 16 spaces but found 8 indent 623:1 error Expected indentation of 16 spaces but found 8 indent 624:1 error Expected indentation of 20 spaces but found 10 indent 625:1 error Expected indentation of 20 spaces but found 10 indent 626:1 error Expected indentation of 16 spaces but found 8 indent 627:1 error Expected indentation of 12 spaces but found 6 indent 628:1 error Expected indentation of 8 spaces but found 4 indent 629:1 error Expected indentation of 8 spaces but found 4 indent 630:1 error Expected indentation of 8 spaces but found 4 indent 631:1 error Expected indentation of 8 spaces but found 4 indent 632:1 error Expected indentation of 8 spaces but found 4 indent 633:1 error Expected indentation of 4 spaces but found 2 indent 635:1 error Expected indentation of 4 spaces but found 2 indent 636:1 error Expected indentation of 4 spaces but found 2 indent 637:1 error Expected indentation of 8 spaces but found 4 indent 638:1 error Expected indentation of 4 spaces but found 2 indent 639:1 error Expected indentation of 4 spaces but found 2 indent 640:1 error Expected indentation of 4 spaces but found 2 indent 641:1 error Expected indentation of 8 spaces but found 4 indent 642:1 error Expected indentation of 8 spaces but found 4 indent 643:1 error Expected indentation of 8 spaces but found 4 indent 644:1 error Expected indentation of 8 spaces but found 4 indent 646:1 error Expected indentation of 8 spaces but found 4 indent 647:1 error Expected indentation of 12 spaces but found 6 indent 648:1 error Expected indentation of 12 spaces but found 6 indent 649:1 error Expected indentation of 8 spaces but found 4 indent 651:1 error Expected indentation of 8 spaces but found 4 indent 652:1 error Expected indentation of 12 spaces but found 6 indent 653:1 error Expected indentation of 12 spaces but found 6 indent 654:1 error Expected indentation of 12 spaces but found 6 indent 655:1 error Expected indentation of 8 spaces but found 4 indent 657:1 error Expected indentation of 8 spaces but found 4 indent 658:1 error Expected indentation of 12 spaces but found 6 indent 659:1 error Expected indentation of 12 spaces but found 6 indent 660:1 error Expected indentation of 12 spaces but found 6 indent 661:1 error Expected indentation of 12 spaces but found 6 indent 662:1 error Expected indentation of 12 spaces but found 6 indent 663:1 error Expected indentation of 12 spaces but found 6 indent 664:1 error Expected indentation of 12 spaces but found 6 indent 665:1 error Expected indentation of 16 spaces but found 8 indent 667:1 error Expected indentation of 16 spaces but found 8 indent 668:1 error Expected indentation of 16 spaces but found 8 indent 669:1 error Expected indentation of 20 spaces but found 10 indent 670:1 error Expected indentation of 16 spaces but found 8 indent 671:1 error Expected indentation of 16 spaces but found 8 indent 672:1 error Expected indentation of 12 spaces but found 6 indent 674:1 error Expected indentation of 12 spaces but found 6 indent 675:1 error Expected indentation of 16 spaces but found 8 indent 677:1 error Expected indentation of 16 spaces but found 8 indent 678:1 error Expected indentation of 16 spaces but found 8 indent 679:1 error Expected indentation of 20 spaces but found 10 indent 680:1 error Expected indentation of 16 spaces but found 8 indent 681:1 error Expected indentation of 16 spaces but found 8 indent 682:1 error Expected indentation of 12 spaces but found 6 indent 683:1 error Expected indentation of 12 spaces but found 6 indent 684:1 error Expected indentation of 16 spaces but found 8 indent 686:1 error Expected indentation of 16 spaces but found 8 indent 687:1 error Expected indentation of 16 spaces but found 8 indent 688:1 error Expected indentation of 20 spaces but found 10 indent 689:1 error Expected indentation of 16 spaces but found 8 indent 690:1 error Expected indentation of 16 spaces but found 8 indent 691:1 error Expected indentation of 12 spaces but found 6 indent 693:1 error Expected indentation of 12 spaces but found 6 indent 694:1 error Expected indentation of 16 spaces but found 8 indent 695:1 error Expected indentation of 16 spaces but found 8 indent 696:1 error Expected indentation of 16 spaces but found 8 indent 697:1 error Expected indentation of 20 spaces but found 10 indent 698:1 error Expected indentation of 16 spaces but found 8 indent 699:1 error Expected indentation of 12 spaces but found 6 indent 700:1 error Expected indentation of 8 spaces but found 4 indent 703:1 error Expected indentation of 8 spaces but found 4 indent 704:1 error Expected indentation of 12 spaces but found 6 indent 705:1 error Expected indentation of 12 spaces but found 6 indent 707:1 error Expected indentation of 12 spaces but found 6 indent 708:1 error Expected indentation of 16 spaces but found 8 indent 709:1 error Expected indentation of 16 spaces but found 8 indent 710:1 error Expected indentation of 16 spaces but found 8 indent 711:1 error Expected indentation of 20 spaces but found 10 indent 712:1 error Expected indentation of 16 spaces but found 8 indent 713:1 error Expected indentation of 16 spaces but found 8 indent 714:1 error Expected indentation of 12 spaces but found 6 indent 717:1 error Expected indentation of 12 spaces but found 6 indent 718:1 error Expected indentation of 16 spaces but found 8 indent 719:1 error Expected indentation of 16 spaces but found 8 indent 720:1 error Expected indentation of 16 spaces but found 8 indent 721:1 error Expected indentation of 20 spaces but found 10 indent 722:1 error Expected indentation of 16 spaces but found 8 indent 723:1 error Expected indentation of 12 spaces but found 6 indent 724:1 error Expected indentation of 8 spaces but found 4 indent 726:1 error Expected indentation of 8 spaces but found 4 indent 729:1 error Expected indentation of 12 spaces but found 6 indent 730:1 error Expected indentation of 12 spaces but found 6 indent 731:1 error Expected indentation of 16 spaces but found 8 indent 732:1 error Expected indentation of 12 spaces but found 6 indent 733:1 error Expected indentation of 16 spaces but found 8 indent 734:1 error Expected indentation of 12 spaces but found 6 indent 735:1 error Expected indentation of 12 spaces but found 6 indent 736:1 error Expected indentation of 16 spaces but found 8 indent 737:1 error Expected indentation of 12 spaces but found 6 indent 738:1 error Expected indentation of 12 spaces but found 6 indent 739:1 error Expected indentation of 8 spaces but found 4 indent 741:1 error Expected indentation of 8 spaces but found 4 indent 744:1 error Expected indentation of 12 spaces but found 6 indent 745:1 error Expected indentation of 12 spaces but found 6 indent 746:1 error Expected indentation of 12 spaces but found 6 indent 747:1 error Expected indentation of 16 spaces but found 8 indent 748:1 error Expected indentation of 12 spaces but found 6 indent 749:1 error Expected indentation of 8 spaces but found 4 indent 751:1 error Expected indentation of 8 spaces but found 4 indent 753:1 error Expected indentation of 12 spaces but found 6 indent 754:1 error Expected indentation of 12 spaces but found 6 indent 755:1 error Expected indentation of 12 spaces but found 6 indent 756:1 error Expected indentation of 12 spaces but found 6 indent 757:1 error Expected indentation of 12 spaces but found 6 indent 758:1 error Expected indentation of 16 spaces but found 8 indent 759:1 error Expected indentation of 12 spaces but found 6 indent 760:1 error Expected indentation of 12 spaces but found 6 indent 761:1 error Expected indentation of 8 spaces but found 4 indent 762:1 error Expected indentation of 12 spaces but found 6 indent 763:1 error Expected indentation of 12 spaces but found 6 indent 764:1 error Expected indentation of 12 spaces but found 6 indent 765:1 error Expected indentation of 12 spaces but found 6 indent 766:1 error Expected indentation of 16 spaces but found 8 indent 767:1 error Expected indentation of 12 spaces but found 6 indent 768:1 error Expected indentation of 8 spaces but found 4 indent 769:1 error Expected indentation of 8 spaces but found 4 indent 770:1 error Expected indentation of 12 spaces but found 6 indent 771:1 error Expected indentation of 12 spaces but found 6 indent 772:1 error Expected indentation of 8 spaces but found 4 indent 774:1 error Expected indentation of 8 spaces but found 4 indent 775:1 error Expected indentation of 8 spaces but found 4 indent 776:1 error Expected indentation of 8 spaces but found 6 indent 777:1 error Expected indentation of 8 spaces but found 6 indent 778:1 error Expected indentation of 12 spaces but found 8 indent 779:1 error Expected indentation of 12 spaces but found 8 indent 780:1 error Expected indentation of 8 spaces but found 6 indent 781:1 error Expected indentation of 8 spaces but found 6 indent 782:1 error Expected indentation of 12 spaces but found 8 indent 783:1 error Expected indentation of 12 spaces but found 8 indent 784:1 error Expected indentation of 8 spaces but found 6 indent 785:1 error Expected indentation of 8 spaces but found 6 indent 786:1 error Expected indentation of 12 spaces but found 8 indent 787:1 error Expected indentation of 12 spaces but found 8 indent 788:1 error Expected indentation of 8 spaces but found 6 indent 791:1 error Expected indentation of 12 spaces but found 8 indent 792:1 error Expected indentation of 12 spaces but found 8 indent 793:1 error Expected indentation of 8 spaces but found 6 indent 794:1 error Expected indentation of 12 spaces but found 8 indent 795:1 error Expected indentation of 8 spaces but found 4 indent 797:1 error Expected indentation of 8 spaces but found 4 indent 798:1 error Expected indentation of 8 spaces but found 4 indent 799:1 error Expected indentation of 8 spaces but found 4 indent 800:1 error Expected indentation of 12 spaces but found 6 indent 801:1 error Expected indentation of 12 spaces but found 6 indent 802:1 error Expected indentation of 12 spaces but found 6 indent 803:1 error Expected indentation of 12 spaces but found 6 indent 804:1 error Expected indentation of 12 spaces but found 6 indent 805:1 error Expected indentation of 8 spaces but found 4 indent 807:1 error Expected indentation of 8 spaces but found 4 indent 808:1 error Expected indentation of 8 spaces but found 4 indent 809:1 error Expected indentation of 8 spaces but found 4 indent 810:1 error Expected indentation of 12 spaces but found 6 indent 811:1 error Expected indentation of 8 spaces but found 4 indent 812:1 error Expected indentation of 12 spaces but found 6 indent 813:1 error Expected indentation of 12 spaces but found 6 indent 814:1 error Expected indentation of 12 spaces but found 6 indent 815:1 error Expected indentation of 8 spaces but found 4 indent 817:1 error Expected indentation of 8 spaces but found 4 indent 818:1 error Expected indentation of 12 spaces but found 6 indent 819:1 error Expected indentation of 12 spaces but found 6 indent 820:1 error Expected indentation of 12 spaces but found 6 indent 821:1 error Expected indentation of 16 spaces but found 8 indent 822:1 error Expected indentation of 16 spaces but found 8 indent 823:1 error Expected indentation of 16 spaces but found 8 indent 824:1 error Expected indentation of 20 spaces but found 10 indent 825:1 error Expected indentation of 16 spaces but found 8 indent 826:1 error Expected indentation of 12 spaces but found 6 indent 827:1 error Expected indentation of 8 spaces but found 4 indent 828:1 error Expected indentation of 4 spaces but found 2 indent 830:1 error Expected indentation of 4 spaces but found 2 indent 834:1 error Expected indentation of 8 spaces but found 4 indent 835:1 error Expected indentation of 12 spaces but found 6 indent 836:1 error Expected indentation of 12 spaces but found 6 indent 836:28 error '$' is not defined no-undef 836:63 error '$' is not defined no-undef 837:1 error Expected indentation of 12 spaces but found 6 indent 838:1 error Expected indentation of 12 spaces but found 6 indent 839:1 error Expected indentation of 16 spaces but found 8 indent 840:1 error Expected indentation of 12 spaces but found 6 indent 841:1 error Expected indentation of 8 spaces but found 4 indent 842:1 error Expected indentation of 4 spaces but found 2 indent 844:1 error Expected indentation of 4 spaces but found 2 indent 845:1 error Expected indentation of 8 spaces but found 4 indent 846:1 error Expected indentation of 12 spaces but found 6 indent 847:1 error Expected indentation of 8 spaces but found 4 indent 848:1 error Expected indentation of 4 spaces but found 2 indent 850:1 error Expected indentation of 4 spaces but found 2 indent 851:1 error Expected indentation of 8 spaces but found 4 indent 852:1 error Expected indentation of 8 spaces but found 4 indent 853:1 error Expected indentation of 8 spaces but found 4 indent 855:1 error Expected indentation of 8 spaces but found 4 indent 856:1 error Expected indentation of 8 spaces but found 6 indent 857:1 error Expected indentation of 8 spaces but found 6 indent 858:1 error Expected indentation of 12 spaces but found 8 indent 859:1 error Expected indentation of 12 spaces but found 8 indent 860:1 error Expected indentation of 8 spaces but found 6 indent 861:1 error Expected indentation of 12 spaces but found 8 indent 862:1 error Expected indentation of 12 spaces but found 8 indent 863:1 error Expected indentation of 8 spaces but found 6 indent 864:1 error Expected indentation of 8 spaces but found 6 indent 865:1 error Expected indentation of 8 spaces but found 6 indent 866:1 error Expected indentation of 12 spaces but found 8 indent 867:1 error Expected indentation of 12 spaces but found 8 indent 868:1 error Expected indentation of 8 spaces but found 6 indent 869:1 error Expected indentation of 8 spaces but found 6 indent 870:1 error Expected indentation of 12 spaces but found 8 indent 871:1 error Expected indentation of 12 spaces but found 8 indent 872:1 error Expected indentation of 8 spaces but found 6 indent 873:1 error Expected indentation of 12 spaces but found 8 indent 874:1 error Expected indentation of 12 spaces but found 8 indent 875:1 error Expected indentation of 8 spaces but found 6 indent 876:1 error Expected indentation of 12 spaces but found 8 indent 877:1 error Expected indentation of 12 spaces but found 8 indent 878:1 error Expected indentation of 8 spaces but found 6 indent 879:1 error Expected indentation of 12 spaces but found 8 indent 880:1 error Expected indentation of 8 spaces but found 4 indent 882:1 error Expected indentation of 8 spaces but found 4 indent 883:1 error Expected indentation of 8 spaces but found 4 indent 884:1 error Expected indentation of 12 spaces but found 6 indent 885:1 error Expected indentation of 16 spaces but found 8 indent 886:1 error Expected indentation of 20 spaces but found 10 indent 887:1 error Expected indentation of 20 spaces but found 10 indent 888:1 error Expected indentation of 20 spaces but found 10 indent 889:1 error Expected indentation of 20 spaces but found 10 indent 890:1 error Expected indentation of 16 spaces but found 8 indent 891:1 error Expected indentation of 12 spaces but found 6 indent 892:1 error Expected indentation of 8 spaces but found 4 indent 893:1 error Expected indentation of 12 spaces but found 6 indent 894:1 error Expected indentation of 12 spaces but found 6 indent 895:1 error Expected indentation of 16 spaces but found 8 indent 896:1 error Expected indentation of 20 spaces but found 10 indent 897:1 error Expected indentation of 20 spaces but found 10 indent 898:1 error Expected indentation of 20 spaces but found 10 indent 899:1 error Expected indentation of 20 spaces but found 10 indent 900:1 error Expected indentation of 16 spaces but found 8 indent 901:1 error Expected indentation of 12 spaces but found 6 indent 902:1 error Expected indentation of 8 spaces but found 4 indent 903:1 error Expected indentation of 8 spaces but found 4 indent 904:1 error Expected indentation of 12 spaces but found 6 indent 905:1 error Expected indentation of 16 spaces but found 8 indent 906:1 error Expected indentation of 16 spaces but found 8 indent 907:1 error Expected indentation of 20 spaces but found 10 indent 908:1 error Expected indentation of 24 spaces but found 12 indent 909:1 error Expected indentation of 24 spaces but found 12 indent 910:1 error Expected indentation of 20 spaces but found 10 indent 911:1 error Expected indentation of 20 spaces but found 10 indent 912:1 error Expected indentation of 20 spaces but found 10 indent 913:1 error Expected indentation of 24 spaces but found 12 indent 914:1 error Expected indentation of 28 spaces but found 14 indent 915:1 error Expected indentation of 24 spaces but found 12 indent 916:1 error Expected indentation of 20 spaces but found 10 indent 917:1 error Expected indentation of 16 spaces but found 8 indent 918:1 error Expected indentation of 12 spaces but found 6 indent 919:1 error Expected indentation of 8 spaces but found 4 indent 920:1 error Expected indentation of 4 spaces but found 2 indent 933:1 error Expected indentation of 4 spaces but found 2 indent 934:1 error Expected indentation of 4 spaces but found 2 indent 935:1 error Expected indentation of 4 spaces but found 2 indent 936:1 error Expected indentation of 4 spaces but found 2 indent 937:1 error Expected indentation of 4 spaces but found 2 indent 938:1 error Expected indentation of 4 spaces but found 2 indent 939:1 error Expected indentation of 4 spaces but found 2 indent 940:1 error Expected indentation of 4 spaces but found 2 indent ? 792 problems (792 errors, 0 warnings) 789 errors and 0 warnings potentially fixable with the `--fix` option. ERROR in ./modules/instrument_manager/jsx/instrumentManagerIndex.js Module Error (from ./node_modules/eslint-loader/index.js): /var/www/loris/modules/instrument_manager/jsx/instrumentManagerIndex.js 1:8 error 'React' is defined but never used no-unused-vars 4:9 error 'Tabs' is defined but never used no-unused-vars 4:15 error 'TabPane' is defined but never used no-unused-vars 5:8 error 'Loader' is defined but never used no-unused-vars 6:8 error 'FilterableDataTable' is defined but never used no-unused-vars 8:8 error 'InstrumentUploadForm' is defined but never used no-unused-vars 11:1 error Expected indentation of 4 spaces but found 2 indent 12:1 error Expected indentation of 8 spaces but found 4 indent 14:1 error Expected indentation of 8 spaces but found 4 indent 15:1 error Expected indentation of 12 spaces but found 6 indent 16:1 error Expected indentation of 12 spaces but found 6 indent 17:1 error Expected indentation of 12 spaces but found 6 indent 18:1 error Expected indentation of 8 spaces but found 4 indent 20:1 error Expected indentation of 8 spaces but found 3 indent 21:1 error Expected indentation of 8 spaces but found 4 indent 22:1 error Expected indentation of 4 spaces but found 2 indent 24:1 error Expected indentation of 4 spaces but found 2 indent 25:1 error Expected indentation of 8 spaces but found 4 indent 26:1 error Expected indentation of 12 spaces but found 6 indent 27:1 error Expected indentation of 4 spaces but found 2 indent 29:1 error Expected indentation of 4 spaces but found 2 indent 36:1 error Expected indentation of 4 spaces but found 2 indent 37:1 error Expected indentation of 8 spaces but found 4 indent 38:1 error Expected indentation of 12 spaces but found 6 indent 39:1 error Expected indentation of 12 spaces but found 6 indent 40:1 error Expected indentation of 12 spaces but found 6 indent 41:1 error Expected indentation of 16 spaces but found 8 indent 42:1 error Expected indentation of 16 spaces but found 8 indent 42:9 error Unexpected console statement no-console 43:1 error Expected indentation of 12 spaces but found 6 indent 44:1 error Expected indentation of 4 spaces but found 2 indent 46:1 error Expected indentation of 4 spaces but found 2 indent 55:1 error Expected indentation of 4 spaces but found 2 indent 55:30 error 'row' is defined but never used no-unused-vars 56:1 error Expected indentation of 8 spaces but found 4 indent 57:1 error Expected indentation of 12 spaces but found 6 indent 58:1 error Expected indentation of 8 spaces but found 4 indent 59:1 error Expected indentation of 4 spaces but found 2 indent 61:1 error Expected indentation of 4 spaces but found 2 indent 64:1 error Expected indentation of 8 spaces but found 4 indent 65:1 error Expected indentation of 12 spaces but found 6 indent 66:1 error Expected indentation of 8 spaces but found 4 indent 68:1 error Expected indentation of 8 spaces but found 4 indent 69:1 error Expected indentation of 8 spaces but found 4 indent 70:1 error Expected indentation of 12 spaces but found 6 indent 71:1 error Expected indentation of 8 spaces but found 4 indent 73:1 error Expected indentation of 8 spaces but found 4 indent 74:1 error Expected indentation of 12 spaces but found 6 indent 75:1 error Expected indentation of 16 spaces but found 8 indent 76:1 error Expected indentation of 16 spaces but found 8 indent 77:1 error Expected indentation of 12 spaces but found 6 indent 78:1 error Expected indentation of 12 spaces but found 6 indent 79:1 error Expected indentation of 16 spaces but found 8 indent 80:1 error Expected indentation of 16 spaces but found 8 indent 81:1 error Expected indentation of 16 spaces but found 8 indent 82:1 error Expected indentation of 20 spaces but found 10 indent 83:1 error Expected indentation of 20 spaces but found 10 indent 84:1 error Expected indentation of 20 spaces but found 10 indent 85:1 error Expected indentation of 16 spaces but found 8 indent 86:1 error Expected indentation of 12 spaces but found 6 indent 87:1 error Expected indentation of 12 spaces but found 6 indent 88:1 error Expected indentation of 16 spaces but found 8 indent 89:1 error Expected indentation of 16 spaces but found 8 indent 90:1 error Expected indentation of 16 spaces but found 8 indent 91:1 error Expected indentation of 20 spaces but found 10 indent 92:1 error Expected indentation of 20 spaces but found 10 indent 93:1 error Expected indentation of 16 spaces but found 8 indent 94:1 error Expected indentation of 12 spaces but found 6 indent 95:1 error Expected indentation of 12 spaces but found 6 indent 96:1 error Expected indentation of 16 spaces but found 8 indent 97:1 error Expected indentation of 16 spaces but found 8 indent 98:1 error Expected indentation of 12 spaces but found 6 indent 99:1 error Expected indentation of 12 spaces but found 6 indent 100:1 error Expected indentation of 16 spaces but found 8 indent 101:1 error Expected indentation of 16 spaces but found 8 indent 102:1 error Expected indentation of 12 spaces but found 6 indent 103:1 error Expected indentation of 8 spaces but found 4 indent 105:1 error Expected indentation of 8 spaces but found 4 indent 106:1 error Expected indentation of 12 spaces but found 6 indent 107:1 error Expected indentation of 12 spaces but found 6 indent 108:1 error Expected indentation of 8 spaces but found 4 indent 110:1 error Expected indentation of 8 spaces but found 4 indent 111:1 error Expected indentation of 12 spaces but found 6 indent 112:1 error Expected indentation of 16 spaces but found 8 indent 113:1 error Expected indentation of 20 spaces but found 10 indent 118:1 error Expected indentation of 20 spaces but found 10 indent 119:1 error Expected indentation of 16 spaces but found 8 indent 120:1 error Expected indentation of 12 spaces but found 6 indent 121:1 error Expected indentation of 8 spaces but found 4 indent 123:1 error Expected indentation of 8 spaces but found 4 indent 124:1 error Expected indentation of 12 spaces but found 6 indent 125:1 error Expected indentation of 12 spaces but found 6 indent 126:1 error Expected indentation of 16 spaces but found 8 indent 126:19 error 'loris' is not defined no-undef 127:1 error Expected indentation of 16 spaces but found 8 indent 128:1 error Expected indentation of 20 spaces but found 10 indent 129:1 error Expected indentation of 16 spaces but found 8 indent 130:1 error Expected indentation of 12 spaces but found 6 indent 131:1 error Expected indentation of 16 spaces but found 8 indent 132:1 error Expected indentation of 20 spaces but found 10 indent 135:1 error Expected indentation of 20 spaces but found 10 indent 136:1 error Expected indentation of 16 spaces but found 8 indent 137:1 error Expected indentation of 12 spaces but found 6 indent 138:1 error Expected indentation of 12 spaces but found 6 indent 139:1 error Expected indentation of 8 spaces but found 4 indent 141:1 error Expected indentation of 8 spaces but found 4 indent 142:1 error Expected indentation of 12 spaces but found 6 indent 143:1 error Expected indentation of 16 spaces but found 8 indent 144:1 error Expected indentation of 20 spaces but found 10 indent 145:1 error Expected indentation of 24 spaces but found 12 indent 146:1 error Expected indentation of 24 spaces but found 12 indent 147:1 error Expected indentation of 24 spaces but found 12 indent 148:1 error Expected indentation of 24 spaces but found 12 indent 149:1 error Expected indentation of 20 spaces but found 10 indent 150:1 error Expected indentation of 16 spaces but found 8 indent 151:1 error Expected indentation of 16 spaces but found 8 indent 152:1 error Expected indentation of 20 spaces but found 10 indent 153:1 error Expected indentation of 20 spaces but found 10 indent 154:1 error Expected indentation of 16 spaces but found 8 indent 155:1 error Expected indentation of 12 spaces but found 6 indent 156:1 error Expected indentation of 8 spaces but found 4 indent 157:1 error Expected indentation of 4 spaces but found 2 indent 161:1 error Expected indentation of 4 spaces but found 2 indent 162:1 error Expected indentation of 4 spaces but found 2 indent 166:1 error Expected indentation of 4 spaces but found 2 indent 166:3 error 'ReactDOM' is not defined no-undef 167:1 error Expected indentation of 8 spaces but found 4 indent 168:1 error Expected indentation of 12 spaces but found 6 indent 168:19 error 'loris' is not defined no-undef 169:1 error Expected indentation of 12 spaces but found 6 indent 169:22 error 'loris' is not defined no-undef 170:1 error Expected indentation of 8 spaces but found 4 indent 171:1 error Expected indentation of 8 spaces but found 4 indent 172:1 error Expected indentation of 4 spaces but found 2 indent ? 134 problems (134 errors, 0 warnings) 122 errors and 0 warnings potentially fixable with the `--fix` option. ERROR in ./modules/issue_tracker/jsx/index.js Module Error (from ./node_modules/eslint-loader/index.js): /var/www/loris/modules/issue_tracker/jsx/index.js 1:8 error 'IssueForm' is defined but never used no-unused-vars 6:1 error '$' is not defined no-undef 7:1 error Expected indentation of 4 spaces but found 2 indent 8:1 error Expected indentation of 4 spaces but found 2 indent 9:1 error Expected indentation of 8 spaces but found 4 indent 10:1 error Expected indentation of 12 spaces but found 6 indent 11:1 error Expected indentation of 16 spaces but found 8 indent 12:1 error Expected indentation of 16 spaces but found 8 indent 12:21 error 'loris' is not defined no-undef 13:1 error Expected indentation of 16 spaces but found 8 indent 13:20 error 'loris' is not defined no-undef 14:1 error Expected indentation of 12 spaces but found 6 indent 15:1 error Expected indentation of 8 spaces but found 4 indent 16:1 error Expected indentation of 4 spaces but found 2 indent 18:1 error Expected indentation of 4 spaces but found 2 indent 18:3 error 'ReactDOM' is not defined no-undef ? 16 problems (16 errors, 0 warnings) 11 errors and 0 warnings potentially fixable with the `--fix` option. ERROR in ./modules/issue_tracker/jsx/issueTrackerIndex.js Module Error (from ./node_modules/eslint-loader/index.js): /var/www/loris/modules/issue_tracker/jsx/issueTrackerIndex.js 1:8 error 'React' is defined but never used no-unused-vars 4:8 error 'Loader' is defined but never used no-unused-vars 5:8 error 'FilterableDataTable' is defined but never used no-unused-vars 8:1 error Expected indentation of 4 spaces but found 2 indent 9:1 error Expected indentation of 8 spaces but found 4 indent 11:1 error Expected indentation of 8 spaces but found 4 indent 12:1 error Expected indentation of 12 spaces but found 6 indent 13:1 error Expected indentation of 12 spaces but found 6 indent 14:1 error Expected indentation of 12 spaces but found 6 indent 15:1 error Expected indentation of 8 spaces but found 4 indent 17:1 error Expected indentation of 8 spaces but found 4 indent 18:1 error Expected indentation of 8 spaces but found 4 indent 19:1 error Expected indentation of 4 spaces but found 2 indent 21:1 error Expected indentation of 4 spaces but found 2 indent 22:1 error Expected indentation of 8 spaces but found 4 indent 23:1 error Expected indentation of 12 spaces but found 6 indent 24:1 error Expected indentation of 4 spaces but found 2 indent 26:1 error Expected indentation of 4 spaces but found 2 indent 33:1 error Expected indentation of 4 spaces but found 2 indent 34:1 error Expected indentation of 8 spaces but found 4 indent 35:1 error Expected indentation of 12 spaces but found 6 indent 36:1 error Expected indentation of 12 spaces but found 6 indent 37:1 error Expected indentation of 12 spaces but found 6 indent 38:1 error Expected indentation of 16 spaces but found 8 indent 39:1 error Expected indentation of 16 spaces but found 8 indent 39:9 error Unexpected console statement no-console 40:1 error Expected indentation of 12 spaces but found 6 indent 41:1 error Expected indentation of 4 spaces but found 2 indent 43:1 error Expected indentation of 4 spaces but found 2 indent 52:1 error Expected indentation of 4 spaces but found 2 indent 53:1 error Expected indentation of 8 spaces but found 4 indent 54:1 error Expected indentation of 8 spaces but found 4 indent 55:1 error Expected indentation of 8 spaces but found 4 indent 56:1 error Expected indentation of 8 spaces but found 4 indent 57:1 error Expected indentation of 12 spaces but found 6 indent 58:1 error Expected indentation of 16 spaces but found 8 indent 59:1 error Expected indentation of 20 spaces but found 10 indent 59:17 error 'loris' is not defined no-undef 60:1 error Expected indentation of 16 spaces but found 8 indent 61:1 error Expected indentation of 20 spaces but found 10 indent 62:1 error Expected indentation of 16 spaces but found 8 indent 63:1 error Expected indentation of 12 spaces but found 6 indent 64:1 error Expected indentation of 12 spaces but found 6 indent 65:1 error Expected indentation of 12 spaces but found 6 indent 66:1 error Expected indentation of 8 spaces but found 4 indent 67:1 error Expected indentation of 12 spaces but found 6 indent 68:1 error Expected indentation of 16 spaces but found 8 indent 69:1 error Expected indentation of 20 spaces but found 10 indent 69:17 error 'loris' is not defined no-undef 70:1 error Expected indentation of 16 spaces but found 8 indent 71:1 error Expected indentation of 20 spaces but found 10 indent 72:1 error Expected indentation of 16 spaces but found 8 indent 73:1 error Expected indentation of 12 spaces but found 6 indent 74:1 error Expected indentation of 12 spaces but found 6 indent 75:1 error Expected indentation of 12 spaces but found 6 indent 76:1 error Expected indentation of 8 spaces but found 4 indent 77:1 error Expected indentation of 12 spaces but found 6 indent 78:1 error Expected indentation of 12 spaces but found 6 indent 79:1 error Expected indentation of 16 spaces but found 8 indent 80:1 error Expected indentation of 16 spaces but found 8 indent 81:1 error Expected indentation of 12 spaces but found 6 indent 82:1 error Expected indentation of 16 spaces but found 8 indent 83:1 error Expected indentation of 16 spaces but found 8 indent 84:1 error Expected indentation of 12 spaces but found 6 indent 85:1 error Expected indentation of 16 spaces but found 8 indent 86:1 error Expected indentation of 16 spaces but found 8 indent 87:1 error Expected indentation of 12 spaces but found 6 indent 88:1 error Expected indentation of 16 spaces but found 8 indent 89:1 error Expected indentation of 16 spaces but found 8 indent 90:1 error Expected indentation of 12 spaces but found 6 indent 91:1 error Expected indentation of 16 spaces but found 8 indent 92:1 error Expected indentation of 16 spaces but found 8 indent 93:1 error Expected indentation of 12 spaces but found 6 indent 94:1 error Expected indentation of 16 spaces but found 8 indent 95:1 error Expected indentation of 12 spaces but found 6 indent 95:8 error Unnecessary semicolon no-extra-semi 96:1 error Expected indentation of 12 spaces but found 6 indent 97:1 error Expected indentation of 8 spaces but found 4 indent 98:1 error Expected indentation of 12 spaces but found 6 indent 99:1 error Expected indentation of 12 spaces but found 6 indent 100:1 error Expected indentation of 8 spaces but found 4 indent 101:1 error Expected indentation of 12 spaces but found 6 indent 102:1 error Expected indentation of 16 spaces but found 8 indent 103:1 error Expected indentation of 20 spaces but found 10 indent 103:20 error 'loris' is not defined no-undef 104:1 error Expected indentation of 24 spaces but found 12 indent 105:1 error Expected indentation of 20 spaces but found 10 indent 106:1 error Expected indentation of 16 spaces but found 8 indent 107:1 error Expected indentation of 16 spaces but found 8 indent 108:1 error Expected indentation of 12 spaces but found 6 indent 109:1 error Expected indentation of 12 spaces but found 6 indent 110:1 error Expected indentation of 8 spaces but found 4 indent 111:1 error Expected indentation of 12 spaces but found 6 indent 112:1 error Expected indentation of 16 spaces but found 8 indent 113:1 error Expected indentation of 20 spaces but found 10 indent 113:20 error 'loris' is not defined no-undef 115:1 error Expected indentation of 24 spaces but found 12 indent 116:1 error Expected indentation of 20 spaces but found 10 indent 117:1 error Expected indentation of 16 spaces but found 8 indent 118:1 error Expected indentation of 16 spaces but found 8 indent 119:1 error Expected indentation of 12 spaces but found 6 indent 120:1 error Expected indentation of 12 spaces but found 6 indent 121:1 error Expected indentation of 8 spaces but found 4 indent 123:1 error Expected indentation of 8 spaces but found 4 indent 124:1 error Expected indentation of 4 spaces but found 2 indent 126:1 error Expected indentation of 4 spaces but found 2 indent 129:1 error Expected indentation of 8 spaces but found 4 indent 130:1 error Expected indentation of 12 spaces but found 6 indent 131:1 error Expected indentation of 8 spaces but found 4 indent 133:1 error Expected indentation of 8 spaces but found 4 indent 134:1 error Expected indentation of 8 spaces but found 4 indent 135:1 error Expected indentation of 12 spaces but found 6 indent 136:1 error Expected indentation of 8 spaces but found 4 indent 138:1 error Expected indentation of 8 spaces but found 3 indent 142:1 error Expected indentation of 8 spaces but found 4 indent 143:1 error Expected indentation of 8 spaces but found 4 indent 144:1 error Expected indentation of 12 spaces but found 6 indent 145:1 error Expected indentation of 16 spaces but found 8 indent 146:1 error Expected indentation of 16 spaces but found 8 indent 147:1 error Expected indentation of 12 spaces but found 6 indent 148:1 error Expected indentation of 12 spaces but found 6 indent 149:1 error Expected indentation of 16 spaces but found 8 indent 150:1 error Expected indentation of 16 spaces but found 8 indent 151:1 error Expected indentation of 12 spaces but found 6 indent 152:1 error Expected indentation of 12 spaces but found 6 indent 153:1 error Expected indentation of 16 spaces but found 8 indent 154:1 error Expected indentation of 16 spaces but found 8 indent 155:1 error Expected indentation of 16 spaces but found 8 indent 156:1 error Expected indentation of 12 spaces but found 6 indent 157:1 error Expected indentation of 12 spaces but found 6 indent 158:1 error Expected indentation of 16 spaces but found 8 indent 159:1 error Expected indentation of 16 spaces but found 8 indent 160:1 error Expected indentation of 16 spaces but found 8 indent 161:1 error Expected indentation of 12 spaces but found 6 indent 162:1 error Expected indentation of 12 spaces but found 6 indent 163:1 error Expected indentation of 16 spaces but found 8 indent 164:1 error Expected indentation of 16 spaces but found 8 indent 165:1 error Expected indentation of 16 spaces but found 8 indent 166:1 error Expected indentation of 12 spaces but found 6 indent 167:1 error Expected indentation of 12 spaces but found 6 indent 168:1 error Expected indentation of 16 spaces but found 8 indent 169:1 error Expected indentation of 16 spaces but found 8 indent 170:1 error Expected indentation of 16 spaces but found 8 indent 171:1 error Expected indentation of 12 spaces but found 6 indent 172:1 error Expected indentation of 12 spaces but found 6 indent 173:1 error Expected indentation of 16 spaces but found 8 indent 174:1 error Expected indentation of 16 spaces but found 8 indent 175:1 error Expected indentation of 16 spaces but found 8 indent 176:1 error Expected indentation of 12 spaces but found 8 indent 177:1 error Expected indentation of 12 spaces but found 6 indent 178:1 error Expected indentation of 16 spaces but found 8 indent 179:1 error Expected indentation of 16 spaces but found 8 indent 180:1 error Expected indentation of 16 spaces but found 8 indent 181:1 error Expected indentation of 12 spaces but found 8 indent 182:1 error Expected indentation of 12 spaces but found 6 indent 183:1 error Expected indentation of 16 spaces but found 8 indent 184:1 error Expected indentation of 16 spaces but found 8 indent 185:1 error Expected indentation of 16 spaces but found 8 indent 186:1 error Expected indentation of 12 spaces but found 8 indent 187:1 error Expected indentation of 12 spaces but found 6 indent 188:1 error Expected indentation of 16 spaces but found 8 indent 189:1 error Expected indentation of 16 spaces but found 8 indent 190:1 error Expected indentation of 12 spaces but found 8 indent 191:1 error Expected indentation of 12 spaces but found 6 indent 192:1 error Expected indentation of 16 spaces but found 8 indent 193:1 error Expected indentation of 16 spaces but found 8 indent 194:1 error Expected indentation of 12 spaces but found 8 indent 195:1 error Expected indentation of 12 spaces but found 6 indent 196:1 error Expected indentation of 16 spaces but found 8 indent 197:1 error Expected indentation of 16 spaces but found 8 indent 198:1 error Expected indentation of 12 spaces but found 6 indent 199:1 error Expected indentation of 12 spaces but found 6 indent 200:1 error Expected indentation of 12 spaces but found 6 indent 201:1 error Expected indentation of 12 spaces but found 6 indent 202:1 error Expected indentation of 12 spaces but found 6 indent 203:1 error Expected indentation of 16 spaces but found 8 indent 204:1 error Expected indentation of 16 spaces but found 8 indent 205:1 error Expected indentation of 12 spaces but found 8 indent 206:1 error Expected indentation of 8 spaces but found 4 indent 208:1 error Expected indentation of 8 spaces but found 4 indent 209:1 error Expected indentation of 12 spaces but found 6 indent 210:1 error Expected indentation of 12 spaces but found 6 indent 211:1 error Expected indentation of 12 spaces but found 6 indent 212:1 error Expected indentation of 12 spaces but found 6 indent 213:1 error Expected indentation of 8 spaces but found 4 indent 215:1 error Expected indentation of 8 spaces but found 4 indent 216:1 error Expected indentation of 12 spaces but found 6 indent 217:1 error Expected indentation of 16 spaces but found 8 indent 217:9 error 'loris' is not defined no-undef 218:1 error Expected indentation of 12 spaces but found 6 indent 219:1 error Expected indentation of 8 spaces but found 4 indent 220:1 error Expected indentation of 8 spaces but found 4 indent 221:1 error Expected indentation of 12 spaces but found 6 indent 222:1 error Expected indentation of 8 spaces but found 4 indent 224:1 error Expected indentation of 8 spaces but found 4 indent 225:1 error Expected indentation of 12 spaces but found 6 indent 226:1 error Expected indentation of 16 spaces but found 8 indent 227:1 error Expected indentation of 16 spaces but found 8 indent 228:1 error Expected indentation of 16 spaces but found 8 indent 229:1 error Expected indentation of 16 spaces but found 8 indent 230:1 error Expected indentation of 16 spaces but found 8 indent 231:1 error Expected indentation of 16 spaces but found 8 indent 232:1 error Expected indentation of 12 spaces but found 6 indent 233:1 error Expected indentation of 8 spaces but found 4 indent 234:1 error Expected indentation of 4 spaces but found 2 indent 238:1 error Expected indentation of 4 spaces but found 2 indent 239:1 error Expected indentation of 4 spaces but found 2 indent 243:1 error Expected indentation of 4 spaces but found 2 indent 243:3 error 'ReactDOM' is not defined no-undef 244:1 error Expected indentation of 8 spaces but found 4 indent 245:1 error Expected indentation of 12 spaces but found 6 indent 245:19 error 'loris' is not defined no-undef 246:1 error Expected indentation of 12 spaces but found 6 indent 246:22 error 'loris' is not defined no-undef 247:1 error Expected indentation of 8 spaces but found 4 indent 248:1 error Expected indentation of 8 spaces but found 4 indent 249:1 error Expected indentation of 4 spaces but found 2 indent ? 217 problems (217 errors, 0 warnings) 205 errors and 0 warnings potentially fixable with the `--fix` option. ERROR in ./modules/media/jsx/mediaIndex.js Module Error (from ./node_modules/eslint-loader/index.js): /var/www/loris/modules/media/jsx/mediaIndex.js 1:8 error 'React' is defined but never used no-unused-vars 4:9 error 'Tabs' is defined but never used no-unused-vars 4:15 error 'TabPane' is defined but never used no-unused-vars 5:8 error 'Loader' is defined but never used no-unused-vars 6:8 error 'FilterableDataTable' is defined but never used no-unused-vars 7:8 error 'TriggerableModal' is defined but never used no-unused-vars 9:8 error 'MediaUploadForm' is defined but never used no-unused-vars 10:8 error 'MediaEditForm' is defined but never used no-unused-vars 13:1 error Expected indentation of 4 spaces but found 2 indent 14:1 error Expected indentation of 8 spaces but found 4 indent 16:1 error Expected indentation of 8 spaces but found 4 indent 17:1 error Expected indentation of 12 spaces but found 6 indent 18:1 error Expected indentation of 12 spaces but found 6 indent 19:1 error Expected indentation of 12 spaces but found 6 indent 20:1 error Expected indentation of 12 spaces but found 6 indent 21:1 error Expected indentation of 8 spaces but found 4 indent 23:1 error Expected indentation of 8 spaces but found 4 indent 24:1 error Expected indentation of 8 spaces but found 4 indent 25:1 error Expected indentation of 4 spaces but found 2 indent 27:1 error Expected indentation of 4 spaces but found 2 indent 28:1 error Expected indentation of 8 spaces but found 4 indent 29:1 error Expected indentation of 12 spaces but found 6 indent 30:1 error Expected indentation of 4 spaces but found 2 indent 32:1 error Expected indentation of 4 spaces but found 2 indent 39:1 error Expected indentation of 4 spaces but found 2 indent 40:1 error Expected indentation of 8 spaces but found 4 indent 41:1 error Expected indentation of 12 spaces but found 6 indent 42:1 error Expected indentation of 12 spaces but found 6 indent 43:1 error Expected indentation of 12 spaces but found 6 indent 44:1 error Expected indentation of 16 spaces but found 8 indent 45:1 error Expected indentation of 16 spaces but found 8 indent 45:9 error Unexpected console statement no-console 46:1 error Expected indentation of 12 spaces but found 6 indent 47:1 error Expected indentation of 4 spaces but found 2 indent 49:1 error Expected indentation of 4 spaces but found 2 indent 58:1 error Expected indentation of 4 spaces but found 2 indent 60:1 error Expected indentation of 8 spaces but found 4 indent 61:1 error Expected indentation of 8 spaces but found 4 indent 62:1 error Expected indentation of 8 spaces but found 4 indent 63:1 error Expected indentation of 8 spaces but found 4 indent 64:1 error Expected indentation of 12 spaces but found 6 indent 65:1 error Expected indentation of 16 spaces but found 8 indent 65:29 error 'loris' is not defined no-undef 67:1 error Expected indentation of 16 spaces but found 8 indent 68:1 error Expected indentation of 20 spaces but found 10 indent 69:1 error Expected indentation of 24 spaces but found 12 indent 70:1 error Expected indentation of 28 spaces but found 14 indent 71:1 error Expected indentation of 24 spaces but found 12 indent 72:1 error Expected indentation of 20 spaces but found 10 indent 73:1 error Expected indentation of 16 spaces but found 8 indent 74:1 error Expected indentation of 12 spaces but found 6 indent 75:1 error Expected indentation of 12 spaces but found 6 indent 76:1 error Expected indentation of 8 spaces but found 4 indent 77:1 error Expected indentation of 12 spaces but found 6 indent 78:1 error Expected indentation of 16 spaces but found 8 indent 78:28 error 'loris' is not defined no-undef 80:1 error Expected indentation of 16 spaces but found 8 indent 81:1 error Expected indentation of 12 spaces but found 6 indent 82:1 error Expected indentation of 12 spaces but found 6 indent 83:1 error Expected indentation of 8 spaces but found 4 indent 84:1 error Expected indentation of 12 spaces but found 6 indent 85:1 error Expected indentation of 12 spaces but found 6 indent 86:1 error Expected indentation of 8 spaces but found 4 indent 87:1 error Expected indentation of 12 spaces but found 6 indent 88:1 error Expected indentation of 16 spaces but found 10 indent 89:1 error Expected indentation of 12 spaces but found 6 indent 90:1 error Expected indentation of 12 spaces but found 6 indent 90:7 error Unexpected lexical declaration in case block no-case-declarations 91:1 error Expected indentation of 16 spaces but found 12 indent 93:1 error Expected indentation of 24 spaces but found 16 indent 93:29 error 'loris' is not defined no-undef 94:1 error Expected indentation of 24 spaces but found 16 indent 94:28 error 'loris' is not defined no-undef 95:1 error Expected indentation of 24 spaces but found 16 indent 97:1 error Expected indentation of 24 spaces but found 16 indent 99:1 error Expected indentation of 16 spaces but found 12 indent 100:1 error Expected indentation of 12 spaces but found 6 indent 101:1 error Expected indentation of 12 spaces but found 6 indent 102:1 error Expected indentation of 12 spaces but found 6 indent 103:1 error Expected indentation of 8 spaces but found 4 indent 105:1 error Expected indentation of 8 spaces but found 4 indent 106:1 error Expected indentation of 4 spaces but found 2 indent 108:1 error Expected indentation of 4 spaces but found 2 indent 111:1 error Expected indentation of 8 spaces but found 4 indent 112:1 error Expected indentation of 12 spaces but found 6 indent 113:1 error Expected indentation of 8 spaces but found 4 indent 115:1 error Expected indentation of 8 spaces but found 4 indent 116:1 error Expected indentation of 8 spaces but found 4 indent 117:1 error Expected indentation of 12 spaces but found 6 indent 118:1 error Expected indentation of 8 spaces but found 4 indent 120:1 error Expected indentation of 8 spaces but found 3 indent 124:1 error Expected indentation of 8 spaces but found 4 indent 125:1 error Expected indentation of 8 spaces but found 4 indent 126:1 error Expected indentation of 12 spaces but found 6 indent 127:1 error Expected indentation of 16 spaces but found 8 indent 128:1 error Expected indentation of 16 spaces but found 8 indent 129:1 error Expected indentation of 12 spaces but found 6 indent 130:1 error Expected indentation of 12 spaces but found 6 indent 131:1 error Expected indentation of 16 spaces but found 8 indent 132:1 error Expected indentation of 16 spaces but found 8 indent 133:1 error Expected indentation of 12 spaces but found 6 indent 134:1 error Expected indentation of 12 spaces but found 6 indent 135:1 error Expected indentation of 16 spaces but found 8 indent 136:1 error Expected indentation of 16 spaces but found 8 indent 137:1 error Expected indentation of 16 spaces but found 8 indent 138:1 error Expected indentation of 12 spaces but found 6 indent 139:1 error Expected indentation of 12 spaces but found 6 indent 140:1 error Expected indentation of 16 spaces but found 8 indent 141:1 error Expected indentation of 16 spaces but found 8 indent 142:1 error Expected indentation of 16 spaces but found 8 indent 143:1 error Expected indentation of 12 spaces but found 6 indent 144:1 error Expected indentation of 12 spaces but found 6 indent 145:1 error Expected indentation of 16 spaces but found 8 indent 146:1 error Expected indentation of 16 spaces but found 8 indent 147:1 error Expected indentation of 16 spaces but found 8 indent 148:1 error Expected indentation of 12 spaces but found 6 indent 149:1 error Expected indentation of 12 spaces but found 6 indent 150:1 error Expected indentation of 16 spaces but found 8 indent 151:1 error Expected indentation of 16 spaces but found 8 indent 152:1 error Expected indentation of 16 spaces but found 8 indent 153:1 error Expected indentation of 12 spaces but found 6 indent 154:1 error Expected indentation of 12 spaces but found 6 indent 155:1 error Expected indentation of 16 spaces but found 8 indent 156:1 error Expected indentation of 16 spaces but found 8 indent 157:1 error Expected indentation of 12 spaces but found 8 indent 158:1 error Expected indentation of 12 spaces but found 6 indent 159:1 error Expected indentation of 12 spaces but found 6 indent 160:1 error Expected indentation of 12 spaces but found 6 indent 161:1 error Expected indentation of 12 spaces but found 6 indent 162:1 error Expected indentation of 16 spaces but found 8 indent 163:1 error Expected indentation of 16 spaces but found 8 indent 164:1 error Expected indentation of 16 spaces but found 8 indent 165:1 error Expected indentation of 12 spaces but found 6 indent 166:1 error Expected indentation of 12 spaces but found 6 indent 167:1 error Expected indentation of 12 spaces but found 6 indent 168:1 error Expected indentation of 12 spaces but found 6 indent 169:1 error Expected indentation of 16 spaces but found 8 indent 170:1 error Expected indentation of 16 spaces but found 8 indent 171:1 error Expected indentation of 16 spaces but found 8 indent 172:1 error Expected indentation of 16 spaces but found 8 indent 173:1 error Expected indentation of 12 spaces but found 6 indent 174:1 error Expected indentation of 8 spaces but found 4 indent 175:1 error Expected indentation of 8 spaces but found 4 indent 176:1 error Expected indentation of 12 spaces but found 6 indent 177:1 error Expected indentation of 8 spaces but found 4 indent 178:1 error Expected indentation of 8 spaces but found 4 indent 179:1 error Expected indentation of 8 spaces but found 4 indent 180:1 error Expected indentation of 12 spaces but found 6 indent 181:1 error Expected indentation of 16 spaces but found 8 indent 182:1 error Expected indentation of 16 spaces but found 8 indent 183:1 error Expected indentation of 20 spaces but found 10 indent 184:1 error Expected indentation of 24 spaces but found 12 indent 185:1 error Expected indentation of 28 spaces but found 14 indent 185:27 error 'loris' is not defined no-undef 186:1 error Expected indentation of 28 spaces but found 14 indent 186:26 error 'loris' is not defined no-undef 187:1 error Expected indentation of 28 spaces but found 14 indent 188:1 error Expected indentation of 24 spaces but found 12 indent 189:1 error Expected indentation of 20 spaces but found 10 indent 190:1 error Expected indentation of 16 spaces but found 8 indent 191:1 error Expected indentation of 12 spaces but found 6 indent 192:1 error Expected indentation of 8 spaces but found 4 indent 194:1 error Expected indentation of 8 spaces but found 4 indent 195:1 error Expected indentation of 12 spaces but found 6 indent 196:1 error Expected indentation of 16 spaces but found 8 indent 197:1 error Expected indentation of 20 spaces but found 10 indent 198:1 error Expected indentation of 24 spaces but found 12 indent 199:1 error Expected indentation of 24 spaces but found 12 indent 200:1 error Expected indentation of 24 spaces but found 12 indent 201:1 error Expected indentation of 24 spaces but found 12 indent 202:1 error Expected indentation of 20 spaces but found 10 indent 203:1 error Expected indentation of 16 spaces but found 8 indent 204:1 error Expected indentation of 16 spaces but found 8 indent 205:1 error Expected indentation of 12 spaces but found 6 indent 206:1 error Expected indentation of 8 spaces but found 4 indent 207:1 error Expected indentation of 4 spaces but found 2 indent 211:1 error Expected indentation of 4 spaces but found 2 indent 212:1 error Expected indentation of 4 spaces but found 2 indent 216:1 error Expected indentation of 4 spaces but found 2 indent 216:3 error 'ReactDOM' is not defined no-undef 217:1 error Expected indentation of 8 spaces but found 4 indent 218:1 error Expected indentation of 12 spaces but found 6 indent 218:19 error 'loris' is not defined no-undef 219:1 error Expected indentation of 12 spaces but found 6 indent 219:22 error 'loris' is not defined no-undef 220:1 error Expected indentation of 8 spaces but found 4 indent 221:1 error Expected indentation of 8 spaces but found 4 indent 222:1 error Expected indentation of 4 spaces but found 2 indent ? 188 problems (188 errors, 0 warnings) 169 errors and 0 warnings potentially fixable with the `--fix` option. ERROR in ./modules/mri_violations/jsx/columnFormatter.js Module Error (from ./node_modules/eslint-loader/index.js): /var/www/loris/modules/mri_violations/jsx/columnFormatter.js 12:1 error Expected indentation of 4 spaces but found 2 indent 12:7 error 'loris' is not defined no-undef 13:1 error Expected indentation of 8 spaces but found 4 indent 14:1 error Expected indentation of 4 spaces but found 2 indent 15:1 error Expected indentation of 4 spaces but found 2 indent 16:1 error Expected indentation of 4 spaces but found 2 indent 17:1 error Expected indentation of 4 spaces but found 2 indent 18:1 error Expected indentation of 8 spaces but found 4 indent 19:1 error Expected indentation of 4 spaces but found 2 indent 20:1 error Expected indentation of 4 spaces but found 2 indent 21:1 error Expected indentation of 4 spaces but found 2 indent 22:1 error Expected indentation of 4 spaces but found 2 indent 23:1 error Expected indentation of 4 spaces but found 2 indent 24:1 error Expected indentation of 4 spaces but found 2 indent 26:1 error Expected indentation of 4 spaces but found 2 indent 27:1 error Expected indentation of 8 spaces but found 4 indent 28:1 error Expected indentation of 8 spaces but found 6 indent 29:1 error Expected indentation of 12 spaces but found 8 indent 30:1 error Expected indentation of 12 spaces but found 8 indent 31:1 error Expected indentation of 12 spaces but found 8 indent 33:1 error Expected indentation of 8 spaces but found 6 indent 34:1 error Expected indentation of 12 spaces but found 8 indent 35:1 error Expected indentation of 12 spaces but found 8 indent 36:1 error Expected indentation of 12 spaces but found 8 indent 38:1 error Expected indentation of 8 spaces but found 6 indent 39:1 error Expected indentation of 12 spaces but found 8 indent 40:1 error Expected indentation of 12 spaces but found 8 indent 41:1 error Expected indentation of 12 spaces but found 8 indent 43:1 error Expected indentation of 8 spaces but found 6 indent 44:1 error Expected indentation of 12 spaces but found 8 indent 45:1 error Expected indentation of 12 spaces but found 8 indent 46:1 error Expected indentation of 12 spaces but found 8 indent 48:1 error Expected indentation of 8 spaces but found 6 indent 49:1 error Expected indentation of 12 spaces but found 8 indent 50:1 error Expected indentation of 12 spaces but found 8 indent 51:1 error Expected indentation of 12 spaces but found 8 indent 53:1 error Expected indentation of 8 spaces but found 6 indent 54:1 error Expected indentation of 12 spaces but found 8 indent 55:1 error Expected indentation of 12 spaces but found 8 indent 56:1 error Expected indentation of 12 spaces but found 8 indent 58:1 error Expected indentation of 8 spaces but found 6 indent 59:1 error Expected indentation of 12 spaces but found 8 indent 60:1 error Expected indentation of 12 spaces but found 8 indent 61:1 error Expected indentation of 12 spaces but found 8 indent 64:1 error Expected indentation of 8 spaces but found 4 indent 66:1 error Expected indentation of 8 spaces but found 4 indent 70:1 error Expected indentation of 8 spaces but found 11 indent 71:1 error Expected indentation of 4 spaces but found 2 indent 72:1 error Expected indentation of 4 spaces but found 2 indent 73:1 error Expected indentation of 8 spaces but found 4 indent 76:1 error Expected indentation of 20 spaces but found 19 indent 76:29 error 'loris' is not defined no-undef 77:1 error Expected indentation of 24 spaces but found 23 indent 78:1 error Expected indentation of 24 spaces but found 23 indent 79:1 error Expected indentation of 28 spaces but found 24 indent 80:1 error Expected indentation of 20 spaces but found 19 indent 82:1 error Expected indentation of 8 spaces but found 11 indent 83:1 error Expected indentation of 4 spaces but found 2 indent 84:1 error Expected indentation of 4 spaces but found 2 indent 85:1 error Expected indentation of 8 spaces but found 4 indent 86:1 error Expected indentation of 12 spaces but found 11 indent 87:1 error Expected indentation of 16 spaces but found 15 indent 88:1 error Expected indentation of 20 spaces but found 18 indent 88:28 error 'loris' is not defined no-undef 89:1 error Expected indentation of 24 spaces but found 22 indent 90:1 error Expected indentation of 24 spaces but found 22 indent 91:1 error Expected indentation of 28 spaces but found 23 indent 92:1 error Expected indentation of 20 spaces but found 18 indent 93:1 error Expected indentation of 12 spaces but found 11 indent 94:1 error Expected indentation of 8 spaces but found 11 indent 95:1 error Expected indentation of 4 spaces but found 2 indent 96:1 error Expected indentation of 4 spaces but found 2 indent ? 72 problems (72 errors, 0 warnings) 69 errors and 0 warnings potentially fixable with the `--fix` option. ERROR in ./modules/mri_violations/jsx/columnFormatterUnresolved.js Module Error (from ./node_modules/eslint-loader/index.js): /var/www/loris/modules/mri_violations/jsx/columnFormatterUnresolved.js 12:1 error Expected indentation of 4 spaces but found 2 indent 12:7 error 'loris' is not defined no-undef 13:1 error Expected indentation of 8 spaces but found 4 indent 14:1 error Expected indentation of 4 spaces but found 2 indent 15:1 error Expected indentation of 4 spaces but found 2 indent 16:1 error Expected indentation of 4 spaces but found 2 indent 17:1 error Expected indentation of 4 spaces but found 2 indent 18:1 error Expected indentation of 8 spaces but found 4 indent 19:1 error Expected indentation of 4 spaces but found 2 indent 21:1 error Expected indentation of 4 spaces but found 2 indent 22:1 error Expected indentation of 4 spaces but found 2 indent 23:1 error Expected indentation of 4 spaces but found 2 indent 24:1 error Expected indentation of 4 spaces but found 2 indent 25:1 error Expected indentation of 4 spaces but found 2 indent 27:1 error Expected indentation of 4 spaces but found 2 indent 28:1 error Expected indentation of 8 spaces but found 4 indent 29:1 error Expected indentation of 12 spaces but found 11 indent 30:1 error Expected indentation of 16 spaces but found 15 indent 31:1 error Expected indentation of 20 spaces but found 18 indent 31:28 error 'loris' is not defined no-undef 32:1 error Expected indentation of 24 spaces but found 22 indent 33:1 error Expected indentation of 24 spaces but found 22 indent 34:1 error Expected indentation of 28 spaces but found 23 indent 35:1 error Expected indentation of 20 spaces but found 18 indent 36:1 error Expected indentation of 12 spaces but found 11 indent 37:1 error Expected indentation of 8 spaces but found 11 indent 38:1 error Expected indentation of 4 spaces but found 2 indent 39:1 error Expected indentation of 4 spaces but found 2 indent 40:1 error Expected indentation of 8 spaces but found 4 indent 41:1 error Expected indentation of 12 spaces but found 11 indent 42:1 error Expected indentation of 16 spaces but found 12 indent 43:1 error Expected indentation of 20 spaces but found 15 indent 43:25 error 'loris' is not defined no-undef 44:1 error Expected indentation of 24 spaces but found 19 indent 45:1 error Expected indentation of 24 spaces but found 22 indent 46:1 error Expected indentation of 28 spaces but found 23 indent 47:1 error Expected indentation of 20 spaces but found 15 indent 48:1 error Expected indentation of 12 spaces but found 11 indent 49:1 error Expected indentation of 8 spaces but found 11 indent 50:1 error Expected indentation of 4 spaces but found 2 indent 51:1 error Expected indentation of 4 spaces but found 2 indent 52:1 error Expected indentation of 8 spaces but found 4 indent 53:1 error Expected indentation of 8 spaces but found 4 indent 54:1 error Expected indentation of 12 spaces but found 13 indent 56:1 error Expected indentation of 20 spaces but found 21 indent 57:1 error Expected indentation of 20 spaces but found 21 indent 58:1 error Expected indentation of 20 spaces but found 21 indent 59:1 error Expected indentation of 20 spaces but found 21 indent 60:1 error Expected indentation of 20 spaces but found 21 indent 61:1 error Expected indentation of 20 spaces but found 21 indent 62:1 error Expected indentation of 20 spaces but found 21 indent 64:1 error Expected indentation of 12 spaces but found 13 indent 65:1 error Expected indentation of 8 spaces but found 11 indent 66:1 error Expected indentation of 4 spaces but found 2 indent 67:1 error Expected indentation of 4 spaces but found 2 indent 68:1 error Expected indentation of 8 spaces but found 4 indent 69:1 error Expected indentation of 12 spaces but found 6 indent 70:1 error Expected indentation of 8 spaces but found 4 indent 71:1 error Expected indentation of 12 spaces but found 6 indent 72:1 error Expected indentation of 8 spaces but found 4 indent 73:1 error Expected indentation of 12 spaces but found 6 indent 74:1 error Expected indentation of 8 spaces but found 4 indent 76:1 error Expected indentation of 8 spaces but found 4 indent 76:11 error 'loris' is not defined no-undef 78:1 error Expected indentation of 8 spaces but found 4 indent 79:1 error Expected indentation of 12 spaces but found 11 indent 80:1 error Expected indentation of 16 spaces but found 12 indent 81:1 error Expected indentation of 20 spaces but found 12 indent 82:1 error Expected indentation of 16 spaces but found 12 indent 83:1 error Expected indentation of 12 spaces but found 11 indent 84:1 error Expected indentation of 8 spaces but found 11 indent 85:1 error Expected indentation of 4 spaces but found 2 indent 86:1 error Expected indentation of 4 spaces but found 2 indent ? 73 problems (73 errors, 0 warnings) 69 errors and 0 warnings potentially fixable with the `--fix` option. ERROR in ./modules/mri_violations/jsx/mri_protocol_check_violations_columnFormatter.js Module Error (from ./node_modules/eslint-loader/index.js): /var/www/loris/modules/mri_violations/jsx/mri_protocol_check_violations_columnFormatter.js 12:1 error Expected indentation of 4 spaces but found 2 indent 12:7 error 'loris' is not defined no-undef 13:1 error Expected indentation of 8 spaces but found 4 indent 14:1 error Expected indentation of 4 spaces but found 2 indent 15:1 error Expected indentation of 4 spaces but found 2 indent 16:1 error Expected indentation of 4 spaces but found 2 indent 17:1 error Expected indentation of 4 spaces but found 2 indent 18:1 error Expected indentation of 8 spaces but found 4 indent 19:1 error Expected indentation of 4 spaces but found 2 indent 21:1 error Expected indentation of 4 spaces but found 2 indent 22:1 error Expected indentation of 8 spaces but found 4 indent 22:15 error 'loris' is not defined no-undef 24:1 error Expected indentation of 8 spaces but found 4 indent 25:1 error Expected indentation of 12 spaces but found 8 indent 26:1 error Expected indentation of 16 spaces but found 10 indent 27:1 error Expected indentation of 12 spaces but found 8 indent 28:1 error Expected indentation of 8 spaces but found 6 indent 29:1 error Expected indentation of 4 spaces but found 2 indent 31:1 error Expected indentation of 4 spaces but found 2 indent ? 19 problems (19 errors, 0 warnings) 17 errors and 0 warnings potentially fixable with the `--fix` option. ERROR in ./modules/mri_violations/jsx/mri_protocol_violations_columnFormatter.js Module Error (from ./node_modules/eslint-loader/index.js): /var/www/loris/modules/mri_violations/jsx/mri_protocol_violations_columnFormatter.js 10:1 error Expected indentation of 4 spaces but found 2 indent 11:1 error Expected indentation of 4 spaces but found 2 indent 11:7 error 'loris' is not defined no-undef 12:1 error Expected indentation of 8 spaces but found 4 indent 13:1 error Expected indentation of 4 spaces but found 2 indent 14:1 error Expected indentation of 4 spaces but found 2 indent 15:1 error Expected indentation of 4 spaces but found 2 indent 16:1 error Expected indentation of 4 spaces but found 2 indent 17:1 error Expected indentation of 8 spaces but found 4 indent 18:1 error Expected indentation of 4 spaces but found 2 indent 20:1 error Expected indentation of 4 spaces but found 2 indent 21:1 error Expected indentation of 8 spaces but found 4 indent 21:11 error 'loris' is not defined no-undef 23:1 error Expected indentation of 8 spaces but found 4 indent 24:1 error Expected indentation of 12 spaces but found 16 indent 25:1 error Expected indentation of 8 spaces but found 13 indent 26:1 error Expected indentation of 4 spaces but found 2 indent 28:1 error Expected indentation of 4 spaces but found 2 indent ? 18 problems (18 errors, 0 warnings) 16 errors and 0 warnings potentially fixable with the `--fix` option. ERROR in ./modules/new_profile/jsx/NewProfileIndex.js Module Error (from ./node_modules/eslint-loader/index.js): /var/www/loris/modules/new_profile/jsx/NewProfileIndex.js 1:8 error 'Panel' is defined but never used no-unused-vars 2:8 error 'Loader' is defined but never used no-unused-vars 13:7 error 'NewProfileIndex' is defined but never used no-unused-vars 13:31 error 'React' is not defined no-undef 14:1 error Expected indentation of 4 spaces but found 2 indent 15:1 error Expected indentation of 8 spaces but found 4 indent 16:1 error Expected indentation of 8 spaces but found 4 indent 17:1 error Expected indentation of 12 spaces but found 6 indent 18:1 error Expected indentation of 12 spaces but found 6 indent 19:1 error Expected indentation of 12 spaces but found 6 indent 20:1 error Expected indentation of 12 spaces but found 6 indent 21:1 error Expected indentation of 12 spaces but found 6 indent 22:1 error Expected indentation of 12 spaces but found 6 indent 23:1 error Expected indentation of 8 spaces but found 4 indent 24:1 error Expected indentation of 8 spaces but found 4 indent 25:1 error Expected indentation of 8 spaces but found 4 indent 26:1 error Expected indentation of 8 spaces but found 4 indent 27:1 error Expected indentation of 4 spaces but found 2 indent 29:1 error Expected indentation of 4 spaces but found 2 indent 30:1 error Expected indentation of 8 spaces but found 4 indent 31:1 error Expected indentation of 12 spaces but found 6 indent 32:1 error Expected indentation of 4 spaces but found 2 indent 34:1 error Expected indentation of 4 spaces but found 2 indent 39:1 error Expected indentation of 4 spaces but found 2 indent 40:1 error Expected indentation of 8 spaces but found 4 indent 41:1 error Expected indentation of 12 spaces but found 6 indent 42:1 error Expected indentation of 12 spaces but found 6 indent 43:1 error Expected indentation of 12 spaces but found 6 indent 44:1 error Expected indentation of 12 spaces but found 6 indent 44:15 error 'error' is defined but never used no-unused-vars 45:1 error Expected indentation of 16 spaces but found 8 indent 46:1 error Expected indentation of 12 spaces but found 6 indent 47:1 error Expected indentation of 4 spaces but found 2 indent 48:1 error Expected indentation of 4 spaces but found 2 indent 55:1 error Expected indentation of 4 spaces but found 2 indent 56:1 error Expected indentation of 8 spaces but found 4 indent 57:1 error Expected indentation of 8 spaces but found 4 indent 58:1 error Expected indentation of 8 spaces but found 4 indent 59:1 error Expected indentation of 12 spaces but found 6 indent 60:1 error Expected indentation of 8 spaces but found 4 indent 62:1 error Expected indentation of 8 spaces but found 4 indent 63:1 error Expected indentation of 12 spaces but found 6 indent 64:1 error Expected indentation of 8 spaces but found 4 indent 65:1 error Expected indentation of 12 spaces but found 6 indent 66:1 error Expected indentation of 8 spaces but found 4 indent 67:1 error Expected indentation of 8 spaces but found 4 indent 68:1 error Expected indentation of 4 spaces but found 2 indent 70:1 error Expected indentation of 4 spaces but found 2 indent 75:1 error Expected indentation of 4 spaces but found 2 indent 76:1 error Expected indentation of 8 spaces but found 4 indent 77:1 error Expected indentation of 8 spaces but found 4 indent 78:1 error Expected indentation of 8 spaces but found 4 indent 79:1 error Expected indentation of 12 spaces but found 6 indent 80:1 error Expected indentation of 16 spaces but found 8 indent 81:1 error Expected indentation of 12 spaces but found 6 indent 82:1 error Expected indentation of 8 spaces but found 4 indent 83:1 error Expected indentation of 12 spaces but found 6 indent 84:1 error Expected indentation of 12 spaces but found 6 indent 85:1 error Expected indentation of 12 spaces but found 6 indent 86:1 error Expected indentation of 16 spaces but found 8 indent 87:1 error Expected indentation of 20 spaces but found 10 indent 88:1 error Expected indentation of 16 spaces but found 8 indent 89:1 error Expected indentation of 12 spaces but found 6 indent 90:1 error Expected indentation of 12 spaces but found 6 indent 92:1 error Expected indentation of 12 spaces but found 6 indent 93:1 error Expected indentation of 16 spaces but found 8 indent 94:1 error Expected indentation of 16 spaces but found 8 indent 95:1 error Expected indentation of 16 spaces but found 8 indent 96:1 error Expected indentation of 16 spaces but found 8 indent 97:1 error Expected indentation of 12 spaces but found 8 indent 98:1 error Expected indentation of 16 spaces but found 6 indent 99:1 error Expected indentation of 20 spaces but found 8 indent 100:1 error Expected indentation of 24 spaces but found 10 indent 101:1 error Expected indentation of 28 spaces but found 12 indent 102:1 error Expected indentation of 28 spaces but found 12 indent 103:1 error Expected indentation of 24 spaces but found 10 indent 104:1 error Expected indentation of 20 spaces but found 8 indent 105:1 error Expected indentation of 24 spaces but found 10 indent 106:1 error Expected indentation of 28 spaces but found 12 indent 107:1 error Expected indentation of 24 spaces but found 10 indent 108:1 error Expected indentation of 20 spaces but found 8 indent 109:1 error Expected indentation of 16 spaces but found 6 indent 110:1 error Expected indentation of 16 spaces but found 6 indent 111:1 error Expected indentation of 20 spaces but found 8 indent 111:9 error Unexpected console statement no-console 112:1 error Expected indentation of 16 spaces but found 6 indent 113:1 error Expected indentation of 8 spaces but found 4 indent 114:1 error Expected indentation of 4 spaces but found 2 indent 116:1 error Expected indentation of 4 spaces but found 2 indent 122:1 error Expected indentation of 4 spaces but found 2 indent 123:1 error Expected indentation of 8 spaces but found 4 indent 124:1 error Expected indentation of 8 spaces but found 4 indent 126:1 error Expected indentation of 8 spaces but found 4 indent 127:1 error Expected indentation of 4 spaces but found 2 indent 129:1 error Expected indentation of 4 spaces but found 2 indent 131:1 error Expected indentation of 8 spaces but found 4 indent 132:1 error Expected indentation of 12 spaces but found 6 indent 133:1 error Expected indentation of 8 spaces but found 4 indent 135:1 error Expected indentation of 8 spaces but found 4 indent 136:1 error Expected indentation of 8 spaces but found 4 indent 137:1 error Expected indentation of 12 spaces but found 6 indent 138:1 error Expected indentation of 8 spaces but found 4 indent 139:1 error Expected indentation of 8 spaces but found 4 indent 140:1 error Expected indentation of 8 spaces but found 4 indent 141:1 error Expected indentation of 8 spaces but found 4 indent 142:1 error Expected indentation of 8 spaces but found 4 indent 143:1 error Expected indentation of 8 spaces but found 4 indent 144:1 error Expected indentation of 8 spaces but found 4 indent 145:1 error Expected indentation of 8 spaces but found 4 indent 147:1 error Expected indentation of 8 spaces but found 4 indent 148:1 error Expected indentation of 12 spaces but found 6 indent 150:1 error Expected indentation of 12 spaces but found 10 indent 151:1 error Expected indentation of 16 spaces but found 12 indent 152:1 error Expected indentation of 16 spaces but found 12 indent 153:1 error Expected indentation of 16 spaces but found 12 indent 154:1 error Expected indentation of 16 spaces but found 12 indent 155:1 error Expected indentation of 16 spaces but found 12 indent 156:1 error Expected indentation of 16 spaces but found 12 indent 157:1 error Expected indentation of 16 spaces but found 12 indent 158:1 error Expected indentation of 16 spaces but found 12 indent 159:1 error Expected indentation of 12 spaces but found 10 indent 160:1 error Expected indentation of 12 spaces but found 10 indent 161:1 error Expected indentation of 16 spaces but found 12 indent 162:1 error Expected indentation of 16 spaces but found 12 indent 163:1 error Expected indentation of 16 spaces but found 12 indent 164:1 error Expected indentation of 16 spaces but found 12 indent 165:1 error Expected indentation of 16 spaces but found 12 indent 166:1 error Expected indentation of 16 spaces but found 12 indent 167:1 error Expected indentation of 16 spaces but found 12 indent 168:1 error Expected indentation of 16 spaces but found 12 indent 169:1 error Expected indentation of 12 spaces but found 10 indent 171:1 error Expected indentation of 8 spaces but found 4 indent 172:1 error Expected indentation of 8 spaces but found 4 indent 173:1 error Expected indentation of 12 spaces but found 6 indent 175:1 error Expected indentation of 12 spaces but found 10 indent 176:1 error Expected indentation of 12 spaces but found 10 indent 177:1 error Expected indentation of 12 spaces but found 10 indent 178:1 error Expected indentation of 12 spaces but found 10 indent 179:1 error Expected indentation of 12 spaces but found 10 indent 181:1 error Expected indentation of 8 spaces but found 4 indent 182:1 error Expected indentation of 8 spaces but found 4 indent 183:1 error Expected indentation of 12 spaces but found 6 indent 185:1 error Expected indentation of 12 spaces but found 10 indent 186:1 error Expected indentation of 12 spaces but found 10 indent 187:1 error Expected indentation of 12 spaces but found 10 indent 188:1 error Expected indentation of 12 spaces but found 10 indent 189:1 error Expected indentation of 12 spaces but found 10 indent 190:1 error Expected indentation of 12 spaces but found 10 indent 192:1 error Expected indentation of 8 spaces but found 4 indent 193:1 error Expected indentation of 8 spaces but found 4 indent 194:1 error Expected indentation of 12 spaces but found 6 indent 195:1 error Expected indentation of 16 spaces but found 8 indent 196:1 error Expected indentation of 20 spaces but found 10 indent 197:1 error Expected indentation of 20 spaces but found 10 indent 198:1 error Expected indentation of 16 spaces but found 8 indent 199:1 error Expected indentation of 20 spaces but found 10 indent 200:1 error Expected indentation of 24 spaces but found 12 indent 201:1 error Expected indentation of 24 spaces but found 12 indent 202:1 error Expected indentation of 24 spaces but found 12 indent 203:1 error Expected indentation of 24 spaces but found 12 indent 204:1 error Expected indentation of 24 spaces but found 12 indent 205:1 error Expected indentation of 24 spaces but found 12 indent 206:1 error Expected indentation of 24 spaces but found 12 indent 207:1 error Expected indentation of 24 spaces but found 12 indent 208:1 error Expected indentation of 20 spaces but found 10 indent 209:1 error Expected indentation of 20 spaces but found 10 indent 210:1 error Expected indentation of 24 spaces but found 12 indent 211:1 error Expected indentation of 24 spaces but found 12 indent 212:1 error Expected indentation of 24 spaces but found 12 indent 213:1 error Expected indentation of 24 spaces but found 12 indent 214:1 error Expected indentation of 24 spaces but found 12 indent 215:1 error Expected indentation of 24 spaces but found 12 indent 216:1 error Expected indentation of 24 spaces but found 12 indent 217:1 error Expected indentation of 24 spaces but found 12 indent 218:1 error Expected indentation of 20 spaces but found 10 indent 219:1 error Expected indentation of 20 spaces but found 10 indent 220:1 error Expected indentation of 20 spaces but found 10 indent 221:1 error Expected indentation of 24 spaces but found 12 indent 222:1 error Expected indentation of 24 spaces but found 12 indent 223:1 error Expected indentation of 24 spaces but found 12 indent 224:1 error Expected indentation of 24 spaces but found 12 indent 225:1 error Expected indentation of 24 spaces but found 12 indent 226:1 error Expected indentation of 24 spaces but found 12 indent 227:1 error Expected indentation of 20 spaces but found 10 indent 228:1 error Expected indentation of 20 spaces but found 10 indent 229:1 error Expected indentation of 20 spaces but found 10 indent 230:1 error Expected indentation of 20 spaces but found 10 indent 231:1 error Expected indentation of 24 spaces but found 12 indent 232:1 error Expected indentation of 24 spaces but found 12 indent 233:1 error Expected indentation of 24 spaces but found 12 indent 234:1 error Expected indentation of 24 spaces but found 12 indent 235:1 error Expected indentation of 24 spaces but found 12 indent 236:1 error Expected indentation of 24 spaces but found 12 indent 237:1 error Expected indentation of 20 spaces but found 10 indent 238:1 error Expected indentation of 20 spaces but found 10 indent 239:1 error Expected indentation of 24 spaces but found 12 indent 240:1 error Expected indentation of 24 spaces but found 12 indent 241:1 error Expected indentation of 24 spaces but found 12 indent 242:1 error Expected indentation of 24 spaces but found 12 indent 243:1 error Expected indentation of 20 spaces but found 10 indent 244:1 error Expected indentation of 16 spaces but found 8 indent 245:1 error Expected indentation of 12 spaces but found 6 indent 246:1 error Expected indentation of 8 spaces but found 4 indent 247:1 error Expected indentation of 12 spaces but found 6 indent 248:1 error Expected indentation of 16 spaces but found 8 indent 249:1 error Expected indentation of 20 spaces but found 10 indent 250:1 error Expected indentation of 20 spaces but found 10 indent 251:1 error Expected indentation of 20 spaces but found 10 indent 252:1 error Expected indentation of 16 spaces but found 8 indent 253:1 error Expected indentation of 12 spaces but found 6 indent 254:1 error Expected indentation of 8 spaces but found 4 indent 255:1 error Expected indentation of 8 spaces but found 4 indent 256:1 error Expected indentation of 4 spaces but found 2 indent 259:1 error Expected indentation of 4 spaces but found 2 indent 259:3 error 'ReactDOM' is not defined no-undef 260:1 error Expected indentation of 8 spaces but found 4 indent 261:1 error Expected indentation of 12 spaces but found 6 indent 261:21 error 'loris' is not defined no-undef 262:1 error Expected indentation of 12 spaces but found 6 indent 262:23 error 'loris' is not defined no-undef 263:1 error Expected indentation of 12 spaces but found 6 indent 263:24 error 'loris' is not defined no-undef 264:1 error Expected indentation of 8 spaces but found 4 indent 265:1 error Expected indentation of 8 spaces but found 4 indent 266:1 error Expected indentation of 4 spaces but found 2 indent ? 225 problems (225 errors, 0 warnings) 215 errors and 0 warnings potentially fixable with the `--fix` option. ERROR in ./modules/publication/jsx/publicationIndex.js Module Error (from ./node_modules/eslint-loader/index.js): /var/www/loris/modules/publication/jsx/publicationIndex.js 1:8 error 'FilterForm' is defined but never used no-unused-vars 2:9 error 'Tabs' is defined but never used no-unused-vars 2:15 error 'TabPane' is defined but never used no-unused-vars 3:8 error 'PublicationUploadForm' is defined but never used no-unused-vars 5:7 error 'PublicationIndex' is defined but never used no-unused-vars 5:32 error 'React' is not defined no-undef 6:1 error Expected indentation of 4 spaces but found 2 indent 7:1 error Expected indentation of 8 spaces but found 4 indent 8:1 error Expected indentation of 8 spaces but found 4 indent 8:5 error 'loris' is not defined no-undef 9:1 error Expected indentation of 8 spaces but found 4 indent 10:1 error Expected indentation of 12 spaces but found 6 indent 11:1 error Expected indentation of 12 spaces but found 6 indent 12:1 error Expected indentation of 8 spaces but found 4 indent 14:1 error Expected indentation of 8 spaces but found 4 indent 15:1 error Expected indentation of 8 spaces but found 4 indent 16:1 error Expected indentation of 8 spaces but found 4 indent 17:1 error Expected indentation of 8 spaces but found 4 indent 18:1 error Expected indentation of 4 spaces but found 2 indent 20:1 error Expected indentation of 4 spaces but found 2 indent 21:1 error Expected indentation of 8 spaces but found 4 indent 22:1 error Expected indentation of 4 spaces but found 2 indent 24:1 error Expected indentation of 4 spaces but found 2 indent 25:1 error Expected indentation of 8 spaces but found 4 indent 25:5 error '$' is not defined no-undef 26:1 error Expected indentation of 12 spaces but found 6 indent 27:1 error Expected indentation of 12 spaces but found 6 indent 28:1 error Expected indentation of 12 spaces but found 6 indent 29:1 error Expected indentation of 16 spaces but found 8 indent 30:1 error Expected indentation of 20 spaces but found 10 indent 31:1 error Expected indentation of 20 spaces but found 10 indent 32:1 error Expected indentation of 16 spaces but found 8 indent 33:1 error Expected indentation of 12 spaces but found 6 indent 34:1 error Expected indentation of 12 spaces but found 6 indent 35:1 error Expected indentation of 16 spaces but found 8 indent 35:9 error Unexpected console statement no-console 36:1 error Expected indentation of 12 spaces but found 6 indent 37:1 error Expected indentation of 8 spaces but found 4 indent 38:1 error Expected indentation of 4 spaces but found 2 indent 40:1 error Expected indentation of 4 spaces but found 2 indent 41:1 error Expected indentation of 8 spaces but found 4 indent 42:1 error Expected indentation of 4 spaces but found 2 indent 44:1 error Expected indentation of 4 spaces but found 2 indent 45:1 error Expected indentation of 8 spaces but found 4 indent 46:1 error Expected indentation of 4 spaces but found 2 indent 48:1 error Expected indentation of 4 spaces but found 2 indent 49:1 error Expected indentation of 8 spaces but found 4 indent 50:1 error Expected indentation of 12 spaces but found 6 indent 51:1 error Expected indentation of 16 spaces but found 8 indent 53:1 error Expected indentation of 20 spaces but found 10 indent 54:1 error Expected indentation of 24 spaces but found 12 indent 55:1 error Expected indentation of 20 spaces but found 10 indent 56:1 error Expected indentation of 16 spaces but found 8 indent 57:1 error Expected indentation of 12 spaces but found 6 indent 58:1 error Expected indentation of 8 spaces but found 4 indent 59:1 error Expected indentation of 8 spaces but found 4 indent 60:1 error Expected indentation of 12 spaces but found 6 indent 61:1 error Expected indentation of 16 spaces but found 8 indent 62:1 error Expected indentation of 16 spaces but found 8 indent 63:1 error Expected indentation of 12 spaces but found 6 indent 64:1 error Expected indentation of 8 spaces but found 4 indent 65:1 error Expected indentation of 8 spaces but found 4 indent 66:1 error Expected indentation of 8 spaces but found 4 indent 66:9 error 'loris' is not defined no-undef 67:1 error Expected indentation of 12 spaces but found 6 indent 68:1 error Expected indentation of 16 spaces but found 8 indent 69:1 error Expected indentation of 16 spaces but found 8 indent 70:1 error Expected indentation of 12 spaces but found 6 indent 72:1 error Expected indentation of 12 spaces but found 6 indent 73:1 error Expected indentation of 16 spaces but found 8 indent 74:1 error Expected indentation of 20 spaces but found 10 indent 75:1 error Expected indentation of 24 spaces but found 12 indent 75:25 error 'loris' is not defined no-undef 76:1 error Expected indentation of 24 spaces but found 12 indent 76:24 error 'loris' is not defined no-undef 77:1 error Expected indentation of 24 spaces but found 12 indent 78:1 error Expected indentation of 20 spaces but found 10 indent 79:1 error Expected indentation of 16 spaces but found 8 indent 80:1 error Expected indentation of 12 spaces but found 6 indent 81:1 error Expected indentation of 8 spaces but found 4 indent 83:1 error Expected indentation of 8 spaces but found 4 indent 84:1 error Expected indentation of 12 spaces but found 6 indent 85:1 error Expected indentation of 8 spaces but found 4 indent 87:1 error Expected indentation of 8 spaces but found 4 indent 88:1 error Expected indentation of 12 spaces but found 6 indent 89:1 error Expected indentation of 16 spaces but found 8 indent 90:1 error Expected indentation of 20 spaces but found 10 indent 91:1 error Expected indentation of 24 spaces but found 12 indent 92:1 error Expected indentation of 24 spaces but found 12 indent 93:1 error Expected indentation of 24 spaces but found 12 indent 94:1 error Expected indentation of 24 spaces but found 12 indent 95:1 error Expected indentation of 24 spaces but found 12 indent 96:1 error Expected indentation of 24 spaces but found 12 indent 97:1 error Expected indentation of 24 spaces but found 12 indent 98:1 error Expected indentation of 24 spaces but found 12 indent 99:1 error Expected indentation of 20 spaces but found 10 indent 100:1 error Expected indentation of 24 spaces but found 12 indent 101:1 error Expected indentation of 24 spaces but found 12 indent 102:1 error Expected indentation of 28 spaces but found 14 indent 103:1 error Expected indentation of 28 spaces but found 14 indent 104:1 error Expected indentation of 28 spaces but found 14 indent 105:1 error Expected indentation of 24 spaces but found 12 indent 106:1 error Expected indentation of 20 spaces but found 10 indent 107:1 error Expected indentation of 20 spaces but found 10 indent 108:1 error Expected indentation of 24 spaces but found 12 indent 109:1 error Expected indentation of 24 spaces but found 12 indent 110:1 error Expected indentation of 24 spaces but found 12 indent 111:1 error Expected indentation of 24 spaces but found 12 indent 112:1 error Expected indentation of 20 spaces but found 10 indent 113:1 error Expected indentation of 16 spaces but found 8 indent 114:1 error Expected indentation of 16 spaces but found 8 indent 115:1 error Expected indentation of 12 spaces but found 6 indent 116:1 error Expected indentation of 8 spaces but found 4 indent 117:1 error Expected indentation of 4 spaces but found 2 indent 119:1 error Expected indentation of 4 spaces but found 2 indent 121:1 error Expected indentation of 8 spaces but found 4 indent 121:9 error 'loris' is not defined no-undef 122:1 error Expected indentation of 12 spaces but found 6 indent 123:1 error Expected indentation of 8 spaces but found 4 indent 124:1 error Expected indentation of 8 spaces but found 4 indent 125:1 error Expected indentation of 8 spaces but found 4 indent 126:1 error Expected indentation of 8 spaces but found 4 indent 127:1 error Expected indentation of 12 spaces but found 6 indent 128:1 error Expected indentation of 8 spaces but found 4 indent 129:1 error Expected indentation of 8 spaces but found 4 indent 130:1 error Expected indentation of 8 spaces but found 4 indent 131:1 error Expected indentation of 12 spaces but found 6 indent 132:1 error Expected indentation of 12 spaces but found 6 indent 132:21 error 'loris' is not defined no-undef 134:1 error Expected indentation of 12 spaces but found 6 indent 135:1 error Expected indentation of 16 spaces but found 8 indent 136:1 error Expected indentation of 20 spaces but found 10 indent 137:1 error Expected indentation of 24 spaces but found 12 indent 138:1 error Expected indentation of 20 spaces but found 10 indent 139:1 error Expected indentation of 16 spaces but found 8 indent 140:1 error Expected indentation of 12 spaces but found 6 indent 141:1 error Expected indentation of 8 spaces but found 4 indent 142:1 error Expected indentation of 8 spaces but found 4 indent 143:1 error Expected indentation of 4 spaces but found 2 indent 146:1 error '$' is not defined no-undef 147:1 error Expected indentation of 4 spaces but found 2 indent 148:1 error Expected indentation of 8 spaces but found 4 indent 149:1 error Expected indentation of 12 spaces but found 6 indent 149:37 error 'loris' is not defined no-undef 150:1 error Expected indentation of 8 spaces but found 4 indent 151:1 error Expected indentation of 4 spaces but found 2 indent 153:1 error Expected indentation of 4 spaces but found 2 indent 153:3 error 'ReactDOM' is not defined no-undef ? 148 problems (148 errors, 0 warnings) 131 errors and 0 warnings potentially fixable with the `--fix` option. ERROR in ./modules/publication/jsx/viewProjectIndex.js Module Error (from ./node_modules/eslint-loader/index.js): /var/www/loris/modules/publication/jsx/viewProjectIndex.js 1:8 error 'ViewProject' is defined but never used no-unused-vars 3:14 error 'QueryString' is not defined no-undef 5:1 error '$' is not defined no-undef 6:1 error Expected indentation of 4 spaces but found 2 indent 7:1 error Expected indentation of 8 spaces but found 4 indent 8:1 error Expected indentation of 12 spaces but found 6 indent 9:1 error Expected indentation of 16 spaces but found 8 indent 10:1 error Expected indentation of 20 spaces but found 10 indent 11:1 error Expected indentation of 24 spaces but found 12 indent 11:25 error 'loris' is not defined no-undef 12:1 error Expected indentation of 24 spaces but found 12 indent 12:24 error 'loris' is not defined no-undef 13:1 error Expected indentation of 20 spaces but found 10 indent 14:1 error Expected indentation of 16 spaces but found 8 indent 15:1 error Expected indentation of 12 spaces but found 6 indent 16:1 error Expected indentation of 8 spaces but found 4 indent 17:1 error Expected indentation of 4 spaces but found 2 indent 19:1 error Expected indentation of 4 spaces but found 2 indent 19:3 error 'ReactDOM' is not defined no-undef ? 19 problems (19 errors, 0 warnings) 13 errors and 0 warnings potentially fixable with the `--fix` option. ERROR in ./modules/quality_control/jsx/qualityControlIndex.js Module Error (from ./node_modules/eslint-loader/index.js): /var/www/loris/modules/quality_control/jsx/qualityControlIndex.js 1:8 error 'React' is defined but never used no-unused-vars 2:8 error 'Loader' is defined but never used no-unused-vars 3:9 error 'Tabs' is defined but never used no-unused-vars 3:15 error 'TabPane' is defined but never used no-unused-vars 4:8 error 'FilterableDataTable' is defined but never used no-unused-vars 8:1 error Expected indentation of 4 spaces but found 2 indent 9:1 error Expected indentation of 8 spaces but found 4 indent 10:1 error Expected indentation of 8 spaces but found 4 indent 11:1 error Expected indentation of 12 spaces but found 6 indent 12:1 error Expected indentation of 12 spaces but found 6 indent 13:1 error Expected indentation of 12 spaces but found 6 indent 14:1 error Expected indentation of 12 spaces but found 6 indent 15:1 error Expected indentation of 12 spaces but found 6 indent 16:1 error Expected indentation of 12 spaces but found 6 indent 17:1 error Expected indentation of 8 spaces but found 4 indent 18:1 error Expected indentation of 8 spaces but found 4 indent 19:1 error Expected indentation of 4 spaces but found 2 indent 21:1 error Expected indentation of 4 spaces but found 2 indent 31:1 error Expected indentation of 4 spaces but found 2 indent 32:1 error Expected indentation of 8 spaces but found 6 indent 33:1 error Expected indentation of 8 spaces but found 6 indent 34:1 error Expected indentation of 8 spaces but found 6 indent 35:1 error Expected indentation of 12 spaces but found 8 indent 36:1 error Expected indentation of 16 spaces but found 10 indent 36:24 error 'loris' is not defined no-undef 39:1 error Expected indentation of 16 spaces but found 10 indent 40:1 error Expected indentation of 12 spaces but found 8 indent 41:1 error Expected indentation of 8 spaces but found 6 indent 41:7 error Expected a 'break' statement before 'case' no-fallthrough 42:1 error Expected indentation of 12 spaces but found 8 indent 43:1 error Expected indentation of 16 spaces but found 10 indent 43:24 error 'loris' is not defined no-undef 45:1 error Expected indentation of 16 spaces but found 10 indent 46:1 error Expected indentation of 12 spaces but found 8 indent 47:1 error Expected indentation of 8 spaces but found 6 indent 47:7 error Expected a 'break' statement before 'case' no-fallthrough 48:1 error Expected indentation of 12 spaces but found 8 indent 49:1 error Expected indentation of 16 spaces but found 10 indent 49:29 error 'loris' is not defined no-undef 51:1 error Expected indentation of 16 spaces but found 10 indent 52:1 error Expected indentation of 12 spaces but found 8 indent 53:1 error Expected indentation of 8 spaces but found 6 indent 54:1 error Expected indentation of 8 spaces but found 6 indent 55:1 error Expected indentation of 4 spaces but found 2 indent 57:1 error Expected indentation of 4 spaces but found 2 indent 58:1 error Expected indentation of 8 spaces but found 4 indent 59:1 error Expected indentation of 12 spaces but found 8 indent 60:1 error Expected indentation of 8 spaces but found 4 indent 61:1 error Expected indentation of 12 spaces but found 8 indent 62:1 error Expected indentation of 4 spaces but found 2 indent 64:1 error Expected indentation of 4 spaces but found 2 indent 65:1 error Expected indentation of 8 spaces but found 4 indent 66:1 error Expected indentation of 12 spaces but found 8 indent 67:1 error Expected indentation of 12 spaces but found 8 indent 68:1 error Expected indentation of 12 spaces but found 8 indent 68:17 error 'error' is defined but never used no-unused-vars 69:1 error Expected indentation of 16 spaces but found 12 indent 70:1 error Expected indentation of 12 spaces but found 6 indent 71:1 error Expected indentation of 4 spaces but found 2 indent 73:1 error Expected indentation of 4 spaces but found 2 indent 74:1 error Expected indentation of 8 spaces but found 4 indent 75:1 error Expected indentation of 12 spaces but found 6 indent 76:1 error Expected indentation of 8 spaces but found 4 indent 77:1 error Expected indentation of 8 spaces but found 4 indent 78:1 error Expected indentation of 12 spaces but found 6 indent 79:1 error Expected indentation of 16 spaces but found 8 indent 80:1 error Expected indentation of 16 spaces but found 8 indent 81:1 error Expected indentation of 12 spaces but found 6 indent 83:1 error Expected indentation of 12 spaces but found 6 indent 84:1 error Expected indentation of 12 spaces but found 6 indent 86:1 error Expected indentation of 12 spaces but found 6 indent 87:1 error Expected indentation of 16 spaces but found 8 indent 88:1 error Expected indentation of 20 spaces but found 10 indent 89:1 error Expected indentation of 24 spaces but found 12 indent 90:1 error Expected indentation of 24 spaces but found 12 indent 91:1 error Expected indentation of 20 spaces but found 10 indent 92:1 error Expected indentation of 16 spaces but found 8 indent 93:1 error Expected indentation of 16 spaces but found 8 indent 94:1 error Expected indentation of 16 spaces but found 8 indent 95:1 error Expected indentation of 20 spaces but found 10 indent 96:1 error Expected indentation of 24 spaces but found 12 indent 97:1 error Expected indentation of 24 spaces but found 12 indent 98:1 error Expected indentation of 20 spaces but found 10 indent 99:1 error Expected indentation of 16 spaces but found 8 indent 100:1 error Expected indentation of 16 spaces but found 8 indent 101:1 error Expected indentation of 20 spaces but found 10 indent 102:1 error Expected indentation of 24 spaces but found 12 indent 103:1 error Expected indentation of 24 spaces but found 12 indent 104:1 error Expected indentation of 24 spaces but found 12 indent 105:1 error Expected indentation of 20 spaces but found 10 indent 106:1 error Expected indentation of 16 spaces but found 8 indent 107:1 error Expected indentation of 16 spaces but found 8 indent 108:1 error Expected indentation of 20 spaces but found 10 indent 109:1 error Expected indentation of 24 spaces but found 12 indent 110:1 error Expected indentation of 24 spaces but found 12 indent 111:1 error Expected indentation of 24 spaces but found 12 indent 112:1 error Expected indentation of 20 spaces but found 10 indent 113:1 error Expected indentation of 16 spaces but found 8 indent 114:1 error Expected indentation of 16 spaces but found 8 indent 115:1 error Expected indentation of 20 spaces but found 10 indent 116:1 error Expected indentation of 24 spaces but found 12 indent 117:1 error Expected indentation of 24 spaces but found 12 indent 118:1 error Expected indentation of 24 spaces but found 12 indent 119:1 error Expected indentation of 20 spaces but found 10 indent 120:1 error Expected indentation of 16 spaces but found 8 indent 121:1 error Expected indentation of 16 spaces but found 8 indent 122:1 error Expected indentation of 20 spaces but found 10 indent 123:1 error Expected indentation of 24 spaces but found 12 indent 124:1 error Expected indentation of 24 spaces but found 12 indent 125:1 error Expected indentation of 24 spaces but found 12 indent 126:1 error Expected indentation of 20 spaces but found 10 indent 127:1 error Expected indentation of 16 spaces but found 8 indent 128:1 error Expected indentation of 16 spaces but found 8 indent 129:1 error Expected indentation of 20 spaces but found 10 indent 130:1 error Expected indentation of 24 spaces but found 12 indent 131:1 error Expected indentation of 24 spaces but found 12 indent 132:1 error Expected indentation of 24 spaces but found 12 indent 133:1 error Expected indentation of 20 spaces but found 10 indent 134:1 error Expected indentation of 16 spaces but found 8 indent 135:1 error Expected indentation of 16 spaces but found 8 indent 136:1 error Expected indentation of 20 spaces but found 10 indent 137:1 error Expected indentation of 24 spaces but found 12 indent 138:1 error Expected indentation of 24 spaces but found 12 indent 139:1 error Expected indentation of 24 spaces but found 12 indent 140:1 error Expected indentation of 20 spaces but found 10 indent 141:1 error Expected indentation of 16 spaces but found 8 indent 142:1 error Expected indentation of 16 spaces but found 8 indent 143:1 error Expected indentation of 20 spaces but found 10 indent 144:1 error Expected indentation of 24 spaces but found 12 indent 145:1 error Expected indentation of 24 spaces but found 12 indent 146:1 error Expected indentation of 24 spaces but found 12 indent 147:1 error Expected indentation of 20 spaces but found 10 indent 148:1 error Expected indentation of 16 spaces but found 8 indent 149:1 error Expected indentation of 16 spaces but found 8 indent 150:1 error Expected indentation of 20 spaces but found 10 indent 151:1 error Expected indentation of 24 spaces but found 12 indent 152:1 error Expected indentation of 24 spaces but found 12 indent 153:1 error Expected indentation of 24 spaces but found 12 indent 154:1 error Expected indentation of 20 spaces but found 10 indent 155:1 error Expected indentation of 16 spaces but found 8 indent 156:1 error Expected indentation of 16 spaces but found 8 indent 157:1 error Expected indentation of 20 spaces but found 10 indent 158:1 error Expected indentation of 24 spaces but found 12 indent 159:1 error Expected indentation of 24 spaces but found 12 indent 160:1 error Expected indentation of 24 spaces but found 12 indent 161:1 error Expected indentation of 20 spaces but found 10 indent 162:1 error Expected indentation of 16 spaces but found 8 indent 163:1 error Expected indentation of 16 spaces but found 8 indent 164:1 error Expected indentation of 20 spaces but found 10 indent 165:1 error Expected indentation of 24 spaces but found 12 indent 166:1 error Expected indentation of 24 spaces but found 12 indent 167:1 error Expected indentation of 24 spaces but found 12 indent 168:1 error Expected indentation of 20 spaces but found 10 indent 169:1 error Expected indentation of 16 spaces but found 8 indent 170:1 error Expected indentation of 16 spaces but found 8 indent 171:1 error Expected indentation of 20 spaces but found 10 indent 172:1 error Expected indentation of 24 spaces but found 12 indent 173:1 error Expected indentation of 24 spaces but found 12 indent 174:1 error Expected indentation of 24 spaces but found 12 indent 175:1 error Expected indentation of 20 spaces but found 10 indent 176:1 error Expected indentation of 16 spaces but found 8 indent 177:1 error Expected indentation of 16 spaces but found 8 indent 178:1 error Expected indentation of 20 spaces but found 10 indent 179:1 error Expected indentation of 24 spaces but found 12 indent 180:1 error Expected indentation of 24 spaces but found 12 indent 181:1 error Expected indentation of 24 spaces but found 12 indent 182:1 error Expected indentation of 20 spaces but found 10 indent 183:1 error Expected indentation of 16 spaces but found 8 indent 184:1 error Expected indentation of 16 spaces but found 8 indent 185:1 error Expected indentation of 16 spaces but found 8 indent 186:1 error Expected indentation of 12 spaces but found 6 indent 188:1 error Expected indentation of 12 spaces but found 6 indent 189:1 error Expected indentation of 16 spaces but found 8 indent 190:1 error Expected indentation of 20 spaces but found 10 indent 191:1 error Expected indentation of 24 spaces but found 12 indent 192:1 error Expected indentation of 24 spaces but found 12 indent 193:1 error Expected indentation of 24 spaces but found 12 indent 194:1 error Expected indentation of 20 spaces but found 10 indent 195:1 error Expected indentation of 16 spaces but found 8 indent 196:1 error Expected indentation of 16 spaces but found 8 indent 197:1 error Expected indentation of 20 spaces but found 10 indent 198:1 error Expected indentation of 24 spaces but found 12 indent 199:1 error Expected indentation of 24 spaces but found 12 indent 200:1 error Expected indentation of 20 spaces but found 10 indent 201:1 error Expected indentation of 16 spaces but found 8 indent 202:1 error Expected indentation of 16 spaces but found 8 indent 203:1 error Expected indentation of 20 spaces but found 10 indent 204:1 error Expected indentation of 24 spaces but found 12 indent 205:1 error Expected indentation of 24 spaces but found 12 indent 206:1 error Expected indentation of 20 spaces but found 10 indent 207:1 error Expected indentation of 16 spaces but found 8 indent 208:1 error Expected indentation of 16 spaces but found 8 indent 209:1 error Expected indentation of 20 spaces but found 10 indent 210:1 error Expected indentation of 24 spaces but found 12 indent 211:1 error Expected indentation of 24 spaces but found 12 indent 212:1 error Expected indentation of 24 spaces but found 12 indent 213:1 error Expected indentation of 20 spaces but found 10 indent 214:1 error Expected indentation of 16 spaces but found 8 indent 215:1 error Expected indentation of 12 spaces but found 6 indent 217:1 error Expected indentation of 12 spaces but found 6 indent 218:1 error Expected indentation of 16 spaces but found 8 indent 219:1 error Expected indentation of 20 spaces but found 10 indent 220:1 error Expected indentation of 24 spaces but found 12 indent 221:1 error Expected indentation of 24 spaces but found 12 indent 222:1 error Expected indentation of 24 spaces but found 12 indent 223:1 error Expected indentation of 24 spaces but found 12 indent 224:1 error Expected indentation of 20 spaces but found 10 indent 225:1 error Expected indentation of 16 spaces but found 8 indent 226:1 error Expected indentation of 12 spaces but found 6 indent 228:1 error Expected indentation of 12 spaces but found 6 indent 229:1 error Expected indentation of 16 spaces but found 8 indent 230:1 error Expected indentation of 20 spaces but found 10 indent 231:1 error Expected indentation of 24 spaces but found 12 indent 232:1 error Expected indentation of 24 spaces but found 12 indent 233:1 error Expected indentation of 24 spaces but found 12 indent 234:1 error Expected indentation of 24 spaces but found 12 indent 235:1 error Expected indentation of 20 spaces but found 10 indent 236:1 error Expected indentation of 16 spaces but found 8 indent 237:1 error Expected indentation of 12 spaces but found 6 indent 238:1 error Expected indentation of 12 spaces but found 6 indent 239:1 error Expected indentation of 16 spaces but found 8 indent 240:1 error Expected indentation of 20 spaces but found 10 indent 241:1 error Expected indentation of 24 spaces but found 16 indent 242:1 error Expected indentation of 24 spaces but found 12 indent 243:1 error Expected indentation of 24 spaces but found 12 indent 244:1 error Expected indentation of 20 spaces but found 10 indent 245:1 error Expected indentation of 16 spaces but found 8 indent 246:1 error Expected indentation of 12 spaces but found 6 indent 247:1 error Expected indentation of 8 spaces but found 4 indent 248:1 error Expected indentation of 12 spaces but found 6 indent 249:1 error Expected indentation of 16 spaces but found 8 indent 250:1 error Expected indentation of 20 spaces but found 10 indent 251:1 error Expected indentation of 16 spaces but found 8 indent 252:1 error Expected indentation of 12 spaces but found 6 indent 253:1 error Expected indentation of 8 spaces but found 4 indent 254:1 error Expected indentation of 4 spaces but found 2 indent 258:1 error Expected indentation of 4 spaces but found 2 indent 259:1 error Expected indentation of 4 spaces but found 2 indent 260:1 error Expected indentation of 4 spaces but found 2 indent 264:1 error Expected indentation of 4 spaces but found 2 indent 264:3 error 'ReactDOM' is not defined no-undef 265:1 error Expected indentation of 8 spaces but found 4 indent 266:1 error Expected indentation of 12 spaces but found 6 indent 266:22 error 'loris' is not defined no-undef 267:1 error Expected indentation of 12 spaces but found 6 indent 267:31 error 'loris' is not defined no-undef 268:1 error Expected indentation of 12 spaces but found 6 indent 268:22 error 'loris' is not defined no-undef 269:1 error Expected indentation of 8 spaces but found 4 indent 270:1 error Expected indentation of 8 spaces but found 4 indent 271:1 error Expected indentation of 4 spaces but found 2 indent ? 251 problems (251 errors, 0 warnings) 236 errors and 0 warnings potentially fixable with the `--fix` option. ERROR in ./modules/server_processes_manager/jsx/server_processes_managerIndex.js Module Error (from ./node_modules/eslint-loader/index.js): /var/www/loris/modules/server_processes_manager/jsx/server_processes_managerIndex.js 1:8 error 'React' is defined but never used no-unused-vars 4:8 error 'Loader' is defined but never used no-unused-vars 5:8 error 'FilterableDataTable' is defined but never used no-unused-vars 8:1 error Expected indentation of 4 spaces but found 2 indent 9:1 error Expected indentation of 8 spaces but found 4 indent 11:1 error Expected indentation of 8 spaces but found 4 indent 12:1 error Expected indentation of 12 spaces but found 6 indent 13:1 error Expected indentation of 12 spaces but found 6 indent 14:1 error Expected indentation of 12 spaces but found 6 indent 15:1 error Expected indentation of 8 spaces but found 4 indent 17:1 error Expected indentation of 8 spaces but found 4 indent 18:1 error Expected indentation of 8 spaces but found 4 indent 19:1 error Expected indentation of 4 spaces but found 2 indent 21:1 error Expected indentation of 4 spaces but found 2 indent 22:1 error Expected indentation of 8 spaces but found 4 indent 23:1 error Expected indentation of 12 spaces but found 6 indent 24:1 error Expected indentation of 4 spaces but found 2 indent 26:1 error Expected indentation of 4 spaces but found 2 indent 31:1 error Expected indentation of 4 spaces but found 2 indent 32:1 error Expected indentation of 8 spaces but found 4 indent 33:1 error Expected indentation of 12 spaces but found 6 indent 34:1 error Expected indentation of 12 spaces but found 6 indent 35:1 error Expected indentation of 12 spaces but found 6 indent 36:1 error Expected indentation of 16 spaces but found 8 indent 37:1 error Expected indentation of 16 spaces but found 8 indent 37:9 error Unexpected console statement no-console 38:1 error Expected indentation of 12 spaces but found 6 indent 39:1 error Expected indentation of 4 spaces but found 2 indent 41:1 error Expected indentation of 4 spaces but found 2 indent 50:1 error Expected indentation of 4 spaces but found 2 indent 50:30 error 'row' is defined but never used no-unused-vars 51:1 error Expected indentation of 8 spaces but found 4 indent 52:1 error Expected indentation of 4 spaces but found 2 indent 54:1 error Expected indentation of 4 spaces but found 2 indent 57:1 error Expected indentation of 8 spaces but found 4 indent 58:1 error Expected indentation of 12 spaces but found 6 indent 59:1 error Expected indentation of 8 spaces but found 4 indent 61:1 error Expected indentation of 8 spaces but found 4 indent 62:1 error Expected indentation of 8 spaces but found 4 indent 63:1 error Expected indentation of 12 spaces but found 6 indent 64:1 error Expected indentation of 8 spaces but found 4 indent 66:1 error Expected indentation of 8 spaces but found 3 indent 70:1 error Expected indentation of 8 spaces but found 4 indent 71:1 error Expected indentation of 12 spaces but found 6 indent 72:1 error Expected indentation of 16 spaces but found 8 indent 73:1 error Expected indentation of 16 spaces but found 8 indent 74:1 error Expected indentation of 12 spaces but found 6 indent 75:1 error Expected indentation of 12 spaces but found 6 indent 76:1 error Expected indentation of 16 spaces but found 8 indent 77:1 error Expected indentation of 16 spaces but found 8 indent 78:1 error Expected indentation of 12 spaces but found 6 indent 79:1 error Expected indentation of 12 spaces but found 6 indent 80:1 error Expected indentation of 12 spaces but found 6 indent 81:1 error Expected indentation of 12 spaces but found 6 indent 82:1 error Expected indentation of 12 spaces but found 6 indent 83:1 error Expected indentation of 12 spaces but found 6 indent 84:1 error Expected indentation of 16 spaces but found 8 indent 85:1 error Expected indentation of 16 spaces but found 8 indent 86:1 error Expected indentation of 12 spaces but found 6 indent 87:1 error Expected indentation of 12 spaces but found 6 indent 88:1 error Expected indentation of 12 spaces but found 6 indent 89:1 error Expected indentation of 12 spaces but found 6 indent 90:1 error Expected indentation of 8 spaces but found 4 indent 92:1 error Expected indentation of 8 spaces but found 4 indent 93:1 error Expected indentation of 12 spaces but found 10 indent 94:1 error Expected indentation of 16 spaces but found 12 indent 95:1 error Expected indentation of 16 spaces but found 12 indent 96:1 error Expected indentation of 16 spaces but found 12 indent 97:1 error Expected indentation of 16 spaces but found 12 indent 98:1 error Expected indentation of 12 spaces but found 10 indent 99:1 error Expected indentation of 8 spaces but found 4 indent 100:1 error Expected indentation of 4 spaces but found 2 indent 104:1 error Expected indentation of 4 spaces but found 2 indent 108:1 error Expected indentation of 4 spaces but found 2 indent 108:3 error 'ReactDOM' is not defined no-undef 109:1 error Expected indentation of 8 spaces but found 4 indent 110:1 error Expected indentation of 12 spaces but found 6 indent 110:19 error 'loris' is not defined no-undef 111:1 error Expected indentation of 8 spaces but found 4 indent 112:1 error Expected indentation of 8 spaces but found 4 indent 113:1 error Expected indentation of 4 spaces but found 2 indent ? 81 problems (81 errors, 0 warnings) 74 errors and 0 warnings potentially fixable with the `--fix` option. ERROR in ./modules/survey_accounts/jsx/surveyAccountsIndex.js Module Error (from ./node_modules/eslint-loader/index.js): /var/www/loris/modules/survey_accounts/jsx/surveyAccountsIndex.js 1:8 error 'React' is defined but never used no-unused-vars 4:8 error 'Loader' is defined but never used no-unused-vars 5:8 error 'FilterableDataTable' is defined but never used no-unused-vars 8:1 error Expected indentation of 4 spaces but found 2 indent 9:1 error Expected indentation of 8 spaces but found 4 indent 11:1 error Expected indentation of 8 spaces but found 4 indent 12:1 error Expected indentation of 12 spaces but found 6 indent 13:1 error Expected indentation of 12 spaces but found 6 indent 14:1 error Expected indentation of 12 spaces but found 6 indent 15:1 error Expected indentation of 8 spaces but found 4 indent 17:1 error Expected indentation of 8 spaces but found 4 indent 18:1 error Expected indentation of 8 spaces but found 4 indent 19:1 error Expected indentation of 4 spaces but found 2 indent 21:1 error Expected indentation of 4 spaces but found 2 indent 22:1 error Expected indentation of 8 spaces but found 4 indent 23:1 error Expected indentation of 12 spaces but found 6 indent 24:1 error Expected indentation of 4 spaces but found 2 indent 26:1 error Expected indentation of 4 spaces but found 2 indent 33:1 error Expected indentation of 4 spaces but found 2 indent 34:1 error Expected indentation of 8 spaces but found 4 indent 35:1 error Expected indentation of 12 spaces but found 6 indent 36:1 error Expected indentation of 12 spaces but found 6 indent 37:1 error Expected indentation of 12 spaces but found 6 indent 38:1 error Expected indentation of 16 spaces but found 8 indent 39:1 error Expected indentation of 16 spaces but found 8 indent 39:9 error Unexpected console statement no-console 40:1 error Expected indentation of 12 spaces but found 6 indent 41:1 error Expected indentation of 4 spaces but found 2 indent 43:1 error Expected indentation of 4 spaces but found 2 indent 52:1 error Expected indentation of 4 spaces but found 2 indent 53:1 error Expected indentation of 8 spaces but found 4 indent 54:1 error Expected indentation of 8 spaces but found 4 indent 55:1 error Expected indentation of 8 spaces but found 4 indent 56:1 error Expected indentation of 12 spaces but found 6 indent 56:7 error Unexpected lexical declaration in case block no-case-declarations 56:19 error 'loris' is not defined no-undef 57:1 error Expected indentation of 12 spaces but found 6 indent 58:1 error Expected indentation of 12 spaces but found 6 indent 59:1 error Expected indentation of 8 spaces but found 4 indent 60:1 error Expected indentation of 12 spaces but found 6 indent 61:1 error Expected indentation of 12 spaces but found 6 indent 62:1 error Expected indentation of 8 spaces but found 4 indent 65:1 error Expected indentation of 8 spaces but found 4 indent 66:1 error Expected indentation of 4 spaces but found 2 indent 68:1 error Expected indentation of 4 spaces but found 2 indent 71:1 error Expected indentation of 8 spaces but found 4 indent 72:1 error Expected indentation of 12 spaces but found 6 indent 73:1 error Expected indentation of 8 spaces but found 4 indent 75:1 error Expected indentation of 8 spaces but found 4 indent 76:1 error Expected indentation of 8 spaces but found 4 indent 77:1 error Expected indentation of 12 spaces but found 6 indent 78:1 error Expected indentation of 8 spaces but found 4 indent 80:1 error Expected indentation of 8 spaces but found 3 indent 84:1 error Expected indentation of 8 spaces but found 4 indent 85:1 error Expected indentation of 8 spaces but found 4 indent 86:1 error Expected indentation of 12 spaces but found 6 indent 87:1 error Expected indentation of 16 spaces but found 8 indent 88:1 error Expected indentation of 16 spaces but found 8 indent 89:1 error Expected indentation of 12 spaces but found 6 indent 90:1 error Expected indentation of 12 spaces but found 6 indent 91:1 error Expected indentation of 16 spaces but found 8 indent 92:1 error Expected indentation of 16 spaces but found 8 indent 93:1 error Expected indentation of 16 spaces but found 8 indent 94:1 error Expected indentation of 12 spaces but found 6 indent 95:1 error Expected indentation of 12 spaces but found 6 indent 96:1 error Expected indentation of 16 spaces but found 8 indent 97:1 error Expected indentation of 16 spaces but found 8 indent 98:1 error Expected indentation of 12 spaces but found 6 indent 99:1 error Expected indentation of 12 spaces but found 6 indent 100:1 error Expected indentation of 16 spaces but found 8 indent 101:1 error Expected indentation of 16 spaces but found 8 indent 102:1 error Expected indentation of 16 spaces but found 8 indent 103:1 error Expected indentation of 12 spaces but found 6 indent 104:1 error Expected indentation of 12 spaces but found 6 indent 105:1 error Expected indentation of 12 spaces but found 6 indent 106:1 error Expected indentation of 8 spaces but found 4 indent 107:1 error Expected indentation of 8 spaces but found 2 indent 108:1 error Expected indentation of 12 spaces but found 4 indent 109:1 error Expected indentation of 8 spaces but found 2 indent 110:1 error Expected indentation of 8 spaces but found 2 indent 111:1 error Expected indentation of 12 spaces but found 4 indent 112:1 error Expected indentation of 8 spaces but found 2 indent 114:1 error Expected indentation of 8 spaces but found 4 indent 115:1 error Expected indentation of 12 spaces but found 7 indent 116:1 error Expected indentation of 16 spaces but found 9 indent 117:1 error Expected indentation of 16 spaces but found 9 indent 118:1 error Expected indentation of 16 spaces but found 9 indent 119:1 error Expected indentation of 16 spaces but found 9 indent 120:1 error Expected indentation of 16 spaces but found 9 indent 121:1 error Expected indentation of 16 spaces but found 9 indent 122:1 error Expected indentation of 12 spaces but found 7 indent 123:1 error Expected indentation of 8 spaces but found 4 indent 124:1 error Expected indentation of 4 spaces but found 2 indent 128:1 error Expected indentation of 4 spaces but found 2 indent 129:1 error Expected indentation of 4 spaces but found 2 indent 133:1 error Expected indentation of 4 spaces but found 2 indent 133:3 error 'ReactDOM' is not defined no-undef 134:1 error Expected indentation of 8 spaces but found 4 indent 135:1 error Expected indentation of 12 spaces but found 6 indent 135:19 error 'loris' is not defined no-undef 136:1 error Expected indentation of 8 spaces but found 4 indent 137:1 error Expected indentation of 8 spaces but found 4 indent 138:1 error Expected indentation of 4 spaces but found 2 indent ? 103 problems (103 errors, 0 warnings) 95 errors and 0 warnings potentially fixable with the `--fix` option. ERROR in ./modules/user_accounts/jsx/userAccountsIndex.js Module Error (from ./node_modules/eslint-loader/index.js): /var/www/loris/modules/user_accounts/jsx/userAccountsIndex.js 1:8 error 'React' is defined but never used no-unused-vars 4:8 error 'Loader' is defined but never used no-unused-vars 5:8 error 'FilterableDataTable' is defined but never used no-unused-vars 8:1 error Expected indentation of 4 spaces but found 2 indent 9:1 error Expected indentation of 8 spaces but found 4 indent 11:1 error Expected indentation of 8 spaces but found 4 indent 12:1 error Expected indentation of 12 spaces but found 6 indent 13:1 error Expected indentation of 12 spaces but found 6 indent 14:1 error Expected indentation of 12 spaces but found 6 indent 15:1 error Expected indentation of 8 spaces but found 4 indent 17:1 error Expected indentation of 8 spaces but found 4 indent 18:1 error Expected indentation of 8 spaces but found 4 indent 19:1 error Expected indentation of 8 spaces but found 4 indent 20:1 error Expected indentation of 4 spaces but found 2 indent 22:1 error Expected indentation of 4 spaces but found 2 indent 23:1 error Expected indentation of 8 spaces but found 4 indent 24:1 error Expected indentation of 12 spaces but found 6 indent 25:1 error Expected indentation of 4 spaces but found 2 indent 27:1 error Expected indentation of 4 spaces but found 2 indent 34:1 error Expected indentation of 4 spaces but found 2 indent 35:1 error Expected indentation of 8 spaces but found 4 indent 36:1 error Expected indentation of 12 spaces but found 6 indent 37:1 error Expected indentation of 12 spaces but found 6 indent 38:1 error Expected indentation of 16 spaces but found 8 indent 39:1 error Expected indentation of 16 spaces but found 8 indent 40:1 error Expected indentation of 20 spaces but found 10 indent 41:1 error Expected indentation of 20 spaces but found 10 indent 42:1 error Expected indentation of 16 spaces but found 8 indent 43:1 error Expected indentation of 16 spaces but found 8 indent 44:1 error Expected indentation of 12 spaces but found 6 indent 45:1 error Expected indentation of 12 spaces but found 6 indent 46:1 error Expected indentation of 16 spaces but found 8 indent 47:1 error Expected indentation of 16 spaces but found 8 indent 47:9 error Unexpected console statement no-console 48:1 error Expected indentation of 12 spaces but found 6 indent 49:1 error Expected indentation of 4 spaces but found 2 indent 51:1 error Expected indentation of 4 spaces but found 2 indent 60:1 error Expected indentation of 4 spaces but found 2 indent 61:1 error Expected indentation of 8 spaces but found 4 indent 62:1 error Expected indentation of 8 spaces but found 4 indent 63:1 error Expected indentation of 8 spaces but found 4 indent 64:1 error Expected indentation of 8 spaces but found 6 indent 66:1 error Expected indentation of 12 spaces but found 8 indent 67:1 error Expected indentation of 12 spaces but found 8 indent 68:1 error Expected indentation of 8 spaces but found 6 indent 69:1 error Expected indentation of 12 spaces but found 8 indent 69:15 error 'loris' is not defined no-undef 70:1 error Expected indentation of 12 spaces but found 8 indent 71:1 error Expected indentation of 12 spaces but found 8 indent 72:1 error Expected indentation of 8 spaces but found 6 indent 73:1 error Expected indentation of 12 spaces but found 8 indent 74:1 error Expected indentation of 16 spaces but found 10 indent 75:1 error Expected indentation of 12 spaces but found 8 indent 76:1 error Expected indentation of 16 spaces but found 10 indent 77:1 error Expected indentation of 12 spaces but found 8 indent 78:1 error Expected indentation of 12 spaces but found 8 indent 79:1 error Expected indentation of 8 spaces but found 6 indent 80:1 error Expected indentation of 12 spaces but found 8 indent 81:1 error Expected indentation of 16 spaces but found 10 indent 82:1 error Expected indentation of 12 spaces but found 8 indent 83:1 error Expected indentation of 16 spaces but found 10 indent 84:1 error Expected indentation of 12 spaces but found 8 indent 85:1 error Expected indentation of 12 spaces but found 8 indent 86:1 error Expected indentation of 8 spaces but found 4 indent 87:1 error Expected indentation of 8 spaces but found 4 indent 88:1 error Expected indentation of 4 spaces but found 2 indent 90:1 error Expected indentation of 4 spaces but found 2 indent 91:1 error Expected indentation of 8 spaces but found 4 indent 92:1 error Expected indentation of 4 spaces but found 2 indent 94:1 error Expected indentation of 4 spaces but found 2 indent 97:1 error Expected indentation of 8 spaces but found 4 indent 98:1 error Expected indentation of 12 spaces but found 6 indent 99:1 error Expected indentation of 8 spaces but found 4 indent 101:1 error Expected indentation of 8 spaces but found 4 indent 102:1 error Expected indentation of 8 spaces but found 4 indent 103:1 error Expected indentation of 12 spaces but found 6 indent 104:1 error Expected indentation of 8 spaces but found 4 indent 106:1 error Expected indentation of 8 spaces but found 3 indent 110:1 error Expected indentation of 8 spaces but found 4 indent 111:1 error Expected indentation of 8 spaces but found 4 indent 112:1 error Expected indentation of 12 spaces but found 6 indent 113:1 error Expected indentation of 16 spaces but found 8 indent 114:1 error Expected indentation of 16 spaces but found 8 indent 115:1 error Expected indentation of 16 spaces but found 8 indent 116:1 error Expected indentation of 12 spaces but found 6 indent 117:1 error Expected indentation of 12 spaces but found 6 indent 118:1 error Expected indentation of 16 spaces but found 8 indent 119:1 error Expected indentation of 16 spaces but found 8 indent 120:1 error Expected indentation of 12 spaces but found 6 indent 121:1 error Expected indentation of 12 spaces but found 6 indent 122:1 error Expected indentation of 16 spaces but found 8 indent 123:1 error Expected indentation of 16 spaces but found 8 indent 124:1 error Expected indentation of 12 spaces but found 6 indent 125:1 error Expected indentation of 12 spaces but found 6 indent 126:1 error Expected indentation of 16 spaces but found 8 indent 127:1 error Expected indentation of 16 spaces but found 8 indent 128:1 error Expected indentation of 12 spaces but found 6 indent 129:1 error Expected indentation of 12 spaces but found 6 indent 130:1 error Expected indentation of 16 spaces but found 8 indent 131:1 error Expected indentation of 16 spaces but found 8 indent 132:1 error Expected indentation of 16 spaces but found 8 indent 133:1 error Expected indentation of 12 spaces but found 6 indent 134:1 error Expected indentation of 12 spaces but found 6 indent 135:1 error Expected indentation of 16 spaces but found 8 indent 136:1 error Expected indentation of 16 spaces but found 8 indent 137:1 error Expected indentation of 16 spaces but found 8 indent 138:1 error Expected indentation of 12 spaces but found 6 indent 139:1 error Expected indentation of 8 spaces but found 4 indent 140:1 error Expected indentation of 8 spaces but found 4 indent 141:1 error Expected indentation of 12 spaces but found 6 indent 142:1 error Expected indentation of 8 spaces but found 4 indent 144:1 error Expected indentation of 8 spaces but found 4 indent 145:1 error Expected indentation of 12 spaces but found 6 indent 146:1 error Expected indentation of 16 spaces but found 8 indent 147:1 error Expected indentation of 16 spaces but found 8 indent 148:1 error Expected indentation of 16 spaces but found 8 indent 149:1 error Expected indentation of 16 spaces but found 8 indent 150:1 error Expected indentation of 16 spaces but found 8 indent 151:1 error Expected indentation of 16 spaces but found 8 indent 152:1 error Expected indentation of 12 spaces but found 6 indent 153:1 error Expected indentation of 8 spaces but found 4 indent 154:1 error Expected indentation of 4 spaces but found 2 indent 158:1 error Expected indentation of 4 spaces but found 2 indent 159:1 error Expected indentation of 4 spaces but found 2 indent 163:1 error Expected indentation of 4 spaces but found 2 indent 163:3 error 'ReactDOM' is not defined no-undef 164:1 error Expected indentation of 8 spaces but found 4 indent 165:1 error Expected indentation of 12 spaces but found 6 indent 165:19 error 'loris' is not defined no-undef 166:1 error Expected indentation of 12 spaces but found 6 indent 166:22 error 'loris' is not defined no-undef 167:1 error Expected indentation of 8 spaces but found 4 indent 168:1 error Expected indentation of 8 spaces but found 4 indent 169:1 error Expected indentation of 4 spaces but found 2 indent ? 134 problems (134 errors, 0 warnings) 126 errors and 0 warnings potentially fixable with the `--fix` option. ERROR in ./modules/document_repository/jsx/docIndex.js Module build failed (from ./node_modules/babel-loader/lib/index.js): SyntaxError: Unexpected token (103:17) 101 | */ 102 | formatColumn(column, cell, row) { > 103 | let result = {cell}; | ^ 104 | switch (column) { 105 | case 'File Name': 106 | let downloadURL = loris.BaseURL + '/document_repository/Files/' + encodeURIComponent(row['File Name']); ERROR in ./modules/instrument_builder/jsx/react.instrument_builder.js Module build failed (from ./node_modules/babel-loader/lib/index.js): SyntaxError: Unexpected token (104:6) 102 | } 103 | return ( > 104 | | ^ 105 |
106 | ERROR in ./jsx/PaginationLinks.js Module build failed (from ./node_modules/babel-loader/lib/index.js): SyntaxError: Unexpected token (42:13) 40 | 41 | if (this.props.Total === 0) { > 42 | return
; | ^ 43 | } 44 | if (this.props.Total < this.props.RowsPerPage) { 45 | return
; ERROR in ./modules/conflict_resolver/jsx/resolvedConflictsIndex.js Module build failed (from ./node_modules/babel-loader/lib/index.js): SyntaxError: Unexpected token (43:13) 41 | 42 | if (column === 'Instrument') { > 43 | return {this.state.Data.form.instrument.options[row.Instrument]}; | ^ 44 | } 45 | 46 | if (column === 'Correct Answer') { ERROR in ./modules/dataquery/jsx/react.app.js Module build failed (from ./node_modules/babel-loader/lib/index.js): SyntaxError: Unexpected token (47:13) 45 | 46 | if (this.props.queriesLoaded === false) { > 47 | return
; | ^ 48 | } 49 | // Build the list for the user queries 50 | for (let i = 0; i < this.props.userQueries.length; i += 1) { ERROR in ./modules/candidate_list/jsx/onLoad.js Module build failed (from ./node_modules/babel-loader/lib/index.js): SyntaxError: Unexpected token (4:18) 2 | 3 | $(function() { > 4 | ReactDOM.render( 50 |
| ^ 51 | 51 | return ({cell}); | ^ 52 | } 53 | 54 | render() { ERROR in ./modules/imaging_browser/jsx/imagingBrowserIndex.js Module build failed (from ./node_modules/babel-loader/lib/index.js): SyntaxError: Unexpected token (51:17) 49 | // Set class to 'bg-danger' if file is hidden. 50 | const style = ''; > 51 | let result = {cell}; | ^ 52 | switch (column) { 53 | case 'New Data': 54 | if (cell === 'new') { ERROR in ./modules/publication/jsx/publicationIndex.js Module build failed (from ./node_modules/babel-loader/lib/index.js): SyntaxError: Unexpected token (51:8) 49 | if (!this.state.isLoaded) { 50 | return ( > 51 | ERROR in ./jsx/DynamicDataTable.js Module build failed (from ./node_modules/babel-loader/lib/index.js): SyntaxError: Unexpected token (77:10) 75 | if (this.state.error !== undefined) { 76 | return ( > 77 |
| ^ 78 | {this.state.error} 79 |
80 | ); ERROR in ./modules/publication/jsx/viewProjectIndex.js Module build failed (from ./node_modules/babel-loader/lib/index.js): SyntaxError: Unexpected token (7:4) 5 | $(function() { 6 | const viewProject = ( > 7 |
| ^ 8 |
9 |
10 | 80 |
  • | ^ 81 | 82 | {element.text} 83 | ERROR in ./jsx/Markdown.js Module build failed (from ./node_modules/babel-loader/lib/index.js): SyntaxError: Unexpected token (81:28) 79 | switch (hlevel) { 80 | case 6: > 81 | paragraphs[i] =
    {paragraphs[i]}
    ; | ^ 82 | break; 83 | 84 | case 5: ERROR in ./modules/candidate_list/jsx/openProfileForm.js Module build failed (from ./node_modules/babel-loader/lib/index.js): SyntaxError: Unexpected token (89:14) 87 | if (this.state.error.message !== '') { 88 | warning = ( > 89 |
    | ^ 90 | {this.state.error.message} 91 |
    92 | ); ERROR in ./modules/candidate_list/jsx/candidateListIndex.js Module build failed (from ./node_modules/babel-loader/lib/index.js): SyntaxError: Unexpected token (97:13) 95 | if (column === 'PSCID' && this.props.hasPermission('access_all_profiles')) { 96 | let url = this.props.baseURL + '/' + row['DCCID'] + '/'; > 97 | return     {cell}; | ^ 98 | } 99 | if (column === 'Feedback') { 100 | switch (cell) { ERROR in ./modules/genomic_browser/jsx/FileUploadModal.js Module build failed (from ./node_modules/babel-loader/lib/index.js): SyntaxError: Unexpected token (97:25) 95 | 96 | if (this.state.submited) { > 97 | footerButtons.push(); | ^ 98 | } else { 99 | if (this.state.readyForUpload) { 100 | footerButtons.push(); ERROR in ./modules/document_repository/jsx/editFormIndex.js Module build failed (from ./node_modules/babel-loader/lib/index.js): SyntaxError: Unexpected token (9:3) 7 | window.addEventListener('load', () => { 8 | ReactDOM.render( > 9 |
    | ^ 10 |
    11 |
    12 | 9 |
    | ^ 10 | References: Message-ID: Hi Yubu, I saw you error log, it is very helpful. It seems like you didn't create the config.xml in you project folder successfully. You need to run this [sudo ./install.sh ] in the tools folder. ex. [ install at install-dev:/var/www/Loris/tools$ sudo ./install.sh] Then check if project/confilg.xml file exists. if it can't create the project folder and config.xml, it is definitely your ubuntu permission issue. Please do it manually in your loris folder. sudo chgrp apache project sudo chmod 770 project Then you need to do [sudo ./install.sh ] , then load the installdb.php again. Please let me know if you have any questions. Regards. Shen On Tue, 13 Aug 2019 at 20:16, ??? wrote: > Dear Shen, > > > 1 Which version of Loris are you using? > We are using Loris-21.0.0 > > 2 Mysql version? > The output of mysql -V is > mysql Ver 14.14 Distrib 5.7.27, for Linux (x86_64) using EditLine wrapper > > 3 [sudo tail -f /var/log/apache2/loris-error.log] Please running this > in the backend, > then try loading the installdb.php again, with a different database > name. Please send us the error message. > > cat loris-error.log does not show any content however loris-error.log.1 > shows the following: > > yubu at data:/var/log/apache2$ cat loris-error.log.1 > > [Tue Aug 13 09:12:41.214417 2019] [php7:error] [pid 17930] [client > ::1:58960] PHP Fatal error: Uncaught ConfigurationException: Config file > config.xml does not exist in the defined locations. in > /var/www/loris/php/libraries/NDB_Config.class.inc:139\nStack trace:\n#0 > /var/www/loris/php/libraries/NDB_Config.class.inc(66): > NDB_Config->configFilePath()\n#1 > /var/www/loris/php/libraries/NDB_Factory.class.inc(118): > NDB_Config::singleton(NULL)\n#2 > /var/www/loris/php/libraries/NDB_Client.class.inc(54): > NDB_Factory->config(NULL)\n#3 /var/www/loris/htdocs/index.php(27): > NDB_Client->initialize()\n#4 {main}\n thrown in > /var/www/loris/php/libraries/NDB_Config.class.inc on line 139, referer: > http://localhost/installdb.php > > [Tue Aug 13 09:14:53.843582 2019] [php7:notice] [pid 17932] [client > ::1:58992] SQLSTATE[HY000] [1698] Access denied for user 'root'@'localhost', > referer: http://localhost/installdb.php > [Tue Aug 13 09:14:53.843708 2019] [php7:error] [pid 17932] [client > ::1:58992] PHP Fatal error: Uncaught Error: Call to a member function > exec() on null in > /var/www/loris/php/installer/Installer.class.inc:374\nStack trace:\n#0 > /var/www/loris/php/installer/Installer.class.inc(235): > LORIS\\Installer\\Installer->_sourceSchemaFile(Object(LORIS\\Installer\\Database), > '00-schema.sql')\n#1 /var/www/loris/htdocs/installdb.php(109): > LORIS\\Installer\\Installer->sourceSchema(Array)\n#2 {main}\n thrown in > /var/www/loris/php/installer/Installer.class.inc on line 374, referer: > http://localhost/installdb.php > > Further, we accidentally deleted the loris-error.log and loris-error.log.1 > files. Is there a way to generate them again? > > Thanks for the prompt reply > > Yours Sincerely, > > ====================================================== > > Yubu Lee, Ph.D. > > Research Professor, > > Center for Neuroscience Imaging Research, Institute for Basic Science > > > #86332, N Center, SungKyunKwan University > 2066, Seobu-Ro, Jangan-gu, Suwon, Gyeonggi-do, 16419, Korea > > E-mail: basilia1123 at gmail.com > > Tel: +82-31-299-4411 > > Fax: +82-31-299-4506 > > ====================================================== > > > 2019? 8? 13? (?) ?? 10:21, Shen Wang ?? ??: > >> Hi Yubu, >> We need more information to debug this issue. >> 1 Which version of Loris are you using? >> 2 Mysql version? >> 3 [sudo tail -f /var/log/apache2/loris-error.log] Please running this >> in the backend, >> then try loading the installdb.php again, with a different database >> name. Please send us the error message. >> >> Your Sincerely, >> Shen >> >> On Mon, 12 Aug 2019 at 22:27, ??? wrote: >> >>> Dear Sir/Madam, >>> >>> We are currently trying to install LORIS on Ubuntu 18.04 platform >>> following the steps from >>> https://github.com/aces/Loris/wiki/Installing-Loris-in-Depth >>> >>> 1. Following the above link, we installed the prerequisites mentioned >>> in >>> https://github.com/aces/Loris/wiki/Installing-Loris-in-Depth#getting-prerequisites, >>> which are all verified to be installed normally. >>> >>> 2. We ensured that mySQL credentials are set up properly (as pasted >>> below) >>> mysql> select host, user, authentication_string from user >>> -> ; >>> >>> +-----------+------------------+-------------------------------------------+ >>> | host | user | authentication_string >>> | >>> >>> +-----------+------------------+-------------------------------------------+ >>> | localhost | root | >>> | >>> | localhost | mysql.session | >>> *THISISNOTAVALIDPASSWORDTHATCANBEUSEDHERE | >>> | localhost | mysql.sys | >>> *THISISNOTAVALIDPASSWORDTHATCANBEUSEDHERE | >>> | localhost | debian-sys-maint | >>> *C9BF7C6E59BFF0FA879E6650D174264C9EE87F25 | >>> >>> +-----------+------------------+-------------------------------------------+ >>> 4 rows in set (0.00 sec) >>> >>> mysql> update user set authentication_string=password('yubu') where >>> user='root'; >>> Query OK, 1 row affected, 1 warning (0.00 sec) >>> Rows matched: 1 Changed: 1 Warnings: 1 >>> >>> mysql> flush privileges; >>> Query OK, 0 rows affected (0.01 sec) >>> >>> mysql> select host, user, authentication_string from user >>> -> ; >>> >>> +-----------+------------------+-------------------------------------------+ >>> | host | user | authentication_string >>> | >>> >>> +-----------+------------------+-------------------------------------------+ >>> | localhost | root | >>> *E311E16EECE7E8900098CFEB4103D5266A343F5F | >>> | localhost | mysql.session | >>> *THISISNOTAVALIDPASSWORDTHATCANBEUSEDHERE | >>> | localhost | mysql.sys | >>> *THISISNOTAVALIDPASSWORDTHATCANBEUSEDHERE | >>> | localhost | debian-sys-maint | >>> *C9BF7C6E59BFF0FA879E6650D174264C9EE87F25 | >>> >>> +-----------+------------------+-------------------------------------------+ >>> 4 rows in set (0.00 sec) >>> >>> 3. We then opened http://localhost/installdb.php and have gotten the >>> login page for LORIS installation and typed the credentials as follows: >>> [image: Screenshot from 2019-08-13 09-14-51.png] >>> 4. Once we submitted the page we obtained error as follows >>> >>> [image: Screenshot from 2019-08-13 09-14-56.png] >>> >>> >>> >>> We really do not know how to proceed further from this point onward. >>> Kindly let us know how to proceed further in order to get the LORIS >>> installed. >>> >>> Thank you. >>> >>> Your Sincerely, >>> >>> ====================================================== >>> >>> Yubu Lee, Ph.D. >>> >>> Research Professor, >>> >>> Center for Neuroscience Imaging Research, Institute for Basic Science >>> >>> >>> #86332, N Center, SungKyunKwan University >>> 2066, Seobu-Ro, Jangan-gu, Suwon, Gyeonggi-do, 16419, Korea >>> >>> E-mail: basilia1123 at gmail.com >>> >>> Tel: +82-31-299-4411 >>> >>> Fax: +82-31-299-4506 >>> >>> ====================================================== >>> _______________________________________________ >>> Loris-dev mailing list >>> Loris-dev at bic.mni.mcgill.ca >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>> >> >> >> -- >> Shen Wang >> Loris Developer >> Montreal Neurological Institute >> McGill University >> >> -- Shen Wang Loris Developer Montreal Neurological Institute McGill University -------------- next part -------------- An HTML attachment was scrubbed... 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Name: Screenshot from 2019-08-13 09-14-56.png Type: image/png Size: 124916 bytes Desc: not available URL: From wangshen.mcin at gmail.com Tue Aug 13 21:02:04 2019 From: wangshen.mcin at gmail.com (Shen Wang) Date: Tue, 13 Aug 2019 21:02:04 -0400 Subject: [Loris-dev] Upgrading to Loris 21 - new make file In-Reply-To: References: Message-ID: Hi Sotirios, step 1: sudo ./node_modules/.bin/eslint --fix /var/www/loris step 2: put the rest error files under this line [# Ignore until ESLint is run] in the .eslintignore file. step 3: sudo make On Tue, 13 Aug 2019 at 20:34, Sotirios Nikoloutsopoulos < sotirisnik at gmail.com> wrote: > I did the modifications, still there are errors. > Thanks > > > ???? ???, 14 ??? 2019 ???? 3:22 ?.?., ?/? Shen Wang < > wangshen.mcin at gmail.com> ??????: > >> Hi Sotirios, >> I saw your output file, the config issue is gone. >> you can use [sudo npm run lintfix:javascript ] to fix these indent >> issues. >> If it still has errors. >> Then try modify this file .eslintignore >> with this >> >> # Ignore until ESLint is run >> >> modules/* >> >> modules/dataquery/ >> >> node_modules/* >> >> htdocs/js/components/* >> >> jsx/* >> >> >> # Ignore external libs >> >> htdocs/js/flot/* >> >> htdocs/js/jquery/* >> >> htdocs/js/jszip/* >> >> htdocs/js/modernizr/* >> >> htdocs/js/modules/* >> >> htdocs/js/react/* >> >> htdocs/js/shims/* >> >> htdocs/js/c3.min.js >> >> htdocs/js/d3.min.js >> >> htdocs/js/FileSaver.min.js >> >> >> then do sudo make. >> It should work. >> Regards >> Shen >> >> >> Sotirios Nikoloutsopoulos ?2019?8?13? ????7:54??? >> >>> No, it didn't work, i also tried space/tabs because most of the errors >>> where about indentation, also there are some errors about React. >>> >>> Thanks >>> >>> lorisadmin at hbp:/var/www/loris$ sudo ./node_modules/.bin/eslint --init >>> ? How would you like to configure ESLint? Answer questions about your >>> style >>> ? Which version of ECMAScript do you use? ES2015 >>> ? Are you using ES6 modules? Yes >>> ? Where will your code run? Browser >>> ? Do you use CommonJS? Yes >>> ? Do you use JSX? Yes >>> ? Do you use React? Yes >>> ? What style of indentation do you use? Spaces >>> ? What quotes do you use for strings? Single >>> ? What line endings do you use? Unix >>> ? Do you require semicolons? Yes >>> ? What format do you want your config file to be in? JSON >>> The config that you've selected requires the following dependencies: >>> >>> eslint-plugin-react at latest >>> Successfully created .eslintrc.json file in /var/www/loris >>> >>> lorisadmin at hbp:/var/www/loris$ sudo make > sudo_make_output >>> npm WARN The package prop-types is included as both a dev and production >>> dependency. >>> npm WARN optional SKIPPING OPTIONAL DEPENDENCY: fsevents at 1.2.4 >>> (node_modules/fsevents): >>> npm WARN notsup SKIPPING OPTIONAL DEPENDENCY: Unsupported platform for >>> fsevents at 1.2.4: wanted {"os":"darwin","arch":"any"} (current: >>> {"os":"linux","arch":"x64"}) >>> >>> npm ERR! code ELIFECYCLE >>> npm ERR! errno 2 >>> npm ERR! loris at 1.0.0 compile: `webpack` >>> npm ERR! Exit status 2 >>> npm ERR! >>> npm ERR! Failed at the loris at 1.0.0 compile script. >>> npm ERR! This is probably not a problem with npm. There is likely >>> additional logging output above. >>> >>> npm ERR! A complete log of this run can be found in: >>> npm ERR! >>> /home/lorisadmin/.npm/_logs/2019-08-13T23_40_58_841Z-debug.log >>> >>> ???? ???, 14 ??? 2019 ???? 2:29 ?.?., ?/? Shen Wang < >>> wangshen.mcin at gmail.com> ??????: >>> >>>> Hi Sotirios, >>>> When you do make command, please make sure with sudo at the beginning. >>>> [sudo make] >>>> If it still doesn't work for you. >>>> Then try the solutions below. >>>> solution 1: >>>> [image: ???? 2019-08-13 19.21.15.png] >>>> Regards >>>> Shen >>>> >>>> >>>> >>>> >>>> On Tue, 13 Aug 2019 at 17:22, Sotirios Nikoloutsopoulos < >>>> sotirisnik at gmail.com> wrote: >>>> >>>>> I think that the files exists although i redownloaded the >>>>> eslintrc.json i checked others files that had similar errors. >>>>> >>>>> lorisadmin at hbp:/var/www/loris$ ls -l >>>>> ./node_modules/eslint-loader/index.js >>>>> -rw-rw-r-- 1 lorisadmin lorisadmin 6463 ??? 26 1985 >>>>> ./node_modules/eslint-loader/index.js >>>>> >>>>> lorisadmin at hbp:/var/www/loris$ ls -l .eslintrc.json >>>>> -rw-rw-r-- 1 lorisadmin lorisadmin 84530 ??? 14 00:04 .eslintrc.json >>>>> >>>>> Maybe this can help >>>>> >>>>> Module build failed (from ./node_modules/eslint-loader/index.js): >>>>> SyntaxError: Cannot read config file: /var/www/loris/.eslintrc.json >>>>> Error: Unexpected token < in JSON at position 6 >>>>> at JSON.parse () >>>>> at loadJSONConfigFile >>>>> (/var/www/loris/node_modules/eslint/lib/config/config-file.js:114:21) >>>>> at loadConfigFile >>>>> (/var/www/loris/node_modules/eslint/lib/config/config-file.js:230:26) >>>>> at loadFromDisk >>>>> (/var/www/loris/node_modules/eslint/lib/config/config-file.js:500:18) >>>>> at Object.load >>>>> (/var/www/loris/node_modules/eslint/lib/config/config-file.js:564:20) >>>>> at Config.getLocalConfigHierarchy >>>>> (/var/www/loris/node_modules/eslint/lib/config.js:227:44) >>>>> at Config.getConfigHierarchy >>>>> (/var/www/loris/node_modules/eslint/lib/config.js:179:43) >>>>> at Config.getConfigVector >>>>> (/var/www/loris/node_modules/eslint/lib/config.js:286:21) >>>>> at Config.getConfig >>>>> (/var/www/loris/node_modules/eslint/lib/config.js:329:29) >>>>> at processText >>>>> (/var/www/loris/node_modules/eslint/lib/cli-engine.js:162:33) >>>>> at CLIEngine.executeOnText >>>>> (/var/www/loris/node_modules/eslint/lib/cli-engine.js:596:17) >>>>> at lint >>>>> (/var/www/loris/node_modules/eslint-loader/index.js:237:17) >>>>> at Object.module.exports >>>>> (/var/www/loris/node_modules/eslint-loader/index.js:232:21) >>>>> >>>>> ERROR in ./modules/imaging_uploader/jsx/index.js >>>>> Module build failed (from ./node_modules/eslint-loader/index.js): >>>>> SyntaxError: Cannot read config file: /var/www/loris/.eslintrc.json >>>>> Error: Unexpected token < in JSON at position 6 >>>>> at JSON.parse () >>>>> at loadJSONConfigFile >>>>> (/var/www/loris/node_modules/eslint/lib/config/config-file.js:114:21) >>>>> at loadConfigFile >>>>> (/var/www/loris/node_modules/eslint/lib/config/config-file.js:230:26) >>>>> at loadFromDisk >>>>> (/var/www/loris/node_modules/eslint/lib/config/config-file.js:500:18) >>>>> at Object.load >>>>> (/var/www/loris/node_modules/eslint/lib/config/config-file.js:564:20) >>>>> at Config.getLocalConfigHierarchy >>>>> (/var/www/loris/node_modules/eslint/lib/config.js:227:44) >>>>> at Config.getConfigHierarchy >>>>> (/var/www/loris/node_modules/eslint/lib/config.js:179:43) >>>>> at Config.getConfigVector >>>>> (/var/www/loris/node_modules/eslint/lib/config.js:286:21) >>>>> at Config.getConfig >>>>> (/var/www/loris/node_modules/eslint/lib/config.js:329:29) >>>>> at processText >>>>> (/var/www/loris/node_modules/eslint/lib/cli-engine.js:162:33) >>>>> at CLIEngine.executeOnText >>>>> (/var/www/loris/node_modules/eslint/lib/cli-engine.js:596:17) >>>>> at lint >>>>> (/var/www/loris/node_modules/eslint-loader/index.js:237:17) >>>>> at Object.module.exports >>>>> (/var/www/loris/node_modules/eslint-loader/index.js:232:21) >>>>> >>>>> >>>>> >>>>> ???? ???, 13 ??? 2019 ???? 11:52 ?.?., ?/? John Saigle < >>>>> john.saigle at mcin.ca> ??????: >>>>> >>>>>> HI Sotirios, >>>>>> >>>>>> The make_output.txt file shows webpack failing because it can't find >>>>>> the ESLint config file. >>>>>> >>>>>> Can you confirm whether the file `.eslintrc.json` exists within your >>>>>> loris root directory (usually `/var/www/loris/`)? When I delete my file I >>>>>> get the same errors as you. >>>>>> >>>>>> If you find that it's missing, you can make a local copy with the >>>>>> contents found here: >>>>>> >>>>>> >>>>>> https://github.com/aces/Loris/blob/e26a6ad49a73fcffef0cd73bb600c4d17b200b62/.eslintrc.json >>>>>> >>>>>> Once you know it exists, try running `make` again. >>>>>> >>>>>> Let us know if that moves you forward. >>>>>> >>>>>> Best, >>>>>> John >>>>>> >>>>>> On Tue, Aug 13, 2019 at 2:21 PM Sotirios Nikoloutsopoulos < >>>>>> sotirisnik at gmail.com> wrote: >>>>>> >>>>>>> Hi, >>>>>>> I executed the commands for the node and now i am get the >>>>>>> followings: >>>>>>> >>>>>>> lorisadmin at hbp:/var/www/loris$ make > ~/make_output >>>>>>> npm WARN The package prop-types is included as both a dev and >>>>>>> production dependency. >>>>>>> npm WARN optional SKIPPING OPTIONAL DEPENDENCY: fsevents at 1.2.4 >>>>>>> (node_modules/fsevents): >>>>>>> npm WARN notsup SKIPPING OPTIONAL DEPENDENCY: Unsupported platform >>>>>>> for fsevents at 1.2.4: wanted {"os":"darwin","arch":"any"} (current: >>>>>>> {"os":"linux","arch":"x64"}) >>>>>>> >>>>>>> npm ERR! code ELIFECYCLE >>>>>>> npm ERR! errno 2 >>>>>>> npm ERR! loris at 1.0.0 compile: `webpack` >>>>>>> npm ERR! Exit status 2 >>>>>>> npm ERR! >>>>>>> npm ERR! Failed at the loris at 1.0.0 compile script. >>>>>>> npm ERR! This is probably not a problem with npm. There is likely >>>>>>> additional logging output above. >>>>>>> >>>>>>> npm ERR! A complete log of this run can be found in: >>>>>>> npm ERR! >>>>>>> /home/lorisadmin/.npm/_logs/2019-08-13T18_12_05_378Z-debug.log >>>>>>> make: *** [javascript] Error 2 >>>>>>> >>>>>>> Thanks, >>>>>>> Sotirios >>>>>>> >>>>>>> >>>>>>> ???? ???, 12 ??? 2019 ???? 10:19 ?.?., ?/? Christine Rogers, Ms. < >>>>>>> christine.rogers at mcgill.ca> ??????: >>>>>>> >>>>>>>> Hi Sotirios, >>>>>>>> >>>>>>>> We've seen some users installing LORIS 21 or upgrading to 21 whose >>>>>>>> version of node doesn't work well with webpack, due to updated packages >>>>>>>> they're missing. >>>>>>>> If so, update your node : >>>>>>>> >>>>>>>> curl -sL https://deb.nodesource.com/setup_8.x | sudo -E bash - >>>>>>>> sudo apt-get install -y nodejs >>>>>>>> >>>>>>>> Let us know how that goes -- please send us output from the same >>>>>>>> log if any issues. >>>>>>>> Best, >>>>>>>> Christine >>>>>>>> >>>>>>>> >>>>>>>> On Thu, Aug 8, 2019 at 2:38 PM Sotirios Nikoloutsopoulos < >>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>> >>>>>>>>> It's not a disk space issue, as you can see below i have still >>>>>>>>> 74GB available. >>>>>>>>> >>>>>>>>> lorisadmin at hbp:/var/www/loris$ df -h >>>>>>>>> Filesystem Size Used Avail Use% Mounted on >>>>>>>>> udev 2,9G 0 2,9G 0% /dev >>>>>>>>> tmpfs 597M 8,6M 588M 2% /run >>>>>>>>> /dev/sda1 98G 19G 74G 21% / >>>>>>>>> >>>>>>>>> Maybe we have to pass a flag to get into strict mode? as stated >>>>>>>>> "SyntaxError: Block-scoped declarations (let, const, function, class) not >>>>>>>>> yet supported outside strict mode" >>>>>>>>> >>>>>>>>> Thanks, >>>>>>>>> Sotirios >>>>>>>>> >>>>>>>>> ???? ???, 8 ??? 2019 ???? 4:32 ?.?., ?/? Dave MacFarlane < >>>>>>>>> dave.macfarlane at mcin.ca> ??????: >>>>>>>>> >>>>>>>>>> It looks like the javascript snippet shown in the error message >>>>>>>>>> when trying to compile the js is truncated. Have you run out of disk space? >>>>>>>>>> >>>>>>>>>> On Thu, Aug 8, 2019 at 8:37 AM Sotirios Nikoloutsopoulos < >>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>> >>>>>>>>>>> Hi, >>>>>>>>>>> >>>>>>>>>>> I runned make and also included the file it reports at the end. >>>>>>>>>>> >>>>>>>>>>> lorisadmin at hbp:/var/www/loris$ make >>>>>>>>>>> npm install >>>>>>>>>>> npm WARN optional Skipping failed optional dependency >>>>>>>>>>> /chokidar/fsevents: >>>>>>>>>>> npm WARN notsup Not compatible with your operating system or >>>>>>>>>>> architecture: fsevents at 1.2.9 >>>>>>>>>>> npm WARN optional Skipping failed optional dependency >>>>>>>>>>> /watchpack/chokidar/fsevents: >>>>>>>>>>> npm WARN notsup Not compatible with your operating system or >>>>>>>>>>> architecture: fsevents at 1.2.9 >>>>>>>>>>> npm run compile >>>>>>>>>>> >>>>>>>>>>> > loris at 1.0.0 compile /var/www/loris >>>>>>>>>>> > webpack >>>>>>>>>>> >>>>>>>>>>> /var/www/loris/node_modules/webpack/bin/webpack.js:86 >>>>>>>>>>> let notify = >>>>>>>>>>> ^^^ >>>>>>>>>>> >>>>>>>>>>> SyntaxError: Block-scoped declarations (let, const, function, >>>>>>>>>>> class) not yet supported outside strict mode >>>>>>>>>>> at exports.runInThisContext (vm.js:53:16) >>>>>>>>>>> at Module._compile (module.js:374:25) >>>>>>>>>>> at Object.Module._extensions..js (module.js:417:10) >>>>>>>>>>> at Module.load (module.js:344:32) >>>>>>>>>>> at Function.Module._load (module.js:301:12) >>>>>>>>>>> at Function.Module.runMain (module.js:442:10) >>>>>>>>>>> at startup (node.js:136:18) >>>>>>>>>>> at node.js:966:3 >>>>>>>>>>> >>>>>>>>>>> npm ERR! Linux 4.15.0-55-generic >>>>>>>>>>> npm ERR! argv "/usr/bin/nodejs" "/usr/bin/npm" "run" "compile" >>>>>>>>>>> npm ERR! node v4.2.6 >>>>>>>>>>> npm ERR! npm v3.5.2 >>>>>>>>>>> npm ERR! code ELIFECYCLE >>>>>>>>>>> npm ERR! loris at 1.0.0 compile: `webpack` >>>>>>>>>>> npm ERR! Exit status 1 >>>>>>>>>>> npm ERR! >>>>>>>>>>> npm ERR! Failed at the loris at 1.0.0 compile script 'webpack'. >>>>>>>>>>> npm ERR! Make sure you have the latest version of node.js and >>>>>>>>>>> npm installed. >>>>>>>>>>> npm ERR! If you do, this is most likely a problem with the loris >>>>>>>>>>> package, >>>>>>>>>>> npm ERR! not with npm itself. >>>>>>>>>>> npm ERR! Tell the author that this fails on your system: >>>>>>>>>>> npm ERR! webpack >>>>>>>>>>> npm ERR! You can get information on how to open an issue for >>>>>>>>>>> this project with: >>>>>>>>>>> npm ERR! npm bugs loris >>>>>>>>>>> npm ERR! Or if that isn't available, you can get their info via: >>>>>>>>>>> npm ERR! npm owner ls loris >>>>>>>>>>> npm ERR! There is likely additional logging output above. >>>>>>>>>>> >>>>>>>>>>> npm ERR! Please include the following file with any support >>>>>>>>>>> request: >>>>>>>>>>> npm ERR! /var/www/loris/npm-debug.log >>>>>>>>>>> Makefile:14: recipe for target 'javascript' failed >>>>>>>>>>> make: *** [javascript] Error 1 >>>>>>>>>>> >>>>>>>>>>> Thanks, >>>>>>>>>>> >>>>>>>>>>> Sotirios >>>>>>>>>>> >>>>>>>>>>> ???? ???, 7 ??? 2019 ???? 5:41 ?.?., ?/? Christine Rogers, Ms. < >>>>>>>>>>> christine.rogers at mcgill.ca> ??????: >>>>>>>>>>> >>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>> >>>>>>>>>>>> Thanks, have you tried all of these steps? >>>>>>>>>>>> - clear your browser cache (and refresh a few times) >>>>>>>>>>>> - delete any files in your smarty/templates_c directory (this >>>>>>>>>>>> will clear the template cache - do Not touch smarty/templates/) >>>>>>>>>>>> - run `make` (per the 21 release notes, this replaces the >>>>>>>>>>>> composer commands used in previous releases to update your dependencies) >>>>>>>>>>>> - restart apache (doesn't hurt) >>>>>>>>>>>> >>>>>>>>>>>> Let us know how it goes -- let us know what difference you see >>>>>>>>>>>> after, with your logs. A >>>>>>>>>>>> lso please send us your Config path settings (see these >>>>>>>>>>>> Troubleshooting Queries >>>>>>>>>>>> ) >>>>>>>>>>>> if you're still seeing front-end issues. >>>>>>>>>>>> >>>>>>>>>>>> Thanks, >>>>>>>>>>>> Christine >>>>>>>>>>>> >>>>>>>>>>>> On Wed, Aug 7, 2019 at 8:02 AM Sotirios Nikoloutsopoulos < >>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>> >>>>>>>>>>>>> Hi, >>>>>>>>>>>>> >>>>>>>>>>>>> lorisadmin at hbp:/var/www/loris$ sudo cat >>>>>>>>>>>>> /var/log/apache2/error.log >>>>>>>>>>>>> [Wed Aug 07 07:35:02.422501 2019] [mpm_prefork:notice] [pid >>>>>>>>>>>>> 1267] AH00163: Apache/2.4.18 (Ubuntu) OpenSSL/1.0.2g configured -- resuming >>>>>>>>>>>>> normal operations >>>>>>>>>>>>> [Wed Aug 07 07:35:02.422514 2019] [core:notice] [pid 1267] >>>>>>>>>>>>> AH00094: Command line: '/usr/sbin/apache2' >>>>>>>>>>>>> >>>>>>>>>>>>> And as for the access.log the content are empty >>>>>>>>>>>>> lorisadmin at hbp:/var/www/loris$ sudo ls -l >>>>>>>>>>>>> /var/log/apache2/access.log >>>>>>>>>>>>> lorisadmin at hbp:/var/www/loris$ sudo ls -l >>>>>>>>>>>>> /var/log/apache2/access.log >>>>>>>>>>>>> -rw-r----- 1 root adm 0 ???? 28 14:09 >>>>>>>>>>>>> /var/log/apache2/access.log >>>>>>>>>>>>> >>>>>>>>>>>>> Also i noticed a loris_access.log. >>>>>>>>>>>>> >>>>>>>>>>>>> The only non-blank pages are: >>>>>>>>>>>>> mri_violations, dataquery does not exist at all, statistics, >>>>>>>>>>>>> data_team_helper, genomic_browser, configuration and >>>>>>>>>>>>> server_processes_manager/ prints "Required configuration settings for >>>>>>>>>>>>> Server Processes Manager are missing. Cannot continue." >>>>>>>>>>>>> >>>>>>>>>>>>> Thanks, >>>>>>>>>>>>> Sotirios >>>>>>>>>>>>> >>>>>>>>>>>>> ???? ???, 6 ??? 2019 ???? 10:13 ?.?., ?/? Christine Rogers, >>>>>>>>>>>>> Ms. ??????: >>>>>>>>>>>>> >>>>>>>>>>>>>> Hi Sotirios and LORIS community -- >>>>>>>>>>>>>> >>>>>>>>>>>>>> When upgrading to brand-new release 21 -- just a reminder to >>>>>>>>>>>>>> follow the release notes and run the new *make* file to >>>>>>>>>>>>>> update your dependencies (instead of using *composer* >>>>>>>>>>>>>> commands). >>>>>>>>>>>>>> We've also updated the Wiki page >>>>>>>>>>>>>> to >>>>>>>>>>>>>> clarify that the release notes for each version will tell you what to run. >>>>>>>>>>>>>> >>>>>>>>>>>>>> If your current version is not the last release (20.3), it's >>>>>>>>>>>>>> still important to upgrade to each minor release increment (e.g. 20.2, >>>>>>>>>>>>>> 20.3) before making the leap to 21.0. >>>>>>>>>>>>>> >>>>>>>>>>>>>> If you're getting blank pages, post-upgrade -- Try clearing >>>>>>>>>>>>>> your cache. >>>>>>>>>>>>>> >>>>>>>>>>>>>> Got questions or feedback e.g. on the Release Notes? please >>>>>>>>>>>>>> don't hesitate to let us know. >>>>>>>>>>>>>> Thanks, >>>>>>>>>>>>>> Christine >>>>>>>>>>>>>> The LORIS team >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> On Tue, Aug 6, 2019 at 10:09 AM Christine Rogers, Ms. < >>>>>>>>>>>>>> christine.rogers at mcgill.ca> wrote: >>>>>>>>>>>>>> >>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>> Could you also let us know -- on which pages is content >>>>>>>>>>>>>>> visible, and on which pages/modules is content not visible for you? >>>>>>>>>>>>>>> Thanks, >>>>>>>>>>>>>>> Christine >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> On Tue, Aug 6, 2019 at 9:54 AM Christine Rogers, Ms. < >>>>>>>>>>>>>>> christine.rogers at mcgill.ca> wrote: >>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Thanks Sotirios, >>>>>>>>>>>>>>>> That's good to know. It sounds like you've checked that >>>>>>>>>>>>>>>> your /var/www/loris/project/config.xml file get populated properly. >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Please send us the last few errors you're seeing in your >>>>>>>>>>>>>>>> apache error log file, and your config paths and we can see what's >>>>>>>>>>>>>>>> happening with your front end -- >>>>>>>>>>>>>>>> Run these Troubleshooting Queries >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> to get your config path settings, given your front end is not displaying >>>>>>>>>>>>>>>> fully. >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> The Loris-MRI repo >>>>>>>>>>>>>>>> 21 >>>>>>>>>>>>>>>> install/upgrade would then be your next steps. >>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>> Christine >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> On Tue, Aug 6, 2019 at 7:53 AM Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> I am using a VM. What i did was: >>>>>>>>>>>>>>>>> 1) Download the files from https://github.com/aces/Loris >>>>>>>>>>>>>>>>> and replace them to my existing /vaw/www/loris folder. >>>>>>>>>>>>>>>>> 2) Execute the composer install --no-dev and then composer >>>>>>>>>>>>>>>>> dump-autoload as mentioned here >>>>>>>>>>>>>>>>> https://github.com/aces/Loris/wiki/Updating-your-LORIS. >>>>>>>>>>>>>>>>> 3) Execute install.sh from /var/www/loris/tools and >>>>>>>>>>>>>>>>> because LORIS already existed i moved a .config file, then re-executed the >>>>>>>>>>>>>>>>> install.sh successfully >>>>>>>>>>>>>>>>> 4 ) As for the database, i dropped the schema and i >>>>>>>>>>>>>>>>> executed the installdb.php >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> ???? ???, 5 ??? 2019 ???? 5:22 ?.?., ?/? Christine Rogers, >>>>>>>>>>>>>>>>> Ms. ??????: >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Hi Sotorios, >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Thanks - when you re-installed did you start on a fresh >>>>>>>>>>>>>>>>>> root path / VM or might some of your old system setting still apply? >>>>>>>>>>>>>>>>>> (And if you did any steps similar to an upgrade, did you >>>>>>>>>>>>>>>>>> follow the Upgrade steps in the Release Notes, from both repos?) >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> About the TR_range column - it was recently split (MRI >>>>>>>>>>>>>>>>>> pr339 ) split >>>>>>>>>>>>>>>>>> into TR_min and _max columns. Given the code was trying to query TR_range >>>>>>>>>>>>>>>>>> which does not exist in your mri_protocol table, double-check which version >>>>>>>>>>>>>>>>>> of the Loris repo (tables) and the Loris-MRI repo (code) you have installed >>>>>>>>>>>>>>>>>> to ensure they match. >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Christine >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> On Mon, Aug 5, 2019 at 9:06 AM Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> I reinstalled LORIS to 21 version and now the content is >>>>>>>>>>>>>>>>>>> not visible at all at most pages. >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> ???? ???, 5 ??? 2019 ???? 3:19 ?.?., ?/? Sotirios >>>>>>>>>>>>>>>>>>> Nikoloutsopoulos ??????: >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Is it easy to upgrade to Loris 21? Also the following >>>>>>>>>>>>>>>>>>>> fails because the line 1985 of NeuroDB/MRIProcessingUtility.pm query >>>>>>>>>>>>>>>>>>>> mri_protocol which doesn't have TR_range >>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris/blob/21.0-release/SQL/0000-00-00-schema.sql#L556 >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> lorisadmin at hbp:/data/loris/bin/mri$ >>>>>>>>>>>>>>>>>>>> ./batch_uploads_imageuploader -profile prod < ~/Desktop/input.txt > log.txt >>>>>>>>>>>>>>>>>>>> Use of uninitialized value $_ in pattern match (m//) at >>>>>>>>>>>>>>>>>>>> ./batch_uploads_imageuploader line 147. >>>>>>>>>>>>>>>>>>>> base is DCC0000_258024_V1 >>>>>>>>>>>>>>>>>>>> path is /data/incoming/ >>>>>>>>>>>>>>>>>>>> type is .tar.gz >>>>>>>>>>>>>>>>>>>> fullpath is /data/incoming/DCC0000_258024_V1.tar.gz >>>>>>>>>>>>>>>>>>>> DBD::mysql::st execute failed: Unknown column >>>>>>>>>>>>>>>>>>>> 'TR_range' in 'where clause' at >>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line 1985. >>>>>>>>>>>>>>>>>>>> DBD::mysql::st fetchrow_array failed: fetch() without >>>>>>>>>>>>>>>>>>>> execute() at >>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line 1986. >>>>>>>>>>>>>>>>>>>> Use of uninitialized value $count_mri_protocol in >>>>>>>>>>>>>>>>>>>> numeric gt (>) at >>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line 1995. >>>>>>>>>>>>>>>>>>>> DBD::mysql::st execute failed: Unknown column >>>>>>>>>>>>>>>>>>>> 'TR_range' in 'field list' at >>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 562. >>>>>>>>>>>>>>>>>>>> Can't exec "mail": No such file or directory at >>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 721. >>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 722. >>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 723. >>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 724. >>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 725. >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> No Mincs inserted >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Thanks, >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> ???? ???, 3 ??? 2019 ???? 1:08 ?.?., ?/? Christine >>>>>>>>>>>>>>>>>>>> Rogers, Ms. ??????: >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> First, just a note: we've released LORIS 21 this week >>>>>>>>>>>>>>>>>>>>> with some major new features and cleanup -- especially if you are early in >>>>>>>>>>>>>>>>>>>>> your setup phase, check out the Release notes for both the >>>>>>>>>>>>>>>>>>>>> LORIS >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> and Loris-MRI >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> repos. >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> Thanks for your screenshots -- your empty mri_protocol >>>>>>>>>>>>>>>>>>>>> table should be at the root of these issues : >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> The mri_protocol table must be populated >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> in order for your scans to be registered in LORIS -- it serves as a >>>>>>>>>>>>>>>>>>>>> whitelist for the insertion pipeline which filters out scans that aren't >>>>>>>>>>>>>>>>>>>>> identified or matched to scan types in this table. >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> By default, this table is populated with entries for >>>>>>>>>>>>>>>>>>>>> t1, t2, fMRI and DTI (Insert statements for 21 >>>>>>>>>>>>>>>>>>>>> release branch are here >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> ) >>>>>>>>>>>>>>>>>>>>> Feel free to restore our default records and broaden >>>>>>>>>>>>>>>>>>>>> their parameters to match all your scan types. >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> re Defaced, native, selected -- these filter the scans >>>>>>>>>>>>>>>>>>>>> displayed as you move to the next page (View Session), instead of viewing >>>>>>>>>>>>>>>>>>>>> "all types" of scans from a given session : >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> - "defaced" means that a defacing script >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> has masked the subject's face in the volume (for patient privacy) >>>>>>>>>>>>>>>>>>>>> - "native" means that no pre-processing has been >>>>>>>>>>>>>>>>>>>>> performed on the scan (it's raw data), >>>>>>>>>>>>>>>>>>>>> - "selected" will show only volumes that have >>>>>>>>>>>>>>>>>>>>> been QC'd and "selected" as the best of their type -- used to display only >>>>>>>>>>>>>>>>>>>>> the best quality T1 image instead of all T1s acquired in a session, e.g. >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> re QC Comments -- >>>>>>>>>>>>>>>>>>>>> Once you have successfully loaded scans (matched to >>>>>>>>>>>>>>>>>>>>> the mri_protocol table), you'll be able to use the Imaging Browser's View >>>>>>>>>>>>>>>>>>>>> Session subpage to enter/view QC comments on each volume, or for each >>>>>>>>>>>>>>>>>>>>> visit. >>>>>>>>>>>>>>>>>>>>> These are stored directly in the database, and linked >>>>>>>>>>>>>>>>>>>>> to each scan. (Table name: feedback_mri_comments) >>>>>>>>>>>>>>>>>>>>> (Visit-level QC comments are linked to the session.) >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> For a walkthrough of the Imaging setup - please see the Imaging >>>>>>>>>>>>>>>>>>>>> Setup guide >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> - >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> An old LORIS walkthrough video >>>>>>>>>>>>>>>>>>>>> can >>>>>>>>>>>>>>>>>>>>> also walk you through some of the Imaging front-end features, starting at >>>>>>>>>>>>>>>>>>>>> 8:00 >>>>>>>>>>>>>>>>>>>>> LORIS' imaging modules have been updated many times >>>>>>>>>>>>>>>>>>>>> since this video, but the functionality and workflow is similar. >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> Let us know how it goes once you have entries in your >>>>>>>>>>>>>>>>>>>>> mri_protocol table - >>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>> Christine >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> On Fri, Aug 2, 2019 at 7:58 AM Sotirios >>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos wrote: >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> Hi Christine, >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> In the candidate_list page i can see this patient >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> If i press the link under PSCID i get to see >>>>>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> and if i press the link under Scan Done it redirects >>>>>>>>>>>>>>>>>>>>>> me to imaging_browser >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> At the mri_violations page i also see No results ( >>>>>>>>>>>>>>>>>>>>>> neither on resolved / not resolved ). >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> At the imaging_uploader i can see the record that >>>>>>>>>>>>>>>>>>>>>> failed. >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> If i click on the tarchive info i get to see the >>>>>>>>>>>>>>>>>>>>>> Protocol Name which i think is the acquisition we wanted? >>>>>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> Also my mri_protocol table is empty. >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> Furthermore i would like to ask about the defaced, >>>>>>>>>>>>>>>>>>>>>> native, selected. What exactly is native and selected? And where are the qc >>>>>>>>>>>>>>>>>>>>>> comments stored? >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> Finally a walkthrough would be helpful. >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> Thanks, >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> ???? ???, 30 ???? 2019 ???? 8:29 ?.?., ?/? Christine >>>>>>>>>>>>>>>>>>>>>> Rogers, Ms. ??????: >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>> Glad to hear you're making progress with the visit >>>>>>>>>>>>>>>>>>>>>>> labels. To follow up on your last few emails: >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> a- The Wiki's Setup Guide contains Sample insert >>>>>>>>>>>>>>>>>>>>>>> statements for the Visit Windows table >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> . >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> As Cecile mentioned, the consistency of visit label >>>>>>>>>>>>>>>>>>>>>>> format is important: V01, v01, V1, 01 -- whichever you select to use is >>>>>>>>>>>>>>>>>>>>>>> fine; we use V01 by default across all documentation. >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> b- For Password reset, there is a script in the >>>>>>>>>>>>>>>>>>>>>>> tools/ directory so that a back-end administrator can reset any front-end >>>>>>>>>>>>>>>>>>>>>>> user password, including Admin. (See info on setting up / resetting User >>>>>>>>>>>>>>>>>>>>>>> passwords in the Wiki's Setup Guide >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> ) >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> c- The minc file not being registered -- due to >>>>>>>>>>>>>>>>>>>>>>> AcquisitionProtocol unknown. >>>>>>>>>>>>>>>>>>>>>>> This means the SeriesDescription (Acquisition >>>>>>>>>>>>>>>>>>>>>>> Protocol) in you Dicom header was not matched to any scan listed in the >>>>>>>>>>>>>>>>>>>>>>> mri_protocol database table. >>>>>>>>>>>>>>>>>>>>>>> (In the online Loris-MRI Troubleshooting Guide, >>>>>>>>>>>>>>>>>>>>>>> this >>>>>>>>>>>>>>>>>>>>>>> is Table 3, 2nd-last item "no MINCs inserted"). >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> The MRI Violations module (Readme here) >>>>>>>>>>>>>>>>>>>>>>> will show >>>>>>>>>>>>>>>>>>>>>>> you the details of this mismatch -- >>>>>>>>>>>>>>>>>>>>>>> Go to the module (under the Imaging menu), find your >>>>>>>>>>>>>>>>>>>>>>> scan and click the link "Could not identify scan type" -- in the next >>>>>>>>>>>>>>>>>>>>>>> subpage you can compare the scan's actual parameters against the >>>>>>>>>>>>>>>>>>>>>>> mri_protocol table. >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> To resolve this, adjust your mri_protocol table >>>>>>>>>>>>>>>>>>>>>>> values or perhaps ensure your DICOMs are labelled consistently. >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> Let us know if this works for you -- we can also >>>>>>>>>>>>>>>>>>>>>>> walk you through an example of non-identified scans on >>>>>>>>>>>>>>>>>>>>>>> Demo.loris.ca (MRI Violations module). >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>> Christine >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> The LORIS team >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> On Tue, Jul 30, 2019 at 10:47 AM Sotirios >>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos wrote: >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> I hope this is sufficient as the error for the >>>>>>>>>>>>>>>>>>>>>>>> visit label disappeared. >>>>>>>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> Please see the attached file. Also something i >>>>>>>>>>>>>>>>>>>>>>>> found. >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> lorisadmin at hbp:/data/loris/bin/mri$ cat >>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data//logs/TarLoad-17-39-xubBdv.log >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> ==> Loading file from disk >>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-17-39-UyQcG2/dcc0000_258024_v1_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> --> mapping DICOM parameter for >>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-17-39-UyQcG2/dcc0000_258024_v1_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> ==> computing md5 hash for MINC body. >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> --> md5: 6b1202fd63e29de4c9be1cd9925888a5 >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> ==> verifying acquisition protocol >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> Acquisition protocol is unknown >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> --> The minc file cannot be registered since the >>>>>>>>>>>>>>>>>>>>>>>> AcquisitionProtocol is unknown >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 30 ???? 2019 ???? 4:58 ?.?., ?/? Sotirios >>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos ??????: >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> Ok I fixed the login problem by using a known hash >>>>>>>>>>>>>>>>>>>>>>>>> and by deleting the rows from the login_history i was able to login. >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 30 ???? 2019 ???? 4:50 ?.?., ?/? >>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos >>>>>>>>>>>>>>>>>>>>>>>>> ??????: >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> there was no visit label 01 in the Visit_Windows >>>>>>>>>>>>>>>>>>>>>>>>>> table and i don't know how to insert it because the record requires lots of >>>>>>>>>>>>>>>>>>>>>>>>>> attributes. Also the system for a reason asked me to update my password and >>>>>>>>>>>>>>>>>>>>>>>>>> now i don't remember it and my account got suspended. Is there a way to >>>>>>>>>>>>>>>>>>>>>>>>>> reset it or set a simple password? I updated the password hash in the >>>>>>>>>>>>>>>>>>>>>>>>>> users table by using the hash from another LORIS setup we had and i still >>>>>>>>>>>>>>>>>>>>>>>>>> couldn't login ( also the attribute password is always NULL and the >>>>>>>>>>>>>>>>>>>>>>>>>> expiration date is 1999-01-01 for some reason ). >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> Thanks >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 29 ???? 2019 ???? 5:21 ?.?., ?/? Cecile >>>>>>>>>>>>>>>>>>>>>>>>>> Madjar ??????: >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> Can you try adding the visit label v01 to the >>>>>>>>>>>>>>>>>>>>>>>>>>> Visit_Windows table? >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> However, I noticed that in a previous dataset, >>>>>>>>>>>>>>>>>>>>>>>>>>> the label was V1. Does that refer to the same visit? If so, you might want >>>>>>>>>>>>>>>>>>>>>>>>>>> to harmonize the visit labels so they are all the same across datasets for >>>>>>>>>>>>>>>>>>>>>>>>>>> a given timepoint, meaning you will need to relabel scans when the visit >>>>>>>>>>>>>>>>>>>>>>>>>>> label is different but referring to the same visit label (v01 = V1 etc...). >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helps, >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> On Mon, Jul 29, 2019 at 10:15 AM Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos wrote: >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> Could you help me with the "Visit label does >>>>>>>>>>>>>>>>>>>>>>>>>>>> not exist"? I had changed $subjectID{'createVisitLabel'} to 1 as you had >>>>>>>>>>>>>>>>>>>>>>>>>>>> suggested but it appears that this problem hasn't been resolved yet. >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> lorisadmin at hbp:/data/loris/bin/mri$ cat >>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data//logs/TarLoad-14-58-9Xog7H.log >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> ==> Loading file from disk >>>>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> --> mapping DICOM parameter for >>>>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> --> using user-defined filterParameters for >>>>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> Candidate Mismatch Error is Visit label does >>>>>>>>>>>>>>>>>>>>>>>>>>>> not exist >>>>>>>>>>>>>>>>>>>>>>>>>>>> -> WARNING: This candidate was invalid. >>>>>>>>>>>>>>>>>>>>>>>>>>>> Logging to >>>>>>>>>>>>>>>>>>>>>>>>>>>> MRICandidateErrors table with >>>>>>>>>>>>>>>>>>>>>>>>>>>> reason Visit label does not exist >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 26 ???? 2019 ???? 3:02 ?.?., ?/? >>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos >>>>>>>>>>>>>>>>>>>>>>>>>>>> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Cecile, >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> The Center error was fixed. Still the >>>>>>>>>>>>>>>>>>>>>>>>>>>>> insertion of mincs fails. Please see the output.txt file i attached. Also >>>>>>>>>>>>>>>>>>>>>>>>>>>>> is there something else i need to change at the paths configuration? >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 25 ???? 2019 ???? 6:55 ?.?., ?/? >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Cecile Madjar ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> We are making progress! >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I have a feeling this error comes from the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> fact that your psc table does not have the MRI_alias populated for the DCC >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> site. Running the following query in the mysql database should fix this: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> UPDATE psc SET MRI_alias="DCC", Alias="DCC" >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> WHERE Name="Data Coordinating Center"; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Repeat the same with all your sites (make >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sure to change the Aliases between sites, they should all be unique). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Let me know how it goes! >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> On Thu, Jul 25, 2019 at 11:43 AM Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> wrote: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Dear Cecile, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> You were right about your guesses. I did the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> modifications you suggested, i still get the "no mincs inserted" error, now >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> i am getting the "No center found this candidate" error ( how do i fix >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> that? from what i see the .dcm files contains a 'Institution Name', is that >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the center? ), so i guess that's why the validation fails, but i changed >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the force variable of tarchiveLoader to 1, shouldn't it have inserted the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> mincs then? Also it is optional to have a mail server, right? ( from what i >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> see the mail error does not affect the $valid_study, so i assume we are >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> okay with that ) >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you a lot, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 25 ???? 2019 ???? 5:48 ?.?., ?/? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Cecile Madjar >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> From what I understand, I believe you just >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> need to update a few config settings from the frontend in the Config module >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> (under the Admin menu). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [image: Screen Shot 2019-07-25 at 10.31.35 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> AM.png] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Then go to the Paths section of the config >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> module and update the "LORIS-MRI code" config setting to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri (my guess is that currently, it is set to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data) and click on the submit button. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [image: Screen Shot 2019-07-25 at 10.32.50 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> AM.png] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Then, go to Imaging Pipeline section of the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Configuration module and update the "Loris-MRI Data Directory" to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/ (my guess is that it is empty at the moment in your >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> database which is why $data_dir is not defined when you run the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> tarchiveLoader step of the insertion pipeline). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [image: Screen Shot 2019-07-25 at 10.40.52 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> AM.png] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Finally, I took a look at your environment >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> file and it might be a good idea to update your PERL5LIB variable to the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> following (it has been added to the code a few releases ago as we realized >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> this was needed for the libraries. Not sure which version of LORIS-MRI you >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> are using but it does not hurt to update this variable to what I suggest >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> below): >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> export >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PERL5LIB=/data/loris/bin/mri/uploadNeuroDB:/data/loris/bin/mri/dicom-archive:$PERL5LIB >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helps. Sorry you are experiencing >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> so much trouble setting things up. We probably need to update our WIKI. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> On Thu, Jul 25, 2019 at 9:48 AM Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> wrote: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The "Loris-MRI Data Directory" should be >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in the environment file? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 25 ???? 2019 ???? 12:59 ?.?., >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ?/? Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The scripts are located in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/. Somewhere I might have messed something up but i >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> remember following the instructions in the wiki.For example when i tried to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> execute the batch_uploads_imageuploader perl script the line >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> my $command = "$bin_dir/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl " >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> was pointing to an invalid path, for >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> example: it was repeating a pattern and had LORIS instead of loris ( i >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> think the mistake was that in the wiki it suggested to use $PROJECT for >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the name of the folder and i choosed 'loris' >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris/wiki/Imaging-Database >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ). See also the in image for the modification i did. Also i didn't find the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> section to config the $data_dir variable. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 24 ???? 2019 ???? 6:05 ?.?., >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ?/? Cecile Madjar >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> It looks like you have one Config >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> setting not set (based on the first error message you got when running it >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the first time). You need to set a value for "Loris-MRI Data Directory" in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the Config module under the Imaging pipeline section (from what I can see, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> it would be /data/loris/data/ for your setup). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The reason you got that error message >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the second time is that the pipeline checks if the DICOM study was already >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> inserted in the tarchive table. Since you ran the study once already, the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> study is inserted into the tarchive, hence the message. However, the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> pipeline did not complete as the MINC files were not created and inserted >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> into the files/parameter_file table. In order to continue the insertion, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> you will then need to run the tarchiveLoader command suggested in the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> terminal during the second run: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -globLocation -profile prod >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive//2012/DCM_2012-12-05_ImagingUpload-17-43-ZUEFjb.tar >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -verbose >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Finally, I am a bit confused by your >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> setup. Where are the scripts located? In /data/loris/bin/mri or >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data? It feels like the Config setting "LORIS-MRI code" in the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Paths section was set to "/data/LORIS/data" but it should have been set to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the directory where the scripts are located (most probably >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helps, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> On Wed, Jul 24, 2019 at 10:55 AM >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Ok first i execute this command: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> "lorisadmin at hbp:/data/loris/bin/mri$ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ./batch_uploads_imageuploader -profile prod < ~/Desktop/input.txt > log.txt >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at ./batch_uploads_imageuploader line 143. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at ./batch_uploads_imageuploader line 143. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $_ in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> pattern match (m//) at ./batch_uploads_imageuploader line 147. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> base is DCC0000_258024_V01 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> path is /data/incoming/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> type is .tar.gz >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> fullpath is >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/incoming/DCC0000_258024_V01.tar.gz >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> source /tmp/ImagingUpload-17-43-ZUEFjb >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> targetlocation /data/loris/data/tarchive >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 256. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 284. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at /data/loris/bin/mri/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> tarchive_validation.pl line 219. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at /data/loris/bin/mri/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl line 270. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 711. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Can't exec "mail": No such file or >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> directory at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 721. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 722. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 723. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 724. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 724. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 725. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 735. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> No Mincs inserted >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The tarchiveLoader insertion script has >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> failed. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Running now the following command: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl -profile prod >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -upload_id 3 /data/incoming/DCC0000_258024_V01.tar.gz -verbose" >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I inserted the VisitLabel, but still >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the Mincs are not inserted and i am getting this error >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> "lorisadmin at hbp:/data/loris/bin/mri$ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl -profile prod >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -upload_id 3 /data/incoming/DCC0000_258024_V01.tar.gz -verbose >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> find -path >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> \/tmp\/ImagingUpload\-17\-45\-5MsWEd -name '__MACOSX' -delete >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Spool message is: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The Scan for the uploadID 3 has already >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> been run with tarchiveID: 7. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> To continue with the rest of the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> insertion pipeline, please run tarchiveLoader from a terminal as follows: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader -globLocation -profile prod >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive//2012/DCM_2012-12-05_ImagingUpload-17-43-ZUEFjb.tar >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -verbose" >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Which files should i delete? I thought >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> that deleting the files from the tarchive was enough. And i executed the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> last proposed command to continue to rest of the insertion pipeline ( check >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the image ). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 24 ???? 2019 ???? 5:05 ?.?., >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ?/? Cecile Madjar < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> cecile.madjar at mcin.ca> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sorry I was not clear before. Every >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visits of candidates are created in the session table with one entry per >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID/VisitLabel. So if the imaging pipeline created visits in the session >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> table (that are not attached to instruments) and you want to clean your >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> database completely, you can delete entries in that table as well. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Regarding your point 2, the imaging >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> pipeline can create the visit in the session table as long as the visit >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> label is present in the Visit_Windows table (which means the visit label >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> stored in the PatientName is a valid visit label). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> However, in your prod file, if the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> variable $subjectID{'createVisitLabel'} is set to 1 for candidates, the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit label should be created in the Visit_Windows table I believe. Here >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> is the line of the prod file you would need to change >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> . >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> In general, we prefer populating the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Visit_Windows table and set the $subjectID{'createVisitLabel'} to 0 for >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> candidate data to avoid insertion of badly labelled MRI data that are >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> complex to relabel. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Finally, regarding the candidate >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> creation, if you execute the following steps, the pipeline should be able >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> to create candidates: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - set in the Imaging Pipeline section >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> of the config module the config setting "Upload creation of candidates" to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Yes >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - manually transfer the scans to the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> LORIS server instead of uploading it via the imaging browser >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - run batch_imaging_upload.pl as you >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> did until now. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helps! >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> On Wed, Jul 24, 2019 at 8:47 AM >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> About my second question i replaced >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the name of the patient in the .dcm files and now i am getting an error >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> that the visit label does not exist. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I thought it was supposed to be >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> automatically created. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> "Done adding archive info into >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> database >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -globLocation -profile prod >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive//DCM_2012-12-05_ImagingUpload-15-42-yUwQQV.tar >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -verbose >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> md5sum >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive/DCM_2012-12-05_ImagingUpload-15-42-yUwQQV.tar >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> candidate id 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> => No Visit labelVisit label does not >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> exist >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Set centerID = 1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Number of MINC files that will be >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> considered for inserting into the database: 1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> log dir is /logs and log file is >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /logs/TarLoad-15-42-L6pocU.log >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> candidate id 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> => No Visit label >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Cleaning up temp files: rm -rf >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-15-42-J2rQms/ImagingUpload-15-42-yUwQQV*" >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 24 ???? 2019 ???? 3:38 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ?.?., ?/? Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 1) What are the records in the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> session table? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 2) I tried to upload a non-phantom >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> file like this >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> input_file.txt: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/incoming/DCC0000_258024_V1.tar.gz >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> N DCC0000_258024_V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Terminal: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ./batch_uploads_imageuploader >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -profile prod < ~/Desktop/input.txt > log.txt >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and i get the following error in the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> log.txt file >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> "Running now the following command: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl -profile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> prod -upload_id 7 /data/incoming/DCC0000_258024_V1.tar.gz -verbose >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> find -path >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> \/tmp\/ImagingUpload\-14\-56\-FeLCB4 -name '__MACOSX' -delete >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Spool message is: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The PatientName read from the DICOM >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> header does not start with DCC0000_258024_V1 from the mri_upload table >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> " >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and the spool message is repeated >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> for each .dcm file. Should i preprocess every .dcm file and change the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PatientName to "DCC0000_258024_V1"? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 3) As far as it concerns the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> candidate profile i have to create a new one each time before i try to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> upload a file? Is there already a way to create a candidate profile and get >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the DCCID and PSCID without the user interface? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 18 ???? 2019 ???? 5:00 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ?.?., ?/? Cecile Madjar < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> cecile.madjar at mcin.ca> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> See answers to your questions below. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> About the 1st case we had a dicom >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> with a blank studyUID, maybe someone accidentally removed it. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> That is strange. Something must >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> have been done to the DICOM files. I have never seen a study with no >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> StudyUID out of the scanner. Usually, you need to manually erase it with >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> some tool. However, DICOMs never cease to surprise me... >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Some other questions: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 1) What are the steps to remove >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> all of my patients and uploads?: because i want to try to reupload all the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> testing dicoms we had with a clean database. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Release 21.0 of LORIS-MRI will >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> offer a script to remove all the entries and files specific to an upload. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> However, this release is not yet out. Hopefully in the next few weeks. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> In the meantime, since your case is >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> particular and that you just want to start with a clean database, the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> following deletes should work (hopefully I won't forget any tables): >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from mri_violations_log; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> mri_protocol_violated_scans; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from MRICandidateErrors; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from parameter_file; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from files_qcstatus; # (if >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> you played with the QC part of the imaging browser for testing) >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from feedback_mri_comments; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> # (if you played with the QC part of the imaging browser for testing) >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from tarchive_series; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from tarchive_files; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from mri_upload; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from tarchive; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from mri_scanner; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from candidate where >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID="scanner"; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I don't know if you want to also >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete entries in the session and candidate table too? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 2) We do not need to create the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> profile of a patient ( are the patients stored in the candidate table? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> because i can't see the ghosts ), because will it automatically be created >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> when importing a dicom? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I am not sure I understand fully >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> this question. All candidates are stored in the candidate table. The >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> phantom scans however are attached to a scanner candidate depending on >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> where the scan happened. It is a bit of a weird concept that we have to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> redesign eventually but never got a chance to get to it. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hopefully this answered your >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> question, otherwise, don't hesitate to let me know. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 3) What is the difference between >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> uploading a dicom as phantom instead of importing as >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCCID_DCCID_VisitLabel? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> When you upload the scan as >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID_DCCID_VisitLabel, there is a check that makes sure the candidate IDs >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and visit label are valid at the time of upload. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> When you upload a scan as phantom, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> it expects that the DICOM field PatientName and uploaded filename contains >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the string "phantom". We enforced this behaviour on the imaging uploader >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> side in recent releases but I can't remember which one. Probably the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> upcoming 21.0 release. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> All those verifications might seem >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> cumbersome but they are here to ensure that the files inserted are all >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> valid and labelled properly as it is a bit messy to have to delete files >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> that were wrongly labelled. At least, the delete script present in release >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 21.0 will make this process easier but it is still good practice to verify >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> those things. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> With pleasure. Hopefully the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> answers to your questions will be helpful. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PS: loris-dev mailing list: you >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> will find the initial answer I gave Sotirios below. I forgot to cc the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> loris-dev in my earlier reply... >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 16 ???? 2019 ???? 12:02 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ?.?., ?/? Cecile Madjar < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> cecile.madjar at mcin.ca> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Dear Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you for reaching out. Since >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> your email was already organized in points, I will reply directly below >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> your questions below. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 1) What do we do when the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> StudyUID is blank on the header? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/minor/docs/AppendixA-Troubleshooting_guideline.md >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> There solution provided at the table 3 does not guide us how to find the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> information ( is possible ). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The StudyUID is the field used in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> our pipeline at the moment to check whether a DICOM study was already >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> inserted into LORIS with that same StudyUID since it is supposed to be >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> unique for every single study. Currently, we do not support insertion of >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DICOM studies if they do not have a StudyUID associated with them. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Is there a specific reason why >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the StudyUID is blank in the DICOM headers in your DICOM files? Did they go >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> through some processes before upload to LORIS? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 2) When i am about to upload a >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> non-phanton case i need a 'Visit Label'. Is there already a script that can >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> create a new visit label for a specific Candidate, so i can provide it as >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> input afterwards to the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> batch_uploads_imageuploader ( See option 5.1.3 https://github.com/aces/Loris-MRI/blob/minor/docs/05-PipelineLaunchOptions.md ) >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I am not sure if the front-end >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> allows for it but if you use batch_uploads_imageuploader, the insertion >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> scripts could create the visit label for you. However, it does need to be >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> included in the patient name in order for the script to know which label it >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> should use. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> For example: you upload V02 for >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> MTL0123 (DCCID: 456789) but V02 was not yet created for MTL0123; the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> insertion scripts will create a V02 visit for MTL0123 if the PatientName >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> field for the dataset is MTL0123_456789_V02 with Stage marked as "Not >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Started". >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> However, *note that for the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> script to create the visit for the candidate, you have to make sure that >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> all the visit label of your projects were inserted in the Visit_Windows >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> table* (otherwise, the visit >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> will never be created as they were not specified as being part of the list >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> of visit label to expect). So in the example above, you should have one row >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in Visit_Windows with Visit_label="V02" set. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 3) Section 4.3 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/minor/docs/04-Scripts.md >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> What do we do when the folder contains multiple mnc files? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> This is a case by case. Most of >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the time, the MINC files that failed insertion into the imaging browser end >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> up in the MRI violation module where you can see what went wrong with the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> acquisitions not inserted. If you notice that the MINC file should be >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> inserted as a specific protocol, you can force the insertion as explained >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in section 4.3. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> In your case, I have a feeling >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> that you want to be able to insert MINC files that did not go through the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> whole pipeline insertion (DICOM archival, then dcm2mnc, then protocol >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> identification, then insertion...). In theory, you could call >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl on any MINC >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> file, provided you have at least the following information: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - path to the MINC file >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - uploadID associated with the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> MINC files or DICOM archive path from which those MINC files were created >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> from >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Then the minc_insertion.pl >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> script will do the subject information and protocol validation etc... >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> If all the MINC files come from >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the same uploadID or TarchiveID, then you could run a loop in bash calling >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the minc_insertion.pl script >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> like this for files deriving from uploadID=1: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ls /path/to/mnc/folder/* | while >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> read f; do minc_insertion.pl >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -profile prod -uploadID 1 -mincPath $f; done >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helped! >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>>>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> -- >>>>>>>>>>>>>> >>>>>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>>>>> >>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> -- >>>>>>>>>>>> >>>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>>> >>>>>>>>>>> _______________________________________________ >>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>> >>>>>>>>>> _______________________________________________ >>>>>>>>> Loris-dev mailing list >>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> -- >>>>>>>> >>>>>>>> christine.rogers at mcgill.ca >>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>> Montreal Neurological Institute >>>>>>>> McGill University | Montreal | Canada >>>>>>>> >>>>>>> _______________________________________________ >>>>>>> Loris-dev mailing list >>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>> >>>>>> _______________________________________________ >>>>> Loris-dev mailing list >>>>> Loris-dev at bic.mni.mcgill.ca >>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>> >>>> >>>> >>>> -- >>>> Shen Wang >>>> Loris Developer >>>> Montreal Neurological Institute >>>> McGill University >>>> >>>> -- Shen Wang Loris Developer Montreal Neurological Institute McGill University -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: ???? 2019-08-13 19.21.15.png Type: image/png Size: 508603 bytes Desc: not available URL: From wangshen.mcin at gmail.com Tue Aug 13 21:21:40 2019 From: wangshen.mcin at gmail.com (Shen Wang) Date: Tue, 13 Aug 2019 21:21:40 -0400 Subject: [Loris-dev] Upgrading to Loris 21 - new make file In-Reply-To: References: Message-ID: Does it work? If still doesn?t work, try to remove project/config.xml file. Do sudo ./install.sh again. To reinstall Loris again. Shen Wang ?2019?8?13? ????9:02??? > Hi Sotirios, > step 1: > sudo ./node_modules/.bin/eslint --fix /var/www/loris > step 2: > put the rest error files under this line [# Ignore until ESLint is run] in > the .eslintignore file. > step 3: > sudo make > > > > On Tue, 13 Aug 2019 at 20:34, Sotirios Nikoloutsopoulos < > sotirisnik at gmail.com> wrote: > >> I did the modifications, still there are errors. >> Thanks >> >> >> ???? ???, 14 ??? 2019 ???? 3:22 ?.?., ?/? Shen Wang < >> wangshen.mcin at gmail.com> ??????: >> >>> Hi Sotirios, >>> I saw your output file, the config issue is gone. >>> you can use [sudo npm run lintfix:javascript ] to fix these indent >>> issues. >>> If it still has errors. >>> Then try modify this file .eslintignore >>> with this >>> >>> # Ignore until ESLint is run >>> >>> modules/* >>> >>> modules/dataquery/ >>> >>> node_modules/* >>> >>> htdocs/js/components/* >>> >>> jsx/* >>> >>> >>> # Ignore external libs >>> >>> htdocs/js/flot/* >>> >>> htdocs/js/jquery/* >>> >>> htdocs/js/jszip/* >>> >>> htdocs/js/modernizr/* >>> >>> htdocs/js/modules/* >>> >>> htdocs/js/react/* >>> >>> htdocs/js/shims/* >>> >>> htdocs/js/c3.min.js >>> >>> htdocs/js/d3.min.js >>> >>> htdocs/js/FileSaver.min.js >>> >>> >>> then do sudo make. >>> It should work. >>> Regards >>> Shen >>> >>> >>> Sotirios Nikoloutsopoulos ?2019?8?13? ????7:54??? >>> >>>> No, it didn't work, i also tried space/tabs because most of the errors >>>> where about indentation, also there are some errors about React. >>>> >>>> Thanks >>>> >>>> lorisadmin at hbp:/var/www/loris$ sudo ./node_modules/.bin/eslint --init >>>> ? How would you like to configure ESLint? Answer questions about your >>>> style >>>> ? Which version of ECMAScript do you use? ES2015 >>>> ? Are you using ES6 modules? Yes >>>> ? Where will your code run? Browser >>>> ? Do you use CommonJS? Yes >>>> ? Do you use JSX? Yes >>>> ? Do you use React? Yes >>>> ? What style of indentation do you use? Spaces >>>> ? What quotes do you use for strings? Single >>>> ? What line endings do you use? Unix >>>> ? Do you require semicolons? Yes >>>> ? What format do you want your config file to be in? JSON >>>> The config that you've selected requires the following dependencies: >>>> >>>> eslint-plugin-react at latest >>>> Successfully created .eslintrc.json file in /var/www/loris >>>> >>>> lorisadmin at hbp:/var/www/loris$ sudo make > sudo_make_output >>>> npm WARN The package prop-types is included as both a dev and >>>> production dependency. >>>> npm WARN optional SKIPPING OPTIONAL DEPENDENCY: fsevents at 1.2.4 >>>> (node_modules/fsevents): >>>> npm WARN notsup SKIPPING OPTIONAL DEPENDENCY: Unsupported platform for >>>> fsevents at 1.2.4: wanted {"os":"darwin","arch":"any"} (current: >>>> {"os":"linux","arch":"x64"}) >>>> >>>> npm ERR! code ELIFECYCLE >>>> npm ERR! errno 2 >>>> npm ERR! loris at 1.0.0 compile: `webpack` >>>> npm ERR! Exit status 2 >>>> npm ERR! >>>> npm ERR! Failed at the loris at 1.0.0 compile script. >>>> npm ERR! This is probably not a problem with npm. There is likely >>>> additional logging output above. >>>> >>>> npm ERR! A complete log of this run can be found in: >>>> npm ERR! >>>> /home/lorisadmin/.npm/_logs/2019-08-13T23_40_58_841Z-debug.log >>>> >>>> ???? ???, 14 ??? 2019 ???? 2:29 ?.?., ?/? Shen Wang < >>>> wangshen.mcin at gmail.com> ??????: >>>> >>>>> Hi Sotirios, >>>>> When you do make command, please make sure with sudo at the >>>>> beginning. [sudo make] >>>>> If it still doesn't work for you. >>>>> Then try the solutions below. >>>>> solution 1: >>>>> [image: ???? 2019-08-13 19.21.15.png] >>>>> Regards >>>>> Shen >>>>> >>>>> >>>>> >>>>> >>>>> On Tue, 13 Aug 2019 at 17:22, Sotirios Nikoloutsopoulos < >>>>> sotirisnik at gmail.com> wrote: >>>>> >>>>>> I think that the files exists although i redownloaded the >>>>>> eslintrc.json i checked others files that had similar errors. >>>>>> >>>>>> lorisadmin at hbp:/var/www/loris$ ls -l >>>>>> ./node_modules/eslint-loader/index.js >>>>>> -rw-rw-r-- 1 lorisadmin lorisadmin 6463 ??? 26 1985 >>>>>> ./node_modules/eslint-loader/index.js >>>>>> >>>>>> lorisadmin at hbp:/var/www/loris$ ls -l .eslintrc.json >>>>>> -rw-rw-r-- 1 lorisadmin lorisadmin 84530 ??? 14 00:04 .eslintrc.json >>>>>> >>>>>> Maybe this can help >>>>>> >>>>>> Module build failed (from ./node_modules/eslint-loader/index.js): >>>>>> SyntaxError: Cannot read config file: >>>>>> /var/www/loris/.eslintrc.json >>>>>> Error: Unexpected token < in JSON at position 6 >>>>>> at JSON.parse () >>>>>> at loadJSONConfigFile >>>>>> (/var/www/loris/node_modules/eslint/lib/config/config-file.js:114:21) >>>>>> at loadConfigFile >>>>>> (/var/www/loris/node_modules/eslint/lib/config/config-file.js:230:26) >>>>>> at loadFromDisk >>>>>> (/var/www/loris/node_modules/eslint/lib/config/config-file.js:500:18) >>>>>> at Object.load >>>>>> (/var/www/loris/node_modules/eslint/lib/config/config-file.js:564:20) >>>>>> at Config.getLocalConfigHierarchy >>>>>> (/var/www/loris/node_modules/eslint/lib/config.js:227:44) >>>>>> at Config.getConfigHierarchy >>>>>> (/var/www/loris/node_modules/eslint/lib/config.js:179:43) >>>>>> at Config.getConfigVector >>>>>> (/var/www/loris/node_modules/eslint/lib/config.js:286:21) >>>>>> at Config.getConfig >>>>>> (/var/www/loris/node_modules/eslint/lib/config.js:329:29) >>>>>> at processText >>>>>> (/var/www/loris/node_modules/eslint/lib/cli-engine.js:162:33) >>>>>> at CLIEngine.executeOnText >>>>>> (/var/www/loris/node_modules/eslint/lib/cli-engine.js:596:17) >>>>>> at lint >>>>>> (/var/www/loris/node_modules/eslint-loader/index.js:237:17) >>>>>> at Object.module.exports >>>>>> (/var/www/loris/node_modules/eslint-loader/index.js:232:21) >>>>>> >>>>>> ERROR in ./modules/imaging_uploader/jsx/index.js >>>>>> Module build failed (from ./node_modules/eslint-loader/index.js): >>>>>> SyntaxError: Cannot read config file: >>>>>> /var/www/loris/.eslintrc.json >>>>>> Error: Unexpected token < in JSON at position 6 >>>>>> at JSON.parse () >>>>>> at loadJSONConfigFile >>>>>> (/var/www/loris/node_modules/eslint/lib/config/config-file.js:114:21) >>>>>> at loadConfigFile >>>>>> (/var/www/loris/node_modules/eslint/lib/config/config-file.js:230:26) >>>>>> at loadFromDisk >>>>>> (/var/www/loris/node_modules/eslint/lib/config/config-file.js:500:18) >>>>>> at Object.load >>>>>> (/var/www/loris/node_modules/eslint/lib/config/config-file.js:564:20) >>>>>> at Config.getLocalConfigHierarchy >>>>>> (/var/www/loris/node_modules/eslint/lib/config.js:227:44) >>>>>> at Config.getConfigHierarchy >>>>>> (/var/www/loris/node_modules/eslint/lib/config.js:179:43) >>>>>> at Config.getConfigVector >>>>>> (/var/www/loris/node_modules/eslint/lib/config.js:286:21) >>>>>> at Config.getConfig >>>>>> (/var/www/loris/node_modules/eslint/lib/config.js:329:29) >>>>>> at processText >>>>>> (/var/www/loris/node_modules/eslint/lib/cli-engine.js:162:33) >>>>>> at CLIEngine.executeOnText >>>>>> (/var/www/loris/node_modules/eslint/lib/cli-engine.js:596:17) >>>>>> at lint >>>>>> (/var/www/loris/node_modules/eslint-loader/index.js:237:17) >>>>>> at Object.module.exports >>>>>> (/var/www/loris/node_modules/eslint-loader/index.js:232:21) >>>>>> >>>>>> >>>>>> >>>>>> ???? ???, 13 ??? 2019 ???? 11:52 ?.?., ?/? John Saigle < >>>>>> john.saigle at mcin.ca> ??????: >>>>>> >>>>>>> HI Sotirios, >>>>>>> >>>>>>> The make_output.txt file shows webpack failing because it can't find >>>>>>> the ESLint config file. >>>>>>> >>>>>>> Can you confirm whether the file `.eslintrc.json` exists within your >>>>>>> loris root directory (usually `/var/www/loris/`)? When I delete my file I >>>>>>> get the same errors as you. >>>>>>> >>>>>>> If you find that it's missing, you can make a local copy with the >>>>>>> contents found here: >>>>>>> >>>>>>> >>>>>>> https://github.com/aces/Loris/blob/e26a6ad49a73fcffef0cd73bb600c4d17b200b62/.eslintrc.json >>>>>>> >>>>>>> Once you know it exists, try running `make` again. >>>>>>> >>>>>>> Let us know if that moves you forward. >>>>>>> >>>>>>> Best, >>>>>>> John >>>>>>> >>>>>>> On Tue, Aug 13, 2019 at 2:21 PM Sotirios Nikoloutsopoulos < >>>>>>> sotirisnik at gmail.com> wrote: >>>>>>> >>>>>>>> Hi, >>>>>>>> I executed the commands for the node and now i am get the >>>>>>>> followings: >>>>>>>> >>>>>>>> lorisadmin at hbp:/var/www/loris$ make > ~/make_output >>>>>>>> npm WARN The package prop-types is included as both a dev and >>>>>>>> production dependency. >>>>>>>> npm WARN optional SKIPPING OPTIONAL DEPENDENCY: fsevents at 1.2.4 >>>>>>>> (node_modules/fsevents): >>>>>>>> npm WARN notsup SKIPPING OPTIONAL DEPENDENCY: Unsupported platform >>>>>>>> for fsevents at 1.2.4: wanted {"os":"darwin","arch":"any"} (current: >>>>>>>> {"os":"linux","arch":"x64"}) >>>>>>>> >>>>>>>> npm ERR! code ELIFECYCLE >>>>>>>> npm ERR! errno 2 >>>>>>>> npm ERR! loris at 1.0.0 compile: `webpack` >>>>>>>> npm ERR! Exit status 2 >>>>>>>> npm ERR! >>>>>>>> npm ERR! Failed at the loris at 1.0.0 compile script. >>>>>>>> npm ERR! This is probably not a problem with npm. There is likely >>>>>>>> additional logging output above. >>>>>>>> >>>>>>>> npm ERR! A complete log of this run can be found in: >>>>>>>> npm ERR! >>>>>>>> /home/lorisadmin/.npm/_logs/2019-08-13T18_12_05_378Z-debug.log >>>>>>>> make: *** [javascript] Error 2 >>>>>>>> >>>>>>>> Thanks, >>>>>>>> Sotirios >>>>>>>> >>>>>>>> >>>>>>>> ???? ???, 12 ??? 2019 ???? 10:19 ?.?., ?/? Christine Rogers, Ms. < >>>>>>>> christine.rogers at mcgill.ca> ??????: >>>>>>>> >>>>>>>>> Hi Sotirios, >>>>>>>>> >>>>>>>>> We've seen some users installing LORIS 21 or upgrading to 21 whose >>>>>>>>> version of node doesn't work well with webpack, due to updated packages >>>>>>>>> they're missing. >>>>>>>>> If so, update your node : >>>>>>>>> >>>>>>>>> curl -sL https://deb.nodesource.com/setup_8.x | sudo -E bash - >>>>>>>>> sudo apt-get install -y nodejs >>>>>>>>> >>>>>>>>> Let us know how that goes -- please send us output from the same >>>>>>>>> log if any issues. >>>>>>>>> Best, >>>>>>>>> Christine >>>>>>>>> >>>>>>>>> >>>>>>>>> On Thu, Aug 8, 2019 at 2:38 PM Sotirios Nikoloutsopoulos < >>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>> >>>>>>>>>> It's not a disk space issue, as you can see below i have still >>>>>>>>>> 74GB available. >>>>>>>>>> >>>>>>>>>> lorisadmin at hbp:/var/www/loris$ df -h >>>>>>>>>> Filesystem Size Used Avail Use% Mounted on >>>>>>>>>> udev 2,9G 0 2,9G 0% /dev >>>>>>>>>> tmpfs 597M 8,6M 588M 2% /run >>>>>>>>>> /dev/sda1 98G 19G 74G 21% / >>>>>>>>>> >>>>>>>>>> Maybe we have to pass a flag to get into strict mode? as stated >>>>>>>>>> "SyntaxError: Block-scoped declarations (let, const, function, class) not >>>>>>>>>> yet supported outside strict mode" >>>>>>>>>> >>>>>>>>>> Thanks, >>>>>>>>>> Sotirios >>>>>>>>>> >>>>>>>>>> ???? ???, 8 ??? 2019 ???? 4:32 ?.?., ?/? Dave MacFarlane < >>>>>>>>>> dave.macfarlane at mcin.ca> ??????: >>>>>>>>>> >>>>>>>>>>> It looks like the javascript snippet shown in the error message >>>>>>>>>>> when trying to compile the js is truncated. Have you run out of disk space? >>>>>>>>>>> >>>>>>>>>>> On Thu, Aug 8, 2019 at 8:37 AM Sotirios Nikoloutsopoulos < >>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>> >>>>>>>>>>>> Hi, >>>>>>>>>>>> >>>>>>>>>>>> I runned make and also included the file it reports at the end. >>>>>>>>>>>> >>>>>>>>>>>> lorisadmin at hbp:/var/www/loris$ make >>>>>>>>>>>> npm install >>>>>>>>>>>> npm WARN optional Skipping failed optional dependency >>>>>>>>>>>> /chokidar/fsevents: >>>>>>>>>>>> npm WARN notsup Not compatible with your operating system or >>>>>>>>>>>> architecture: fsevents at 1.2.9 >>>>>>>>>>>> npm WARN optional Skipping failed optional dependency >>>>>>>>>>>> /watchpack/chokidar/fsevents: >>>>>>>>>>>> npm WARN notsup Not compatible with your operating system or >>>>>>>>>>>> architecture: fsevents at 1.2.9 >>>>>>>>>>>> npm run compile >>>>>>>>>>>> >>>>>>>>>>>> > loris at 1.0.0 compile /var/www/loris >>>>>>>>>>>> > webpack >>>>>>>>>>>> >>>>>>>>>>>> /var/www/loris/node_modules/webpack/bin/webpack.js:86 >>>>>>>>>>>> let notify = >>>>>>>>>>>> ^^^ >>>>>>>>>>>> >>>>>>>>>>>> SyntaxError: Block-scoped declarations (let, const, function, >>>>>>>>>>>> class) not yet supported outside strict mode >>>>>>>>>>>> at exports.runInThisContext (vm.js:53:16) >>>>>>>>>>>> at Module._compile (module.js:374:25) >>>>>>>>>>>> at Object.Module._extensions..js (module.js:417:10) >>>>>>>>>>>> at Module.load (module.js:344:32) >>>>>>>>>>>> at Function.Module._load (module.js:301:12) >>>>>>>>>>>> at Function.Module.runMain (module.js:442:10) >>>>>>>>>>>> at startup (node.js:136:18) >>>>>>>>>>>> at node.js:966:3 >>>>>>>>>>>> >>>>>>>>>>>> npm ERR! Linux 4.15.0-55-generic >>>>>>>>>>>> npm ERR! argv "/usr/bin/nodejs" "/usr/bin/npm" "run" "compile" >>>>>>>>>>>> npm ERR! node v4.2.6 >>>>>>>>>>>> npm ERR! npm v3.5.2 >>>>>>>>>>>> npm ERR! code ELIFECYCLE >>>>>>>>>>>> npm ERR! loris at 1.0.0 compile: `webpack` >>>>>>>>>>>> npm ERR! Exit status 1 >>>>>>>>>>>> npm ERR! >>>>>>>>>>>> npm ERR! Failed at the loris at 1.0.0 compile script 'webpack'. >>>>>>>>>>>> npm ERR! Make sure you have the latest version of node.js and >>>>>>>>>>>> npm installed. >>>>>>>>>>>> npm ERR! If you do, this is most likely a problem with the >>>>>>>>>>>> loris package, >>>>>>>>>>>> npm ERR! not with npm itself. >>>>>>>>>>>> npm ERR! Tell the author that this fails on your system: >>>>>>>>>>>> npm ERR! webpack >>>>>>>>>>>> npm ERR! You can get information on how to open an issue for >>>>>>>>>>>> this project with: >>>>>>>>>>>> npm ERR! npm bugs loris >>>>>>>>>>>> npm ERR! Or if that isn't available, you can get their info via: >>>>>>>>>>>> npm ERR! npm owner ls loris >>>>>>>>>>>> npm ERR! There is likely additional logging output above. >>>>>>>>>>>> >>>>>>>>>>>> npm ERR! Please include the following file with any support >>>>>>>>>>>> request: >>>>>>>>>>>> npm ERR! /var/www/loris/npm-debug.log >>>>>>>>>>>> Makefile:14: recipe for target 'javascript' failed >>>>>>>>>>>> make: *** [javascript] Error 1 >>>>>>>>>>>> >>>>>>>>>>>> Thanks, >>>>>>>>>>>> >>>>>>>>>>>> Sotirios >>>>>>>>>>>> >>>>>>>>>>>> ???? ???, 7 ??? 2019 ???? 5:41 ?.?., ?/? Christine Rogers, Ms. < >>>>>>>>>>>> christine.rogers at mcgill.ca> ??????: >>>>>>>>>>>> >>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>> >>>>>>>>>>>>> Thanks, have you tried all of these steps? >>>>>>>>>>>>> - clear your browser cache (and refresh a few times) >>>>>>>>>>>>> - delete any files in your smarty/templates_c directory (this >>>>>>>>>>>>> will clear the template cache - do Not touch smarty/templates/) >>>>>>>>>>>>> - run `make` (per the 21 release notes, this replaces the >>>>>>>>>>>>> composer commands used in previous releases to update your dependencies) >>>>>>>>>>>>> - restart apache (doesn't hurt) >>>>>>>>>>>>> >>>>>>>>>>>>> Let us know how it goes -- let us know what difference you see >>>>>>>>>>>>> after, with your logs. A >>>>>>>>>>>>> lso please send us your Config path settings (see these >>>>>>>>>>>>> Troubleshooting Queries >>>>>>>>>>>>> ) >>>>>>>>>>>>> if you're still seeing front-end issues. >>>>>>>>>>>>> >>>>>>>>>>>>> Thanks, >>>>>>>>>>>>> Christine >>>>>>>>>>>>> >>>>>>>>>>>>> On Wed, Aug 7, 2019 at 8:02 AM Sotirios Nikoloutsopoulos < >>>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>> >>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>> >>>>>>>>>>>>>> lorisadmin at hbp:/var/www/loris$ sudo cat >>>>>>>>>>>>>> /var/log/apache2/error.log >>>>>>>>>>>>>> [Wed Aug 07 07:35:02.422501 2019] [mpm_prefork:notice] [pid >>>>>>>>>>>>>> 1267] AH00163: Apache/2.4.18 (Ubuntu) OpenSSL/1.0.2g configured -- resuming >>>>>>>>>>>>>> normal operations >>>>>>>>>>>>>> [Wed Aug 07 07:35:02.422514 2019] [core:notice] [pid 1267] >>>>>>>>>>>>>> AH00094: Command line: '/usr/sbin/apache2' >>>>>>>>>>>>>> >>>>>>>>>>>>>> And as for the access.log the content are empty >>>>>>>>>>>>>> lorisadmin at hbp:/var/www/loris$ sudo ls -l >>>>>>>>>>>>>> /var/log/apache2/access.log >>>>>>>>>>>>>> lorisadmin at hbp:/var/www/loris$ sudo ls -l >>>>>>>>>>>>>> /var/log/apache2/access.log >>>>>>>>>>>>>> -rw-r----- 1 root adm 0 ???? 28 14:09 >>>>>>>>>>>>>> /var/log/apache2/access.log >>>>>>>>>>>>>> >>>>>>>>>>>>>> Also i noticed a loris_access.log. >>>>>>>>>>>>>> >>>>>>>>>>>>>> The only non-blank pages are: >>>>>>>>>>>>>> mri_violations, dataquery does not exist at all, statistics, >>>>>>>>>>>>>> data_team_helper, genomic_browser, configuration and >>>>>>>>>>>>>> server_processes_manager/ prints "Required configuration settings for >>>>>>>>>>>>>> Server Processes Manager are missing. Cannot continue." >>>>>>>>>>>>>> >>>>>>>>>>>>>> Thanks, >>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>> >>>>>>>>>>>>>> ???? ???, 6 ??? 2019 ???? 10:13 ?.?., ?/? Christine Rogers, >>>>>>>>>>>>>> Ms. ??????: >>>>>>>>>>>>>> >>>>>>>>>>>>>>> Hi Sotirios and LORIS community -- >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> When upgrading to brand-new release 21 -- just a reminder >>>>>>>>>>>>>>> to follow the release notes and run the new *make* file to >>>>>>>>>>>>>>> update your dependencies (instead of using *composer* >>>>>>>>>>>>>>> commands). >>>>>>>>>>>>>>> We've also updated the Wiki page >>>>>>>>>>>>>>> to >>>>>>>>>>>>>>> clarify that the release notes for each version will tell you what to run. >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> If your current version is not the last release (20.3), it's >>>>>>>>>>>>>>> still important to upgrade to each minor release increment (e.g. 20.2, >>>>>>>>>>>>>>> 20.3) before making the leap to 21.0. >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> If you're getting blank pages, post-upgrade -- Try clearing >>>>>>>>>>>>>>> your cache. >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> Got questions or feedback e.g. on the Release Notes? please >>>>>>>>>>>>>>> don't hesitate to let us know. >>>>>>>>>>>>>>> Thanks, >>>>>>>>>>>>>>> Christine >>>>>>>>>>>>>>> The LORIS team >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> On Tue, Aug 6, 2019 at 10:09 AM Christine Rogers, Ms. < >>>>>>>>>>>>>>> christine.rogers at mcgill.ca> wrote: >>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>> Could you also let us know -- on which pages is content >>>>>>>>>>>>>>>> visible, and on which pages/modules is content not visible for you? >>>>>>>>>>>>>>>> Thanks, >>>>>>>>>>>>>>>> Christine >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> On Tue, Aug 6, 2019 at 9:54 AM Christine Rogers, Ms. < >>>>>>>>>>>>>>>> christine.rogers at mcgill.ca> wrote: >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Thanks Sotirios, >>>>>>>>>>>>>>>>> That's good to know. It sounds like you've checked that >>>>>>>>>>>>>>>>> your /var/www/loris/project/config.xml file get populated properly. >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Please send us the last few errors you're seeing in your >>>>>>>>>>>>>>>>> apache error log file, and your config paths and we can see what's >>>>>>>>>>>>>>>>> happening with your front end -- >>>>>>>>>>>>>>>>> Run these Troubleshooting Queries >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> to get your config path settings, given your front end is not displaying >>>>>>>>>>>>>>>>> fully. >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> The Loris-MRI repo >>>>>>>>>>>>>>>>> 21 >>>>>>>>>>>>>>>>> install/upgrade would then be your next steps. >>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>> Christine >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> On Tue, Aug 6, 2019 at 7:53 AM Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> I am using a VM. What i did was: >>>>>>>>>>>>>>>>>> 1) Download the files from https://github.com/aces/Loris >>>>>>>>>>>>>>>>>> and replace them to my existing /vaw/www/loris folder. >>>>>>>>>>>>>>>>>> 2) Execute the composer install --no-dev and then composer >>>>>>>>>>>>>>>>>> dump-autoload as mentioned here >>>>>>>>>>>>>>>>>> https://github.com/aces/Loris/wiki/Updating-your-LORIS. >>>>>>>>>>>>>>>>>> 3) Execute install.sh from /var/www/loris/tools and >>>>>>>>>>>>>>>>>> because LORIS already existed i moved a .config file, then re-executed the >>>>>>>>>>>>>>>>>> install.sh successfully >>>>>>>>>>>>>>>>>> 4 ) As for the database, i dropped the schema and i >>>>>>>>>>>>>>>>>> executed the installdb.php >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> ???? ???, 5 ??? 2019 ???? 5:22 ?.?., ?/? Christine >>>>>>>>>>>>>>>>>> Rogers, Ms. ??????: >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Hi Sotorios, >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Thanks - when you re-installed did you start on a fresh >>>>>>>>>>>>>>>>>>> root path / VM or might some of your old system setting still apply? >>>>>>>>>>>>>>>>>>> (And if you did any steps similar to an upgrade, did you >>>>>>>>>>>>>>>>>>> follow the Upgrade steps in the Release Notes, from both repos?) >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> About the TR_range column - it was recently split (MRI >>>>>>>>>>>>>>>>>>> pr339 ) split >>>>>>>>>>>>>>>>>>> into TR_min and _max columns. Given the code was trying to query TR_range >>>>>>>>>>>>>>>>>>> which does not exist in your mri_protocol table, double-check which version >>>>>>>>>>>>>>>>>>> of the Loris repo (tables) and the Loris-MRI repo (code) you have installed >>>>>>>>>>>>>>>>>>> to ensure they match. >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Christine >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> On Mon, Aug 5, 2019 at 9:06 AM Sotirios Nikoloutsopoulos >>>>>>>>>>>>>>>>>>> wrote: >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> I reinstalled LORIS to 21 version and now the content >>>>>>>>>>>>>>>>>>>> is not visible at all at most pages. >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> ???? ???, 5 ??? 2019 ???? 3:19 ?.?., ?/? Sotirios >>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos ??????: >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> Is it easy to upgrade to Loris 21? Also the following >>>>>>>>>>>>>>>>>>>>> fails because the line 1985 of NeuroDB/MRIProcessingUtility.pm query >>>>>>>>>>>>>>>>>>>>> mri_protocol which doesn't have TR_range >>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris/blob/21.0-release/SQL/0000-00-00-schema.sql#L556 >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> lorisadmin at hbp:/data/loris/bin/mri$ >>>>>>>>>>>>>>>>>>>>> ./batch_uploads_imageuploader -profile prod < ~/Desktop/input.txt > log.txt >>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $_ in pattern match (m//) >>>>>>>>>>>>>>>>>>>>> at ./batch_uploads_imageuploader line 147. >>>>>>>>>>>>>>>>>>>>> base is DCC0000_258024_V1 >>>>>>>>>>>>>>>>>>>>> path is /data/incoming/ >>>>>>>>>>>>>>>>>>>>> type is .tar.gz >>>>>>>>>>>>>>>>>>>>> fullpath is /data/incoming/DCC0000_258024_V1.tar.gz >>>>>>>>>>>>>>>>>>>>> DBD::mysql::st execute failed: Unknown column >>>>>>>>>>>>>>>>>>>>> 'TR_range' in 'where clause' at >>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line 1985. >>>>>>>>>>>>>>>>>>>>> DBD::mysql::st fetchrow_array failed: fetch() without >>>>>>>>>>>>>>>>>>>>> execute() at >>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line 1986. >>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $count_mri_protocol in >>>>>>>>>>>>>>>>>>>>> numeric gt (>) at >>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line 1995. >>>>>>>>>>>>>>>>>>>>> DBD::mysql::st execute failed: Unknown column >>>>>>>>>>>>>>>>>>>>> 'TR_range' in 'field list' at >>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 562. >>>>>>>>>>>>>>>>>>>>> Can't exec "mail": No such file or directory at >>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 721. >>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 722. >>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 723. >>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 724. >>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 725. >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> No Mincs inserted >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> Thanks, >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> ???? ???, 3 ??? 2019 ???? 1:08 ?.?., ?/? Christine >>>>>>>>>>>>>>>>>>>>> Rogers, Ms. ??????: >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> First, just a note: we've released LORIS 21 this >>>>>>>>>>>>>>>>>>>>>> week with some major new features and cleanup -- especially if you are >>>>>>>>>>>>>>>>>>>>>> early in your setup phase, check out the Release notes for both the >>>>>>>>>>>>>>>>>>>>>> LORIS >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> and Loris-MRI >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> repos. >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> Thanks for your screenshots -- your empty >>>>>>>>>>>>>>>>>>>>>> mri_protocol table should be at the root of these issues : >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> The mri_protocol table must be populated >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> in order for your scans to be registered in LORIS -- it serves as a >>>>>>>>>>>>>>>>>>>>>> whitelist for the insertion pipeline which filters out scans that aren't >>>>>>>>>>>>>>>>>>>>>> identified or matched to scan types in this table. >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> By default, this table is populated with entries for >>>>>>>>>>>>>>>>>>>>>> t1, t2, fMRI and DTI (Insert statements for 21 >>>>>>>>>>>>>>>>>>>>>> release branch are here >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> ) >>>>>>>>>>>>>>>>>>>>>> Feel free to restore our default records and broaden >>>>>>>>>>>>>>>>>>>>>> their parameters to match all your scan types. >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> re Defaced, native, selected -- these filter the >>>>>>>>>>>>>>>>>>>>>> scans displayed as you move to the next page (View Session), instead of >>>>>>>>>>>>>>>>>>>>>> viewing "all types" of scans from a given session : >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> - "defaced" means that a defacing script >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> has masked the subject's face in the volume (for patient privacy) >>>>>>>>>>>>>>>>>>>>>> - "native" means that no pre-processing has been >>>>>>>>>>>>>>>>>>>>>> performed on the scan (it's raw data), >>>>>>>>>>>>>>>>>>>>>> - "selected" will show only volumes that have >>>>>>>>>>>>>>>>>>>>>> been QC'd and "selected" as the best of their type -- used to display only >>>>>>>>>>>>>>>>>>>>>> the best quality T1 image instead of all T1s acquired in a session, e.g. >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> re QC Comments -- >>>>>>>>>>>>>>>>>>>>>> Once you have successfully loaded scans (matched to >>>>>>>>>>>>>>>>>>>>>> the mri_protocol table), you'll be able to use the Imaging Browser's View >>>>>>>>>>>>>>>>>>>>>> Session subpage to enter/view QC comments on each volume, or for each >>>>>>>>>>>>>>>>>>>>>> visit. >>>>>>>>>>>>>>>>>>>>>> These are stored directly in the database, and linked >>>>>>>>>>>>>>>>>>>>>> to each scan. (Table name: feedback_mri_comments) >>>>>>>>>>>>>>>>>>>>>> (Visit-level QC comments are linked to the session.) >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> For a walkthrough of the Imaging setup - please see >>>>>>>>>>>>>>>>>>>>>> the Imaging Setup guide >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> - >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> An old LORIS walkthrough video >>>>>>>>>>>>>>>>>>>>>> can >>>>>>>>>>>>>>>>>>>>>> also walk you through some of the Imaging front-end features, starting at >>>>>>>>>>>>>>>>>>>>>> 8:00 >>>>>>>>>>>>>>>>>>>>>> LORIS' imaging modules have been updated many times >>>>>>>>>>>>>>>>>>>>>> since this video, but the functionality and workflow is similar. >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> Let us know how it goes once you have entries in your >>>>>>>>>>>>>>>>>>>>>> mri_protocol table - >>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>> Christine >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> On Fri, Aug 2, 2019 at 7:58 AM Sotirios >>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos wrote: >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> Hi Christine, >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> In the candidate_list page i can see this patient >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> If i press the link under PSCID i get to see >>>>>>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> and if i press the link under Scan Done it redirects >>>>>>>>>>>>>>>>>>>>>>> me to imaging_browser >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> At the mri_violations page i also see No results ( >>>>>>>>>>>>>>>>>>>>>>> neither on resolved / not resolved ). >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> At the imaging_uploader i can see the record that >>>>>>>>>>>>>>>>>>>>>>> failed. >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> If i click on the tarchive info i get to see the >>>>>>>>>>>>>>>>>>>>>>> Protocol Name which i think is the acquisition we wanted? >>>>>>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> Also my mri_protocol table is empty. >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> Furthermore i would like to ask about the defaced, >>>>>>>>>>>>>>>>>>>>>>> native, selected. What exactly is native and selected? And where are the qc >>>>>>>>>>>>>>>>>>>>>>> comments stored? >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> Finally a walkthrough would be helpful. >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> Thanks, >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> ???? ???, 30 ???? 2019 ???? 8:29 ?.?., ?/? Christine >>>>>>>>>>>>>>>>>>>>>>> Rogers, Ms. ??????: >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>> Glad to hear you're making progress with the visit >>>>>>>>>>>>>>>>>>>>>>>> labels. To follow up on your last few emails: >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> a- The Wiki's Setup Guide contains Sample insert >>>>>>>>>>>>>>>>>>>>>>>> statements for the Visit Windows table >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> . >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> As Cecile mentioned, the consistency of visit label >>>>>>>>>>>>>>>>>>>>>>>> format is important: V01, v01, V1, 01 -- whichever you select to use is >>>>>>>>>>>>>>>>>>>>>>>> fine; we use V01 by default across all documentation. >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> b- For Password reset, there is a script in the >>>>>>>>>>>>>>>>>>>>>>>> tools/ directory so that a back-end administrator can reset any front-end >>>>>>>>>>>>>>>>>>>>>>>> user password, including Admin. (See info on setting up / resetting User >>>>>>>>>>>>>>>>>>>>>>>> passwords in the Wiki's Setup Guide >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> ) >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> c- The minc file not being registered -- due to >>>>>>>>>>>>>>>>>>>>>>>> AcquisitionProtocol unknown. >>>>>>>>>>>>>>>>>>>>>>>> This means the SeriesDescription (Acquisition >>>>>>>>>>>>>>>>>>>>>>>> Protocol) in you Dicom header was not matched to any scan listed in the >>>>>>>>>>>>>>>>>>>>>>>> mri_protocol database table. >>>>>>>>>>>>>>>>>>>>>>>> (In the online Loris-MRI Troubleshooting Guide, >>>>>>>>>>>>>>>>>>>>>>>> this >>>>>>>>>>>>>>>>>>>>>>>> is Table 3, 2nd-last item "no MINCs inserted"). >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> The MRI Violations module (Readme here) >>>>>>>>>>>>>>>>>>>>>>>> will show >>>>>>>>>>>>>>>>>>>>>>>> you the details of this mismatch -- >>>>>>>>>>>>>>>>>>>>>>>> Go to the module (under the Imaging menu), find >>>>>>>>>>>>>>>>>>>>>>>> your scan and click the link "Could not identify scan type" -- in the next >>>>>>>>>>>>>>>>>>>>>>>> subpage you can compare the scan's actual parameters against the >>>>>>>>>>>>>>>>>>>>>>>> mri_protocol table. >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> To resolve this, adjust your mri_protocol table >>>>>>>>>>>>>>>>>>>>>>>> values or perhaps ensure your DICOMs are labelled consistently. >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> Let us know if this works for you -- we can also >>>>>>>>>>>>>>>>>>>>>>>> walk you through an example of non-identified scans on >>>>>>>>>>>>>>>>>>>>>>>> Demo.loris.ca (MRI Violations module). >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>> Christine >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> The LORIS team >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> On Tue, Jul 30, 2019 at 10:47 AM Sotirios >>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos wrote: >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> I hope this is sufficient as the error for the >>>>>>>>>>>>>>>>>>>>>>>>> visit label disappeared. >>>>>>>>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> Please see the attached file. Also something i >>>>>>>>>>>>>>>>>>>>>>>>> found. >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> lorisadmin at hbp:/data/loris/bin/mri$ cat >>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data//logs/TarLoad-17-39-xubBdv.log >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> ==> Loading file from disk >>>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-17-39-UyQcG2/dcc0000_258024_v1_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> --> mapping DICOM parameter for >>>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-17-39-UyQcG2/dcc0000_258024_v1_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> ==> computing md5 hash for MINC body. >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> --> md5: 6b1202fd63e29de4c9be1cd9925888a5 >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> ==> verifying acquisition protocol >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> Acquisition protocol is unknown >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> --> The minc file cannot be registered since the >>>>>>>>>>>>>>>>>>>>>>>>> AcquisitionProtocol is unknown >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 30 ???? 2019 ???? 4:58 ?.?., ?/? >>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos >>>>>>>>>>>>>>>>>>>>>>>>> ??????: >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> Ok I fixed the login problem by using a known >>>>>>>>>>>>>>>>>>>>>>>>>> hash and by deleting the rows from the login_history i was able to login. >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 30 ???? 2019 ???? 4:50 ?.?., ?/? >>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos >>>>>>>>>>>>>>>>>>>>>>>>>> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> there was no visit label 01 in the Visit_Windows >>>>>>>>>>>>>>>>>>>>>>>>>>> table and i don't know how to insert it because the record requires lots of >>>>>>>>>>>>>>>>>>>>>>>>>>> attributes. Also the system for a reason asked me to update my password and >>>>>>>>>>>>>>>>>>>>>>>>>>> now i don't remember it and my account got suspended. Is there a way to >>>>>>>>>>>>>>>>>>>>>>>>>>> reset it or set a simple password? I updated the password hash in the >>>>>>>>>>>>>>>>>>>>>>>>>>> users table by using the hash from another LORIS setup we had and i still >>>>>>>>>>>>>>>>>>>>>>>>>>> couldn't login ( also the attribute password is always NULL and the >>>>>>>>>>>>>>>>>>>>>>>>>>> expiration date is 1999-01-01 for some reason ). >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> Thanks >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 29 ???? 2019 ???? 5:21 ?.?., ?/? >>>>>>>>>>>>>>>>>>>>>>>>>>> Cecile Madjar ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> Can you try adding the visit label v01 to the >>>>>>>>>>>>>>>>>>>>>>>>>>>> Visit_Windows table? >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> However, I noticed that in a previous dataset, >>>>>>>>>>>>>>>>>>>>>>>>>>>> the label was V1. Does that refer to the same visit? If so, you might want >>>>>>>>>>>>>>>>>>>>>>>>>>>> to harmonize the visit labels so they are all the same across datasets for >>>>>>>>>>>>>>>>>>>>>>>>>>>> a given timepoint, meaning you will need to relabel scans when the visit >>>>>>>>>>>>>>>>>>>>>>>>>>>> label is different but referring to the same visit label (v01 = V1 etc...). >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helps, >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> On Mon, Jul 29, 2019 at 10:15 AM Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos wrote: >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Could you help me with the "Visit label does >>>>>>>>>>>>>>>>>>>>>>>>>>>>> not exist"? I had changed $subjectID{'createVisitLabel'} to 1 as you had >>>>>>>>>>>>>>>>>>>>>>>>>>>>> suggested but it appears that this problem hasn't been resolved yet. >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> lorisadmin at hbp:/data/loris/bin/mri$ cat >>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data//logs/TarLoad-14-58-9Xog7H.log >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> ==> Loading file from disk >>>>>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> --> mapping DICOM parameter for >>>>>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> --> using user-defined filterParameters for >>>>>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Candidate Mismatch Error is Visit label does >>>>>>>>>>>>>>>>>>>>>>>>>>>>> not exist >>>>>>>>>>>>>>>>>>>>>>>>>>>>> -> WARNING: This candidate was invalid. >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Logging to >>>>>>>>>>>>>>>>>>>>>>>>>>>>> MRICandidateErrors table with >>>>>>>>>>>>>>>>>>>>>>>>>>>>> reason Visit label does not exist >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 26 ???? 2019 ???? 3:02 ?.?., ?/? >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Cecile, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The Center error was fixed. Still the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> insertion of mincs fails. Please see the output.txt file i attached. Also >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> is there something else i need to change at the paths configuration? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 25 ???? 2019 ???? 6:55 ?.?., ?/? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Cecile Madjar ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> We are making progress! >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I have a feeling this error comes from the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> fact that your psc table does not have the MRI_alias populated for the DCC >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> site. Running the following query in the mysql database should fix this: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> UPDATE psc SET MRI_alias="DCC", Alias="DCC" >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> WHERE Name="Data Coordinating Center"; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Repeat the same with all your sites (make >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sure to change the Aliases between sites, they should all be unique). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Let me know how it goes! >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> On Thu, Jul 25, 2019 at 11:43 AM Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> wrote: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Dear Cecile, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> You were right about your guesses. I did >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the modifications you suggested, i still get the "no mincs inserted" error, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> now i am getting the "No center found this candidate" error ( how do i fix >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> that? from what i see the .dcm files contains a 'Institution Name', is that >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the center? ), so i guess that's why the validation fails, but i changed >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the force variable of tarchiveLoader to 1, shouldn't it have inserted the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> mincs then? Also it is optional to have a mail server, right? ( from what i >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> see the mail error does not affect the $valid_study, so i assume we are >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> okay with that ) >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you a lot, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 25 ???? 2019 ???? 5:48 ?.?., ?/? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Cecile Madjar >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> From what I understand, I believe you just >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> need to update a few config settings from the frontend in the Config module >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> (under the Admin menu). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [image: Screen Shot 2019-07-25 at 10.31.35 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> AM.png] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Then go to the Paths section of the config >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> module and update the "LORIS-MRI code" config setting to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri (my guess is that currently, it is set to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data) and click on the submit button. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [image: Screen Shot 2019-07-25 at 10.32.50 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> AM.png] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Then, go to Imaging Pipeline section of >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the Configuration module and update the "Loris-MRI Data Directory" to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/ (my guess is that it is empty at the moment in your >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> database which is why $data_dir is not defined when you run the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> tarchiveLoader step of the insertion pipeline). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [image: Screen Shot 2019-07-25 at 10.40.52 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> AM.png] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Finally, I took a look at your environment >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> file and it might be a good idea to update your PERL5LIB variable to the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> following (it has been added to the code a few releases ago as we realized >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> this was needed for the libraries. Not sure which version of LORIS-MRI you >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> are using but it does not hurt to update this variable to what I suggest >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> below): >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> export >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PERL5LIB=/data/loris/bin/mri/uploadNeuroDB:/data/loris/bin/mri/dicom-archive:$PERL5LIB >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helps. Sorry you are >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> experiencing so much trouble setting things up. We probably need to update >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> our WIKI. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> On Thu, Jul 25, 2019 at 9:48 AM Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> wrote: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The "Loris-MRI Data Directory" should be >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in the environment file? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 25 ???? 2019 ???? 12:59 ?.?., >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ?/? Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The scripts are located in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/. Somewhere I might have messed something up but i >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> remember following the instructions in the wiki.For example when i tried to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> execute the batch_uploads_imageuploader perl script the line >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> my $command = "$bin_dir/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl " >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> was pointing to an invalid path, for >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> example: it was repeating a pattern and had LORIS instead of loris ( i >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> think the mistake was that in the wiki it suggested to use $PROJECT for >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the name of the folder and i choosed 'loris' >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris/wiki/Imaging-Database >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ). See also the in image for the modification i did. Also i didn't find the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> section to config the $data_dir variable. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 24 ???? 2019 ???? 6:05 ?.?., >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ?/? Cecile Madjar >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> It looks like you have one Config >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> setting not set (based on the first error message you got when running it >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the first time). You need to set a value for "Loris-MRI Data Directory" in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the Config module under the Imaging pipeline section (from what I can see, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> it would be /data/loris/data/ for your setup). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The reason you got that error message >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the second time is that the pipeline checks if the DICOM study was already >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> inserted in the tarchive table. Since you ran the study once already, the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> study is inserted into the tarchive, hence the message. However, the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> pipeline did not complete as the MINC files were not created and inserted >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> into the files/parameter_file table. In order to continue the insertion, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> you will then need to run the tarchiveLoader command suggested in the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> terminal during the second run: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -globLocation -profile prod >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive//2012/DCM_2012-12-05_ImagingUpload-17-43-ZUEFjb.tar >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -verbose >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Finally, I am a bit confused by your >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> setup. Where are the scripts located? In /data/loris/bin/mri or >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data? It feels like the Config setting "LORIS-MRI code" in the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Paths section was set to "/data/LORIS/data" but it should have been set to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the directory where the scripts are located (most probably >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helps, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> On Wed, Jul 24, 2019 at 10:55 AM >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Ok first i execute this command: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> "lorisadmin at hbp:/data/loris/bin/mri$ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ./batch_uploads_imageuploader -profile prod < ~/Desktop/input.txt > log.txt >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in concatenation (.) or string at ./batch_uploads_imageuploader line 143. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in concatenation (.) or string at ./batch_uploads_imageuploader line 143. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $_ in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> pattern match (m//) at ./batch_uploads_imageuploader line 147. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> base is DCC0000_258024_V01 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> path is /data/incoming/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> type is .tar.gz >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> fullpath is >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/incoming/DCC0000_258024_V01.tar.gz >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> source /tmp/ImagingUpload-17-43-ZUEFjb >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> targetlocation >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 256. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 284. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in concatenation (.) or string at /data/loris/bin/mri/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> tarchive_validation.pl line 219. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in concatenation (.) or string at /data/loris/bin/mri/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl line 270. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 711. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Can't exec "mail": No such file or >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> directory at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 721. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 722. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 723. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 724. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 724. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 725. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 735. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> No Mincs inserted >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The tarchiveLoader insertion script >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> has failed. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Running now the following command: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl -profile prod >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -upload_id 3 /data/incoming/DCC0000_258024_V01.tar.gz -verbose" >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I inserted the VisitLabel, but still >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the Mincs are not inserted and i am getting this error >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> "lorisadmin at hbp:/data/loris/bin/mri$ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl -profile prod >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -upload_id 3 /data/incoming/DCC0000_258024_V01.tar.gz -verbose >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> find -path >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> \/tmp\/ImagingUpload\-17\-45\-5MsWEd -name '__MACOSX' -delete >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Spool message is: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The Scan for the uploadID 3 has >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> already been run with tarchiveID: 7. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> To continue with the rest of the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> insertion pipeline, please run tarchiveLoader from a terminal as follows: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader -globLocation -profile prod >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive//2012/DCM_2012-12-05_ImagingUpload-17-43-ZUEFjb.tar >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -verbose" >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Which files should i delete? I thought >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> that deleting the files from the tarchive was enough. And i executed the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> last proposed command to continue to rest of the insertion pipeline ( check >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the image ). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 24 ???? 2019 ???? 5:05 ?.?., >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ?/? Cecile Madjar < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> cecile.madjar at mcin.ca> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sorry I was not clear before. Every >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visits of candidates are created in the session table with one entry per >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID/VisitLabel. So if the imaging pipeline created visits in the session >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> table (that are not attached to instruments) and you want to clean your >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> database completely, you can delete entries in that table as well. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Regarding your point 2, the imaging >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> pipeline can create the visit in the session table as long as the visit >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> label is present in the Visit_Windows table (which means the visit label >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> stored in the PatientName is a valid visit label). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> However, in your prod file, if the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> variable $subjectID{'createVisitLabel'} is set to 1 for candidates, the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit label should be created in the Visit_Windows table I believe. Here >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> is the line of the prod file you would need to change >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> . >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> In general, we prefer populating the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Visit_Windows table and set the $subjectID{'createVisitLabel'} to 0 for >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> candidate data to avoid insertion of badly labelled MRI data that are >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> complex to relabel. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Finally, regarding the candidate >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> creation, if you execute the following steps, the pipeline should be able >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> to create candidates: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - set in the Imaging Pipeline section >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> of the config module the config setting "Upload creation of candidates" to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Yes >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - manually transfer the scans to the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> LORIS server instead of uploading it via the imaging browser >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - run batch_imaging_upload.pl as you >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> did until now. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helps! >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> On Wed, Jul 24, 2019 at 8:47 AM >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> About my second question i replaced >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the name of the patient in the .dcm files and now i am getting an error >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> that the visit label does not exist. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I thought it was supposed to be >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> automatically created. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> "Done adding archive info into >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> database >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -globLocation -profile prod >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive//DCM_2012-12-05_ImagingUpload-15-42-yUwQQV.tar >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -verbose >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> md5sum >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive/DCM_2012-12-05_ImagingUpload-15-42-yUwQQV.tar >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> candidate id 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> => No Visit labelVisit label does >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> not exist >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Set centerID = 1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Number of MINC files that will be >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> considered for inserting into the database: 1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> log dir is /logs and log file is >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /logs/TarLoad-15-42-L6pocU.log >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> candidate id 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> => No Visit label >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Cleaning up temp files: rm -rf >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-15-42-J2rQms/ImagingUpload-15-42-yUwQQV*" >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 24 ???? 2019 ???? 3:38 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ?.?., ?/? Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 1) What are the records in the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> session table? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 2) I tried to upload a non-phantom >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> file like this >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> input_file.txt: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/incoming/DCC0000_258024_V1.tar.gz >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> N DCC0000_258024_V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Terminal: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ./batch_uploads_imageuploader >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -profile prod < ~/Desktop/input.txt > log.txt >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and i get the following error in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the log.txt file >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> "Running now the following command: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl -profile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> prod -upload_id 7 /data/incoming/DCC0000_258024_V1.tar.gz -verbose >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> find -path >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> \/tmp\/ImagingUpload\-14\-56\-FeLCB4 -name '__MACOSX' -delete >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Spool message is: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The PatientName read from the DICOM >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> header does not start with DCC0000_258024_V1 from the mri_upload table >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> " >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and the spool message is repeated >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> for each .dcm file. Should i preprocess every .dcm file and change the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PatientName to "DCC0000_258024_V1"? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 3) As far as it concerns the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> candidate profile i have to create a new one each time before i try to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> upload a file? Is there already a way to create a candidate profile and get >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the DCCID and PSCID without the user interface? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 18 ???? 2019 ???? 5:00 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ?.?., ?/? Cecile Madjar < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> cecile.madjar at mcin.ca> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> See answers to your questions >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> below. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> About the 1st case we had a dicom >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> with a blank studyUID, maybe someone accidentally removed it. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> That is strange. Something must >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> have been done to the DICOM files. I have never seen a study with no >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> StudyUID out of the scanner. Usually, you need to manually erase it with >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> some tool. However, DICOMs never cease to surprise me... >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Some other questions: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 1) What are the steps to remove >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> all of my patients and uploads?: because i want to try to reupload all the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> testing dicoms we had with a clean database. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Release 21.0 of LORIS-MRI will >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> offer a script to remove all the entries and files specific to an upload. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> However, this release is not yet out. Hopefully in the next few weeks. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> In the meantime, since your case >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> is particular and that you just want to start with a clean database, the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> following deletes should work (hopefully I won't forget any tables): >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from mri_violations_log; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> mri_protocol_violated_scans; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from MRICandidateErrors; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from parameter_file; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from files_qcstatus; # (if >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> you played with the QC part of the imaging browser for testing) >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from feedback_mri_comments; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> # (if you played with the QC part of the imaging browser for testing) >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from tarchive_series; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from tarchive_files; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from mri_upload; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from tarchive; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from mri_scanner; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from candidate where >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID="scanner"; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I don't know if you want to also >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete entries in the session and candidate table too? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 2) We do not need to create the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> profile of a patient ( are the patients stored in the candidate table? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> because i can't see the ghosts ), because will it automatically be created >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> when importing a dicom? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I am not sure I understand fully >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> this question. All candidates are stored in the candidate table. The >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> phantom scans however are attached to a scanner candidate depending on >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> where the scan happened. It is a bit of a weird concept that we have to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> redesign eventually but never got a chance to get to it. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hopefully this answered your >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> question, otherwise, don't hesitate to let me know. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 3) What is the difference between >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> uploading a dicom as phantom instead of importing as >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCCID_DCCID_VisitLabel? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> When you upload the scan as >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID_DCCID_VisitLabel, there is a check that makes sure the candidate IDs >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and visit label are valid at the time of upload. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> When you upload a scan as phantom, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> it expects that the DICOM field PatientName and uploaded filename contains >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the string "phantom". We enforced this behaviour on the imaging uploader >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> side in recent releases but I can't remember which one. Probably the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> upcoming 21.0 release. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> All those verifications might seem >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> cumbersome but they are here to ensure that the files inserted are all >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> valid and labelled properly as it is a bit messy to have to delete files >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> that were wrongly labelled. At least, the delete script present in release >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 21.0 will make this process easier but it is still good practice to verify >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> those things. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> With pleasure. Hopefully the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> answers to your questions will be helpful. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PS: loris-dev mailing list: you >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> will find the initial answer I gave Sotirios below. I forgot to cc the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> loris-dev in my earlier reply... >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 16 ???? 2019 ???? 12:02 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ?.?., ?/? Cecile Madjar < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> cecile.madjar at mcin.ca> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Dear Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you for reaching out. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Since your email was already organized in points, I will reply directly >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> below your questions below. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 1) What do we do when the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> StudyUID is blank on the header? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/minor/docs/AppendixA-Troubleshooting_guideline.md >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> There solution provided at the table 3 does not guide us how to find the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> information ( is possible ). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The StudyUID is the field used >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in our pipeline at the moment to check whether a DICOM study was already >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> inserted into LORIS with that same StudyUID since it is supposed to be >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> unique for every single study. Currently, we do not support insertion of >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DICOM studies if they do not have a StudyUID associated with them. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Is there a specific reason why >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the StudyUID is blank in the DICOM headers in your DICOM files? Did they go >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> through some processes before upload to LORIS? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 2) When i am about to upload a >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> non-phanton case i need a 'Visit Label'. Is there already a script that can >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> create a new visit label for a specific Candidate, so i can provide it as >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> input afterwards to the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> batch_uploads_imageuploader ( See option 5.1.3 https://github.com/aces/Loris-MRI/blob/minor/docs/05-PipelineLaunchOptions.md ) >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I am not sure if the front-end >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> allows for it but if you use batch_uploads_imageuploader, the insertion >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> scripts could create the visit label for you. However, it does need to be >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> included in the patient name in order for the script to know which label it >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> should use. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> For example: you upload V02 for >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> MTL0123 (DCCID: 456789) but V02 was not yet created for MTL0123; the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> insertion scripts will create a V02 visit for MTL0123 if the PatientName >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> field for the dataset is MTL0123_456789_V02 with Stage marked as "Not >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Started". >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> However, *note that for the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> script to create the visit for the candidate, you have to make sure that >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> all the visit label of your projects were inserted in the Visit_Windows >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> table* (otherwise, the visit >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> will never be created as they were not specified as being part of the list >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> of visit label to expect). So in the example above, you should have one row >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in Visit_Windows with Visit_label="V02" set. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 3) Section 4.3 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/minor/docs/04-Scripts.md >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> What do we do when the folder contains multiple mnc files? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> This is a case by case. Most of >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the time, the MINC files that failed insertion into the imaging browser end >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> up in the MRI violation module where you can see what went wrong with the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> acquisitions not inserted. If you notice that the MINC file should be >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> inserted as a specific protocol, you can force the insertion as explained >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in section 4.3. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> In your case, I have a feeling >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> that you want to be able to insert MINC files that did not go through the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> whole pipeline insertion (DICOM archival, then dcm2mnc, then protocol >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> identification, then insertion...). In theory, you could call >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl on any MINC >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> file, provided you have at least the following information: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - path to the MINC file >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - uploadID associated with the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> MINC files or DICOM archive path from which those MINC files were created >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> from >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Then the minc_insertion.pl >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> script will do the subject information and protocol validation etc... >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> If all the MINC files come from >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the same uploadID or TarchiveID, then you could run a loop in bash calling >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the minc_insertion.pl script >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> like this for files deriving from uploadID=1: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ls /path/to/mnc/folder/* | while >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> read f; do minc_insertion.pl >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -profile prod -uploadID 1 -mincPath $f; done >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helped! >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>>>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>>>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>>>>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>>>>>> >>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> -- >>>>>>>>>>>>> >>>>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>>>> >>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>> >>>>>>>>>>> _______________________________________________ >>>>>>>>>> Loris-dev mailing list >>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> -- >>>>>>>>> >>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>> Montreal Neurological Institute >>>>>>>>> McGill University | Montreal | Canada >>>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> Loris-dev mailing list >>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>> >>>>>>> _______________________________________________ >>>>>> Loris-dev mailing list >>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>> >>>>> >>>>> >>>>> -- >>>>> Shen Wang >>>>> Loris Developer >>>>> Montreal Neurological Institute >>>>> McGill University >>>>> >>>>> > > -- > Shen Wang > Loris Developer > Montreal Neurological Institute > McGill University > > -- Shen Wang Loris Developer Montreal Neurological Institute McGill University -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: ???? 2019-08-13 19.21.15.png Type: image/png Size: 508603 bytes Desc: not available URL: From christine.rogers at mcgill.ca Wed Aug 14 00:50:54 2019 From: christine.rogers at mcgill.ca (Christine Rogers, Ms.) Date: Wed, 14 Aug 2019 04:50:54 +0000 Subject: [Loris-dev] Upgrading to Loris 21 - new make file In-Reply-To: References: Message-ID: Hi Shen and Sotirios - just a note, For the 21 release, it's best to run the install script without sudoing it. (Shen, I believe we discovered a minor issue with the sudo last week #5008) Best, Christine On Tue, Aug 13, 2019 at 9:22 PM Shen Wang > wrote: Does it work? If still doesn?t work, try to remove project/config.xml file. Do sudo ./install.sh again. To reinstall Loris again. Shen Wang >?2019?8?13? ????9:02??? Hi Sotirios, step 1: sudo ./node_modules/.bin/eslint --fix /var/www/loris step 2: put the rest error files under this line [# Ignore until ESLint is run] in the .eslintignore file. step 3: sudo make On Tue, 13 Aug 2019 at 20:34, Sotirios Nikoloutsopoulos > wrote: I did the modifications, still there are errors. Thanks ???? ???, 14 ??? 2019 ???? 3:22 ?.?., ?/? Shen Wang > ??????: Hi Sotirios, I saw your output file, the config issue is gone. you can use [sudo npm run lintfix:javascript ] to fix these indent issues. If it still has errors. Then try modify this file .eslintignore with this # Ignore until ESLint is run modules/* modules/dataquery/ node_modules/* htdocs/js/components/* jsx/* # Ignore external libs htdocs/js/flot/* htdocs/js/jquery/* htdocs/js/jszip/* htdocs/js/modernizr/* htdocs/js/modules/* htdocs/js/react/* htdocs/js/shims/* htdocs/js/c3.min.js htdocs/js/d3.min.js htdocs/js/FileSaver.min.js then do sudo make. It should work. Regards Shen Sotirios Nikoloutsopoulos >?2019?8?13? ????7:54??? No, it didn't work, i also tried space/tabs because most of the errors where about indentation, also there are some errors about React. Thanks lorisadmin at hbp:/var/www/loris$ sudo ./node_modules/.bin/eslint --init ? How would you like to configure ESLint? Answer questions about your style ? Which version of ECMAScript do you use? ES2015 ? Are you using ES6 modules? Yes ? Where will your code run? Browser ? Do you use CommonJS? Yes ? Do you use JSX? Yes ? Do you use React? Yes ? What style of indentation do you use? Spaces ? What quotes do you use for strings? Single ? What line endings do you use? Unix ? Do you require semicolons? Yes ? What format do you want your config file to be in? JSON The config that you've selected requires the following dependencies: eslint-plugin-react at latest Successfully created .eslintrc.json file in /var/www/loris lorisadmin at hbp:/var/www/loris$ sudo make > sudo_make_output npm WARN The package prop-types is included as both a dev and production dependency. npm WARN optional SKIPPING OPTIONAL DEPENDENCY: fsevents at 1.2.4 (node_modules/fsevents): npm WARN notsup SKIPPING OPTIONAL DEPENDENCY: Unsupported platform for fsevents at 1.2.4: wanted {"os":"darwin","arch":"any"} (current: {"os":"linux","arch":"x64"}) npm ERR! code ELIFECYCLE npm ERR! errno 2 npm ERR! loris at 1.0.0 compile: `webpack` npm ERR! Exit status 2 npm ERR! npm ERR! Failed at the loris at 1.0.0 compile script. npm ERR! This is probably not a problem with npm. There is likely additional logging output above. npm ERR! A complete log of this run can be found in: npm ERR! /home/lorisadmin/.npm/_logs/2019-08-13T23_40_58_841Z-debug.log ???? ???, 14 ??? 2019 ???? 2:29 ?.?., ?/? Shen Wang > ??????: Hi Sotirios, When you do make command, please make sure with sudo at the beginning. [sudo make] If it still doesn't work for you. Then try the solutions below. solution 1: [???? 2019-08-13 19.21.15.png] Regards Shen On Tue, 13 Aug 2019 at 17:22, Sotirios Nikoloutsopoulos > wrote: I think that the files exists although i redownloaded the eslintrc.json i checked others files that had similar errors. lorisadmin at hbp:/var/www/loris$ ls -l ./node_modules/eslint-loader/index.js -rw-rw-r-- 1 lorisadmin lorisadmin 6463 ??? 26 1985 ./node_modules/eslint-loader/index.js lorisadmin at hbp:/var/www/loris$ ls -l .eslintrc.json -rw-rw-r-- 1 lorisadmin lorisadmin 84530 ??? 14 00:04 .eslintrc.json Maybe this can help Module build failed (from ./node_modules/eslint-loader/index.js): SyntaxError: Cannot read config file: /var/www/loris/.eslintrc.json Error: Unexpected token < in JSON at position 6 at JSON.parse () at loadJSONConfigFile (/var/www/loris/node_modules/eslint/lib/config/config-file.js:114:21) at loadConfigFile (/var/www/loris/node_modules/eslint/lib/config/config-file.js:230:26) at loadFromDisk (/var/www/loris/node_modules/eslint/lib/config/config-file.js:500:18) at Object.load (/var/www/loris/node_modules/eslint/lib/config/config-file.js:564:20) at Config.getLocalConfigHierarchy (/var/www/loris/node_modules/eslint/lib/config.js:227:44) at Config.getConfigHierarchy (/var/www/loris/node_modules/eslint/lib/config.js:179:43) at Config.getConfigVector (/var/www/loris/node_modules/eslint/lib/config.js:286:21) at Config.getConfig (/var/www/loris/node_modules/eslint/lib/config.js:329:29) at processText (/var/www/loris/node_modules/eslint/lib/cli-engine.js:162:33) at CLIEngine.executeOnText (/var/www/loris/node_modules/eslint/lib/cli-engine.js:596:17) at lint (/var/www/loris/node_modules/eslint-loader/index.js:237:17) at Object.module.exports (/var/www/loris/node_modules/eslint-loader/index.js:232:21) ERROR in ./modules/imaging_uploader/jsx/index.js Module build failed (from ./node_modules/eslint-loader/index.js): SyntaxError: Cannot read config file: /var/www/loris/.eslintrc.json Error: Unexpected token < in JSON at position 6 at JSON.parse () at loadJSONConfigFile (/var/www/loris/node_modules/eslint/lib/config/config-file.js:114:21) at loadConfigFile (/var/www/loris/node_modules/eslint/lib/config/config-file.js:230:26) at loadFromDisk (/var/www/loris/node_modules/eslint/lib/config/config-file.js:500:18) at Object.load (/var/www/loris/node_modules/eslint/lib/config/config-file.js:564:20) at Config.getLocalConfigHierarchy (/var/www/loris/node_modules/eslint/lib/config.js:227:44) at Config.getConfigHierarchy (/var/www/loris/node_modules/eslint/lib/config.js:179:43) at Config.getConfigVector (/var/www/loris/node_modules/eslint/lib/config.js:286:21) at Config.getConfig (/var/www/loris/node_modules/eslint/lib/config.js:329:29) at processText (/var/www/loris/node_modules/eslint/lib/cli-engine.js:162:33) at CLIEngine.executeOnText (/var/www/loris/node_modules/eslint/lib/cli-engine.js:596:17) at lint (/var/www/loris/node_modules/eslint-loader/index.js:237:17) at Object.module.exports (/var/www/loris/node_modules/eslint-loader/index.js:232:21) ???? ???, 13 ??? 2019 ???? 11:52 ?.?., ?/? John Saigle > ??????: HI Sotirios, The make_output.txt file shows webpack failing because it can't find the ESLint config file. Can you confirm whether the file `.eslintrc.json` exists within your loris root directory (usually `/var/www/loris/`)? When I delete my file I get the same errors as you. If you find that it's missing, you can make a local copy with the contents found here: https://github.com/aces/Loris/blob/e26a6ad49a73fcffef0cd73bb600c4d17b200b62/.eslintrc.json Once you know it exists, try running `make` again. Let us know if that moves you forward. Best, John On Tue, Aug 13, 2019 at 2:21 PM Sotirios Nikoloutsopoulos > wrote: Hi, I executed the commands for the node and now i am get the followings: lorisadmin at hbp:/var/www/loris$ make > ~/make_output npm WARN The package prop-types is included as both a dev and production dependency. npm WARN optional SKIPPING OPTIONAL DEPENDENCY: fsevents at 1.2.4 (node_modules/fsevents): npm WARN notsup SKIPPING OPTIONAL DEPENDENCY: Unsupported platform for fsevents at 1.2.4: wanted {"os":"darwin","arch":"any"} (current: {"os":"linux","arch":"x64"}) npm ERR! code ELIFECYCLE npm ERR! errno 2 npm ERR! loris at 1.0.0 compile: `webpack` npm ERR! Exit status 2 npm ERR! npm ERR! Failed at the loris at 1.0.0 compile script. npm ERR! This is probably not a problem with npm. There is likely additional logging output above. npm ERR! A complete log of this run can be found in: npm ERR! /home/lorisadmin/.npm/_logs/2019-08-13T18_12_05_378Z-debug.log make: *** [javascript] Error 2 Thanks, Sotirios ???? ???, 12 ??? 2019 ???? 10:19 ?.?., ?/? Christine Rogers, Ms. > ??????: Hi Sotirios, We've seen some users installing LORIS 21 or upgrading to 21 whose version of node doesn't work well with webpack, due to updated packages they're missing. If so, update your node : curl -sL https://deb.nodesource.com/setup_8.x | sudo -E bash - sudo apt-get install -y nodejs Let us know how that goes -- please send us output from the same log if any issues. Best, Christine On Thu, Aug 8, 2019 at 2:38 PM Sotirios Nikoloutsopoulos > wrote: It's not a disk space issue, as you can see below i have still 74GB available. lorisadmin at hbp:/var/www/loris$ df -h Filesystem Size Used Avail Use% Mounted on udev 2,9G 0 2,9G 0% /dev tmpfs 597M 8,6M 588M 2% /run /dev/sda1 98G 19G 74G 21% / Maybe we have to pass a flag to get into strict mode? as stated "SyntaxError: Block-scoped declarations (let, const, function, class) not yet supported outside strict mode" Thanks, Sotirios ???? ???, 8 ??? 2019 ???? 4:32 ?.?., ?/? Dave MacFarlane > ??????: It looks like the javascript snippet shown in the error message when trying to compile the js is truncated. Have you run out of disk space? On Thu, Aug 8, 2019 at 8:37 AM Sotirios Nikoloutsopoulos > wrote: Hi, I runned make and also included the file it reports at the end. lorisadmin at hbp:/var/www/loris$ make npm install npm WARN optional Skipping failed optional dependency /chokidar/fsevents: npm WARN notsup Not compatible with your operating system or architecture: fsevents at 1.2.9 npm WARN optional Skipping failed optional dependency /watchpack/chokidar/fsevents: npm WARN notsup Not compatible with your operating system or architecture: fsevents at 1.2.9 npm run compile > loris at 1.0.0 compile /var/www/loris > webpack /var/www/loris/node_modules/webpack/bin/webpack.js:86 let notify = ^^^ SyntaxError: Block-scoped declarations (let, const, function, class) not yet supported outside strict mode at exports.runInThisContext (vm.js:53:16) at Module._compile (module.js:374:25) at Object.Module._extensions..js (module.js:417:10) at Module.load (module.js:344:32) at Function.Module._load (module.js:301:12) at Function.Module.runMain (module.js:442:10) at startup (node.js:136:18) at node.js:966:3 npm ERR! Linux 4.15.0-55-generic npm ERR! argv "/usr/bin/nodejs" "/usr/bin/npm" "run" "compile" npm ERR! node v4.2.6 npm ERR! npm v3.5.2 npm ERR! code ELIFECYCLE npm ERR! loris at 1.0.0 compile: `webpack` npm ERR! Exit status 1 npm ERR! npm ERR! Failed at the loris at 1.0.0 compile script 'webpack'. npm ERR! Make sure you have the latest version of node.js and npm installed. npm ERR! If you do, this is most likely a problem with the loris package, npm ERR! not with npm itself. npm ERR! Tell the author that this fails on your system: npm ERR! webpack npm ERR! You can get information on how to open an issue for this project with: npm ERR! npm bugs loris npm ERR! Or if that isn't available, you can get their info via: npm ERR! npm owner ls loris npm ERR! There is likely additional logging output above. npm ERR! Please include the following file with any support request: npm ERR! /var/www/loris/npm-debug.log Makefile:14: recipe for target 'javascript' failed make: *** [javascript] Error 1 Thanks, Sotirios ???? ???, 7 ??? 2019 ???? 5:41 ?.?., ?/? Christine Rogers, Ms. > ??????: Hi Sotirios, Thanks, have you tried all of these steps? - clear your browser cache (and refresh a few times) - delete any files in your smarty/templates_c directory (this will clear the template cache - do Not touch smarty/templates/) - run `make` (per the 21 release notes, this replaces the composer commands used in previous releases to update your dependencies) - restart apache (doesn't hurt) Let us know how it goes -- let us know what difference you see after, with your logs. A lso please send us your Config path settings (see these Troubleshooting Queries) if you're still seeing front-end issues. Thanks, Christine On Wed, Aug 7, 2019 at 8:02 AM Sotirios Nikoloutsopoulos > wrote: Hi, lorisadmin at hbp:/var/www/loris$ sudo cat /var/log/apache2/error.log [Wed Aug 07 07:35:02.422501 2019] [mpm_prefork:notice] [pid 1267] AH00163: Apache/2.4.18 (Ubuntu) OpenSSL/1.0.2g configured -- resuming normal operations [Wed Aug 07 07:35:02.422514 2019] [core:notice] [pid 1267] AH00094: Command line: '/usr/sbin/apache2' And as for the access.log the content are empty lorisadmin at hbp:/var/www/loris$ sudo ls -l /var/log/apache2/access.log lorisadmin at hbp:/var/www/loris$ sudo ls -l /var/log/apache2/access.log -rw-r----- 1 root adm 0 ???? 28 14:09 /var/log/apache2/access.log Also i noticed a loris_access.log. The only non-blank pages are: mri_violations, dataquery does not exist at all, statistics, data_team_helper, genomic_browser, configuration and server_processes_manager/ prints "Required configuration settings for Server Processes Manager are missing. Cannot continue." Thanks, Sotirios ???? ???, 6 ??? 2019 ???? 10:13 ?.?., ?/? Christine Rogers, Ms. > ??????: Hi Sotirios and LORIS community -- When upgrading to brand-new release 21 -- just a reminder to follow the release notes and run the new make file to update your dependencies (instead of using composer commands). We've also updated the Wiki page to clarify that the release notes for each version will tell you what to run. If your current version is not the last release (20.3), it's still important to upgrade to each minor release increment (e.g. 20.2, 20.3) before making the leap to 21.0. If you're getting blank pages, post-upgrade -- Try clearing your cache. Got questions or feedback e.g. on the Release Notes? please don't hesitate to let us know. Thanks, Christine The LORIS team On Tue, Aug 6, 2019 at 10:09 AM Christine Rogers, Ms. > wrote: Hi Sotirios, Could you also let us know -- on which pages is content visible, and on which pages/modules is content not visible for you? Thanks, Christine On Tue, Aug 6, 2019 at 9:54 AM Christine Rogers, Ms. > wrote: Thanks Sotirios, That's good to know. It sounds like you've checked that your /var/www/loris/project/config.xml file get populated properly. Please send us the last few errors you're seeing in your apache error log file, and your config paths and we can see what's happening with your front end -- Run these Troubleshooting Queries to get your config path settings, given your front end is not displaying fully. The Loris-MRI repo 21 install/upgrade would then be your next steps. Best, Christine On Tue, Aug 6, 2019 at 7:53 AM Sotirios Nikoloutsopoulos > wrote: I am using a VM. What i did was: 1) Download the files from https://github.com/aces/Loris and replace them to my existing /vaw/www/loris folder. 2) Execute the composer install --no-dev and then composer dump-autoload as mentioned here https://github.com/aces/Loris/wiki/Updating-your-LORIS. 3) Execute install.sh from /var/www/loris/tools and because LORIS already existed i moved a .config file, then re-executed the install.sh successfully 4 ) As for the database, i dropped the schema and i executed the installdb.php ???? ???, 5 ??? 2019 ???? 5:22 ?.?., ?/? Christine Rogers, Ms. > ??????: Hi Sotorios, Thanks - when you re-installed did you start on a fresh root path / VM or might some of your old system setting still apply? (And if you did any steps similar to an upgrade, did you follow the Upgrade steps in the Release Notes, from both repos?) About the TR_range column - it was recently split (MRI pr339) split into TR_min and _max columns. Given the code was trying to query TR_range which does not exist in your mri_protocol table, double-check which version of the Loris repo (tables) and the Loris-MRI repo (code) you have installed to ensure they match. Christine On Mon, Aug 5, 2019 at 9:06 AM Sotirios Nikoloutsopoulos > wrote: I reinstalled LORIS to 21 version and now the content is not visible at all at most pages. [image.png] ???? ???, 5 ??? 2019 ???? 3:19 ?.?., ?/? Sotirios Nikoloutsopoulos > ??????: Hi, Is it easy to upgrade to Loris 21? Also the following fails because the line 1985 of NeuroDB/MRIProcessingUtility.pm query mri_protocol which doesn't have TR_range https://github.com/aces/Loris/blob/21.0-release/SQL/0000-00-00-schema.sql#L556 [image.png] lorisadmin at hbp:/data/loris/bin/mri$ ./batch_uploads_imageuploader -profile prod < ~/Desktop/input.txt > log.txt Use of uninitialized value $_ in pattern match (m//) at ./batch_uploads_imageuploader line 147. base is DCC0000_258024_V1 path is /data/incoming/ type is .tar.gz fullpath is /data/incoming/DCC0000_258024_V1.tar.gz DBD::mysql::st execute failed: Unknown column 'TR_range' in 'where clause' at /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line 1985. DBD::mysql::st fetchrow_array failed: fetch() without execute() at /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line 1986. Use of uninitialized value $count_mri_protocol in numeric gt (>) at /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line 1995. DBD::mysql::st execute failed: Unknown column 'TR_range' in 'field list' at /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 562. Can't exec "mail": No such file or directory at /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 721. print() on closed filehandle MAIL at /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 722. print() on closed filehandle MAIL at /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 723. print() on closed filehandle MAIL at /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 724. print() on closed filehandle MAIL at /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 725. No Mincs inserted Thanks, Sotirios ???? ???, 3 ??? 2019 ???? 1:08 ?.?., ?/? Christine Rogers, Ms. > ??????: Hi Sotirios, First, just a note: we've released LORIS 21 this week with some major new features and cleanup -- especially if you are early in your setup phase, check out the Release notes for both the LORIS and Loris-MRI repos. Thanks for your screenshots -- your empty mri_protocol table should be at the root of these issues : The mri_protocol table must be populated in order for your scans to be registered in LORIS -- it serves as a whitelist for the insertion pipeline which filters out scans that aren't identified or matched to scan types in this table. By default, this table is populated with entries for t1, t2, fMRI and DTI (Insert statements for 21 release branch are here) Feel free to restore our default records and broaden their parameters to match all your scan types. re Defaced, native, selected -- these filter the scans displayed as you move to the next page (View Session), instead of viewing "all types" of scans from a given session : * "defaced" means that a defacing script has masked the subject's face in the volume (for patient privacy) * "native" means that no pre-processing has been performed on the scan (it's raw data), * "selected" will show only volumes that have been QC'd and "selected" as the best of their type -- used to display only the best quality T1 image instead of all T1s acquired in a session, e.g. re QC Comments -- Once you have successfully loaded scans (matched to the mri_protocol table), you'll be able to use the Imaging Browser's View Session subpage to enter/view QC comments on each volume, or for each visit. These are stored directly in the database, and linked to each scan. (Table name: feedback_mri_comments) (Visit-level QC comments are linked to the session.) For a walkthrough of the Imaging setup - please see the Imaging Setup guide - An old LORIS walkthrough video can also walk you through some of the Imaging front-end features, starting at 8:00 LORIS' imaging modules have been updated many times since this video, but the functionality and workflow is similar. Let us know how it goes once you have entries in your mri_protocol table - Best, Christine On Fri, Aug 2, 2019 at 7:58 AM Sotirios Nikoloutsopoulos > wrote: Hi Christine, In the candidate_list page i can see this patient [image.png] If i press the link under PSCID i get to see [image.png] and if i press the link under Scan Done it redirects me to imaging_browser [image.png] At the mri_violations page i also see No results ( neither on resolved / not resolved ). At the imaging_uploader i can see the record that failed. [image.png] If i click on the tarchive info i get to see the Protocol Name which i think is the acquisition we wanted? [image.png] Also my mri_protocol table is empty. Furthermore i would like to ask about the defaced, native, selected. What exactly is native and selected? And where are the qc comments stored? [image.png] Finally a walkthrough would be helpful. Thanks, Sotirios ???? ???, 30 ???? 2019 ???? 8:29 ?.?., ?/? Christine Rogers, Ms. > ??????: Hi Sotirios, Glad to hear you're making progress with the visit labels. To follow up on your last few emails: a- The Wiki's Setup Guide contains Sample insert statements for the Visit Windows table. As Cecile mentioned, the consistency of visit label format is important: V01, v01, V1, 01 -- whichever you select to use is fine; we use V01 by default across all documentation. b- For Password reset, there is a script in the tools/ directory so that a back-end administrator can reset any front-end user password, including Admin. (See info on setting up / resetting User passwords in the Wiki's Setup Guide) c- The minc file not being registered -- due to AcquisitionProtocol unknown. This means the SeriesDescription (Acquisition Protocol) in you Dicom header was not matched to any scan listed in the mri_protocol database table. (In the online Loris-MRI Troubleshooting Guide, this is Table 3, 2nd-last item "no MINCs inserted"). The MRI Violations module (Readme here) will show you the details of this mismatch -- Go to the module (under the Imaging menu), find your scan and click the link "Could not identify scan type" -- in the next subpage you can compare the scan's actual parameters against the mri_protocol table. To resolve this, adjust your mri_protocol table values or perhaps ensure your DICOMs are labelled consistently. Let us know if this works for you -- we can also walk you through an example of non-identified scans on Demo.loris.ca (MRI Violations module). Best, Christine The LORIS team On Tue, Jul 30, 2019 at 10:47 AM Sotirios Nikoloutsopoulos > wrote: I hope this is sufficient as the error for the visit label disappeared. [image.png] Please see the attached file. Also something i found. lorisadmin at hbp:/data/loris/bin/mri$ cat /data/loris/data//logs/TarLoad-17-39-xubBdv.log ==> Loading file from disk /tmp/TarLoad-17-39-UyQcG2/dcc0000_258024_v1_20121205_102108_501e1_mri.mnc --> mapping DICOM parameter for /tmp/TarLoad-17-39-UyQcG2/dcc0000_258024_v1_20121205_102108_501e1_mri.mnc ==> computing md5 hash for MINC body. --> md5: 6b1202fd63e29de4c9be1cd9925888a5 ==> verifying acquisition protocol Acquisition protocol is unknown --> The minc file cannot be registered since the AcquisitionProtocol is unknown ???? ???, 30 ???? 2019 ???? 4:58 ?.?., ?/? Sotirios Nikoloutsopoulos > ??????: Ok I fixed the login problem by using a known hash and by deleting the rows from the login_history i was able to login. ???? ???, 30 ???? 2019 ???? 4:50 ?.?., ?/? Sotirios Nikoloutsopoulos > ??????: Hi, there was no visit label 01 in the Visit_Windows table and i don't know how to insert it because the record requires lots of attributes. Also the system for a reason asked me to update my password and now i don't remember it and my account got suspended. Is there a way to reset it or set a simple password? I updated the password hash in the users table by using the hash from another LORIS setup we had and i still couldn't login ( also the attribute password is always NULL and the expiration date is 1999-01-01 for some reason ). Thanks ???? ???, 29 ???? 2019 ???? 5:21 ?.?., ?/? Cecile Madjar > ??????: Hi Sotirios, Can you try adding the visit label v01 to the Visit_Windows table? However, I noticed that in a previous dataset, the label was V1. Does that refer to the same visit? If so, you might want to harmonize the visit labels so they are all the same across datasets for a given timepoint, meaning you will need to relabel scans when the visit label is different but referring to the same visit label (v01 = V1 etc...). Hope this helps, C?cile On Mon, Jul 29, 2019 at 10:15 AM Sotirios Nikoloutsopoulos > wrote: Hi, Could you help me with the "Visit label does not exist"? I had changed $subjectID{'createVisitLabel'} to 1 as you had suggested but it appears that this problem hasn't been resolved yet. lorisadmin at hbp:/data/loris/bin/mri$ cat /data/loris/data//logs/TarLoad-14-58-9Xog7H.log ==> Loading file from disk /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc --> mapping DICOM parameter for /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc --> using user-defined filterParameters for /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc Candidate Mismatch Error is Visit label does not exist -> WARNING: This candidate was invalid. Logging to MRICandidateErrors table with reason Visit label does not exist Thank you, Sotirios ???? ???, 26 ???? 2019 ???? 3:02 ?.?., ?/? Sotirios Nikoloutsopoulos > ??????: Hi Cecile, The Center error was fixed. Still the insertion of mincs fails. Please see the output.txt file i attached. Also is there something else i need to change at the paths configuration? Thank you, Sotirios ???? ???, 25 ???? 2019 ???? 6:55 ?.?., ?/? Cecile Madjar > ??????: Hi Sotirios, We are making progress! I have a feeling this error comes from the fact that your psc table does not have the MRI_alias populated for the DCC site. Running the following query in the mysql database should fix this: UPDATE psc SET MRI_alias="DCC", Alias="DCC" WHERE Name="Data Coordinating Center"; Repeat the same with all your sites (make sure to change the Aliases between sites, they should all be unique). Let me know how it goes! Best, C?cile On Thu, Jul 25, 2019 at 11:43 AM Sotirios Nikoloutsopoulos > wrote: Dear Cecile, You were right about your guesses. I did the modifications you suggested, i still get the "no mincs inserted" error, now i am getting the "No center found this candidate" error ( how do i fix that? from what i see the .dcm files contains a 'Institution Name', is that the center? ), so i guess that's why the validation fails, but i changed the force variable of tarchiveLoader to 1, shouldn't it have inserted the mincs then? Also it is optional to have a mail server, right? ( from what i see the mail error does not affect the $valid_study, so i assume we are okay with that ) Thank you a lot, Sotirios ???? ???, 25 ???? 2019 ???? 5:48 ?.?., ?/? Cecile Madjar > ??????: Hi Sotirios, From what I understand, I believe you just need to update a few config settings from the frontend in the Config module (under the Admin menu). [Screen Shot 2019-07-25 at 10.31.35 AM.png] Then go to the Paths section of the config module and update the "LORIS-MRI code" config setting to /data/loris/bin/mri (my guess is that currently, it is set to /data/LORIS/data) and click on the submit button. [Screen Shot 2019-07-25 at 10.32.50 AM.png] Then, go to Imaging Pipeline section of the Configuration module and update the "Loris-MRI Data Directory" to /data/loris/data/ (my guess is that it is empty at the moment in your database which is why $data_dir is not defined when you run the tarchiveLoader step of the insertion pipeline). [Screen Shot 2019-07-25 at 10.40.52 AM.png] Finally, I took a look at your environment file and it might be a good idea to update your PERL5LIB variable to the following (it has been added to the code a few releases ago as we realized this was needed for the libraries. Not sure which version of LORIS-MRI you are using but it does not hurt to update this variable to what I suggest below): export PERL5LIB=/data/loris/bin/mri/uploadNeuroDB:/data/loris/bin/mri/dicom-archive:$PERL5LIB Hope this helps. Sorry you are experiencing so much trouble setting things up. We probably need to update our WIKI. Best, C?cile On Thu, Jul 25, 2019 at 9:48 AM Sotirios Nikoloutsopoulos > wrote: The "Loris-MRI Data Directory" should be in the environment file? ???? ???, 25 ???? 2019 ???? 12:59 ?.?., ?/? Sotirios Nikoloutsopoulos > ??????: The scripts are located in /data/loris/bin/mri/. Somewhere I might have messed something up but i remember following the instructions in the wiki.For example when i tried to execute the batch_uploads_imageuploader perl script the line my $command = "$bin_dir/uploadNeuroDB/imaging_upload_file.pl " was pointing to an invalid path, for example: it was repeating a pattern and had LORIS instead of loris ( i think the mistake was that in the wiki it suggested to use $PROJECT for the name of the folder and i choosed 'loris' https://github.com/aces/Loris/wiki/Imaging-Database ). See also the in image for the modification i did. Also i didn't find the section to config the $data_dir variable. Thank you, Sotirios ???? ???, 24 ???? 2019 ???? 6:05 ?.?., ?/? Cecile Madjar > ??????: Hi Sotirios, It looks like you have one Config setting not set (based on the first error message you got when running it the first time). You need to set a value for "Loris-MRI Data Directory" in the Config module under the Imaging pipeline section (from what I can see, it would be /data/loris/data/ for your setup). The reason you got that error message the second time is that the pipeline checks if the DICOM study was already inserted in the tarchive table. Since you ran the study once already, the study is inserted into the tarchive, hence the message. However, the pipeline did not complete as the MINC files were not created and inserted into the files/parameter_file table. In order to continue the insertion, you will then need to run the tarchiveLoader command suggested in the terminal during the second run: /data/LORIS/data//uploadNeuroDB/tarchiveLoader -globLocation -profile prod /data/loris/data/tarchive//2012/DCM_2012-12-05_ImagingUpload-17-43-ZUEFjb.tar -verbose Finally, I am a bit confused by your setup. Where are the scripts located? In /data/loris/bin/mri or /data/loris/data? It feels like the Config setting "LORIS-MRI code" in the Paths section was set to "/data/LORIS/data" but it should have been set to the directory where the scripts are located (most probably /data/loris/bin/mri). Hope this helps, C?cile On Wed, Jul 24, 2019 at 10:55 AM Sotirios Nikoloutsopoulos > wrote: Ok first i execute this command: "lorisadmin at hbp:/data/loris/bin/mri$ ./batch_uploads_imageuploader -profile prod < ~/Desktop/input.txt > log.txt Use of uninitialized value $data_dir in concatenation (.) or string at ./batch_uploads_imageuploader line 143. Use of uninitialized value $data_dir in concatenation (.) or string at ./batch_uploads_imageuploader line 143. Use of uninitialized value $_ in pattern match (m//) at ./batch_uploads_imageuploader line 147. base is DCC0000_258024_V01 path is /data/incoming/ type is .tar.gz fullpath is /data/incoming/DCC0000_258024_V01.tar.gz source /tmp/ImagingUpload-17-43-ZUEFjb targetlocation /data/loris/data/tarchive Use of uninitialized value $data_dir in concatenation (.) or string at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 256. Use of uninitialized value $data_dir in concatenation (.) or string at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 284. Use of uninitialized value $data_dir in concatenation (.) or string at /data/loris/bin/mri/uploadNeuroDB/tarchive_validation.pl line 219. Use of uninitialized value $data_dir in concatenation (.) or string at /data/loris/bin/mri/uploadNeuroDB/minc_insertion.pl line 270. Use of uninitialized value $data_dir in concatenation (.) or string at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 711. Can't exec "mail": No such file or directory at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 721. print() on closed filehandle MAIL at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 722. print() on closed filehandle MAIL at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 723. Use of uninitialized value $data_dir in concatenation (.) or string at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 724. print() on closed filehandle MAIL at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 724. print() on closed filehandle MAIL at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 725. Use of uninitialized value $data_dir in concatenation (.) or string at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 735. No Mincs inserted The tarchiveLoader insertion script has failed. Running now the following command: /data/loris/data/uploadNeuroDB/imaging_upload_file.pl -profile prod -upload_id 3 /data/incoming/DCC0000_258024_V01.tar.gz -verbose" I inserted the VisitLabel, but still the Mincs are not inserted and i am getting this error "lorisadmin at hbp:/data/loris/bin/mri$ /data/loris/data/uploadNeuroDB/imaging_upload_file.pl -profile prod -upload_id 3 /data/incoming/DCC0000_258024_V01.tar.gz -verbose find -path \/tmp\/ImagingUpload\-17\-45\-5MsWEd -name '__MACOSX' -delete Spool message is: The Scan for the uploadID 3 has already been run with tarchiveID: 7. To continue with the rest of the insertion pipeline, please run tarchiveLoader from a terminal as follows: /data/LORIS/data//uploadNeuroDB/tarchiveLoader -globLocation -profile prod /data/loris/data/tarchive//2012/DCM_2012-12-05_ImagingUpload-17-43-ZUEFjb.tar -verbose" Which files should i delete? I thought that deleting the files from the tarchive was enough. And i executed the last proposed command to continue to rest of the insertion pipeline ( check the image ). Thank you ???? ???, 24 ???? 2019 ???? 5:05 ?.?., ?/? Cecile Madjar > ??????: Hi Sotirios, Sorry I was not clear before. Every visits of candidates are created in the session table with one entry per CandID/VisitLabel. So if the imaging pipeline created visits in the session table (that are not attached to instruments) and you want to clean your database completely, you can delete entries in that table as well. Regarding your point 2, the imaging pipeline can create the visit in the session table as long as the visit label is present in the Visit_Windows table (which means the visit label stored in the PatientName is a valid visit label). However, in your prod file, if the variable $subjectID{'createVisitLabel'} is set to 1 for candidates, the visit label should be created in the Visit_Windows table I believe. Here is the line of the prod file you would need to change. In general, we prefer populating the Visit_Windows table and set the $subjectID{'createVisitLabel'} to 0 for candidate data to avoid insertion of badly labelled MRI data that are complex to relabel. Finally, regarding the candidate creation, if you execute the following steps, the pipeline should be able to create candidates: - set in the Imaging Pipeline section of the config module the config setting "Upload creation of candidates" to Yes - manually transfer the scans to the LORIS server instead of uploading it via the imaging browser - run batch_imaging_upload.pl as you did until now. Hope this helps! Best, C?cile On Wed, Jul 24, 2019 at 8:47 AM Sotirios Nikoloutsopoulos > wrote: About my second question i replaced the name of the patient in the .dcm files and now i am getting an error that the visit label does not exist. I thought it was supposed to be automatically created. "Done adding archive info into database /data/LORIS/data//uploadNeuroDB/tarchiveLoader -globLocation -profile prod /data/loris/data/tarchive//DCM_2012-12-05_ImagingUpload-15-42-yUwQQV.tar -verbose md5sum /data/loris/data/tarchive/DCM_2012-12-05_ImagingUpload-15-42-yUwQQV.tar PSCID is: DCC0000 CandID id: 258024 visit_label is: V1 PSCID is: DCC0000 CandID id: 258024 visit_label is: V1 candidate id 258024 => No Visit labelVisit label does not exist Set centerID = 1 PSCID is: DCC0000 CandID id: 258024 visit_label is: V1 PSCID is: DCC0000 CandID id: 258024 visit_label is: V1 Number of MINC files that will be considered for inserting into the database: 1 log dir is /logs and log file is /logs/TarLoad-15-42-L6pocU.log PSCID is: DCC0000 CandID id: 258024 visit_label is: V1 PSCID is: DCC0000 CandID id: 258024 visit_label is: V1 candidate id 258024 => No Visit label Cleaning up temp files: rm -rf /tmp/TarLoad-15-42-J2rQms/ImagingUpload-15-42-yUwQQV*" ???? ???, 24 ???? 2019 ???? 3:38 ?.?., ?/? Sotirios Nikoloutsopoulos > ??????: Hi, 1) What are the records in the session table? 2) I tried to upload a non-phantom file like this input_file.txt: /data/incoming/DCC0000_258024_V1.tar.gz N DCC0000_258024_V1 Terminal: ./batch_uploads_imageuploader -profile prod < ~/Desktop/input.txt > log.txt and i get the following error in the log.txt file "Running now the following command: /data/loris/data/uploadNeuroDB/imaging_upload_file.pl -profile prod -upload_id 7 /data/incoming/DCC0000_258024_V1.tar.gz -verbose find -path \/tmp\/ImagingUpload\-14\-56\-FeLCB4 -name '__MACOSX' -delete Spool message is: The PatientName read from the DICOM header does not start with DCC0000_258024_V1 from the mri_upload table " and the spool message is repeated for each .dcm file. Should i preprocess every .dcm file and change the PatientName to "DCC0000_258024_V1"? 3) As far as it concerns the candidate profile i have to create a new one each time before i try to upload a file? Is there already a way to create a candidate profile and get the DCCID and PSCID without the user interface? Thank you, Sotirios ???? ???, 18 ???? 2019 ???? 5:00 ?.?., ?/? Cecile Madjar > ??????: Hi Sotirios, See answers to your questions below. About the 1st case we had a dicom with a blank studyUID, maybe someone accidentally removed it. That is strange. Something must have been done to the DICOM files. I have never seen a study with no StudyUID out of the scanner. Usually, you need to manually erase it with some tool. However, DICOMs never cease to surprise me... Some other questions: 1) What are the steps to remove all of my patients and uploads?: because i want to try to reupload all the testing dicoms we had with a clean database. Release 21.0 of LORIS-MRI will offer a script to remove all the entries and files specific to an upload. However, this release is not yet out. Hopefully in the next few weeks. In the meantime, since your case is particular and that you just want to start with a clean database, the following deletes should work (hopefully I won't forget any tables): delete from mri_violations_log; delete from mri_protocol_violated_scans; delete from MRICandidateErrors; delete from parameter_file; delete from files_qcstatus; # (if you played with the QC part of the imaging browser for testing) delete from feedback_mri_comments; # (if you played with the QC part of the imaging browser for testing) delete from tarchive_series; delete from tarchive_files; delete from mri_upload; delete from tarchive; delete from mri_scanner; delete from candidate where PSCID="scanner"; I don't know if you want to also delete entries in the session and candidate table too? 2) We do not need to create the profile of a patient ( are the patients stored in the candidate table? because i can't see the ghosts ), because will it automatically be created when importing a dicom? I am not sure I understand fully this question. All candidates are stored in the candidate table. The phantom scans however are attached to a scanner candidate depending on where the scan happened. It is a bit of a weird concept that we have to redesign eventually but never got a chance to get to it. Hopefully this answered your question, otherwise, don't hesitate to let me know. 3) What is the difference between uploading a dicom as phantom instead of importing as PSCCID_DCCID_VisitLabel? When you upload the scan as PSCID_DCCID_VisitLabel, there is a check that makes sure the candidate IDs and visit label are valid at the time of upload. When you upload a scan as phantom, it expects that the DICOM field PatientName and uploaded filename contains the string "phantom". We enforced this behaviour on the imaging uploader side in recent releases but I can't remember which one. Probably the upcoming 21.0 release. All those verifications might seem cumbersome but they are here to ensure that the files inserted are all valid and labelled properly as it is a bit messy to have to delete files that were wrongly labelled. At least, the delete script present in release 21.0 will make this process easier but it is still good practice to verify those things. Thank you, With pleasure. Hopefully the answers to your questions will be helpful. Best, C?cile PS: loris-dev mailing list: you will find the initial answer I gave Sotirios below. I forgot to cc the loris-dev in my earlier reply... ???? ???, 16 ???? 2019 ???? 12:02 ?.?., ?/? Cecile Madjar > ??????: Dear Sotirios, Thank you for reaching out. Since your email was already organized in points, I will reply directly below your questions below. Best, C?cile 1) What do we do when the StudyUID is blank on the header? https://github.com/aces/Loris-MRI/blob/minor/docs/AppendixA-Troubleshooting_guideline.md There solution provided at the table 3 does not guide us how to find the information ( is possible ). The StudyUID is the field used in our pipeline at the moment to check whether a DICOM study was already inserted into LORIS with that same StudyUID since it is supposed to be unique for every single study. Currently, we do not support insertion of DICOM studies if they do not have a StudyUID associated with them. Is there a specific reason why the StudyUID is blank in the DICOM headers in your DICOM files? Did they go through some processes before upload to LORIS? 2) When i am about to upload a non-phanton case i need a 'Visit Label'. Is there already a script that can create a new visit label for a specific Candidate, so i can provide it as input afterwards to the batch_uploads_imageuploader ( See option 5.1.3 https://github.com/aces/Loris-MRI/blob/minor/docs/05-PipelineLaunchOptions.md ) I am not sure if the front-end allows for it but if you use batch_uploads_imageuploader, the insertion scripts could create the visit label for you. However, it does need to be included in the patient name in order for the script to know which label it should use. For example: you upload V02 for MTL0123 (DCCID: 456789) but V02 was not yet created for MTL0123; the insertion scripts will create a V02 visit for MTL0123 if the PatientName field for the dataset is MTL0123_456789_V02 with Stage marked as "Not Started". However, note that for the script to create the visit for the candidate, you have to make sure that all the visit label of your projects were inserted in the Visit_Windows table (otherwise, the visit will never be created as they were not specified as being part of the list of visit label to expect). So in the example above, you should have one row in Visit_Windows with Visit_label="V02" set. 3) Section 4.3 https://github.com/aces/Loris-MRI/blob/minor/docs/04-Scripts.md What do we do when the folder contains multiple mnc files? This is a case by case. Most of the time, the MINC files that failed insertion into the imaging browser end up in the MRI violation module where you can see what went wrong with the acquisitions not inserted. If you notice that the MINC file should be inserted as a specific protocol, you can force the insertion as explained in section 4.3. In your case, I have a feeling that you want to be able to insert MINC files that did not go through the whole pipeline insertion (DICOM archival, then dcm2mnc, then protocol identification, then insertion...). In theory, you could call minc_insertion.pl on any MINC file, provided you have at least the following information: - path to the MINC file - uploadID associated with the MINC files or DICOM archive path from which those MINC files were created from Then the minc_insertion.pl script will do the subject information and protocol validation etc... If all the MINC files come from the same uploadID or TarchiveID, then you could run a loop in bash calling the minc_insertion.pl script like this for files deriving from uploadID=1: ls /path/to/mnc/folder/* | while read f; do minc_insertion.pl -profile prod -uploadID 1 -mincPath $f; done Thank you, Hope this helped! _______________________________________________ Loris-dev mailing list Loris-dev at bic.mni.mcgill.ca https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev -- christine.rogers at mcgill.ca McGill Centre for Integrative Neuroscience | MCIN.ca Montreal Neurological Institute McGill University | Montreal | Canada -- christine.rogers at mcgill.ca McGill Centre for Integrative Neuroscience | MCIN.ca Montreal Neurological Institute McGill University | Montreal | Canada _______________________________________________ Loris-dev mailing list Loris-dev at bic.mni.mcgill.ca https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev -- christine.rogers at mcgill.ca McGill Centre for Integrative Neuroscience | MCIN.ca Montreal Neurological Institute McGill University | Montreal | Canada _______________________________________________ Loris-dev mailing list Loris-dev at bic.mni.mcgill.ca https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev -- christine.rogers at mcgill.ca McGill Centre for Integrative Neuroscience | MCIN.ca Montreal Neurological Institute McGill University | Montreal | Canada _______________________________________________ Loris-dev mailing list Loris-dev at bic.mni.mcgill.ca https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev -- christine.rogers at mcgill.ca McGill Centre for Integrative Neuroscience | MCIN.ca Montreal Neurological Institute McGill University | Montreal | Canada _______________________________________________ Loris-dev mailing list Loris-dev at bic.mni.mcgill.ca https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev -- christine.rogers at mcgill.ca McGill Centre for Integrative Neuroscience | MCIN.ca Montreal Neurological Institute McGill University | Montreal | Canada _______________________________________________ Loris-dev mailing list Loris-dev at bic.mni.mcgill.ca https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev -- christine.rogers at mcgill.ca McGill Centre for Integrative Neuroscience | MCIN.ca Montreal Neurological Institute McGill University | Montreal | Canada _______________________________________________ Loris-dev mailing list Loris-dev at bic.mni.mcgill.ca https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev _______________________________________________ Loris-dev mailing list Loris-dev at bic.mni.mcgill.ca https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev -- christine.rogers at mcgill.ca McGill Centre for Integrative Neuroscience | MCIN.ca Montreal Neurological Institute McGill University | Montreal | Canada _______________________________________________ Loris-dev mailing list Loris-dev at bic.mni.mcgill.ca https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev _______________________________________________ Loris-dev mailing list Loris-dev at bic.mni.mcgill.ca https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev -- Shen Wang Loris Developer Montreal Neurological Institute McGill University -- Shen Wang Loris Developer Montreal Neurological Institute McGill University -- Shen Wang Loris Developer Montreal Neurological Institute McGill University _______________________________________________ Loris-dev mailing list Loris-dev at bic.mni.mcgill.ca https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev -- christine.rogers at mcgill.ca McGill Centre for Integrative Neuroscience | MCIN.ca Montreal Neurological Institute McGill University | Montreal | Canada -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: ???? 2019-08-13 19.21.15.png Type: image/png Size: 508603 bytes Desc: ???? 2019-08-13 19.21.15.png URL: From sotirisnik at gmail.com Wed Aug 14 08:26:38 2019 From: sotirisnik at gmail.com (Sotirios Nikoloutsopoulos) Date: Wed, 14 Aug 2019 15:26:38 +0300 Subject: [Loris-dev] Upgrading to Loris 21 - new make file In-Reply-To: References: Message-ID: Hi, Step 1 worked and the indentation errors were fixed. About step2 i added all of these( there are more to include in the list) these to .eslintignore which were reported to fail at being built, but they still appear on the errors at the make_output file. /jsx/DynamicDataTable.js /jsx/StaticDataTable.js /jsx/MultiSelectDropdown.js /jsx/Breadcrumbs.js /jsx/Form.js /jsx/Markdown.js /modules/media/jsx/mediaIndex.js /modules/issue_tracker/jsx/issueTrackerIndex.js /modules/issue_tracker/jsx/index.js /modules/candidate_parameters/jsx/CandidateParameters.js /modules/configuration/jsx/SubprojectRelations.js /modules/conflict_resolver/jsx/conflictResolverIndex.js /modules/conflict_resolver/jsx/resolvedConflictsIndex.js /modules/bvl_feedback/jsx/react.behavioural_feedback_panel.js /modules/dataquery/jsx/react.tabs.js /modules/document_repository/jsx/docIndex.js /modules/instrument_builder/jsx/react.instrument_builder.js /modules/imaging_uploader/jsx/index.js /modules/datadict/jsx/dataDictIndex.js /modules/bvl_feedback/jsx/react.behavioural_feedback_panel.js /modules/new_profile/jsx/NewProfileIndex.js /modules/examiner/jsx/examinerIndex.js /modules/configuration/jsx/SubprojectRelations.js /modules/data_team_helper/jsx/behavioural_qc_module.js /modules/acknowledgements/jsx/acknowledgementsIndex.js /modules/candidate_parameters/jsx/CandidateParameters.js /modules/imaging_browser/jsx/ImagePanel.js /modules/mri_violations/jsx/mri_protocol_violations_columnFormatter.js /modules/mri_violations/jsx/mri_protocol_check_violations_columnFormatter.js /modules/genomic_browser/jsx/profileColumnFormatter.js /modules/dataquery/jsx/react.tabs.js /jsx/MultiSelectDropdown.js /modules/mri_violations/jsx/columnFormatterUnresolved.js /modules/dataquery/jsx/react.sidebar.js /modules/dataquery/jsx/react.fieldselector.js /modules/quality_control/jsx/qualityControlIndex.js /modules/dataquery/jsx/react.paginator.js /modules/instrument_builder/jsx/react.questions.js /modules/dataquery/jsx/react.filterBuilder.js /modules/conflict_resolver/jsx/conflictResolverIndex.js /jsx/PaginationLinks.js /modules/conflict_resolver/jsx/resolvedConflictsIndex.js /modules/dataquery/jsx/react.app.js /modules/candidate_list/jsx/onLoad.js /jsx/Form.js /modules/publication/jsx/publicationIndex.js /modules/server_processes_manager/jsx/server_processes_managerIndex.js /modules/imaging_browser/jsx/imagingBrowserIndex.js /modules/issue_tracker/jsx/issueTrackerIndex.js /modules/survey_accounts/jsx/surveyAccountsIndex.js /modules/data_integrity_flag/jsx/dataIntegrityFlagIndex.js /modules/instrument_manager/jsx/instrumentManagerIndex.js /modules/media/jsx/mediaIndex.js /modules/user_accounts/jsx/userAccountsIndex.js /modules/help_editor/jsx/help_editor.js /modules/dicom_archive/jsx/dicom_archive.js /modules/mri_violations/jsx/columnFormatter.js /modules/brainbrowser/jsx/Brainbrowser.js /node_modules/babel-loader/lib/index.js /modules/document_repository/jsx/editFormIndex.js Thanks ???? ???, 14 ??? 2019 ???? 7:50 ?.?., ?/? Christine Rogers, Ms. < christine.rogers at mcgill.ca> ??????: > Hi Shen and Sotirios - just a note, > > For the 21 release, it's best to run the install script without sudoing > it. > > (Shen, I believe we discovered a minor issue with the sudo last week #5008) > > Best, > Christine > > On Tue, Aug 13, 2019 at 9:22 PM Shen Wang wrote: > >> Does it work? If still doesn?t work, try to remove project/config.xml >> file. Do sudo ./install.sh again. To reinstall Loris again. >> >> >> Shen Wang ?2019?8?13? ????9:02??? >> >>> Hi Sotirios, >>> step 1: >>> sudo ./node_modules/.bin/eslint --fix /var/www/loris >>> step 2: >>> put the rest error files under this line [# Ignore until ESLint is run] in >>> the .eslintignore file. >>> step 3: >>> sudo make >>> >>> >>> >>> On Tue, 13 Aug 2019 at 20:34, Sotirios Nikoloutsopoulos < >>> sotirisnik at gmail.com> wrote: >>> >>>> I did the modifications, still there are errors. >>>> Thanks >>>> >>>> >>>> ???? ???, 14 ??? 2019 ???? 3:22 ?.?., ?/? Shen Wang < >>>> wangshen.mcin at gmail.com> ??????: >>>> >>>>> Hi Sotirios, >>>>> I saw your output file, the config issue is gone. >>>>> you can use [sudo npm run lintfix:javascript ] to fix these indent >>>>> issues. >>>>> If it still has errors. >>>>> Then try modify this file .eslintignore >>>>> with this >>>>> >>>>> # Ignore until ESLint is run >>>>> >>>>> modules/* >>>>> >>>>> modules/dataquery/ >>>>> >>>>> node_modules/* >>>>> >>>>> htdocs/js/components/* >>>>> >>>>> jsx/* >>>>> >>>>> >>>>> # Ignore external libs >>>>> >>>>> htdocs/js/flot/* >>>>> >>>>> htdocs/js/jquery/* >>>>> >>>>> htdocs/js/jszip/* >>>>> >>>>> htdocs/js/modernizr/* >>>>> >>>>> htdocs/js/modules/* >>>>> >>>>> htdocs/js/react/* >>>>> >>>>> htdocs/js/shims/* >>>>> >>>>> htdocs/js/c3.min.js >>>>> >>>>> htdocs/js/d3.min.js >>>>> >>>>> htdocs/js/FileSaver.min.js >>>>> >>>>> >>>>> then do sudo make. >>>>> It should work. >>>>> Regards >>>>> Shen >>>>> >>>>> >>>>> Sotirios Nikoloutsopoulos ?2019?8?13? >>>>> ????7:54??? >>>>> >>>>>> No, it didn't work, i also tried space/tabs because most of the >>>>>> errors where about indentation, also there are some errors about React. >>>>>> >>>>>> Thanks >>>>>> >>>>>> lorisadmin at hbp:/var/www/loris$ sudo ./node_modules/.bin/eslint --init >>>>>> ? How would you like to configure ESLint? Answer questions about your >>>>>> style >>>>>> ? Which version of ECMAScript do you use? ES2015 >>>>>> ? Are you using ES6 modules? Yes >>>>>> ? Where will your code run? Browser >>>>>> ? Do you use CommonJS? Yes >>>>>> ? Do you use JSX? Yes >>>>>> ? Do you use React? Yes >>>>>> ? What style of indentation do you use? Spaces >>>>>> ? What quotes do you use for strings? Single >>>>>> ? What line endings do you use? Unix >>>>>> ? Do you require semicolons? Yes >>>>>> ? What format do you want your config file to be in? JSON >>>>>> The config that you've selected requires the following dependencies: >>>>>> >>>>>> eslint-plugin-react at latest >>>>>> Successfully created .eslintrc.json file in /var/www/loris >>>>>> >>>>>> lorisadmin at hbp:/var/www/loris$ sudo make > sudo_make_output >>>>>> npm WARN The package prop-types is included as both a dev and >>>>>> production dependency. >>>>>> npm WARN optional SKIPPING OPTIONAL DEPENDENCY: fsevents at 1.2.4 >>>>>> (node_modules/fsevents): >>>>>> npm WARN notsup SKIPPING OPTIONAL DEPENDENCY: Unsupported platform >>>>>> for fsevents at 1.2.4: wanted {"os":"darwin","arch":"any"} (current: >>>>>> {"os":"linux","arch":"x64"}) >>>>>> >>>>>> npm ERR! code ELIFECYCLE >>>>>> npm ERR! errno 2 >>>>>> npm ERR! loris at 1.0.0 compile: `webpack` >>>>>> npm ERR! Exit status 2 >>>>>> npm ERR! >>>>>> npm ERR! Failed at the loris at 1.0.0 compile script. >>>>>> npm ERR! This is probably not a problem with npm. There is likely >>>>>> additional logging output above. >>>>>> >>>>>> npm ERR! A complete log of this run can be found in: >>>>>> npm ERR! >>>>>> /home/lorisadmin/.npm/_logs/2019-08-13T23_40_58_841Z-debug.log >>>>>> >>>>>> ???? ???, 14 ??? 2019 ???? 2:29 ?.?., ?/? Shen Wang < >>>>>> wangshen.mcin at gmail.com> ??????: >>>>>> >>>>>>> Hi Sotirios, >>>>>>> When you do make command, please make sure with sudo at the >>>>>>> beginning. [sudo make] >>>>>>> If it still doesn't work for you. >>>>>>> Then try the solutions below. >>>>>>> solution 1: >>>>>>> [image: ???? 2019-08-13 19.21.15.png] >>>>>>> Regards >>>>>>> Shen >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> On Tue, 13 Aug 2019 at 17:22, Sotirios Nikoloutsopoulos < >>>>>>> sotirisnik at gmail.com> wrote: >>>>>>> >>>>>>>> I think that the files exists although i redownloaded the >>>>>>>> eslintrc.json i checked others files that had similar errors. >>>>>>>> >>>>>>>> lorisadmin at hbp:/var/www/loris$ ls -l >>>>>>>> ./node_modules/eslint-loader/index.js >>>>>>>> -rw-rw-r-- 1 lorisadmin lorisadmin 6463 ??? 26 1985 >>>>>>>> ./node_modules/eslint-loader/index.js >>>>>>>> >>>>>>>> lorisadmin at hbp:/var/www/loris$ ls -l .eslintrc.json >>>>>>>> -rw-rw-r-- 1 lorisadmin lorisadmin 84530 ??? 14 00:04 >>>>>>>> .eslintrc.json >>>>>>>> >>>>>>>> Maybe this can help >>>>>>>> >>>>>>>> Module build failed (from ./node_modules/eslint-loader/index.js): >>>>>>>> SyntaxError: Cannot read config file: >>>>>>>> /var/www/loris/.eslintrc.json >>>>>>>> Error: Unexpected token < in JSON at position 6 >>>>>>>> at JSON.parse () >>>>>>>> at loadJSONConfigFile >>>>>>>> (/var/www/loris/node_modules/eslint/lib/config/config-file.js:114:21) >>>>>>>> at loadConfigFile >>>>>>>> (/var/www/loris/node_modules/eslint/lib/config/config-file.js:230:26) >>>>>>>> at loadFromDisk >>>>>>>> (/var/www/loris/node_modules/eslint/lib/config/config-file.js:500:18) >>>>>>>> at Object.load >>>>>>>> (/var/www/loris/node_modules/eslint/lib/config/config-file.js:564:20) >>>>>>>> at Config.getLocalConfigHierarchy >>>>>>>> (/var/www/loris/node_modules/eslint/lib/config.js:227:44) >>>>>>>> at Config.getConfigHierarchy >>>>>>>> (/var/www/loris/node_modules/eslint/lib/config.js:179:43) >>>>>>>> at Config.getConfigVector >>>>>>>> (/var/www/loris/node_modules/eslint/lib/config.js:286:21) >>>>>>>> at Config.getConfig >>>>>>>> (/var/www/loris/node_modules/eslint/lib/config.js:329:29) >>>>>>>> at processText >>>>>>>> (/var/www/loris/node_modules/eslint/lib/cli-engine.js:162:33) >>>>>>>> at CLIEngine.executeOnText >>>>>>>> (/var/www/loris/node_modules/eslint/lib/cli-engine.js:596:17) >>>>>>>> at lint >>>>>>>> (/var/www/loris/node_modules/eslint-loader/index.js:237:17) >>>>>>>> at Object.module.exports >>>>>>>> (/var/www/loris/node_modules/eslint-loader/index.js:232:21) >>>>>>>> >>>>>>>> ERROR in ./modules/imaging_uploader/jsx/index.js >>>>>>>> Module build failed (from >>>>>>>> ./node_modules/eslint-loader/index.js): >>>>>>>> SyntaxError: Cannot read config file: >>>>>>>> /var/www/loris/.eslintrc.json >>>>>>>> Error: Unexpected token < in JSON at position 6 >>>>>>>> at JSON.parse () >>>>>>>> at loadJSONConfigFile >>>>>>>> (/var/www/loris/node_modules/eslint/lib/config/config-file.js:114:21) >>>>>>>> at loadConfigFile >>>>>>>> (/var/www/loris/node_modules/eslint/lib/config/config-file.js:230:26) >>>>>>>> at loadFromDisk >>>>>>>> (/var/www/loris/node_modules/eslint/lib/config/config-file.js:500:18) >>>>>>>> at Object.load >>>>>>>> (/var/www/loris/node_modules/eslint/lib/config/config-file.js:564:20) >>>>>>>> at Config.getLocalConfigHierarchy >>>>>>>> (/var/www/loris/node_modules/eslint/lib/config.js:227:44) >>>>>>>> at Config.getConfigHierarchy >>>>>>>> (/var/www/loris/node_modules/eslint/lib/config.js:179:43) >>>>>>>> at Config.getConfigVector >>>>>>>> (/var/www/loris/node_modules/eslint/lib/config.js:286:21) >>>>>>>> at Config.getConfig >>>>>>>> (/var/www/loris/node_modules/eslint/lib/config.js:329:29) >>>>>>>> at processText >>>>>>>> (/var/www/loris/node_modules/eslint/lib/cli-engine.js:162:33) >>>>>>>> at CLIEngine.executeOnText >>>>>>>> (/var/www/loris/node_modules/eslint/lib/cli-engine.js:596:17) >>>>>>>> at lint >>>>>>>> (/var/www/loris/node_modules/eslint-loader/index.js:237:17) >>>>>>>> at Object.module.exports >>>>>>>> (/var/www/loris/node_modules/eslint-loader/index.js:232:21) >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> ???? ???, 13 ??? 2019 ???? 11:52 ?.?., ?/? John Saigle < >>>>>>>> john.saigle at mcin.ca> ??????: >>>>>>>> >>>>>>>>> HI Sotirios, >>>>>>>>> >>>>>>>>> The make_output.txt file shows webpack failing because it can't >>>>>>>>> find the ESLint config file. >>>>>>>>> >>>>>>>>> Can you confirm whether the file `.eslintrc.json` exists within >>>>>>>>> your loris root directory (usually `/var/www/loris/`)? When I delete my >>>>>>>>> file I get the same errors as you. >>>>>>>>> >>>>>>>>> If you find that it's missing, you can make a local copy with the >>>>>>>>> contents found here: >>>>>>>>> >>>>>>>>> >>>>>>>>> https://github.com/aces/Loris/blob/e26a6ad49a73fcffef0cd73bb600c4d17b200b62/.eslintrc.json >>>>>>>>> >>>>>>>>> Once you know it exists, try running `make` again. >>>>>>>>> >>>>>>>>> Let us know if that moves you forward. >>>>>>>>> >>>>>>>>> Best, >>>>>>>>> John >>>>>>>>> >>>>>>>>> On Tue, Aug 13, 2019 at 2:21 PM Sotirios Nikoloutsopoulos < >>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>> >>>>>>>>>> Hi, >>>>>>>>>> I executed the commands for the node and now i am get the >>>>>>>>>> followings: >>>>>>>>>> >>>>>>>>>> lorisadmin at hbp:/var/www/loris$ make > ~/make_output >>>>>>>>>> npm WARN The package prop-types is included as both a dev and >>>>>>>>>> production dependency. >>>>>>>>>> npm WARN optional SKIPPING OPTIONAL DEPENDENCY: fsevents at 1.2.4 >>>>>>>>>> (node_modules/fsevents): >>>>>>>>>> npm WARN notsup SKIPPING OPTIONAL DEPENDENCY: Unsupported >>>>>>>>>> platform for fsevents at 1.2.4: wanted {"os":"darwin","arch":"any"} >>>>>>>>>> (current: {"os":"linux","arch":"x64"}) >>>>>>>>>> >>>>>>>>>> npm ERR! code ELIFECYCLE >>>>>>>>>> npm ERR! errno 2 >>>>>>>>>> npm ERR! loris at 1.0.0 compile: `webpack` >>>>>>>>>> npm ERR! Exit status 2 >>>>>>>>>> npm ERR! >>>>>>>>>> npm ERR! Failed at the loris at 1.0.0 compile script. >>>>>>>>>> npm ERR! This is probably not a problem with npm. There is likely >>>>>>>>>> additional logging output above. >>>>>>>>>> >>>>>>>>>> npm ERR! A complete log of this run can be found in: >>>>>>>>>> npm ERR! >>>>>>>>>> /home/lorisadmin/.npm/_logs/2019-08-13T18_12_05_378Z-debug.log >>>>>>>>>> make: *** [javascript] Error 2 >>>>>>>>>> >>>>>>>>>> Thanks, >>>>>>>>>> Sotirios >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> ???? ???, 12 ??? 2019 ???? 10:19 ?.?., ?/? Christine Rogers, Ms. < >>>>>>>>>> christine.rogers at mcgill.ca> ??????: >>>>>>>>>> >>>>>>>>>>> Hi Sotirios, >>>>>>>>>>> >>>>>>>>>>> We've seen some users installing LORIS 21 or upgrading to 21 >>>>>>>>>>> whose version of node doesn't work well with webpack, due to updated >>>>>>>>>>> packages they're missing. >>>>>>>>>>> If so, update your node : >>>>>>>>>>> >>>>>>>>>>> curl -sL https://deb.nodesource.com/setup_8.x | sudo -E bash - >>>>>>>>>>> sudo apt-get install -y nodejs >>>>>>>>>>> >>>>>>>>>>> Let us know how that goes -- please send us output from the same >>>>>>>>>>> log if any issues. >>>>>>>>>>> Best, >>>>>>>>>>> Christine >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> On Thu, Aug 8, 2019 at 2:38 PM Sotirios Nikoloutsopoulos < >>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>> >>>>>>>>>>>> It's not a disk space issue, as you can see below i have still >>>>>>>>>>>> 74GB available. >>>>>>>>>>>> >>>>>>>>>>>> lorisadmin at hbp:/var/www/loris$ df -h >>>>>>>>>>>> Filesystem Size Used Avail Use% Mounted on >>>>>>>>>>>> udev 2,9G 0 2,9G 0% /dev >>>>>>>>>>>> tmpfs 597M 8,6M 588M 2% /run >>>>>>>>>>>> /dev/sda1 98G 19G 74G 21% / >>>>>>>>>>>> >>>>>>>>>>>> Maybe we have to pass a flag to get into strict mode? as stated >>>>>>>>>>>> "SyntaxError: Block-scoped declarations (let, const, function, class) not >>>>>>>>>>>> yet supported outside strict mode" >>>>>>>>>>>> >>>>>>>>>>>> Thanks, >>>>>>>>>>>> Sotirios >>>>>>>>>>>> >>>>>>>>>>>> ???? ???, 8 ??? 2019 ???? 4:32 ?.?., ?/? Dave MacFarlane < >>>>>>>>>>>> dave.macfarlane at mcin.ca> ??????: >>>>>>>>>>>> >>>>>>>>>>>>> It looks like the javascript snippet shown in the error >>>>>>>>>>>>> message when trying to compile the js is truncated. Have you run out of >>>>>>>>>>>>> disk space? >>>>>>>>>>>>> >>>>>>>>>>>>> On Thu, Aug 8, 2019 at 8:37 AM Sotirios Nikoloutsopoulos < >>>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>> >>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>> >>>>>>>>>>>>>> I runned make and also included the file it reports at the >>>>>>>>>>>>>> end. >>>>>>>>>>>>>> >>>>>>>>>>>>>> lorisadmin at hbp:/var/www/loris$ make >>>>>>>>>>>>>> npm install >>>>>>>>>>>>>> npm WARN optional Skipping failed optional dependency >>>>>>>>>>>>>> /chokidar/fsevents: >>>>>>>>>>>>>> npm WARN notsup Not compatible with your operating system or >>>>>>>>>>>>>> architecture: fsevents at 1.2.9 >>>>>>>>>>>>>> npm WARN optional Skipping failed optional dependency >>>>>>>>>>>>>> /watchpack/chokidar/fsevents: >>>>>>>>>>>>>> npm WARN notsup Not compatible with your operating system or >>>>>>>>>>>>>> architecture: fsevents at 1.2.9 >>>>>>>>>>>>>> npm run compile >>>>>>>>>>>>>> >>>>>>>>>>>>>> > loris at 1.0.0 compile /var/www/loris >>>>>>>>>>>>>> > webpack >>>>>>>>>>>>>> >>>>>>>>>>>>>> /var/www/loris/node_modules/webpack/bin/webpack.js:86 >>>>>>>>>>>>>> let notify = >>>>>>>>>>>>>> ^^^ >>>>>>>>>>>>>> >>>>>>>>>>>>>> SyntaxError: Block-scoped declarations (let, const, function, >>>>>>>>>>>>>> class) not yet supported outside strict mode >>>>>>>>>>>>>> at exports.runInThisContext (vm.js:53:16) >>>>>>>>>>>>>> at Module._compile (module.js:374:25) >>>>>>>>>>>>>> at Object.Module._extensions..js (module.js:417:10) >>>>>>>>>>>>>> at Module.load (module.js:344:32) >>>>>>>>>>>>>> at Function.Module._load (module.js:301:12) >>>>>>>>>>>>>> at Function.Module.runMain (module.js:442:10) >>>>>>>>>>>>>> at startup (node.js:136:18) >>>>>>>>>>>>>> at node.js:966:3 >>>>>>>>>>>>>> >>>>>>>>>>>>>> npm ERR! Linux 4.15.0-55-generic >>>>>>>>>>>>>> npm ERR! argv "/usr/bin/nodejs" "/usr/bin/npm" "run" "compile" >>>>>>>>>>>>>> npm ERR! node v4.2.6 >>>>>>>>>>>>>> npm ERR! npm v3.5.2 >>>>>>>>>>>>>> npm ERR! code ELIFECYCLE >>>>>>>>>>>>>> npm ERR! loris at 1.0.0 compile: `webpack` >>>>>>>>>>>>>> npm ERR! Exit status 1 >>>>>>>>>>>>>> npm ERR! >>>>>>>>>>>>>> npm ERR! Failed at the loris at 1.0.0 compile script 'webpack'. >>>>>>>>>>>>>> npm ERR! Make sure you have the latest version of node.js and >>>>>>>>>>>>>> npm installed. >>>>>>>>>>>>>> npm ERR! If you do, this is most likely a problem with the >>>>>>>>>>>>>> loris package, >>>>>>>>>>>>>> npm ERR! not with npm itself. >>>>>>>>>>>>>> npm ERR! Tell the author that this fails on your system: >>>>>>>>>>>>>> npm ERR! webpack >>>>>>>>>>>>>> npm ERR! You can get information on how to open an issue for >>>>>>>>>>>>>> this project with: >>>>>>>>>>>>>> npm ERR! npm bugs loris >>>>>>>>>>>>>> npm ERR! Or if that isn't available, you can get their info >>>>>>>>>>>>>> via: >>>>>>>>>>>>>> npm ERR! npm owner ls loris >>>>>>>>>>>>>> npm ERR! There is likely additional logging output above. >>>>>>>>>>>>>> >>>>>>>>>>>>>> npm ERR! Please include the following file with any support >>>>>>>>>>>>>> request: >>>>>>>>>>>>>> npm ERR! /var/www/loris/npm-debug.log >>>>>>>>>>>>>> Makefile:14: recipe for target 'javascript' failed >>>>>>>>>>>>>> make: *** [javascript] Error 1 >>>>>>>>>>>>>> >>>>>>>>>>>>>> Thanks, >>>>>>>>>>>>>> >>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>> >>>>>>>>>>>>>> ???? ???, 7 ??? 2019 ???? 5:41 ?.?., ?/? Christine Rogers, >>>>>>>>>>>>>> Ms. ??????: >>>>>>>>>>>>>> >>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> Thanks, have you tried all of these steps? >>>>>>>>>>>>>>> - clear your browser cache (and refresh a few times) >>>>>>>>>>>>>>> - delete any files in your smarty/templates_c directory >>>>>>>>>>>>>>> (this will clear the template cache - do Not touch smarty/templates/) >>>>>>>>>>>>>>> - run `make` (per the 21 release notes, this replaces the >>>>>>>>>>>>>>> composer commands used in previous releases to update your dependencies) >>>>>>>>>>>>>>> - restart apache (doesn't hurt) >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> Let us know how it goes -- let us know what difference you >>>>>>>>>>>>>>> see after, with your logs. A >>>>>>>>>>>>>>> lso please send us your Config path settings (see these >>>>>>>>>>>>>>> Troubleshooting Queries >>>>>>>>>>>>>>> ) >>>>>>>>>>>>>>> if you're still seeing front-end issues. >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> Thanks, >>>>>>>>>>>>>>> Christine >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> On Wed, Aug 7, 2019 at 8:02 AM Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> lorisadmin at hbp:/var/www/loris$ sudo cat >>>>>>>>>>>>>>>> /var/log/apache2/error.log >>>>>>>>>>>>>>>> [Wed Aug 07 07:35:02.422501 2019] [mpm_prefork:notice] [pid >>>>>>>>>>>>>>>> 1267] AH00163: Apache/2.4.18 (Ubuntu) OpenSSL/1.0.2g configured -- resuming >>>>>>>>>>>>>>>> normal operations >>>>>>>>>>>>>>>> [Wed Aug 07 07:35:02.422514 2019] [core:notice] [pid 1267] >>>>>>>>>>>>>>>> AH00094: Command line: '/usr/sbin/apache2' >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> And as for the access.log the content are empty >>>>>>>>>>>>>>>> lorisadmin at hbp:/var/www/loris$ sudo ls -l >>>>>>>>>>>>>>>> /var/log/apache2/access.log >>>>>>>>>>>>>>>> lorisadmin at hbp:/var/www/loris$ sudo ls -l >>>>>>>>>>>>>>>> /var/log/apache2/access.log >>>>>>>>>>>>>>>> -rw-r----- 1 root adm 0 ???? 28 14:09 >>>>>>>>>>>>>>>> /var/log/apache2/access.log >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Also i noticed a loris_access.log. >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> The only non-blank pages are: >>>>>>>>>>>>>>>> mri_violations, dataquery does not exist at all, >>>>>>>>>>>>>>>> statistics, data_team_helper, genomic_browser, configuration and >>>>>>>>>>>>>>>> server_processes_manager/ prints "Required configuration settings for >>>>>>>>>>>>>>>> Server Processes Manager are missing. Cannot continue." >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Thanks, >>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> ???? ???, 6 ??? 2019 ???? 10:13 ?.?., ?/? Christine Rogers, >>>>>>>>>>>>>>>> Ms. ??????: >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Hi Sotirios and LORIS community -- >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> When upgrading to brand-new release 21 -- just a reminder >>>>>>>>>>>>>>>>> to follow the release notes and run the new *make* file >>>>>>>>>>>>>>>>> to update your dependencies (instead of using *composer* >>>>>>>>>>>>>>>>> commands). >>>>>>>>>>>>>>>>> We've also updated the Wiki page >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> to clarify that the release notes for each version will tell you what to >>>>>>>>>>>>>>>>> run. >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> If your current version is not the last release (20.3), >>>>>>>>>>>>>>>>> it's still important to upgrade to each minor release increment (e.g. 20.2, >>>>>>>>>>>>>>>>> 20.3) before making the leap to 21.0. >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> If you're getting blank pages, post-upgrade -- Try >>>>>>>>>>>>>>>>> clearing your cache. >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Got questions or feedback e.g. on the Release Notes? >>>>>>>>>>>>>>>>> please don't hesitate to let us know. >>>>>>>>>>>>>>>>> Thanks, >>>>>>>>>>>>>>>>> Christine >>>>>>>>>>>>>>>>> The LORIS team >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> On Tue, Aug 6, 2019 at 10:09 AM Christine Rogers, Ms. < >>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca> wrote: >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>> Could you also let us know -- on which pages is content >>>>>>>>>>>>>>>>>> visible, and on which pages/modules is content not visible for you? >>>>>>>>>>>>>>>>>> Thanks, >>>>>>>>>>>>>>>>>> Christine >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> On Tue, Aug 6, 2019 at 9:54 AM Christine Rogers, Ms. < >>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca> wrote: >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Thanks Sotirios, >>>>>>>>>>>>>>>>>>> That's good to know. It sounds like you've checked that >>>>>>>>>>>>>>>>>>> your /var/www/loris/project/config.xml file get populated properly. >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Please send us the last few errors you're seeing in your >>>>>>>>>>>>>>>>>>> apache error log file, and your config paths and we can see what's >>>>>>>>>>>>>>>>>>> happening with your front end -- >>>>>>>>>>>>>>>>>>> Run these Troubleshooting Queries >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> to get your config path settings, given your front end is not displaying >>>>>>>>>>>>>>>>>>> fully. >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> The Loris-MRI repo >>>>>>>>>>>>>>>>>>> 21 >>>>>>>>>>>>>>>>>>> install/upgrade would then be your next steps. >>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>> Christine >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> On Tue, Aug 6, 2019 at 7:53 AM Sotirios Nikoloutsopoulos >>>>>>>>>>>>>>>>>>> wrote: >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> I am using a VM. What i did was: >>>>>>>>>>>>>>>>>>>> 1) Download the files from >>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris and replace them to my >>>>>>>>>>>>>>>>>>>> existing /vaw/www/loris folder. >>>>>>>>>>>>>>>>>>>> 2) Execute the composer install --no-dev and then composer >>>>>>>>>>>>>>>>>>>> dump-autoload as mentioned here >>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris/wiki/Updating-your-LORIS. >>>>>>>>>>>>>>>>>>>> 3) Execute install.sh from /var/www/loris/tools and >>>>>>>>>>>>>>>>>>>> because LORIS already existed i moved a .config file, then re-executed the >>>>>>>>>>>>>>>>>>>> install.sh successfully >>>>>>>>>>>>>>>>>>>> 4 ) As for the database, i dropped the schema and i >>>>>>>>>>>>>>>>>>>> executed the installdb.php >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> ???? ???, 5 ??? 2019 ???? 5:22 ?.?., ?/? Christine >>>>>>>>>>>>>>>>>>>> Rogers, Ms. ??????: >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> Hi Sotorios, >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> Thanks - when you re-installed did you start on a >>>>>>>>>>>>>>>>>>>>> fresh root path / VM or might some of your old system setting still apply? >>>>>>>>>>>>>>>>>>>>> (And if you did any steps similar to an upgrade, did >>>>>>>>>>>>>>>>>>>>> you follow the Upgrade steps in the Release Notes, from both repos?) >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> About the TR_range column - it was recently split (MRI >>>>>>>>>>>>>>>>>>>>> pr339 ) split >>>>>>>>>>>>>>>>>>>>> into TR_min and _max columns. Given the code was trying to query TR_range >>>>>>>>>>>>>>>>>>>>> which does not exist in your mri_protocol table, double-check which version >>>>>>>>>>>>>>>>>>>>> of the Loris repo (tables) and the Loris-MRI repo (code) you have installed >>>>>>>>>>>>>>>>>>>>> to ensure they match. >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> Christine >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> On Mon, Aug 5, 2019 at 9:06 AM Sotirios >>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos wrote: >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> I reinstalled LORIS to 21 version and now the content >>>>>>>>>>>>>>>>>>>>>> is not visible at all at most pages. >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> ???? ???, 5 ??? 2019 ???? 3:19 ?.?., ?/? Sotirios >>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos ??????: >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> Is it easy to upgrade to Loris 21? Also the >>>>>>>>>>>>>>>>>>>>>>> following fails because the line 1985 of NeuroDB/MRIProcessingUtility.pm >>>>>>>>>>>>>>>>>>>>>>> query mri_protocol which doesn't have TR_range >>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris/blob/21.0-release/SQL/0000-00-00-schema.sql#L556 >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> lorisadmin at hbp:/data/loris/bin/mri$ >>>>>>>>>>>>>>>>>>>>>>> ./batch_uploads_imageuploader -profile prod < ~/Desktop/input.txt > log.txt >>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $_ in pattern match (m//) >>>>>>>>>>>>>>>>>>>>>>> at ./batch_uploads_imageuploader line 147. >>>>>>>>>>>>>>>>>>>>>>> base is DCC0000_258024_V1 >>>>>>>>>>>>>>>>>>>>>>> path is /data/incoming/ >>>>>>>>>>>>>>>>>>>>>>> type is .tar.gz >>>>>>>>>>>>>>>>>>>>>>> fullpath is /data/incoming/DCC0000_258024_V1.tar.gz >>>>>>>>>>>>>>>>>>>>>>> DBD::mysql::st execute failed: Unknown column >>>>>>>>>>>>>>>>>>>>>>> 'TR_range' in 'where clause' at >>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line 1985. >>>>>>>>>>>>>>>>>>>>>>> DBD::mysql::st fetchrow_array failed: fetch() >>>>>>>>>>>>>>>>>>>>>>> without execute() at >>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line 1986. >>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $count_mri_protocol in >>>>>>>>>>>>>>>>>>>>>>> numeric gt (>) at >>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line 1995. >>>>>>>>>>>>>>>>>>>>>>> DBD::mysql::st execute failed: Unknown column >>>>>>>>>>>>>>>>>>>>>>> 'TR_range' in 'field list' at >>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 562. >>>>>>>>>>>>>>>>>>>>>>> Can't exec "mail": No such file or directory at >>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 721. >>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 722. >>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 723. >>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 724. >>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 725. >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> No Mincs inserted >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> Thanks, >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> ???? ???, 3 ??? 2019 ???? 1:08 ?.?., ?/? Christine >>>>>>>>>>>>>>>>>>>>>>> Rogers, Ms. ??????: >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> First, just a note: we've released LORIS 21 this >>>>>>>>>>>>>>>>>>>>>>>> week with some major new features and cleanup -- especially if you are >>>>>>>>>>>>>>>>>>>>>>>> early in your setup phase, check out the Release notes for both the >>>>>>>>>>>>>>>>>>>>>>>> LORIS >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> and Loris-MRI >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> repos. >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> Thanks for your screenshots -- your empty >>>>>>>>>>>>>>>>>>>>>>>> mri_protocol table should be at the root of these issues : >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> The mri_protocol table must be populated >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> in order for your scans to be registered in LORIS -- it serves as a >>>>>>>>>>>>>>>>>>>>>>>> whitelist for the insertion pipeline which filters out scans that aren't >>>>>>>>>>>>>>>>>>>>>>>> identified or matched to scan types in this table. >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> By default, this table is populated with entries >>>>>>>>>>>>>>>>>>>>>>>> for t1, t2, fMRI and DTI (Insert statements for 21 >>>>>>>>>>>>>>>>>>>>>>>> release branch are here >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> ) >>>>>>>>>>>>>>>>>>>>>>>> Feel free to restore our default records and >>>>>>>>>>>>>>>>>>>>>>>> broaden their parameters to match all your scan types. >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> re Defaced, native, selected -- these filter the >>>>>>>>>>>>>>>>>>>>>>>> scans displayed as you move to the next page (View Session), instead of >>>>>>>>>>>>>>>>>>>>>>>> viewing "all types" of scans from a given session : >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> - "defaced" means that a defacing script >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> has masked the subject's face in the volume (for patient privacy) >>>>>>>>>>>>>>>>>>>>>>>> - "native" means that no pre-processing has >>>>>>>>>>>>>>>>>>>>>>>> been performed on the scan (it's raw data), >>>>>>>>>>>>>>>>>>>>>>>> - "selected" will show only volumes that have >>>>>>>>>>>>>>>>>>>>>>>> been QC'd and "selected" as the best of their type -- used to display only >>>>>>>>>>>>>>>>>>>>>>>> the best quality T1 image instead of all T1s acquired in a session, e.g. >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> re QC Comments -- >>>>>>>>>>>>>>>>>>>>>>>> Once you have successfully loaded scans (matched to >>>>>>>>>>>>>>>>>>>>>>>> the mri_protocol table), you'll be able to use the Imaging Browser's View >>>>>>>>>>>>>>>>>>>>>>>> Session subpage to enter/view QC comments on each volume, or for each >>>>>>>>>>>>>>>>>>>>>>>> visit. >>>>>>>>>>>>>>>>>>>>>>>> These are stored directly in the database, and >>>>>>>>>>>>>>>>>>>>>>>> linked to each scan. (Table name: >>>>>>>>>>>>>>>>>>>>>>>> feedback_mri_comments) >>>>>>>>>>>>>>>>>>>>>>>> (Visit-level QC comments are linked to the session.) >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> For a walkthrough of the Imaging setup - please see >>>>>>>>>>>>>>>>>>>>>>>> the Imaging Setup guide >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> - >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> An old LORIS walkthrough video >>>>>>>>>>>>>>>>>>>>>>>> can >>>>>>>>>>>>>>>>>>>>>>>> also walk you through some of the Imaging front-end features, starting at >>>>>>>>>>>>>>>>>>>>>>>> 8:00 >>>>>>>>>>>>>>>>>>>>>>>> LORIS' imaging modules have been updated many times >>>>>>>>>>>>>>>>>>>>>>>> since this video, but the functionality and workflow is similar. >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> Let us know how it goes once you have entries in >>>>>>>>>>>>>>>>>>>>>>>> your mri_protocol table - >>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>> Christine >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> On Fri, Aug 2, 2019 at 7:58 AM Sotirios >>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos wrote: >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> Hi Christine, >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> In the candidate_list page i can see this patient >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> If i press the link under PSCID i get to see >>>>>>>>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> and if i press the link under Scan Done it >>>>>>>>>>>>>>>>>>>>>>>>> redirects me to imaging_browser >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> At the mri_violations page i also see No results ( >>>>>>>>>>>>>>>>>>>>>>>>> neither on resolved / not resolved ). >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> At the imaging_uploader i can see the record that >>>>>>>>>>>>>>>>>>>>>>>>> failed. >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> If i click on the tarchive info i get to see the >>>>>>>>>>>>>>>>>>>>>>>>> Protocol Name which i think is the acquisition we wanted? >>>>>>>>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> Also my mri_protocol table is empty. >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> Furthermore i would like to ask about the defaced, >>>>>>>>>>>>>>>>>>>>>>>>> native, selected. What exactly is native and selected? And where are the qc >>>>>>>>>>>>>>>>>>>>>>>>> comments stored? >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> Finally a walkthrough would be helpful. >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> Thanks, >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 30 ???? 2019 ???? 8:29 ?.?., ?/? >>>>>>>>>>>>>>>>>>>>>>>>> Christine Rogers, Ms. >>>>>>>>>>>>>>>>>>>>>>>>> ??????: >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>> Glad to hear you're making progress with the >>>>>>>>>>>>>>>>>>>>>>>>>> visit labels. To follow up on your last few emails: >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> a- The Wiki's Setup Guide contains Sample insert >>>>>>>>>>>>>>>>>>>>>>>>>> statements for the Visit Windows table >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> . >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> As Cecile mentioned, the consistency of visit >>>>>>>>>>>>>>>>>>>>>>>>>> label format is important: V01, v01, V1, 01 -- whichever you select to use >>>>>>>>>>>>>>>>>>>>>>>>>> is fine; we use V01 by default across all documentation. >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> b- For Password reset, there is a script in the >>>>>>>>>>>>>>>>>>>>>>>>>> tools/ directory so that a back-end administrator can reset any front-end >>>>>>>>>>>>>>>>>>>>>>>>>> user password, including Admin. (See info on setting up / resetting User >>>>>>>>>>>>>>>>>>>>>>>>>> passwords in the Wiki's Setup Guide >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> ) >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> c- The minc file not being registered -- due to >>>>>>>>>>>>>>>>>>>>>>>>>> AcquisitionProtocol unknown. >>>>>>>>>>>>>>>>>>>>>>>>>> This means the SeriesDescription (Acquisition >>>>>>>>>>>>>>>>>>>>>>>>>> Protocol) in you Dicom header was not matched to any scan listed in the >>>>>>>>>>>>>>>>>>>>>>>>>> mri_protocol database table. >>>>>>>>>>>>>>>>>>>>>>>>>> (In the online Loris-MRI Troubleshooting Guide, >>>>>>>>>>>>>>>>>>>>>>>>>> this >>>>>>>>>>>>>>>>>>>>>>>>>> is Table 3, 2nd-last item "no MINCs inserted"). >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> The MRI Violations module (Readme here) >>>>>>>>>>>>>>>>>>>>>>>>>> will show >>>>>>>>>>>>>>>>>>>>>>>>>> you the details of this mismatch -- >>>>>>>>>>>>>>>>>>>>>>>>>> Go to the module (under the Imaging menu), find >>>>>>>>>>>>>>>>>>>>>>>>>> your scan and click the link "Could not identify scan type" -- in the next >>>>>>>>>>>>>>>>>>>>>>>>>> subpage you can compare the scan's actual parameters against the >>>>>>>>>>>>>>>>>>>>>>>>>> mri_protocol table. >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> To resolve this, adjust your mri_protocol table >>>>>>>>>>>>>>>>>>>>>>>>>> values or perhaps ensure your DICOMs are labelled consistently. >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> Let us know if this works for you -- we can also >>>>>>>>>>>>>>>>>>>>>>>>>> walk you through an example of non-identified scans on >>>>>>>>>>>>>>>>>>>>>>>>>> Demo.loris.ca (MRI Violations module). >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>> Christine >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> The LORIS team >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> On Tue, Jul 30, 2019 at 10:47 AM Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos wrote: >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> I hope this is sufficient as the error for the >>>>>>>>>>>>>>>>>>>>>>>>>>> visit label disappeared. >>>>>>>>>>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> Please see the attached file. Also something i >>>>>>>>>>>>>>>>>>>>>>>>>>> found. >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> lorisadmin at hbp:/data/loris/bin/mri$ cat >>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data//logs/TarLoad-17-39-xubBdv.log >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> ==> Loading file from disk >>>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-17-39-UyQcG2/dcc0000_258024_v1_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> --> mapping DICOM parameter for >>>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-17-39-UyQcG2/dcc0000_258024_v1_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> ==> computing md5 hash for MINC body. >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> --> md5: 6b1202fd63e29de4c9be1cd9925888a5 >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> ==> verifying acquisition protocol >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> Acquisition protocol is unknown >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> --> The minc file cannot be registered since >>>>>>>>>>>>>>>>>>>>>>>>>>> the AcquisitionProtocol is unknown >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 30 ???? 2019 ???? 4:58 ?.?., ?/? >>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos >>>>>>>>>>>>>>>>>>>>>>>>>>> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> Ok I fixed the login problem by using a known >>>>>>>>>>>>>>>>>>>>>>>>>>>> hash and by deleting the rows from the login_history i was able to login. >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 30 ???? 2019 ???? 4:50 ?.?., ?/? >>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos >>>>>>>>>>>>>>>>>>>>>>>>>>>> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> there was no visit label 01 in the >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Visit_Windows table and i don't know how to insert it because the record >>>>>>>>>>>>>>>>>>>>>>>>>>>>> requires lots of attributes. Also the system for a reason asked me to >>>>>>>>>>>>>>>>>>>>>>>>>>>>> update my password and now i don't remember it and my account got >>>>>>>>>>>>>>>>>>>>>>>>>>>>> suspended. Is there a way to reset it or set a simple password? I updated >>>>>>>>>>>>>>>>>>>>>>>>>>>>> the password hash in the users table by using the hash from another LORIS >>>>>>>>>>>>>>>>>>>>>>>>>>>>> setup we had and i still couldn't login ( also the attribute password is >>>>>>>>>>>>>>>>>>>>>>>>>>>>> always NULL and the expiration date is 1999-01-01 for some reason ). >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thanks >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 29 ???? 2019 ???? 5:21 ?.?., ?/? >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Cecile Madjar ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Can you try adding the visit label v01 to the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Visit_Windows table? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> However, I noticed that in a previous >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> dataset, the label was V1. Does that refer to the same visit? If so, you >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> might want to harmonize the visit labels so they are all the same across >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> datasets for a given timepoint, meaning you will need to relabel scans when >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the visit label is different but referring to the same visit label (v01 = >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> V1 etc...). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helps, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> On Mon, Jul 29, 2019 at 10:15 AM Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> wrote: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Could you help me with the "Visit label does >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> not exist"? I had changed $subjectID{'createVisitLabel'} to 1 as you had >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> suggested but it appears that this problem hasn't been resolved yet. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> lorisadmin at hbp:/data/loris/bin/mri$ cat >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data//logs/TarLoad-14-58-9Xog7H.log >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ==> Loading file from disk >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> --> mapping DICOM parameter for >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> --> using user-defined filterParameters for >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Candidate Mismatch Error is Visit label does >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> not exist >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -> WARNING: This candidate was invalid. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Logging to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> MRICandidateErrors table with >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> reason Visit label does not exist >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 26 ???? 2019 ???? 3:02 ?.?., ?/? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Cecile, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The Center error was fixed. Still the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> insertion of mincs fails. Please see the output.txt file i attached. Also >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> is there something else i need to change at the paths configuration? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 25 ???? 2019 ???? 6:55 ?.?., ?/? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Cecile Madjar >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> We are making progress! >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I have a feeling this error comes from the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> fact that your psc table does not have the MRI_alias populated for the DCC >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> site. Running the following query in the mysql database should fix this: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> UPDATE psc SET MRI_alias="DCC", >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Alias="DCC" WHERE Name="Data Coordinating Center"; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Repeat the same with all your sites (make >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sure to change the Aliases between sites, they should all be unique). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Let me know how it goes! >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> On Thu, Jul 25, 2019 at 11:43 AM Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> wrote: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Dear Cecile, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> You were right about your guesses. I did >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the modifications you suggested, i still get the "no mincs inserted" error, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> now i am getting the "No center found this candidate" error ( how do i fix >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> that? from what i see the .dcm files contains a 'Institution Name', is that >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the center? ), so i guess that's why the validation fails, but i changed >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the force variable of tarchiveLoader to 1, shouldn't it have inserted the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> mincs then? Also it is optional to have a mail server, right? ( from what i >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> see the mail error does not affect the $valid_study, so i assume we are >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> okay with that ) >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you a lot, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 25 ???? 2019 ???? 5:48 ?.?., >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ?/? Cecile Madjar >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> From what I understand, I believe you >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> just need to update a few config settings from the frontend in the Config >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> module (under the Admin menu). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [image: Screen Shot 2019-07-25 at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 10.31.35 AM.png] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Then go to the Paths section of the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> config module and update the "LORIS-MRI code" config setting to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri (my guess is that currently, it is set to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data) and click on the submit button. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [image: Screen Shot 2019-07-25 at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 10.32.50 AM.png] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Then, go to Imaging Pipeline section of >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the Configuration module and update the "Loris-MRI Data Directory" to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/ (my guess is that it is empty at the moment in your >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> database which is why $data_dir is not defined when you run the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> tarchiveLoader step of the insertion pipeline). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [image: Screen Shot 2019-07-25 at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 10.40.52 AM.png] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Finally, I took a look at your >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> environment file and it might be a good idea to update your PERL5LIB >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> variable to the following (it has been added to the code a few releases ago >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> as we realized this was needed for the libraries. Not sure which version of >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> LORIS-MRI you are using but it does not hurt to update this variable to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> what I suggest below): >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> export >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PERL5LIB=/data/loris/bin/mri/uploadNeuroDB:/data/loris/bin/mri/dicom-archive:$PERL5LIB >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helps. Sorry you are >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> experiencing so much trouble setting things up. We probably need to update >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> our WIKI. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> On Thu, Jul 25, 2019 at 9:48 AM Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> wrote: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The "Loris-MRI Data Directory" should >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> be in the environment file? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 25 ???? 2019 ???? 12:59 ?.?., >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ?/? Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The scripts are located in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/. Somewhere I might have messed something up but i >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> remember following the instructions in the wiki.For example when i tried to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> execute the batch_uploads_imageuploader perl script the line >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> my $command = "$bin_dir/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl " >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> was pointing to an invalid path, for >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> example: it was repeating a pattern and had LORIS instead of loris ( i >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> think the mistake was that in the wiki it suggested to use $PROJECT for >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the name of the folder and i choosed 'loris' >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris/wiki/Imaging-Database >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ). See also the in image for the modification i did. Also i didn't find the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> section to config the $data_dir variable. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 24 ???? 2019 ???? 6:05 ?.?., >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ?/? Cecile Madjar < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> cecile.madjar at mcin.ca> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> It looks like you have one Config >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> setting not set (based on the first error message you got when running it >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the first time). You need to set a value for "Loris-MRI Data Directory" in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the Config module under the Imaging pipeline section (from what I can see, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> it would be /data/loris/data/ for your setup). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The reason you got that error message >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the second time is that the pipeline checks if the DICOM study was already >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> inserted in the tarchive table. Since you ran the study once already, the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> study is inserted into the tarchive, hence the message. However, the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> pipeline did not complete as the MINC files were not created and inserted >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> into the files/parameter_file table. In order to continue the insertion, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> you will then need to run the tarchiveLoader command suggested in the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> terminal during the second run: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -globLocation -profile prod >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive//2012/DCM_2012-12-05_ImagingUpload-17-43-ZUEFjb.tar >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -verbose >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Finally, I am a bit confused by your >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> setup. Where are the scripts located? In /data/loris/bin/mri or >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data? It feels like the Config setting "LORIS-MRI code" in the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Paths section was set to "/data/LORIS/data" but it should have been set to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the directory where the scripts are located (most probably >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helps, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> On Wed, Jul 24, 2019 at 10:55 AM >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Ok first i execute this command: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> "lorisadmin at hbp:/data/loris/bin/mri$ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ./batch_uploads_imageuploader -profile prod < ~/Desktop/input.txt > log.txt >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in concatenation (.) or string at ./batch_uploads_imageuploader line 143. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in concatenation (.) or string at ./batch_uploads_imageuploader line 143. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $_ in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> pattern match (m//) at ./batch_uploads_imageuploader line 147. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> base is DCC0000_258024_V01 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> path is /data/incoming/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> type is .tar.gz >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> fullpath is >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/incoming/DCC0000_258024_V01.tar.gz >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> source >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/ImagingUpload-17-43-ZUEFjb >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> targetlocation >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 256. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 284. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in concatenation (.) or string at /data/loris/bin/mri/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> tarchive_validation.pl line 219. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in concatenation (.) or string at /data/loris/bin/mri/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl line 270. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 711. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Can't exec "mail": No such file or >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> directory at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 721. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 722. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 723. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 724. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 724. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 725. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 735. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> No Mincs inserted >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The tarchiveLoader insertion script >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> has failed. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Running now the following command: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl -profile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> prod -upload_id 3 /data/incoming/DCC0000_258024_V01.tar.gz -verbose" >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I inserted the VisitLabel, but still >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the Mincs are not inserted and i am getting this error >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> "lorisadmin at hbp:/data/loris/bin/mri$ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl -profile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> prod -upload_id 3 /data/incoming/DCC0000_258024_V01.tar.gz -verbose >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> find -path >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> \/tmp\/ImagingUpload\-17\-45\-5MsWEd -name '__MACOSX' -delete >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Spool message is: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The Scan for the uploadID 3 has >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> already been run with tarchiveID: 7. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> To continue with the rest of the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> insertion pipeline, please run tarchiveLoader from a terminal as follows: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader -globLocation -profile prod >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive//2012/DCM_2012-12-05_ImagingUpload-17-43-ZUEFjb.tar >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -verbose" >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Which files should i delete? I >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> thought that deleting the files from the tarchive was enough. And i >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> executed the last proposed command to continue to rest of the insertion >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> pipeline ( check the image ). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 24 ???? 2019 ???? 5:05 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ?.?., ?/? Cecile Madjar < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> cecile.madjar at mcin.ca> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sorry I was not clear before. Every >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visits of candidates are created in the session table with one entry per >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID/VisitLabel. So if the imaging pipeline created visits in the session >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> table (that are not attached to instruments) and you want to clean your >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> database completely, you can delete entries in that table as well. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Regarding your point 2, the imaging >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> pipeline can create the visit in the session table as long as the visit >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> label is present in the Visit_Windows table (which means the visit label >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> stored in the PatientName is a valid visit label). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> However, in your prod file, if the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> variable $subjectID{'createVisitLabel'} is set to 1 for candidates, the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit label should be created in the Visit_Windows table I believe. Here >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> is the line of the prod file you would need to change >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> . >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> In general, we prefer populating >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the Visit_Windows table and set the $subjectID{'createVisitLabel'} to 0 for >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> candidate data to avoid insertion of badly labelled MRI data that are >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> complex to relabel. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Finally, regarding the candidate >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> creation, if you execute the following steps, the pipeline should be able >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> to create candidates: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - set in the Imaging Pipeline >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> section of the config module the config setting "Upload creation of >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> candidates" to Yes >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - manually transfer the scans to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the LORIS server instead of uploading it via the imaging browser >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - run batch_imaging_upload.pl as >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> you did until now. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helps! >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> On Wed, Jul 24, 2019 at 8:47 AM >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> About my second question i >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> replaced the name of the patient in the .dcm files and now i am getting an >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> error that the visit label does not exist. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I thought it was supposed to be >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> automatically created. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> "Done adding archive info into >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> database >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -globLocation -profile prod >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive//DCM_2012-12-05_ImagingUpload-15-42-yUwQQV.tar >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -verbose >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> md5sum >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive/DCM_2012-12-05_ImagingUpload-15-42-yUwQQV.tar >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> candidate id 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> => No Visit labelVisit label does >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> not exist >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Set centerID = 1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Number of MINC files that will be >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> considered for inserting into the database: 1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> log dir is /logs and log file is >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /logs/TarLoad-15-42-L6pocU.log >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> candidate id 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> => No Visit label >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Cleaning up temp files: rm -rf >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-15-42-J2rQms/ImagingUpload-15-42-yUwQQV*" >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 24 ???? 2019 ???? 3:38 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ?.?., ?/? Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 1) What are the records in the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> session table? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 2) I tried to upload a >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> non-phantom file like this >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> input_file.txt: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/incoming/DCC0000_258024_V1.tar.gz >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> N DCC0000_258024_V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Terminal: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ./batch_uploads_imageuploader >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -profile prod < ~/Desktop/input.txt > log.txt >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and i get the following error in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the log.txt file >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> "Running now the following >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> command: /data/loris/data/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl -profile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> prod -upload_id 7 /data/incoming/DCC0000_258024_V1.tar.gz -verbose >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> find -path >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> \/tmp\/ImagingUpload\-14\-56\-FeLCB4 -name '__MACOSX' -delete >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Spool message is: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The PatientName read from the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DICOM header does not start with DCC0000_258024_V1 from the mri_upload table >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> " >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and the spool message is repeated >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> for each .dcm file. Should i preprocess every .dcm file and change the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PatientName to "DCC0000_258024_V1"? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 3) As far as it concerns the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> candidate profile i have to create a new one each time before i try to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> upload a file? Is there already a way to create a candidate profile and get >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the DCCID and PSCID without the user interface? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 18 ???? 2019 ???? 5:00 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ?.?., ?/? Cecile Madjar < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> cecile.madjar at mcin.ca> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> See answers to your questions >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> below. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> About the 1st case we had a >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> dicom with a blank studyUID, maybe someone accidentally removed it. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> That is strange. Something must >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> have been done to the DICOM files. I have never seen a study with no >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> StudyUID out of the scanner. Usually, you need to manually erase it with >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> some tool. However, DICOMs never cease to surprise me... >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Some other questions: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 1) What are the steps to remove >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> all of my patients and uploads?: because i want to try to reupload all the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> testing dicoms we had with a clean database. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Release 21.0 of LORIS-MRI will >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> offer a script to remove all the entries and files specific to an upload. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> However, this release is not yet out. Hopefully in the next few weeks. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> In the meantime, since your case >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> is particular and that you just want to start with a clean database, the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> following deletes should work (hopefully I won't forget any tables): >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from mri_violations_log; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> mri_protocol_violated_scans; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from MRICandidateErrors; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from parameter_file; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from files_qcstatus; # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> (if you played with the QC part of the imaging browser for testing) >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> feedback_mri_comments; # (if you played with the QC part of the imaging >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> browser for testing) >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from tarchive_series; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from tarchive_files; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from mri_upload; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from tarchive; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from mri_scanner; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from candidate where >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID="scanner"; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I don't know if you want to also >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete entries in the session and candidate table too? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 2) We do not need to create the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> profile of a patient ( are the patients stored in the candidate table? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> because i can't see the ghosts ), because will it automatically be created >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> when importing a dicom? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I am not sure I understand fully >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> this question. All candidates are stored in the candidate table. The >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> phantom scans however are attached to a scanner candidate depending on >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> where the scan happened. It is a bit of a weird concept that we have to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> redesign eventually but never got a chance to get to it. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hopefully this answered your >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> question, otherwise, don't hesitate to let me know. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 3) What is the difference >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> between uploading a dicom as phantom instead of importing as >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCCID_DCCID_VisitLabel? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> When you upload the scan as >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID_DCCID_VisitLabel, there is a check that makes sure the candidate IDs >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and visit label are valid at the time of upload. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> When you upload a scan as >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> phantom, it expects that the DICOM field PatientName and uploaded filename >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> contains the string "phantom". We enforced this behaviour on the imaging >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> uploader side in recent releases but I can't remember which one. Probably >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the upcoming 21.0 release. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> All those verifications might >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> seem cumbersome but they are here to ensure that the files inserted are all >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> valid and labelled properly as it is a bit messy to have to delete files >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> that were wrongly labelled. At least, the delete script present in release >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 21.0 will make this process easier but it is still good practice to verify >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> those things. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> With pleasure. Hopefully the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> answers to your questions will be helpful. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PS: loris-dev mailing list: you >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> will find the initial answer I gave Sotirios below. I forgot to cc the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> loris-dev in my earlier reply... >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 16 ???? 2019 ???? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 12:02 ?.?., ?/? Cecile Madjar < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> cecile.madjar at mcin.ca> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Dear Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you for reaching out. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Since your email was already organized in points, I will reply directly >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> below your questions below. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 1) What do we do when the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> StudyUID is blank on the header? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/minor/docs/AppendixA-Troubleshooting_guideline.md >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> There solution provided at the table 3 does not guide us how to find the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> information ( is possible ). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The StudyUID is the field used >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in our pipeline at the moment to check whether a DICOM study was already >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> inserted into LORIS with that same StudyUID since it is supposed to be >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> unique for every single study. Currently, we do not support insertion of >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DICOM studies if they do not have a StudyUID associated with them. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Is there a specific reason why >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the StudyUID is blank in the DICOM headers in your DICOM files? Did they go >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> through some processes before upload to LORIS? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 2) When i am about to upload a >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> non-phanton case i need a 'Visit Label'. Is there already a script that can >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> create a new visit label for a specific Candidate, so i can provide it as >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> input afterwards to the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> batch_uploads_imageuploader ( See option 5.1.3 https://github.com/aces/Loris-MRI/blob/minor/docs/05-PipelineLaunchOptions.md ) >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I am not sure if the front-end >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> allows for it but if you use batch_uploads_imageuploader, the insertion >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> scripts could create the visit label for you. However, it does need to be >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> included in the patient name in order for the script to know which label it >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> should use. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> For example: you upload V02 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> for MTL0123 (DCCID: 456789) but V02 was not yet created for MTL0123; the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> insertion scripts will create a V02 visit for MTL0123 if the PatientName >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> field for the dataset is MTL0123_456789_V02 with Stage marked as "Not >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Started". >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> However, *note that for the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> script to create the visit for the candidate, you have to make sure that >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> all the visit label of your projects were inserted in the Visit_Windows >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> table* (otherwise, the visit >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> will never be created as they were not specified as being part of the list >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> of visit label to expect). So in the example above, you should have one row >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in Visit_Windows with Visit_label="V02" set. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 3) Section 4.3 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/minor/docs/04-Scripts.md >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> What do we do when the folder contains multiple mnc files? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> This is a case by case. Most >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> of the time, the MINC files that failed insertion into the imaging browser >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> end up in the MRI violation module where you can see what went wrong with >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the acquisitions not inserted. If you notice that the MINC file should be >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> inserted as a specific protocol, you can force the insertion as explained >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in section 4.3. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> In your case, I have a feeling >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> that you want to be able to insert MINC files that did not go through the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> whole pipeline insertion (DICOM archival, then dcm2mnc, then protocol >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> identification, then insertion...). In theory, you could call >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl on any MINC >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> file, provided you have at least the following information: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - path to the MINC file >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - uploadID associated with the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> MINC files or DICOM archive path from which those MINC files were created >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> from >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Then the minc_insertion.pl >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> script will do the subject information and protocol validation etc... >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> If all the MINC files come >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> from the same uploadID or TarchiveID, then you could run a loop in bash >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> calling the minc_insertion.pl >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> script like this for files deriving from uploadID=1: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ls /path/to/mnc/folder/* | >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> while read f; do >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl -profile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> prod -uploadID 1 -mincPath $f; done >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helped! >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>>>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>>>>>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | >>>>>>>>>>>>>>>>>>>>>>>>>> MCIN.ca >>>>>>>>>>>>>>>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>>>>>>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>>>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>>>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>>>>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>>>>>> >>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>> >>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> -- >>>>>>>>>>> >>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>> >>>>>>>>>> _______________________________________________ >>>>>>>>>> Loris-dev mailing list >>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>> >>>>>>>>> _______________________________________________ >>>>>>>> Loris-dev mailing list >>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>> >>>>>>> >>>>>>> >>>>>>> -- >>>>>>> Shen Wang >>>>>>> Loris Developer >>>>>>> Montreal Neurological Institute >>>>>>> McGill University >>>>>>> >>>>>>> >>> >>> -- >>> Shen Wang >>> Loris Developer >>> Montreal Neurological Institute >>> McGill University >>> >>> -- >> Shen Wang >> Loris Developer >> Montreal Neurological Institute >> McGill University >> >> _______________________________________________ >> Loris-dev mailing list >> Loris-dev at bic.mni.mcgill.ca >> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >> > > > -- > > christine.rogers at mcgill.ca > McGill Centre for Integrative Neuroscience | MCIN.ca > Montreal Neurological Institute > McGill University | Montreal | Canada > 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Name: ???? 2019-08-13 19.21.15.png Type: image/png Size: 508603 bytes Desc: not available URL: -------------- next part -------------- 0 info it worked if it ends with ok 1 verbose cli [ '/usr/bin/node', '/usr/bin/npm', 'run', 'compile' ] 2 info using npm at 6.4.1 3 info using node at v8.16.0 4 verbose run-script [ 'precompile', 'compile', 'postcompile' ] 5 info lifecycle loris at 1.0.0~precompile: loris at 1.0.0 6 info lifecycle loris at 1.0.0~compile: loris at 1.0.0 7 verbose lifecycle loris at 1.0.0~compile: unsafe-perm in lifecycle true 8 verbose lifecycle loris at 1.0.0~compile: PATH: /usr/lib/node_modules/npm/node_modules/npm-lifecycle/node-gyp-bin:/var/www/loris/node_modules/.bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/snap/bin 9 verbose lifecycle loris at 1.0.0~compile: CWD: /var/www/loris 10 silly lifecycle loris at 1.0.0~compile: Args: [ '-c', 'webpack' ] 11 silly lifecycle loris at 1.0.0~compile: Returned: code: 2 signal: null 12 info lifecycle loris at 1.0.0~compile: Failed to exec compile script 13 verbose stack Error: loris at 1.0.0 compile: `webpack` 13 verbose stack Exit status 2 13 verbose stack at EventEmitter. (/usr/lib/node_modules/npm/node_modules/npm-lifecycle/index.js:301:16) 13 verbose stack at emitTwo (events.js:126:13) 13 verbose stack at EventEmitter.emit (events.js:214:7) 13 verbose stack at ChildProcess. (/usr/lib/node_modules/npm/node_modules/npm-lifecycle/lib/spawn.js:55:14) 13 verbose stack at emitTwo (events.js:126:13) 13 verbose stack at ChildProcess.emit (events.js:214:7) 13 verbose stack at maybeClose (internal/child_process.js:915:16) 13 verbose stack at Process.ChildProcess._handle.onexit (internal/child_process.js:209:5) 14 verbose pkgid loris at 1.0.0 15 verbose cwd /var/www/loris 16 verbose Linux 4.15.0-55-generic 17 verbose argv "/usr/bin/node" "/usr/bin/npm" "run" "compile" 18 verbose node v8.16.0 19 verbose npm v6.4.1 20 error code ELIFECYCLE 21 error errno 2 22 error loris at 1.0.0 compile: `webpack` 22 error Exit status 2 23 error Failed at the loris at 1.0.0 compile script. 23 error This is probably not a problem with npm. 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./modules/candidate_list/js/openProfileForm.js = ./modules/candidate_list/js/openProfileForm.js ./modules/candidate_list/js/openProfileForm.js.map Entrypoint ./modules/candidate_list/js/onLoad.js = ./modules/candidate_list/js/onLoad.js ./modules/candidate_list/js/onLoad.js.map Entrypoint ./modules/candidate_list/js/candidateListIndex.js = ./modules/candidate_list/js/candidateListIndex.js ./modules/candidate_list/js/candidateListIndex.js.map Entrypoint ./modules/datadict/js/dataDictIndex.js = ./modules/datadict/js/dataDictIndex.js ./modules/datadict/js/dataDictIndex.js.map Entrypoint ./modules/data_integrity_flag/js/dataIntegrityFlagIndex.js = ./modules/data_integrity_flag/js/dataIntegrityFlagIndex.js ./modules/data_integrity_flag/js/dataIntegrityFlagIndex.js.map Entrypoint ./modules/dataquery/js/react.app.js = ./modules/dataquery/js/react.app.js ./modules/dataquery/js/react.app.js.map Entrypoint ./modules/dataquery/js/react.fieldselector.js = ./modules/dataquery/js/react.fieldselector.js ./modules/dataquery/js/react.fieldselector.js.map Entrypoint ./modules/dataquery/js/react.filterBuilder.js = ./modules/dataquery/js/react.filterBuilder.js ./modules/dataquery/js/react.filterBuilder.js.map Entrypoint ./modules/dataquery/js/react.paginator.js = ./modules/dataquery/js/react.paginator.js ./modules/dataquery/js/react.paginator.js.map Entrypoint ./modules/dataquery/js/react.sidebar.js = ./modules/dataquery/js/react.sidebar.js ./modules/dataquery/js/react.sidebar.js.map Entrypoint ./modules/dataquery/js/react.tabs.js = ./modules/dataquery/js/react.tabs.js ./modules/dataquery/js/react.tabs.js.map Entrypoint ./modules/dicom_archive/js/dicom_archive.js = ./modules/dicom_archive/js/dicom_archive.js ./modules/dicom_archive/js/dicom_archive.js.map Entrypoint ./modules/genomic_browser/js/FileUploadModal.js = ./modules/genomic_browser/js/FileUploadModal.js ./modules/genomic_browser/js/FileUploadModal.js.map Entrypoint ./modules/genomic_browser/js/profileColumnFormatter.js = ./modules/genomic_browser/js/profileColumnFormatter.js ./modules/genomic_browser/js/profileColumnFormatter.js.map Entrypoint ./modules/imaging_browser/js/ImagePanel.js = ./modules/imaging_browser/js/ImagePanel.js ./modules/imaging_browser/js/ImagePanel.js.map Entrypoint ./modules/imaging_browser/js/imagingBrowserIndex.js = ./modules/imaging_browser/js/imagingBrowserIndex.js ./modules/imaging_browser/js/imagingBrowserIndex.js.map Entrypoint ./modules/instrument_builder/js/react.instrument_builder.js = ./modules/instrument_builder/js/react.instrument_builder.js ./modules/instrument_builder/js/react.instrument_builder.js.map Entrypoint ./modules/instrument_builder/js/react.questions.js = ./modules/instrument_builder/js/react.questions.js ./modules/instrument_builder/js/react.questions.js.map Entrypoint ./modules/instrument_manager/js/instrumentManagerIndex.js = ./modules/instrument_manager/js/instrumentManagerIndex.js ./modules/instrument_manager/js/instrumentManagerIndex.js.map Entrypoint ./modules/survey_accounts/js/surveyAccountsIndex.js = ./modules/survey_accounts/js/surveyAccountsIndex.js ./modules/survey_accounts/js/surveyAccountsIndex.js.map Entrypoint ./modules/mri_violations/js/mri_protocol_check_violations_columnFormatter.js = ./modules/mri_violations/js/mri_protocol_check_violations_columnFormatter.js ./modules/mri_violations/js/mri_protocol_check_violations_columnFormatter.js.map Entrypoint ./modules/mri_violations/js/columnFormatter.js = ./modules/mri_violations/js/columnFormatter.js ./modules/mri_violations/js/columnFormatter.js.map Entrypoint ./modules/mri_violations/js/columnFormatterUnresolved.js = ./modules/mri_violations/js/columnFormatterUnresolved.js ./modules/mri_violations/js/columnFormatterUnresolved.js.map Entrypoint ./modules/mri_violations/js/mri_protocol_violations_columnFormatter.js = ./modules/mri_violations/js/mri_protocol_violations_columnFormatter.js ./modules/mri_violations/js/mri_protocol_violations_columnFormatter.js.map Entrypoint ./modules/user_accounts/js/userAccountsIndex.js = ./modules/user_accounts/js/userAccountsIndex.js ./modules/user_accounts/js/userAccountsIndex.js.map Entrypoint ./modules/examiner/js/examinerIndex.js = ./modules/examiner/js/examinerIndex.js ./modules/examiner/js/examinerIndex.js.map Entrypoint ./modules/help_editor/js/help_editor.js = ./modules/help_editor/js/help_editor.js ./modules/help_editor/js/help_editor.js.map Entrypoint ./modules/brainbrowser/js/Brainbrowser.js = ./modules/brainbrowser/js/Brainbrowser.js ./modules/brainbrowser/js/Brainbrowser.js.map Entrypoint ./modules/imaging_uploader/js/index.js = ./modules/imaging_uploader/js/index.js ./modules/imaging_uploader/js/index.js.map Entrypoint ./modules/acknowledgements/js/acknowledgementsIndex.js = ./modules/acknowledgements/js/acknowledgementsIndex.js ./modules/acknowledgements/js/acknowledgementsIndex.js.map Entrypoint ./modules/new_profile/js/NewProfileIndex.js = ./modules/new_profile/js/NewProfileIndex.js ./modules/new_profile/js/NewProfileIndex.js.map Entrypoint ./modules/quality_control/js/qualityControlIndex.js = ./modules/quality_control/js/qualityControlIndex.js ./modules/quality_control/js/qualityControlIndex.js.map Entrypoint ./modules/server_processes_manager/js/server_processes_managerIndex.js = ./modules/server_processes_manager/js/server_processes_managerIndex.js ./modules/server_processes_manager/js/server_processes_managerIndex.js.map Entrypoint ./modules/document_repository/js/docIndex.js = ./modules/document_repository/js/docIndex.js ./modules/document_repository/js/docIndex.js.map Entrypoint ./modules/document_repository/js/editFormIndex.js = ./modules/document_repository/js/editFormIndex.js ./modules/document_repository/js/editFormIndex.js.map Entrypoint ./modules/publication/js/publicationIndex.js = ./modules/publication/js/publicationIndex.js ./modules/publication/js/publicationIndex.js.map Entrypoint ./modules/publication/js/viewProjectIndex.js = ./modules/publication/js/viewProjectIndex.js ./modules/publication/js/viewProjectIndex.js.map [0] ./jsx/DynamicDataTable.js 447 bytes {0} [built] [failed] [1 error] [2] ./jsx/StaticDataTable.js 471 bytes {2} [built] [failed] [1 error] [3] ./jsx/MultiSelectDropdown.js 403 bytes {3} [built] [failed] [1 error] [4] ./jsx/Breadcrumbs.js 473 bytes {4} [built] [failed] [1 error] [5] ./jsx/Form.js 510 bytes {5} [built] [failed] [1 error] [6] ./jsx/Markdown.js 425 bytes {6} [built] [failed] [1 error] [7] ./modules/media/jsx/mediaIndex.js 503 bytes {7} [built] [failed] [1 error] [8] ./modules/issue_tracker/jsx/issueTrackerIndex.js 358 bytes {8} [built] [failed] [1 error] [9] ./modules/issue_tracker/jsx/index.js 490 bytes {9} [built] [failed] [1 error] [10] ./modules/candidate_parameters/jsx/CandidateParameters.js 487 bytes {10} [built] [failed] [1 error] [11] ./modules/configuration/jsx/SubprojectRelations.js 383 bytes {11} [built] [failed] [1 error] [12] ./modules/conflict_resolver/jsx/conflictResolverIndex.js 389 bytes {12} [built] [failed] [1 error] [13] ./modules/conflict_resolver/jsx/resolvedConflictsIndex.js 389 bytes {13} [built] [failed] [1 error] [14] ./modules/bvl_feedback/jsx/react.behavioural_feedback_panel.js 441 bytes {14} [built] [failed] [1 error] [26] ./modules/dataquery/jsx/react.tabs.js 427 bytes {26} [built] [failed] [1 error] + 38 hidden modules WARNING in configuration The 'mode' option has not been set, webpack will fallback to 'production' for this value. Set 'mode' option to 'development' or 'production' to enable defaults for each environment. You can also set it to 'none' to disable any default behavior. Learn more: https://webpack.js.org/concepts/mode/ ERROR in ./modules/document_repository/jsx/docIndex.js Module build failed (from ./node_modules/babel-loader/lib/index.js): SyntaxError: Unexpected token (103:21) 101 | */ 102 | formatColumn(column, cell, row) { > 103 | let result = {cell}; | ^ 104 | switch (column) { 105 | case 'File Name': 106 | let downloadURL = loris.BaseURL + '/document_repository/Files/' + encodeURIComponent(row['File Name']); ERROR in ./modules/instrument_builder/jsx/react.instrument_builder.js Module build failed (from ./node_modules/babel-loader/lib/index.js): SyntaxError: Unexpected token (104:12) 102 | } 103 | return ( > 104 | | ^ 105 |
    106 | ERROR in ./modules/conflict_resolver/jsx/conflictResolverIndex.js Module build failed (from ./node_modules/babel-loader/lib/index.js): SyntaxError: Unexpected token (40:19) 38 | 39 | if (column === 'Instrument') { > 40 | return {this.state.Data.form.instrument.options[row.Instrument]}; | ^ 41 | } 42 | 43 | if (column === 'Correct Answer') { ERROR in ./jsx/PaginationLinks.js Module build failed (from ./node_modules/babel-loader/lib/index.js): SyntaxError: Unexpected token (42:19) 40 | 41 | if (this.props.Total === 0) { > 42 | return
    ; | ^ 43 | } 44 | if (this.props.Total < this.props.RowsPerPage) { 45 | return
    ; ERROR in ./modules/conflict_resolver/jsx/resolvedConflictsIndex.js Module build failed (from ./node_modules/babel-loader/lib/index.js): SyntaxError: Unexpected token (43:19) 41 | 42 | if (column === 'Instrument') { > 43 | return {this.state.Data.form.instrument.options[row.Instrument]}; | ^ 44 | } 45 | 46 | if (column === 'Correct Answer') { ERROR in ./modules/dataquery/jsx/react.app.js Module build failed (from ./node_modules/babel-loader/lib/index.js): SyntaxError: Unexpected token (47:19) 45 | 46 | if (this.props.queriesLoaded === false) { > 47 | return
    ; | ^ 48 | } 49 | // Build the list for the user queries 50 | for (let i = 0; i < this.props.userQueries.length; i += 1) { ERROR in ./modules/candidate_list/jsx/onLoad.js Module build failed (from ./node_modules/babel-loader/lib/index.js): SyntaxError: Unexpected token (4:20) 2 | 3 | $(function() { > 4 | ReactDOM.render( 50 |
    | ^ 51 | 51 | ERROR in ./jsx/DynamicDataTable.js Module build failed (from ./node_modules/babel-loader/lib/index.js): SyntaxError: Unexpected token (77:20) 75 | if (this.state.error !== undefined) { 76 | return ( > 77 |
    | ^ 78 | {this.state.error} 79 |
    80 | ); ERROR in ./modules/publication/jsx/viewProjectIndex.js Module build failed (from ./node_modules/babel-loader/lib/index.js): SyntaxError: Unexpected token (7:8) 5 | $(function() { 6 | const viewProject = ( > 7 |
    | ^ 8 |
    9 |
    10 | 80 |
  • | ^ 81 | 82 | {element.text} 83 | ERROR in ./jsx/Markdown.js Module build failed (from ./node_modules/babel-loader/lib/index.js): SyntaxError: Unexpected token (81:36) 79 | switch (hlevel) { 80 | case 6: > 81 | paragraphs[i] =
    {paragraphs[i]}
    ; | ^ 82 | break; 83 | 84 | case 5: ERROR in ./modules/candidate_list/jsx/openProfileForm.js Module build failed (from ./node_modules/babel-loader/lib/index.js): SyntaxError: Unexpected token (89:16) 87 | if (this.state.error.message !== '') { 88 | warning = ( > 89 |
    | ^ 90 | {this.state.error.message} 91 |
    92 | ); ERROR in ./modules/candidate_list/jsx/candidateListIndex.js Module build failed (from ./node_modules/babel-loader/lib/index.js): SyntaxError: Unexpected token (97:19) 95 | if (column === 'PSCID' && this.props.hasPermission('access_all_profiles')) { 96 | let url = this.props.baseURL + '/' + row['DCCID'] + '/'; > 97 | return {cell}; | ^ 98 | } 99 | if (column === 'Feedback') { 100 | switch (cell) { ERROR in ./modules/genomic_browser/jsx/FileUploadModal.js Module build failed (from ./node_modules/babel-loader/lib/index.js): SyntaxError: Unexpected token (97:31) 95 | 96 | if (this.state.submited) { > 97 | footerButtons.push(); | ^ 98 | } else { 99 | if (this.state.readyForUpload) { 100 | footerButtons.push(); ERROR in ./modules/issue_tracker/jsx/index.js Module build failed (from ./node_modules/babel-loader/lib/index.js): SyntaxError: Unexpected token (9:8) 7 | const id = location.href.split('/issue/')[1]; 8 | const issueTracker = ( > 9 |
    | ^ 10 | { 8 | ReactDOM.render( > 9 |
    | ^ 10 |
    11 |
    12 | References: Message-ID: I forgot to mention that i had already moved my previous config file and re-executed the installation script. ???? ???, 14 ??? 2019 ???? 3:26 ?.?., ?/? Sotirios Nikoloutsopoulos < sotirisnik at gmail.com> ??????: > Hi, > > Step 1 worked and the indentation errors were fixed. About step2 i added > all of these( there are more to include in the list) these to .eslintignore > which were reported to fail at being built, but they still appear on the > errors at the make_output file. > > /jsx/DynamicDataTable.js > /jsx/StaticDataTable.js > /jsx/MultiSelectDropdown.js > /jsx/Breadcrumbs.js > /jsx/Form.js > /jsx/Markdown.js > /modules/media/jsx/mediaIndex.js > /modules/issue_tracker/jsx/issueTrackerIndex.js > /modules/issue_tracker/jsx/index.js > /modules/candidate_parameters/jsx/CandidateParameters.js > /modules/configuration/jsx/SubprojectRelations.js > /modules/conflict_resolver/jsx/conflictResolverIndex.js > /modules/conflict_resolver/jsx/resolvedConflictsIndex.js > /modules/bvl_feedback/jsx/react.behavioural_feedback_panel.js > /modules/dataquery/jsx/react.tabs.js > /modules/document_repository/jsx/docIndex.js > /modules/instrument_builder/jsx/react.instrument_builder.js > /modules/imaging_uploader/jsx/index.js > /modules/datadict/jsx/dataDictIndex.js > /modules/bvl_feedback/jsx/react.behavioural_feedback_panel.js > /modules/new_profile/jsx/NewProfileIndex.js > /modules/examiner/jsx/examinerIndex.js > /modules/configuration/jsx/SubprojectRelations.js > /modules/data_team_helper/jsx/behavioural_qc_module.js > /modules/acknowledgements/jsx/acknowledgementsIndex.js > /modules/candidate_parameters/jsx/CandidateParameters.js > /modules/imaging_browser/jsx/ImagePanel.js > /modules/mri_violations/jsx/mri_protocol_violations_columnFormatter.js > > /modules/mri_violations/jsx/mri_protocol_check_violations_columnFormatter.js > /modules/genomic_browser/jsx/profileColumnFormatter.js > /modules/dataquery/jsx/react.tabs.js > /jsx/MultiSelectDropdown.js > /modules/mri_violations/jsx/columnFormatterUnresolved.js > /modules/dataquery/jsx/react.sidebar.js > /modules/dataquery/jsx/react.fieldselector.js > /modules/quality_control/jsx/qualityControlIndex.js > /modules/dataquery/jsx/react.paginator.js > /modules/instrument_builder/jsx/react.questions.js > /modules/dataquery/jsx/react.filterBuilder.js > /modules/conflict_resolver/jsx/conflictResolverIndex.js > /jsx/PaginationLinks.js > /modules/conflict_resolver/jsx/resolvedConflictsIndex.js > /modules/dataquery/jsx/react.app.js > /modules/candidate_list/jsx/onLoad.js > /jsx/Form.js > /modules/publication/jsx/publicationIndex.js > /modules/server_processes_manager/jsx/server_processes_managerIndex.js > /modules/imaging_browser/jsx/imagingBrowserIndex.js > /modules/issue_tracker/jsx/issueTrackerIndex.js > /modules/survey_accounts/jsx/surveyAccountsIndex.js > /modules/data_integrity_flag/jsx/dataIntegrityFlagIndex.js > /modules/instrument_manager/jsx/instrumentManagerIndex.js > /modules/media/jsx/mediaIndex.js > /modules/user_accounts/jsx/userAccountsIndex.js > /modules/help_editor/jsx/help_editor.js > /modules/dicom_archive/jsx/dicom_archive.js > /modules/mri_violations/jsx/columnFormatter.js > /modules/brainbrowser/jsx/Brainbrowser.js > /node_modules/babel-loader/lib/index.js > /modules/document_repository/jsx/editFormIndex.js > > Thanks > > ???? ???, 14 ??? 2019 ???? 7:50 ?.?., ?/? Christine Rogers, Ms. < > christine.rogers at mcgill.ca> ??????: > >> Hi Shen and Sotirios - just a note, >> >> For the 21 release, it's best to run the install script without sudoing >> it. >> >> (Shen, I believe we discovered a minor issue with the sudo last week >> #5008) >> >> Best, >> Christine >> >> On Tue, Aug 13, 2019 at 9:22 PM Shen Wang >> wrote: >> >>> Does it work? If still doesn?t work, try to remove project/config.xml >>> file. Do sudo ./install.sh again. To reinstall Loris again. >>> >>> >>> Shen Wang ?2019?8?13? ????9:02??? >>> >>>> Hi Sotirios, >>>> step 1: >>>> sudo ./node_modules/.bin/eslint --fix /var/www/loris >>>> step 2: >>>> put the rest error files under this line [# Ignore until ESLint is run] in >>>> the .eslintignore file. >>>> step 3: >>>> sudo make >>>> >>>> >>>> >>>> On Tue, 13 Aug 2019 at 20:34, Sotirios Nikoloutsopoulos < >>>> sotirisnik at gmail.com> wrote: >>>> >>>>> I did the modifications, still there are errors. >>>>> Thanks >>>>> >>>>> >>>>> ???? ???, 14 ??? 2019 ???? 3:22 ?.?., ?/? Shen Wang < >>>>> wangshen.mcin at gmail.com> ??????: >>>>> >>>>>> Hi Sotirios, >>>>>> I saw your output file, the config issue is gone. >>>>>> you can use [sudo npm run lintfix:javascript ] to fix these indent >>>>>> issues. >>>>>> If it still has errors. >>>>>> Then try modify this file .eslintignore >>>>>> with this >>>>>> >>>>>> # Ignore until ESLint is run >>>>>> >>>>>> modules/* >>>>>> >>>>>> modules/dataquery/ >>>>>> >>>>>> node_modules/* >>>>>> >>>>>> htdocs/js/components/* >>>>>> >>>>>> jsx/* >>>>>> >>>>>> >>>>>> # Ignore external libs >>>>>> >>>>>> htdocs/js/flot/* >>>>>> >>>>>> htdocs/js/jquery/* >>>>>> >>>>>> htdocs/js/jszip/* >>>>>> >>>>>> htdocs/js/modernizr/* >>>>>> >>>>>> htdocs/js/modules/* >>>>>> >>>>>> htdocs/js/react/* >>>>>> >>>>>> htdocs/js/shims/* >>>>>> >>>>>> htdocs/js/c3.min.js >>>>>> >>>>>> htdocs/js/d3.min.js >>>>>> >>>>>> htdocs/js/FileSaver.min.js >>>>>> >>>>>> >>>>>> then do sudo make. >>>>>> It should work. >>>>>> Regards >>>>>> Shen >>>>>> >>>>>> >>>>>> Sotirios Nikoloutsopoulos ?2019?8?13? >>>>>> ????7:54??? >>>>>> >>>>>>> No, it didn't work, i also tried space/tabs because most of the >>>>>>> errors where about indentation, also there are some errors about React. >>>>>>> >>>>>>> Thanks >>>>>>> >>>>>>> lorisadmin at hbp:/var/www/loris$ sudo ./node_modules/.bin/eslint >>>>>>> --init >>>>>>> ? How would you like to configure ESLint? Answer questions about >>>>>>> your style >>>>>>> ? Which version of ECMAScript do you use? ES2015 >>>>>>> ? Are you using ES6 modules? Yes >>>>>>> ? Where will your code run? Browser >>>>>>> ? Do you use CommonJS? Yes >>>>>>> ? Do you use JSX? Yes >>>>>>> ? Do you use React? Yes >>>>>>> ? What style of indentation do you use? Spaces >>>>>>> ? What quotes do you use for strings? Single >>>>>>> ? What line endings do you use? Unix >>>>>>> ? Do you require semicolons? Yes >>>>>>> ? What format do you want your config file to be in? JSON >>>>>>> The config that you've selected requires the following dependencies: >>>>>>> >>>>>>> eslint-plugin-react at latest >>>>>>> Successfully created .eslintrc.json file in /var/www/loris >>>>>>> >>>>>>> lorisadmin at hbp:/var/www/loris$ sudo make > sudo_make_output >>>>>>> npm WARN The package prop-types is included as both a dev and >>>>>>> production dependency. >>>>>>> npm WARN optional SKIPPING OPTIONAL DEPENDENCY: fsevents at 1.2.4 >>>>>>> (node_modules/fsevents): >>>>>>> npm WARN notsup SKIPPING OPTIONAL DEPENDENCY: Unsupported platform >>>>>>> for fsevents at 1.2.4: wanted {"os":"darwin","arch":"any"} (current: >>>>>>> {"os":"linux","arch":"x64"}) >>>>>>> >>>>>>> npm ERR! code ELIFECYCLE >>>>>>> npm ERR! errno 2 >>>>>>> npm ERR! loris at 1.0.0 compile: `webpack` >>>>>>> npm ERR! Exit status 2 >>>>>>> npm ERR! >>>>>>> npm ERR! Failed at the loris at 1.0.0 compile script. >>>>>>> npm ERR! This is probably not a problem with npm. There is likely >>>>>>> additional logging output above. >>>>>>> >>>>>>> npm ERR! A complete log of this run can be found in: >>>>>>> npm ERR! >>>>>>> /home/lorisadmin/.npm/_logs/2019-08-13T23_40_58_841Z-debug.log >>>>>>> >>>>>>> ???? ???, 14 ??? 2019 ???? 2:29 ?.?., ?/? Shen Wang < >>>>>>> wangshen.mcin at gmail.com> ??????: >>>>>>> >>>>>>>> Hi Sotirios, >>>>>>>> When you do make command, please make sure with sudo at the >>>>>>>> beginning. [sudo make] >>>>>>>> If it still doesn't work for you. >>>>>>>> Then try the solutions below. >>>>>>>> solution 1: >>>>>>>> [image: ???? 2019-08-13 19.21.15.png] >>>>>>>> Regards >>>>>>>> Shen >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> On Tue, 13 Aug 2019 at 17:22, Sotirios Nikoloutsopoulos < >>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>> >>>>>>>>> I think that the files exists although i redownloaded the >>>>>>>>> eslintrc.json i checked others files that had similar errors. >>>>>>>>> >>>>>>>>> lorisadmin at hbp:/var/www/loris$ ls -l >>>>>>>>> ./node_modules/eslint-loader/index.js >>>>>>>>> -rw-rw-r-- 1 lorisadmin lorisadmin 6463 ??? 26 1985 >>>>>>>>> ./node_modules/eslint-loader/index.js >>>>>>>>> >>>>>>>>> lorisadmin at hbp:/var/www/loris$ ls -l .eslintrc.json >>>>>>>>> -rw-rw-r-- 1 lorisadmin lorisadmin 84530 ??? 14 00:04 >>>>>>>>> .eslintrc.json >>>>>>>>> >>>>>>>>> Maybe this can help >>>>>>>>> >>>>>>>>> Module build failed (from ./node_modules/eslint-loader/index.js): >>>>>>>>> SyntaxError: Cannot read config file: >>>>>>>>> /var/www/loris/.eslintrc.json >>>>>>>>> Error: Unexpected token < in JSON at position 6 >>>>>>>>> at JSON.parse () >>>>>>>>> at loadJSONConfigFile >>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config/config-file.js:114:21) >>>>>>>>> at loadConfigFile >>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config/config-file.js:230:26) >>>>>>>>> at loadFromDisk >>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config/config-file.js:500:18) >>>>>>>>> at Object.load >>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config/config-file.js:564:20) >>>>>>>>> at Config.getLocalConfigHierarchy >>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config.js:227:44) >>>>>>>>> at Config.getConfigHierarchy >>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config.js:179:43) >>>>>>>>> at Config.getConfigVector >>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config.js:286:21) >>>>>>>>> at Config.getConfig >>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config.js:329:29) >>>>>>>>> at processText >>>>>>>>> (/var/www/loris/node_modules/eslint/lib/cli-engine.js:162:33) >>>>>>>>> at CLIEngine.executeOnText >>>>>>>>> (/var/www/loris/node_modules/eslint/lib/cli-engine.js:596:17) >>>>>>>>> at lint >>>>>>>>> (/var/www/loris/node_modules/eslint-loader/index.js:237:17) >>>>>>>>> at Object.module.exports >>>>>>>>> (/var/www/loris/node_modules/eslint-loader/index.js:232:21) >>>>>>>>> >>>>>>>>> ERROR in ./modules/imaging_uploader/jsx/index.js >>>>>>>>> Module build failed (from >>>>>>>>> ./node_modules/eslint-loader/index.js): >>>>>>>>> SyntaxError: Cannot read config file: >>>>>>>>> /var/www/loris/.eslintrc.json >>>>>>>>> Error: Unexpected token < in JSON at position 6 >>>>>>>>> at JSON.parse () >>>>>>>>> at loadJSONConfigFile >>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config/config-file.js:114:21) >>>>>>>>> at loadConfigFile >>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config/config-file.js:230:26) >>>>>>>>> at loadFromDisk >>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config/config-file.js:500:18) >>>>>>>>> at Object.load >>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config/config-file.js:564:20) >>>>>>>>> at Config.getLocalConfigHierarchy >>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config.js:227:44) >>>>>>>>> at Config.getConfigHierarchy >>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config.js:179:43) >>>>>>>>> at Config.getConfigVector >>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config.js:286:21) >>>>>>>>> at Config.getConfig >>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config.js:329:29) >>>>>>>>> at processText >>>>>>>>> (/var/www/loris/node_modules/eslint/lib/cli-engine.js:162:33) >>>>>>>>> at CLIEngine.executeOnText >>>>>>>>> (/var/www/loris/node_modules/eslint/lib/cli-engine.js:596:17) >>>>>>>>> at lint >>>>>>>>> (/var/www/loris/node_modules/eslint-loader/index.js:237:17) >>>>>>>>> at Object.module.exports >>>>>>>>> (/var/www/loris/node_modules/eslint-loader/index.js:232:21) >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> ???? ???, 13 ??? 2019 ???? 11:52 ?.?., ?/? John Saigle < >>>>>>>>> john.saigle at mcin.ca> ??????: >>>>>>>>> >>>>>>>>>> HI Sotirios, >>>>>>>>>> >>>>>>>>>> The make_output.txt file shows webpack failing because it can't >>>>>>>>>> find the ESLint config file. >>>>>>>>>> >>>>>>>>>> Can you confirm whether the file `.eslintrc.json` exists within >>>>>>>>>> your loris root directory (usually `/var/www/loris/`)? When I delete my >>>>>>>>>> file I get the same errors as you. >>>>>>>>>> >>>>>>>>>> If you find that it's missing, you can make a local copy with the >>>>>>>>>> contents found here: >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> https://github.com/aces/Loris/blob/e26a6ad49a73fcffef0cd73bb600c4d17b200b62/.eslintrc.json >>>>>>>>>> >>>>>>>>>> Once you know it exists, try running `make` again. >>>>>>>>>> >>>>>>>>>> Let us know if that moves you forward. >>>>>>>>>> >>>>>>>>>> Best, >>>>>>>>>> John >>>>>>>>>> >>>>>>>>>> On Tue, Aug 13, 2019 at 2:21 PM Sotirios Nikoloutsopoulos < >>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>> >>>>>>>>>>> Hi, >>>>>>>>>>> I executed the commands for the node and now i am get the >>>>>>>>>>> followings: >>>>>>>>>>> >>>>>>>>>>> lorisadmin at hbp:/var/www/loris$ make > ~/make_output >>>>>>>>>>> npm WARN The package prop-types is included as both a dev and >>>>>>>>>>> production dependency. >>>>>>>>>>> npm WARN optional SKIPPING OPTIONAL DEPENDENCY: fsevents at 1.2.4 >>>>>>>>>>> (node_modules/fsevents): >>>>>>>>>>> npm WARN notsup SKIPPING OPTIONAL DEPENDENCY: Unsupported >>>>>>>>>>> platform for fsevents at 1.2.4: wanted >>>>>>>>>>> {"os":"darwin","arch":"any"} (current: {"os":"linux","arch":"x64"}) >>>>>>>>>>> >>>>>>>>>>> npm ERR! code ELIFECYCLE >>>>>>>>>>> npm ERR! errno 2 >>>>>>>>>>> npm ERR! loris at 1.0.0 compile: `webpack` >>>>>>>>>>> npm ERR! Exit status 2 >>>>>>>>>>> npm ERR! >>>>>>>>>>> npm ERR! Failed at the loris at 1.0.0 compile script. >>>>>>>>>>> npm ERR! This is probably not a problem with npm. There is >>>>>>>>>>> likely additional logging output above. >>>>>>>>>>> >>>>>>>>>>> npm ERR! A complete log of this run can be found in: >>>>>>>>>>> npm ERR! >>>>>>>>>>> /home/lorisadmin/.npm/_logs/2019-08-13T18_12_05_378Z-debug.log >>>>>>>>>>> make: *** [javascript] Error 2 >>>>>>>>>>> >>>>>>>>>>> Thanks, >>>>>>>>>>> Sotirios >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> ???? ???, 12 ??? 2019 ???? 10:19 ?.?., ?/? Christine Rogers, Ms. >>>>>>>>>>> ??????: >>>>>>>>>>> >>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>> >>>>>>>>>>>> We've seen some users installing LORIS 21 or upgrading to 21 >>>>>>>>>>>> whose version of node doesn't work well with webpack, due to updated >>>>>>>>>>>> packages they're missing. >>>>>>>>>>>> If so, update your node : >>>>>>>>>>>> >>>>>>>>>>>> curl -sL https://deb.nodesource.com/setup_8.x | sudo -E bash - >>>>>>>>>>>> sudo apt-get install -y nodejs >>>>>>>>>>>> >>>>>>>>>>>> Let us know how that goes -- please send us output from the >>>>>>>>>>>> same log if any issues. >>>>>>>>>>>> Best, >>>>>>>>>>>> Christine >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> On Thu, Aug 8, 2019 at 2:38 PM Sotirios Nikoloutsopoulos < >>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>> >>>>>>>>>>>>> It's not a disk space issue, as you can see below i have still >>>>>>>>>>>>> 74GB available. >>>>>>>>>>>>> >>>>>>>>>>>>> lorisadmin at hbp:/var/www/loris$ df -h >>>>>>>>>>>>> Filesystem Size Used Avail Use% Mounted on >>>>>>>>>>>>> udev 2,9G 0 2,9G 0% /dev >>>>>>>>>>>>> tmpfs 597M 8,6M 588M 2% /run >>>>>>>>>>>>> /dev/sda1 98G 19G 74G 21% / >>>>>>>>>>>>> >>>>>>>>>>>>> Maybe we have to pass a flag to get into strict mode? as >>>>>>>>>>>>> stated "SyntaxError: Block-scoped declarations (let, const, function, >>>>>>>>>>>>> class) not yet supported outside strict mode" >>>>>>>>>>>>> >>>>>>>>>>>>> Thanks, >>>>>>>>>>>>> Sotirios >>>>>>>>>>>>> >>>>>>>>>>>>> ???? ???, 8 ??? 2019 ???? 4:32 ?.?., ?/? Dave MacFarlane < >>>>>>>>>>>>> dave.macfarlane at mcin.ca> ??????: >>>>>>>>>>>>> >>>>>>>>>>>>>> It looks like the javascript snippet shown in the error >>>>>>>>>>>>>> message when trying to compile the js is truncated. Have you run out of >>>>>>>>>>>>>> disk space? >>>>>>>>>>>>>> >>>>>>>>>>>>>> On Thu, Aug 8, 2019 at 8:37 AM Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>> >>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> I runned make and also included the file it reports at the >>>>>>>>>>>>>>> end. >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> lorisadmin at hbp:/var/www/loris$ make >>>>>>>>>>>>>>> npm install >>>>>>>>>>>>>>> npm WARN optional Skipping failed optional dependency >>>>>>>>>>>>>>> /chokidar/fsevents: >>>>>>>>>>>>>>> npm WARN notsup Not compatible with your operating system or >>>>>>>>>>>>>>> architecture: fsevents at 1.2.9 >>>>>>>>>>>>>>> npm WARN optional Skipping failed optional dependency >>>>>>>>>>>>>>> /watchpack/chokidar/fsevents: >>>>>>>>>>>>>>> npm WARN notsup Not compatible with your operating system or >>>>>>>>>>>>>>> architecture: fsevents at 1.2.9 >>>>>>>>>>>>>>> npm run compile >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> > loris at 1.0.0 compile /var/www/loris >>>>>>>>>>>>>>> > webpack >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> /var/www/loris/node_modules/webpack/bin/webpack.js:86 >>>>>>>>>>>>>>> let notify = >>>>>>>>>>>>>>> ^^^ >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> SyntaxError: Block-scoped declarations (let, const, >>>>>>>>>>>>>>> function, class) not yet supported outside strict mode >>>>>>>>>>>>>>> at exports.runInThisContext (vm.js:53:16) >>>>>>>>>>>>>>> at Module._compile (module.js:374:25) >>>>>>>>>>>>>>> at Object.Module._extensions..js (module.js:417:10) >>>>>>>>>>>>>>> at Module.load (module.js:344:32) >>>>>>>>>>>>>>> at Function.Module._load (module.js:301:12) >>>>>>>>>>>>>>> at Function.Module.runMain (module.js:442:10) >>>>>>>>>>>>>>> at startup (node.js:136:18) >>>>>>>>>>>>>>> at node.js:966:3 >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> npm ERR! Linux 4.15.0-55-generic >>>>>>>>>>>>>>> npm ERR! argv "/usr/bin/nodejs" "/usr/bin/npm" "run" >>>>>>>>>>>>>>> "compile" >>>>>>>>>>>>>>> npm ERR! node v4.2.6 >>>>>>>>>>>>>>> npm ERR! npm v3.5.2 >>>>>>>>>>>>>>> npm ERR! code ELIFECYCLE >>>>>>>>>>>>>>> npm ERR! loris at 1.0.0 compile: `webpack` >>>>>>>>>>>>>>> npm ERR! Exit status 1 >>>>>>>>>>>>>>> npm ERR! >>>>>>>>>>>>>>> npm ERR! Failed at the loris at 1.0.0 compile script 'webpack'. >>>>>>>>>>>>>>> npm ERR! Make sure you have the latest version of node.js >>>>>>>>>>>>>>> and npm installed. >>>>>>>>>>>>>>> npm ERR! If you do, this is most likely a problem with the >>>>>>>>>>>>>>> loris package, >>>>>>>>>>>>>>> npm ERR! not with npm itself. >>>>>>>>>>>>>>> npm ERR! Tell the author that this fails on your system: >>>>>>>>>>>>>>> npm ERR! webpack >>>>>>>>>>>>>>> npm ERR! You can get information on how to open an issue for >>>>>>>>>>>>>>> this project with: >>>>>>>>>>>>>>> npm ERR! npm bugs loris >>>>>>>>>>>>>>> npm ERR! Or if that isn't available, you can get their info >>>>>>>>>>>>>>> via: >>>>>>>>>>>>>>> npm ERR! npm owner ls loris >>>>>>>>>>>>>>> npm ERR! There is likely additional logging output above. >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> npm ERR! Please include the following file with any support >>>>>>>>>>>>>>> request: >>>>>>>>>>>>>>> npm ERR! /var/www/loris/npm-debug.log >>>>>>>>>>>>>>> Makefile:14: recipe for target 'javascript' failed >>>>>>>>>>>>>>> make: *** [javascript] Error 1 >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> Thanks, >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> ???? ???, 7 ??? 2019 ???? 5:41 ?.?., ?/? Christine Rogers, >>>>>>>>>>>>>>> Ms. ??????: >>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Thanks, have you tried all of these steps? >>>>>>>>>>>>>>>> - clear your browser cache (and refresh a few times) >>>>>>>>>>>>>>>> - delete any files in your smarty/templates_c directory >>>>>>>>>>>>>>>> (this will clear the template cache - do Not touch smarty/templates/) >>>>>>>>>>>>>>>> - run `make` (per the 21 release notes, this replaces the >>>>>>>>>>>>>>>> composer commands used in previous releases to update your dependencies) >>>>>>>>>>>>>>>> - restart apache (doesn't hurt) >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Let us know how it goes -- let us know what difference you >>>>>>>>>>>>>>>> see after, with your logs. A >>>>>>>>>>>>>>>> lso please send us your Config path settings (see these >>>>>>>>>>>>>>>> Troubleshooting Queries >>>>>>>>>>>>>>>> ) >>>>>>>>>>>>>>>> if you're still seeing front-end issues. >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Thanks, >>>>>>>>>>>>>>>> Christine >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> On Wed, Aug 7, 2019 at 8:02 AM Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> lorisadmin at hbp:/var/www/loris$ sudo cat >>>>>>>>>>>>>>>>> /var/log/apache2/error.log >>>>>>>>>>>>>>>>> [Wed Aug 07 07:35:02.422501 2019] [mpm_prefork:notice] >>>>>>>>>>>>>>>>> [pid 1267] AH00163: Apache/2.4.18 (Ubuntu) OpenSSL/1.0.2g configured -- >>>>>>>>>>>>>>>>> resuming normal operations >>>>>>>>>>>>>>>>> [Wed Aug 07 07:35:02.422514 2019] [core:notice] [pid 1267] >>>>>>>>>>>>>>>>> AH00094: Command line: '/usr/sbin/apache2' >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> And as for the access.log the content are empty >>>>>>>>>>>>>>>>> lorisadmin at hbp:/var/www/loris$ sudo ls -l >>>>>>>>>>>>>>>>> /var/log/apache2/access.log >>>>>>>>>>>>>>>>> lorisadmin at hbp:/var/www/loris$ sudo ls -l >>>>>>>>>>>>>>>>> /var/log/apache2/access.log >>>>>>>>>>>>>>>>> -rw-r----- 1 root adm 0 ???? 28 14:09 >>>>>>>>>>>>>>>>> /var/log/apache2/access.log >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Also i noticed a loris_access.log. >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> The only non-blank pages are: >>>>>>>>>>>>>>>>> mri_violations, dataquery does not exist at all, >>>>>>>>>>>>>>>>> statistics, data_team_helper, genomic_browser, configuration and >>>>>>>>>>>>>>>>> server_processes_manager/ prints "Required configuration settings for >>>>>>>>>>>>>>>>> Server Processes Manager are missing. Cannot continue." >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Thanks, >>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> ???? ???, 6 ??? 2019 ???? 10:13 ?.?., ?/? Christine >>>>>>>>>>>>>>>>> Rogers, Ms. ??????: >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Hi Sotirios and LORIS community -- >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> When upgrading to brand-new release 21 -- just a >>>>>>>>>>>>>>>>>> reminder to follow the release notes and run the new >>>>>>>>>>>>>>>>>> *make* file to update your dependencies (instead of >>>>>>>>>>>>>>>>>> using *composer* commands). >>>>>>>>>>>>>>>>>> We've also updated the Wiki page >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> to clarify that the release notes for each version will tell you what to >>>>>>>>>>>>>>>>>> run. >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> If your current version is not the last release (20.3), >>>>>>>>>>>>>>>>>> it's still important to upgrade to each minor release increment (e.g. 20.2, >>>>>>>>>>>>>>>>>> 20.3) before making the leap to 21.0. >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> If you're getting blank pages, post-upgrade -- Try >>>>>>>>>>>>>>>>>> clearing your cache. >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Got questions or feedback e.g. on the Release Notes? >>>>>>>>>>>>>>>>>> please don't hesitate to let us know. >>>>>>>>>>>>>>>>>> Thanks, >>>>>>>>>>>>>>>>>> Christine >>>>>>>>>>>>>>>>>> The LORIS team >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> On Tue, Aug 6, 2019 at 10:09 AM Christine Rogers, Ms. < >>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca> wrote: >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>> Could you also let us know -- on which pages is content >>>>>>>>>>>>>>>>>>> visible, and on which pages/modules is content not visible for you? >>>>>>>>>>>>>>>>>>> Thanks, >>>>>>>>>>>>>>>>>>> Christine >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> On Tue, Aug 6, 2019 at 9:54 AM Christine Rogers, Ms. < >>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca> wrote: >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Thanks Sotirios, >>>>>>>>>>>>>>>>>>>> That's good to know. It sounds like you've checked >>>>>>>>>>>>>>>>>>>> that your /var/www/loris/project/config.xml file get populated properly. >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Please send us the last few errors you're seeing in >>>>>>>>>>>>>>>>>>>> your apache error log file, and your config paths and we can see what's >>>>>>>>>>>>>>>>>>>> happening with your front end -- >>>>>>>>>>>>>>>>>>>> Run these Troubleshooting Queries >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> to get your config path settings, given your front end is not displaying >>>>>>>>>>>>>>>>>>>> fully. >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> The Loris-MRI repo >>>>>>>>>>>>>>>>>>>> 21 >>>>>>>>>>>>>>>>>>>> install/upgrade would then be your next steps. >>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>> Christine >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> On Tue, Aug 6, 2019 at 7:53 AM Sotirios >>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos wrote: >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> I am using a VM. What i did was: >>>>>>>>>>>>>>>>>>>>> 1) Download the files from >>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris and replace them to my >>>>>>>>>>>>>>>>>>>>> existing /vaw/www/loris folder. >>>>>>>>>>>>>>>>>>>>> 2) Execute the composer install --no-dev and then composer >>>>>>>>>>>>>>>>>>>>> dump-autoload as mentioned here >>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris/wiki/Updating-your-LORIS >>>>>>>>>>>>>>>>>>>>> . >>>>>>>>>>>>>>>>>>>>> 3) Execute install.sh from /var/www/loris/tools and >>>>>>>>>>>>>>>>>>>>> because LORIS already existed i moved a .config file, then re-executed the >>>>>>>>>>>>>>>>>>>>> install.sh successfully >>>>>>>>>>>>>>>>>>>>> 4 ) As for the database, i dropped the schema and i >>>>>>>>>>>>>>>>>>>>> executed the installdb.php >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> ???? ???, 5 ??? 2019 ???? 5:22 ?.?., ?/? Christine >>>>>>>>>>>>>>>>>>>>> Rogers, Ms. ??????: >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> Hi Sotorios, >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> Thanks - when you re-installed did you start on a >>>>>>>>>>>>>>>>>>>>>> fresh root path / VM or might some of your old system setting still apply? >>>>>>>>>>>>>>>>>>>>>> (And if you did any steps similar to an upgrade, did >>>>>>>>>>>>>>>>>>>>>> you follow the Upgrade steps in the Release Notes, from both repos?) >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> About the TR_range column - it was recently split (MRI >>>>>>>>>>>>>>>>>>>>>> pr339 ) split >>>>>>>>>>>>>>>>>>>>>> into TR_min and _max columns. Given the code was trying to query TR_range >>>>>>>>>>>>>>>>>>>>>> which does not exist in your mri_protocol table, double-check which version >>>>>>>>>>>>>>>>>>>>>> of the Loris repo (tables) and the Loris-MRI repo (code) you have installed >>>>>>>>>>>>>>>>>>>>>> to ensure they match. >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> Christine >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> On Mon, Aug 5, 2019 at 9:06 AM Sotirios >>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos wrote: >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> I reinstalled LORIS to 21 version and now the >>>>>>>>>>>>>>>>>>>>>>> content is not visible at all at most pages. >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> ???? ???, 5 ??? 2019 ???? 3:19 ?.?., ?/? Sotirios >>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos ??????: >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> Is it easy to upgrade to Loris 21? Also the >>>>>>>>>>>>>>>>>>>>>>>> following fails because the line 1985 of NeuroDB/MRIProcessingUtility.pm >>>>>>>>>>>>>>>>>>>>>>>> query mri_protocol which doesn't have TR_range >>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris/blob/21.0-release/SQL/0000-00-00-schema.sql#L556 >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> lorisadmin at hbp:/data/loris/bin/mri$ >>>>>>>>>>>>>>>>>>>>>>>> ./batch_uploads_imageuploader -profile prod < ~/Desktop/input.txt > log.txt >>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $_ in pattern match >>>>>>>>>>>>>>>>>>>>>>>> (m//) at ./batch_uploads_imageuploader line 147. >>>>>>>>>>>>>>>>>>>>>>>> base is DCC0000_258024_V1 >>>>>>>>>>>>>>>>>>>>>>>> path is /data/incoming/ >>>>>>>>>>>>>>>>>>>>>>>> type is .tar.gz >>>>>>>>>>>>>>>>>>>>>>>> fullpath is /data/incoming/DCC0000_258024_V1.tar.gz >>>>>>>>>>>>>>>>>>>>>>>> DBD::mysql::st execute failed: Unknown column >>>>>>>>>>>>>>>>>>>>>>>> 'TR_range' in 'where clause' at >>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line 1985. >>>>>>>>>>>>>>>>>>>>>>>> DBD::mysql::st fetchrow_array failed: fetch() >>>>>>>>>>>>>>>>>>>>>>>> without execute() at >>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line 1986. >>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $count_mri_protocol in >>>>>>>>>>>>>>>>>>>>>>>> numeric gt (>) at >>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line 1995. >>>>>>>>>>>>>>>>>>>>>>>> DBD::mysql::st execute failed: Unknown column >>>>>>>>>>>>>>>>>>>>>>>> 'TR_range' in 'field list' at >>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 562. >>>>>>>>>>>>>>>>>>>>>>>> Can't exec "mail": No such file or directory at >>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 721. >>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 722. >>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 723. >>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 724. >>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 725. >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> No Mincs inserted >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> Thanks, >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 3 ??? 2019 ???? 1:08 ?.?., ?/? Christine >>>>>>>>>>>>>>>>>>>>>>>> Rogers, Ms. ??????: >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> First, just a note: we've released LORIS 21 this >>>>>>>>>>>>>>>>>>>>>>>>> week with some major new features and cleanup -- especially if you are >>>>>>>>>>>>>>>>>>>>>>>>> early in your setup phase, check out the Release notes for both the >>>>>>>>>>>>>>>>>>>>>>>>> LORIS >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> and Loris-MRI >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> repos. >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> Thanks for your screenshots -- your empty >>>>>>>>>>>>>>>>>>>>>>>>> mri_protocol table should be at the root of these issues : >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> The mri_protocol table must be populated >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> in order for your scans to be registered in LORIS -- it serves as a >>>>>>>>>>>>>>>>>>>>>>>>> whitelist for the insertion pipeline which filters out scans that aren't >>>>>>>>>>>>>>>>>>>>>>>>> identified or matched to scan types in this table. >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> By default, this table is populated with entries >>>>>>>>>>>>>>>>>>>>>>>>> for t1, t2, fMRI and DTI (Insert statements for >>>>>>>>>>>>>>>>>>>>>>>>> 21 release branch are here >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> ) >>>>>>>>>>>>>>>>>>>>>>>>> Feel free to restore our default records and >>>>>>>>>>>>>>>>>>>>>>>>> broaden their parameters to match all your scan types. >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> re Defaced, native, selected -- these filter the >>>>>>>>>>>>>>>>>>>>>>>>> scans displayed as you move to the next page (View Session), instead of >>>>>>>>>>>>>>>>>>>>>>>>> viewing "all types" of scans from a given session : >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> - "defaced" means that a defacing script >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> has masked the subject's face in the volume (for patient privacy) >>>>>>>>>>>>>>>>>>>>>>>>> - "native" means that no pre-processing has >>>>>>>>>>>>>>>>>>>>>>>>> been performed on the scan (it's raw data), >>>>>>>>>>>>>>>>>>>>>>>>> - "selected" will show only volumes that have >>>>>>>>>>>>>>>>>>>>>>>>> been QC'd and "selected" as the best of their type -- used to display only >>>>>>>>>>>>>>>>>>>>>>>>> the best quality T1 image instead of all T1s acquired in a session, e.g. >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> re QC Comments -- >>>>>>>>>>>>>>>>>>>>>>>>> Once you have successfully loaded scans (matched >>>>>>>>>>>>>>>>>>>>>>>>> to the mri_protocol table), you'll be able to use the Imaging Browser's >>>>>>>>>>>>>>>>>>>>>>>>> View Session subpage to enter/view QC comments on each volume, or for each >>>>>>>>>>>>>>>>>>>>>>>>> visit. >>>>>>>>>>>>>>>>>>>>>>>>> These are stored directly in the database, and >>>>>>>>>>>>>>>>>>>>>>>>> linked to each scan. (Table name: >>>>>>>>>>>>>>>>>>>>>>>>> feedback_mri_comments) >>>>>>>>>>>>>>>>>>>>>>>>> (Visit-level QC comments are linked to the >>>>>>>>>>>>>>>>>>>>>>>>> session.) >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> For a walkthrough of the Imaging setup - please >>>>>>>>>>>>>>>>>>>>>>>>> see the Imaging Setup guide >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> - >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> An old LORIS walkthrough video >>>>>>>>>>>>>>>>>>>>>>>>> can >>>>>>>>>>>>>>>>>>>>>>>>> also walk you through some of the Imaging front-end features, starting at >>>>>>>>>>>>>>>>>>>>>>>>> 8:00 >>>>>>>>>>>>>>>>>>>>>>>>> LORIS' imaging modules have been updated many >>>>>>>>>>>>>>>>>>>>>>>>> times since this video, but the functionality and workflow is similar. >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> Let us know how it goes once you have entries in >>>>>>>>>>>>>>>>>>>>>>>>> your mri_protocol table - >>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>> Christine >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> On Fri, Aug 2, 2019 at 7:58 AM Sotirios >>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos wrote: >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> Hi Christine, >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> In the candidate_list page i can see this patient >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> If i press the link under PSCID i get to see >>>>>>>>>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> and if i press the link under Scan Done it >>>>>>>>>>>>>>>>>>>>>>>>>> redirects me to imaging_browser >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> At the mri_violations page i also see No results >>>>>>>>>>>>>>>>>>>>>>>>>> ( neither on resolved / not resolved ). >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> At the imaging_uploader i can see the record that >>>>>>>>>>>>>>>>>>>>>>>>>> failed. >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> If i click on the tarchive info i get to see the >>>>>>>>>>>>>>>>>>>>>>>>>> Protocol Name which i think is the acquisition we wanted? >>>>>>>>>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> Also my mri_protocol table is empty. >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> Furthermore i would like to ask about the >>>>>>>>>>>>>>>>>>>>>>>>>> defaced, native, selected. What exactly is native and selected? And where >>>>>>>>>>>>>>>>>>>>>>>>>> are the qc comments stored? >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> Finally a walkthrough would be helpful. >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> Thanks, >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 30 ???? 2019 ???? 8:29 ?.?., ?/? >>>>>>>>>>>>>>>>>>>>>>>>>> Christine Rogers, Ms. >>>>>>>>>>>>>>>>>>>>>>>>>> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>> Glad to hear you're making progress with the >>>>>>>>>>>>>>>>>>>>>>>>>>> visit labels. To follow up on your last few emails: >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> a- The Wiki's Setup Guide contains Sample >>>>>>>>>>>>>>>>>>>>>>>>>>> insert statements for the Visit Windows table >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> . >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> As Cecile mentioned, the consistency of visit >>>>>>>>>>>>>>>>>>>>>>>>>>> label format is important: V01, v01, V1, 01 -- whichever you select to use >>>>>>>>>>>>>>>>>>>>>>>>>>> is fine; we use V01 by default across all documentation. >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> b- For Password reset, there is a script in the >>>>>>>>>>>>>>>>>>>>>>>>>>> tools/ directory so that a back-end administrator can reset any front-end >>>>>>>>>>>>>>>>>>>>>>>>>>> user password, including Admin. (See info on setting up / resetting User >>>>>>>>>>>>>>>>>>>>>>>>>>> passwords in the Wiki's Setup Guide >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> ) >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> c- The minc file not being registered -- due to >>>>>>>>>>>>>>>>>>>>>>>>>>> AcquisitionProtocol unknown. >>>>>>>>>>>>>>>>>>>>>>>>>>> This means the SeriesDescription (Acquisition >>>>>>>>>>>>>>>>>>>>>>>>>>> Protocol) in you Dicom header was not matched to any scan listed in the >>>>>>>>>>>>>>>>>>>>>>>>>>> mri_protocol database table. >>>>>>>>>>>>>>>>>>>>>>>>>>> (In the online Loris-MRI Troubleshooting Guide, >>>>>>>>>>>>>>>>>>>>>>>>>>> this >>>>>>>>>>>>>>>>>>>>>>>>>>> is Table 3, 2nd-last item "no MINCs inserted"). >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> The MRI Violations module (Readme here) >>>>>>>>>>>>>>>>>>>>>>>>>>> will show >>>>>>>>>>>>>>>>>>>>>>>>>>> you the details of this mismatch -- >>>>>>>>>>>>>>>>>>>>>>>>>>> Go to the module (under the Imaging menu), find >>>>>>>>>>>>>>>>>>>>>>>>>>> your scan and click the link "Could not identify scan type" -- in the next >>>>>>>>>>>>>>>>>>>>>>>>>>> subpage you can compare the scan's actual parameters against the >>>>>>>>>>>>>>>>>>>>>>>>>>> mri_protocol table. >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> To resolve this, adjust your mri_protocol table >>>>>>>>>>>>>>>>>>>>>>>>>>> values or perhaps ensure your DICOMs are labelled consistently. >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> Let us know if this works for you -- we can also >>>>>>>>>>>>>>>>>>>>>>>>>>> walk you through an example of non-identified scans on >>>>>>>>>>>>>>>>>>>>>>>>>>> Demo.loris.ca (MRI Violations module). >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>> Christine >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> The LORIS team >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> On Tue, Jul 30, 2019 at 10:47 AM Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos wrote: >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> I hope this is sufficient as the error for the >>>>>>>>>>>>>>>>>>>>>>>>>>>> visit label disappeared. >>>>>>>>>>>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> Please see the attached file. Also something i >>>>>>>>>>>>>>>>>>>>>>>>>>>> found. >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> lorisadmin at hbp:/data/loris/bin/mri$ cat >>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data//logs/TarLoad-17-39-xubBdv.log >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> ==> Loading file from disk >>>>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-17-39-UyQcG2/dcc0000_258024_v1_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> --> mapping DICOM parameter for >>>>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-17-39-UyQcG2/dcc0000_258024_v1_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> ==> computing md5 hash for MINC body. >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> --> md5: 6b1202fd63e29de4c9be1cd9925888a5 >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> ==> verifying acquisition protocol >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> Acquisition protocol is unknown >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> --> The minc file cannot be registered since >>>>>>>>>>>>>>>>>>>>>>>>>>>> the AcquisitionProtocol is unknown >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 30 ???? 2019 ???? 4:58 ?.?., ?/? >>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos >>>>>>>>>>>>>>>>>>>>>>>>>>>> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Ok I fixed the login problem by using a known >>>>>>>>>>>>>>>>>>>>>>>>>>>>> hash and by deleting the rows from the login_history i was able to login. >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 30 ???? 2019 ???? 4:50 ?.?., ?/? >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> there was no visit label 01 in the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Visit_Windows table and i don't know how to insert it because the record >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> requires lots of attributes. Also the system for a reason asked me to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> update my password and now i don't remember it and my account got >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> suspended. Is there a way to reset it or set a simple password? I updated >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the password hash in the users table by using the hash from another LORIS >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> setup we had and i still couldn't login ( also the attribute password is >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> always NULL and the expiration date is 1999-01-01 for some reason ). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thanks >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 29 ???? 2019 ???? 5:21 ?.?., ?/? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Cecile Madjar ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Can you try adding the visit label v01 to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the Visit_Windows table? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> However, I noticed that in a previous >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> dataset, the label was V1. Does that refer to the same visit? If so, you >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> might want to harmonize the visit labels so they are all the same across >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> datasets for a given timepoint, meaning you will need to relabel scans when >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the visit label is different but referring to the same visit label (v01 = >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> V1 etc...). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helps, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> On Mon, Jul 29, 2019 at 10:15 AM Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> wrote: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Could you help me with the "Visit label >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> does not exist"? I had changed $subjectID{'createVisitLabel'} to 1 as you >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> had suggested but it appears that this problem hasn't been resolved yet. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> lorisadmin at hbp:/data/loris/bin/mri$ cat >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data//logs/TarLoad-14-58-9Xog7H.log >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ==> Loading file from disk >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> --> mapping DICOM parameter for >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> --> using user-defined filterParameters for >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Candidate Mismatch Error is Visit label >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> does not exist >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -> WARNING: This candidate was invalid. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Logging to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> MRICandidateErrors table with >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> reason Visit label does not exist >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 26 ???? 2019 ???? 3:02 ?.?., ?/? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Cecile, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The Center error was fixed. Still the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> insertion of mincs fails. Please see the output.txt file i attached. Also >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> is there something else i need to change at the paths configuration? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 25 ???? 2019 ???? 6:55 ?.?., ?/? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Cecile Madjar >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> We are making progress! >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I have a feeling this error comes from >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the fact that your psc table does not have the MRI_alias populated for the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DCC site. Running the following query in the mysql database should fix this: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> UPDATE psc SET MRI_alias="DCC", >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Alias="DCC" WHERE Name="Data Coordinating Center"; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Repeat the same with all your sites (make >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sure to change the Aliases between sites, they should all be unique). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Let me know how it goes! >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> On Thu, Jul 25, 2019 at 11:43 AM Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> wrote: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Dear Cecile, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> You were right about your guesses. I did >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the modifications you suggested, i still get the "no mincs inserted" error, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> now i am getting the "No center found this candidate" error ( how do i fix >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> that? from what i see the .dcm files contains a 'Institution Name', is that >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the center? ), so i guess that's why the validation fails, but i changed >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the force variable of tarchiveLoader to 1, shouldn't it have inserted the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> mincs then? Also it is optional to have a mail server, right? ( from what i >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> see the mail error does not affect the $valid_study, so i assume we are >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> okay with that ) >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you a lot, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 25 ???? 2019 ???? 5:48 ?.?., >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ?/? Cecile Madjar >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> From what I understand, I believe you >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> just need to update a few config settings from the frontend in the Config >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> module (under the Admin menu). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [image: Screen Shot 2019-07-25 at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 10.31.35 AM.png] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Then go to the Paths section of the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> config module and update the "LORIS-MRI code" config setting to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri (my guess is that currently, it is set to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data) and click on the submit button. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [image: Screen Shot 2019-07-25 at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 10.32.50 AM.png] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Then, go to Imaging Pipeline section of >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the Configuration module and update the "Loris-MRI Data Directory" to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/ (my guess is that it is empty at the moment in your >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> database which is why $data_dir is not defined when you run the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> tarchiveLoader step of the insertion pipeline). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [image: Screen Shot 2019-07-25 at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 10.40.52 AM.png] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Finally, I took a look at your >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> environment file and it might be a good idea to update your PERL5LIB >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> variable to the following (it has been added to the code a few releases ago >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> as we realized this was needed for the libraries. Not sure which version of >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> LORIS-MRI you are using but it does not hurt to update this variable to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> what I suggest below): >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> export >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PERL5LIB=/data/loris/bin/mri/uploadNeuroDB:/data/loris/bin/mri/dicom-archive:$PERL5LIB >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helps. Sorry you are >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> experiencing so much trouble setting things up. We probably need to update >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> our WIKI. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> On Thu, Jul 25, 2019 at 9:48 AM >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The "Loris-MRI Data Directory" should >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> be in the environment file? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 25 ???? 2019 ???? 12:59 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ?.?., ?/? Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The scripts are located in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/. Somewhere I might have messed something up but i >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> remember following the instructions in the wiki.For example when i tried to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> execute the batch_uploads_imageuploader perl script the line >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> my $command = "$bin_dir/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl " >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> was pointing to an invalid path, for >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> example: it was repeating a pattern and had LORIS instead of loris ( i >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> think the mistake was that in the wiki it suggested to use $PROJECT for >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the name of the folder and i choosed 'loris' >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris/wiki/Imaging-Database >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ). See also the in image for the modification i did. Also i didn't find the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> section to config the $data_dir variable. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 24 ???? 2019 ???? 6:05 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ?.?., ?/? Cecile Madjar < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> cecile.madjar at mcin.ca> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> It looks like you have one Config >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> setting not set (based on the first error message you got when running it >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the first time). You need to set a value for "Loris-MRI Data Directory" in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the Config module under the Imaging pipeline section (from what I can see, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> it would be /data/loris/data/ for your setup). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The reason you got that error >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> message the second time is that the pipeline checks if the DICOM study was >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> already inserted in the tarchive table. Since you ran the study once >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> already, the study is inserted into the tarchive, hence the message. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> However, the pipeline did not complete as the MINC files were not created >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and inserted into the files/parameter_file table. In order to continue the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> insertion, you will then need to run the tarchiveLoader command suggested >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in the terminal during the second run: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -globLocation -profile prod >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive//2012/DCM_2012-12-05_ImagingUpload-17-43-ZUEFjb.tar >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -verbose >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Finally, I am a bit confused by your >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> setup. Where are the scripts located? In /data/loris/bin/mri or >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data? It feels like the Config setting "LORIS-MRI code" in the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Paths section was set to "/data/LORIS/data" but it should have been set to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the directory where the scripts are located (most probably >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helps, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> On Wed, Jul 24, 2019 at 10:55 AM >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Ok first i execute this command: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> "lorisadmin at hbp:/data/loris/bin/mri$ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ./batch_uploads_imageuploader -profile prod < ~/Desktop/input.txt > log.txt >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> $data_dir in concatenation (.) or string at ./batch_uploads_imageuploader >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> line 143. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> $data_dir in concatenation (.) or string at ./batch_uploads_imageuploader >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> line 143. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $_ in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> pattern match (m//) at ./batch_uploads_imageuploader line 147. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> base is DCC0000_258024_V01 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> path is /data/incoming/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> type is .tar.gz >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> fullpath is >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/incoming/DCC0000_258024_V01.tar.gz >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> source >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/ImagingUpload-17-43-ZUEFjb >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> targetlocation >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> $data_dir in concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 256. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> $data_dir in concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 284. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> $data_dir in concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> tarchive_validation.pl line 219. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> $data_dir in concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl line 270. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> $data_dir in concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 711. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Can't exec "mail": No such file or >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> directory at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 721. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 722. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 723. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> $data_dir in concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 724. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 724. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 725. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> $data_dir in concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 735. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> No Mincs inserted >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The tarchiveLoader insertion script >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> has failed. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Running now the following command: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl -profile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> prod -upload_id 3 /data/incoming/DCC0000_258024_V01.tar.gz -verbose" >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I inserted the VisitLabel, but >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> still the Mincs are not inserted and i am getting this error >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> "lorisadmin at hbp:/data/loris/bin/mri$ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl -profile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> prod -upload_id 3 /data/incoming/DCC0000_258024_V01.tar.gz -verbose >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> find -path >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> \/tmp\/ImagingUpload\-17\-45\-5MsWEd -name '__MACOSX' -delete >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Spool message is: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The Scan for the uploadID 3 has >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> already been run with tarchiveID: 7. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> To continue with the rest of the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> insertion pipeline, please run tarchiveLoader from a terminal as follows: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader -globLocation -profile prod >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive//2012/DCM_2012-12-05_ImagingUpload-17-43-ZUEFjb.tar >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -verbose" >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Which files should i delete? I >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> thought that deleting the files from the tarchive was enough. And i >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> executed the last proposed command to continue to rest of the insertion >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> pipeline ( check the image ). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 24 ???? 2019 ???? 5:05 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ?.?., ?/? Cecile Madjar < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> cecile.madjar at mcin.ca> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sorry I was not clear before. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Every visits of candidates are created in the session table with one entry >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> per CandID/VisitLabel. So if the imaging pipeline created visits in the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> session table (that are not attached to instruments) and you want to clean >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> your database completely, you can delete entries in that table as well. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Regarding your point 2, the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> imaging pipeline can create the visit in the session table as long as the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit label is present in the Visit_Windows table (which means the visit >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> label stored in the PatientName is a valid visit label). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> However, in your prod file, if the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> variable $subjectID{'createVisitLabel'} is set to 1 for candidates, the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit label should be created in the Visit_Windows table I believe. Here >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> is the line of the prod file you would need to change >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> . >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> In general, we prefer populating >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the Visit_Windows table and set the $subjectID{'createVisitLabel'} to 0 for >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> candidate data to avoid insertion of badly labelled MRI data that are >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> complex to relabel. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Finally, regarding the candidate >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> creation, if you execute the following steps, the pipeline should be able >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> to create candidates: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - set in the Imaging Pipeline >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> section of the config module the config setting "Upload creation of >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> candidates" to Yes >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - manually transfer the scans to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the LORIS server instead of uploading it via the imaging browser >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - run batch_imaging_upload.pl as >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> you did until now. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helps! >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> On Wed, Jul 24, 2019 at 8:47 AM >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> About my second question i >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> replaced the name of the patient in the .dcm files and now i am getting an >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> error that the visit label does not exist. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I thought it was supposed to be >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> automatically created. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> "Done adding archive info into >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> database >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -globLocation -profile prod >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive//DCM_2012-12-05_ImagingUpload-15-42-yUwQQV.tar >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -verbose >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> md5sum >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive/DCM_2012-12-05_ImagingUpload-15-42-yUwQQV.tar >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> candidate id 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> => No Visit labelVisit label does >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> not exist >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Set centerID = 1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Number of MINC files that will be >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> considered for inserting into the database: 1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> log dir is /logs and log file is >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /logs/TarLoad-15-42-L6pocU.log >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> candidate id 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> => No Visit label >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Cleaning up temp files: rm -rf >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-15-42-J2rQms/ImagingUpload-15-42-yUwQQV*" >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 24 ???? 2019 ???? 3:38 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ?.?., ?/? Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 1) What are the records in the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> session table? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 2) I tried to upload a >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> non-phantom file like this >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> input_file.txt: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/incoming/DCC0000_258024_V1.tar.gz >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> N DCC0000_258024_V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Terminal: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ./batch_uploads_imageuploader >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -profile prod < ~/Desktop/input.txt > log.txt >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and i get the following error in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the log.txt file >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> "Running now the following >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> command: /data/loris/data/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl -profile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> prod -upload_id 7 /data/incoming/DCC0000_258024_V1.tar.gz -verbose >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> find -path >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> \/tmp\/ImagingUpload\-14\-56\-FeLCB4 -name '__MACOSX' -delete >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Spool message is: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The PatientName read from the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DICOM header does not start with DCC0000_258024_V1 from the mri_upload table >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> " >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and the spool message is >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> repeated for each .dcm file. Should i preprocess every .dcm file and change >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the PatientName to "DCC0000_258024_V1"? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 3) As far as it concerns the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> candidate profile i have to create a new one each time before i try to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> upload a file? Is there already a way to create a candidate profile and get >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the DCCID and PSCID without the user interface? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 18 ???? 2019 ???? 5:00 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ?.?., ?/? Cecile Madjar < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> cecile.madjar at mcin.ca> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> See answers to your questions >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> below. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> About the 1st case we had a >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> dicom with a blank studyUID, maybe someone accidentally removed it. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> That is strange. Something must >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> have been done to the DICOM files. I have never seen a study with no >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> StudyUID out of the scanner. Usually, you need to manually erase it with >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> some tool. However, DICOMs never cease to surprise me... >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Some other questions: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 1) What are the steps to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> remove all of my patients and uploads?: because i want to try to reupload >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> all the testing dicoms we had with a clean database. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Release 21.0 of LORIS-MRI will >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> offer a script to remove all the entries and files specific to an upload. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> However, this release is not yet out. Hopefully in the next few weeks. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> In the meantime, since your >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> case is particular and that you just want to start with a clean database, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the following deletes should work (hopefully I won't forget any tables): >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from mri_violations_log; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> mri_protocol_violated_scans; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from MRICandidateErrors; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from parameter_file; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from files_qcstatus; # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> (if you played with the QC part of the imaging browser for testing) >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> feedback_mri_comments; # (if you played with the QC part of the imaging >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> browser for testing) >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from tarchive_series; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from tarchive_files; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from mri_upload; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from tarchive; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from mri_scanner; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from candidate where >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID="scanner"; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I don't know if you want to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> also delete entries in the session and candidate table too? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 2) We do not need to create the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> profile of a patient ( are the patients stored in the candidate table? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> because i can't see the ghosts ), because will it automatically be created >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> when importing a dicom? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I am not sure I understand >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> fully this question. All candidates are stored in the candidate table. The >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> phantom scans however are attached to a scanner candidate depending on >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> where the scan happened. It is a bit of a weird concept that we have to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> redesign eventually but never got a chance to get to it. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hopefully this answered your >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> question, otherwise, don't hesitate to let me know. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 3) What is the difference >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> between uploading a dicom as phantom instead of importing as >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCCID_DCCID_VisitLabel? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> When you upload the scan as >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID_DCCID_VisitLabel, there is a check that makes sure the candidate IDs >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and visit label are valid at the time of upload. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> When you upload a scan as >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> phantom, it expects that the DICOM field PatientName and uploaded filename >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> contains the string "phantom". We enforced this behaviour on the imaging >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> uploader side in recent releases but I can't remember which one. Probably >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the upcoming 21.0 release. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> All those verifications might >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> seem cumbersome but they are here to ensure that the files inserted are all >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> valid and labelled properly as it is a bit messy to have to delete files >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> that were wrongly labelled. At least, the delete script present in release >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 21.0 will make this process easier but it is still good practice to verify >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> those things. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> With pleasure. Hopefully the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> answers to your questions will be helpful. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PS: loris-dev mailing list: you >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> will find the initial answer I gave Sotirios below. I forgot to cc the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> loris-dev in my earlier reply... >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 16 ???? 2019 ???? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 12:02 ?.?., ?/? Cecile Madjar < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> cecile.madjar at mcin.ca> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Dear Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you for reaching out. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Since your email was already organized in points, I will reply directly >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> below your questions below. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 1) What do we do when the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> StudyUID is blank on the header? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/minor/docs/AppendixA-Troubleshooting_guideline.md >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> There solution provided at the table 3 does not guide us how to find the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> information ( is possible ). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The StudyUID is the field >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> used in our pipeline at the moment to check whether a DICOM study was >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> already inserted into LORIS with that same StudyUID since it is supposed to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> be unique for every single study. Currently, we do not support insertion of >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DICOM studies if they do not have a StudyUID associated with them. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Is there a specific reason >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> why the StudyUID is blank in the DICOM headers in your DICOM files? Did >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> they go through some processes before upload to LORIS? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 2) When i am about to upload >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> a non-phanton case i need a 'Visit Label'. Is there already a script that >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> can create a new visit label for a specific Candidate, so i can provide it >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> as input afterwards to the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> batch_uploads_imageuploader ( See option 5.1.3 https://github.com/aces/Loris-MRI/blob/minor/docs/05-PipelineLaunchOptions.md ) >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I am not sure if the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> front-end allows for it but if you use batch_uploads_imageuploader, the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> insertion scripts could create the visit label for you. However, it does >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> need to be included in the patient name in order for the script to know >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> which label it should use. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> For example: you upload V02 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> for MTL0123 (DCCID: 456789) but V02 was not yet created for MTL0123; the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> insertion scripts will create a V02 visit for MTL0123 if the PatientName >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> field for the dataset is MTL0123_456789_V02 with Stage marked as "Not >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Started". >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> However, *note that for the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> script to create the visit for the candidate, you have to make sure that >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> all the visit label of your projects were inserted in the Visit_Windows >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> table* (otherwise, the visit >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> will never be created as they were not specified as being part of the list >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> of visit label to expect). So in the example above, you should have one row >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in Visit_Windows with Visit_label="V02" set. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 3) Section 4.3 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/minor/docs/04-Scripts.md >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> What do we do when the folder contains multiple mnc files? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> This is a case by case. Most >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> of the time, the MINC files that failed insertion into the imaging browser >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> end up in the MRI violation module where you can see what went wrong with >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the acquisitions not inserted. If you notice that the MINC file should be >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> inserted as a specific protocol, you can force the insertion as explained >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in section 4.3. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> In your case, I have a >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> feeling that you want to be able to insert MINC files that did not go >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> through the whole pipeline insertion (DICOM archival, then dcm2mnc, then >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> protocol identification, then insertion...). In theory, you could call >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl on any >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> MINC file, provided you have at least the following information: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - path to the MINC file >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - uploadID associated with >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the MINC files or DICOM archive path from which those MINC files were >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> created from >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Then the minc_insertion.pl >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> script will do the subject information and protocol validation etc... >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> If all the MINC files come >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> from the same uploadID or TarchiveID, then you could run a loop in bash >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> calling the minc_insertion.pl >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> script like this for files deriving from uploadID=1: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ls /path/to/mnc/folder/* | >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> while read f; do >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl -profile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> prod -uploadID 1 -mincPath $f; done >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helped! >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>>>>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>>>>>>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | >>>>>>>>>>>>>>>>>>>>>>>>>>> MCIN.ca >>>>>>>>>>>>>>>>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>>>>>>>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>>>>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | >>>>>>>>>>>>>>>>>>>>>>>>> MCIN.ca >>>>>>>>>>>>>>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>>>>>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>>> >>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> -- >>>>>>>>>>>> >>>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>>> >>>>>>>>>>> _______________________________________________ >>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>> >>>>>>>>>> _______________________________________________ >>>>>>>>> Loris-dev mailing list >>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> -- >>>>>>>> Shen Wang >>>>>>>> Loris Developer >>>>>>>> Montreal Neurological Institute >>>>>>>> McGill University >>>>>>>> >>>>>>>> >>>> >>>> -- >>>> Shen Wang >>>> Loris Developer >>>> Montreal Neurological Institute >>>> McGill University >>>> >>>> -- >>> Shen Wang >>> Loris Developer >>> Montreal Neurological Institute >>> McGill University >>> >>> _______________________________________________ >>> Loris-dev mailing list >>> Loris-dev at bic.mni.mcgill.ca >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>> >> >> >> -- >> >> christine.rogers at mcgill.ca >> McGill Centre for Integrative Neuroscience | MCIN.ca >> Montreal Neurological Institute >> McGill University | Montreal | Canada >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: ???? 2019-08-13 19.21.15.png Type: image/png Size: 508603 bytes Desc: not available URL: From dave.macfarlane at mcin.ca Wed Aug 14 08:50:17 2019 From: dave.macfarlane at mcin.ca (Dave MacFarlane) Date: Wed, 14 Aug 2019 08:50:17 -0400 Subject: [Loris-dev] LORIS installation inquiry -- regarding In-Reply-To: References: Message-ID: Hi Yubu, The error log says that the account 'root'@'localhost' can't connect. Are you sure you're providing valid credentials and not making a typo in the password? Have you tried the account from the MySQL command line on the same server that Apache is running on? I just tried putting in incorrect credentials for myself and got a blank page with the same seemingly unrelated error message about "Call to a member function exec() on null", so I'm fairly sure that the account access is the root of the problem. On Tue, Aug 13, 2019 at 8:43 PM Shen Wang wrote: > Hi Yubu, > I saw you error log, it is very helpful. It seems like you didn't create > the config.xml in you project folder successfully. > You need to run this [sudo ./install.sh ] in the tools folder. ex. [ > install at install-dev:/var/www/Loris/tools$ sudo ./install.sh] > Then check if project/confilg.xml file exists. if it can't create the > project folder and config.xml, it is definitely your ubuntu permission > issue. > Please do it manually in your loris folder. sudo chgrp apache project sudo > chmod 770 project > > Then you need to do [sudo ./install.sh ] , then load the installdb.php > again. > Please let me know if you have any questions. > Regards. > Shen > > On Tue, 13 Aug 2019 at 20:16, ??? wrote: > >> Dear Shen, >> >> >> 1 Which version of Loris are you using? >> We are using Loris-21.0.0 >> >> 2 Mysql version? >> The output of mysql -V is >> mysql Ver 14.14 Distrib 5.7.27, for Linux (x86_64) using EditLine >> wrapper >> >> 3 [sudo tail -f /var/log/apache2/loris-error.log] Please running this >> in the backend, >> then try loading the installdb.php again, with a different database >> name. Please send us the error message. >> >> cat loris-error.log does not show any content however loris-error.log.1 >> shows the following: >> >> yubu at data:/var/log/apache2$ cat loris-error.log.1 >> >> [Tue Aug 13 09:12:41.214417 2019] [php7:error] [pid 17930] [client >> ::1:58960] PHP Fatal error: Uncaught ConfigurationException: Config file >> config.xml does not exist in the defined locations. in >> /var/www/loris/php/libraries/NDB_Config.class.inc:139\nStack trace:\n#0 >> /var/www/loris/php/libraries/NDB_Config.class.inc(66): >> NDB_Config->configFilePath()\n#1 >> /var/www/loris/php/libraries/NDB_Factory.class.inc(118): >> NDB_Config::singleton(NULL)\n#2 >> /var/www/loris/php/libraries/NDB_Client.class.inc(54): >> NDB_Factory->config(NULL)\n#3 /var/www/loris/htdocs/index.php(27): >> NDB_Client->initialize()\n#4 {main}\n thrown in >> /var/www/loris/php/libraries/NDB_Config.class.inc on line 139, referer: >> http://localhost/installdb.php >> >> [Tue Aug 13 09:14:53.843582 2019] [php7:notice] [pid 17932] [client >> ::1:58992] SQLSTATE[HY000] [1698] Access denied for user 'root'@'localhost', >> referer: http://localhost/installdb.php >> [Tue Aug 13 09:14:53.843708 2019] [php7:error] [pid 17932] [client >> ::1:58992] PHP Fatal error: Uncaught Error: Call to a member function >> exec() on null in >> /var/www/loris/php/installer/Installer.class.inc:374\nStack trace:\n#0 >> /var/www/loris/php/installer/Installer.class.inc(235): >> LORIS\\Installer\\Installer->_sourceSchemaFile(Object(LORIS\\Installer\\Database), >> '00-schema.sql')\n#1 /var/www/loris/htdocs/installdb.php(109): >> LORIS\\Installer\\Installer->sourceSchema(Array)\n#2 {main}\n thrown in >> /var/www/loris/php/installer/Installer.class.inc on line 374, referer: >> http://localhost/installdb.php >> >> Further, we accidentally deleted the loris-error.log and >> loris-error.log.1 files. Is there a way to generate them again? >> >> Thanks for the prompt reply >> >> Yours Sincerely, >> >> ====================================================== >> >> Yubu Lee, Ph.D. >> >> Research Professor, >> >> Center for Neuroscience Imaging Research, Institute for Basic Science >> >> >> #86332, N Center, SungKyunKwan University >> 2066, Seobu-Ro, Jangan-gu, Suwon, Gyeonggi-do, 16419, Korea >> >> E-mail: basilia1123 at gmail.com >> >> Tel: +82-31-299-4411 >> >> Fax: +82-31-299-4506 >> >> ====================================================== >> >> >> 2019? 8? 13? (?) ?? 10:21, Shen Wang ?? ??: >> >>> Hi Yubu, >>> We need more information to debug this issue. >>> 1 Which version of Loris are you using? >>> 2 Mysql version? >>> 3 [sudo tail -f /var/log/apache2/loris-error.log] Please running this >>> in the backend, >>> then try loading the installdb.php again, with a different database >>> name. Please send us the error message. >>> >>> Your Sincerely, >>> Shen >>> >>> On Mon, 12 Aug 2019 at 22:27, ??? wrote: >>> >>>> Dear Sir/Madam, >>>> >>>> We are currently trying to install LORIS on Ubuntu 18.04 platform >>>> following the steps from >>>> https://github.com/aces/Loris/wiki/Installing-Loris-in-Depth >>>> >>>> 1. Following the above link, we installed the prerequisites mentioned >>>> in >>>> https://github.com/aces/Loris/wiki/Installing-Loris-in-Depth#getting-prerequisites, >>>> which are all verified to be installed normally. >>>> >>>> 2. We ensured that mySQL credentials are set up properly (as pasted >>>> below) >>>> mysql> select host, user, authentication_string from user >>>> -> ; >>>> >>>> +-----------+------------------+-------------------------------------------+ >>>> | host | user | authentication_string >>>> | >>>> >>>> +-----------+------------------+-------------------------------------------+ >>>> | localhost | root | >>>> | >>>> | localhost | mysql.session | >>>> *THISISNOTAVALIDPASSWORDTHATCANBEUSEDHERE | >>>> | localhost | mysql.sys | >>>> *THISISNOTAVALIDPASSWORDTHATCANBEUSEDHERE | >>>> | localhost | debian-sys-maint | >>>> *C9BF7C6E59BFF0FA879E6650D174264C9EE87F25 | >>>> >>>> +-----------+------------------+-------------------------------------------+ >>>> 4 rows in set (0.00 sec) >>>> >>>> mysql> update user set authentication_string=password('yubu') where >>>> user='root'; >>>> Query OK, 1 row affected, 1 warning (0.00 sec) >>>> Rows matched: 1 Changed: 1 Warnings: 1 >>>> >>>> mysql> flush privileges; >>>> Query OK, 0 rows affected (0.01 sec) >>>> >>>> mysql> select host, user, authentication_string from user >>>> -> ; >>>> >>>> +-----------+------------------+-------------------------------------------+ >>>> | host | user | authentication_string >>>> | >>>> >>>> +-----------+------------------+-------------------------------------------+ >>>> | localhost | root | >>>> *E311E16EECE7E8900098CFEB4103D5266A343F5F | >>>> | localhost | mysql.session | >>>> *THISISNOTAVALIDPASSWORDTHATCANBEUSEDHERE | >>>> | localhost | mysql.sys | >>>> *THISISNOTAVALIDPASSWORDTHATCANBEUSEDHERE | >>>> | localhost | debian-sys-maint | >>>> *C9BF7C6E59BFF0FA879E6650D174264C9EE87F25 | >>>> >>>> +-----------+------------------+-------------------------------------------+ >>>> 4 rows in set (0.00 sec) >>>> >>>> 3. We then opened http://localhost/installdb.php and have gotten the >>>> login page for LORIS installation and typed the credentials as follows: >>>> [image: Screenshot from 2019-08-13 09-14-51.png] >>>> 4. Once we submitted the page we obtained error as follows >>>> >>>> [image: Screenshot from 2019-08-13 09-14-56.png] >>>> >>>> >>>> >>>> We really do not know how to proceed further from this point onward. >>>> Kindly let us know how to proceed further in order to get the LORIS >>>> installed. >>>> >>>> Thank you. >>>> >>>> Your Sincerely, >>>> >>>> ====================================================== >>>> >>>> Yubu Lee, Ph.D. >>>> >>>> Research Professor, >>>> >>>> Center for Neuroscience Imaging Research, Institute for Basic Science >>>> >>>> >>>> #86332, N Center, SungKyunKwan University >>>> 2066, Seobu-Ro, Jangan-gu, Suwon, Gyeonggi-do, 16419, Korea >>>> >>>> E-mail: basilia1123 at gmail.com >>>> >>>> Tel: +82-31-299-4411 >>>> >>>> Fax: +82-31-299-4506 >>>> >>>> ====================================================== >>>> _______________________________________________ >>>> Loris-dev mailing list >>>> Loris-dev at bic.mni.mcgill.ca >>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>> >>> >>> >>> -- >>> Shen Wang >>> Loris Developer >>> Montreal Neurological Institute >>> McGill University >>> >>> > > -- > Shen Wang > Loris Developer > Montreal Neurological Institute > McGill University > > _______________________________________________ > Loris-dev mailing list > Loris-dev at bic.mni.mcgill.ca > https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Screenshot from 2019-08-13 09-14-51.png Type: image/png Size: 283124 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Screenshot from 2019-08-13 09-14-56.png Type: image/png Size: 124916 bytes Desc: not available URL: From wangshen.mcin at gmail.com Wed Aug 14 18:36:38 2019 From: wangshen.mcin at gmail.com (Shen Wang) Date: Wed, 14 Aug 2019 18:36:38 -0400 Subject: [Loris-dev] Upgrading to Loris 21 - new make file In-Reply-To: References: Message-ID: Hi,Sotirios In your special situation, there is a temporary fix. step 1. sudo git stash step 2. open webpack.config.js file remove line 75 use: ['babel-loader', 'eslint-loader'], save it. step 3. sudo make I hope this could help you to compile the js files. On Wed, 14 Aug 2019 at 08:28, Sotirios Nikoloutsopoulos < sotirisnik at gmail.com> wrote: > I forgot to mention that i had already moved my previous config file and > re-executed the installation script. > > ???? ???, 14 ??? 2019 ???? 3:26 ?.?., ?/? Sotirios Nikoloutsopoulos < > sotirisnik at gmail.com> ??????: > >> Hi, >> >> Step 1 worked and the indentation errors were fixed. About step2 i added >> all of these( there are more to include in the list) these to .eslintignore >> which were reported to fail at being built, but they still appear on the >> errors at the make_output file. >> >> /jsx/DynamicDataTable.js >> /jsx/StaticDataTable.js >> /jsx/MultiSelectDropdown.js >> /jsx/Breadcrumbs.js >> /jsx/Form.js >> /jsx/Markdown.js >> /modules/media/jsx/mediaIndex.js >> /modules/issue_tracker/jsx/issueTrackerIndex.js >> /modules/issue_tracker/jsx/index.js >> /modules/candidate_parameters/jsx/CandidateParameters.js >> /modules/configuration/jsx/SubprojectRelations.js >> /modules/conflict_resolver/jsx/conflictResolverIndex.js >> /modules/conflict_resolver/jsx/resolvedConflictsIndex.js >> /modules/bvl_feedback/jsx/react.behavioural_feedback_panel.js >> /modules/dataquery/jsx/react.tabs.js >> /modules/document_repository/jsx/docIndex.js >> /modules/instrument_builder/jsx/react.instrument_builder.js >> /modules/imaging_uploader/jsx/index.js >> /modules/datadict/jsx/dataDictIndex.js >> /modules/bvl_feedback/jsx/react.behavioural_feedback_panel.js >> /modules/new_profile/jsx/NewProfileIndex.js >> /modules/examiner/jsx/examinerIndex.js >> /modules/configuration/jsx/SubprojectRelations.js >> /modules/data_team_helper/jsx/behavioural_qc_module.js >> /modules/acknowledgements/jsx/acknowledgementsIndex.js >> /modules/candidate_parameters/jsx/CandidateParameters.js >> /modules/imaging_browser/jsx/ImagePanel.js >> /modules/mri_violations/jsx/mri_protocol_violations_columnFormatter.js >> >> /modules/mri_violations/jsx/mri_protocol_check_violations_columnFormatter.js >> /modules/genomic_browser/jsx/profileColumnFormatter.js >> /modules/dataquery/jsx/react.tabs.js >> /jsx/MultiSelectDropdown.js >> /modules/mri_violations/jsx/columnFormatterUnresolved.js >> /modules/dataquery/jsx/react.sidebar.js >> /modules/dataquery/jsx/react.fieldselector.js >> /modules/quality_control/jsx/qualityControlIndex.js >> /modules/dataquery/jsx/react.paginator.js >> /modules/instrument_builder/jsx/react.questions.js >> /modules/dataquery/jsx/react.filterBuilder.js >> /modules/conflict_resolver/jsx/conflictResolverIndex.js >> /jsx/PaginationLinks.js >> /modules/conflict_resolver/jsx/resolvedConflictsIndex.js >> /modules/dataquery/jsx/react.app.js >> /modules/candidate_list/jsx/onLoad.js >> /jsx/Form.js >> /modules/publication/jsx/publicationIndex.js >> /modules/server_processes_manager/jsx/server_processes_managerIndex.js >> /modules/imaging_browser/jsx/imagingBrowserIndex.js >> /modules/issue_tracker/jsx/issueTrackerIndex.js >> /modules/survey_accounts/jsx/surveyAccountsIndex.js >> /modules/data_integrity_flag/jsx/dataIntegrityFlagIndex.js >> /modules/instrument_manager/jsx/instrumentManagerIndex.js >> /modules/media/jsx/mediaIndex.js >> /modules/user_accounts/jsx/userAccountsIndex.js >> /modules/help_editor/jsx/help_editor.js >> /modules/dicom_archive/jsx/dicom_archive.js >> /modules/mri_violations/jsx/columnFormatter.js >> /modules/brainbrowser/jsx/Brainbrowser.js >> /node_modules/babel-loader/lib/index.js >> /modules/document_repository/jsx/editFormIndex.js >> >> Thanks >> >> ???? ???, 14 ??? 2019 ???? 7:50 ?.?., ?/? Christine Rogers, Ms. < >> christine.rogers at mcgill.ca> ??????: >> >>> Hi Shen and Sotirios - just a note, >>> >>> For the 21 release, it's best to run the install script without sudoing >>> it. >>> >>> (Shen, I believe we discovered a minor issue with the sudo last week >>> #5008) >>> >>> Best, >>> Christine >>> >>> On Tue, Aug 13, 2019 at 9:22 PM Shen Wang >>> wrote: >>> >>>> Does it work? If still doesn?t work, try to remove project/config.xml >>>> file. Do sudo ./install.sh again. To reinstall Loris again. >>>> >>>> >>>> Shen Wang ?2019?8?13? ????9:02??? >>>> >>>>> Hi Sotirios, >>>>> step 1: >>>>> sudo ./node_modules/.bin/eslint --fix /var/www/loris >>>>> step 2: >>>>> put the rest error files under this line [# Ignore until ESLint is run >>>>> ] in the .eslintignore file. >>>>> step 3: >>>>> sudo make >>>>> >>>>> >>>>> >>>>> On Tue, 13 Aug 2019 at 20:34, Sotirios Nikoloutsopoulos < >>>>> sotirisnik at gmail.com> wrote: >>>>> >>>>>> I did the modifications, still there are errors. >>>>>> Thanks >>>>>> >>>>>> >>>>>> ???? ???, 14 ??? 2019 ???? 3:22 ?.?., ?/? Shen Wang < >>>>>> wangshen.mcin at gmail.com> ??????: >>>>>> >>>>>>> Hi Sotirios, >>>>>>> I saw your output file, the config issue is gone. >>>>>>> you can use [sudo npm run lintfix:javascript ] to fix these indent >>>>>>> issues. >>>>>>> If it still has errors. >>>>>>> Then try modify this file .eslintignore >>>>>>> with this >>>>>>> >>>>>>> # Ignore until ESLint is run >>>>>>> >>>>>>> modules/* >>>>>>> >>>>>>> modules/dataquery/ >>>>>>> >>>>>>> node_modules/* >>>>>>> >>>>>>> htdocs/js/components/* >>>>>>> >>>>>>> jsx/* >>>>>>> >>>>>>> >>>>>>> # Ignore external libs >>>>>>> >>>>>>> htdocs/js/flot/* >>>>>>> >>>>>>> htdocs/js/jquery/* >>>>>>> >>>>>>> htdocs/js/jszip/* >>>>>>> >>>>>>> htdocs/js/modernizr/* >>>>>>> >>>>>>> htdocs/js/modules/* >>>>>>> >>>>>>> htdocs/js/react/* >>>>>>> >>>>>>> htdocs/js/shims/* >>>>>>> >>>>>>> htdocs/js/c3.min.js >>>>>>> >>>>>>> htdocs/js/d3.min.js >>>>>>> >>>>>>> htdocs/js/FileSaver.min.js >>>>>>> >>>>>>> >>>>>>> then do sudo make. >>>>>>> It should work. >>>>>>> Regards >>>>>>> Shen >>>>>>> >>>>>>> >>>>>>> Sotirios Nikoloutsopoulos ?2019?8?13? >>>>>>> ????7:54??? >>>>>>> >>>>>>>> No, it didn't work, i also tried space/tabs because most of the >>>>>>>> errors where about indentation, also there are some errors about React. >>>>>>>> >>>>>>>> Thanks >>>>>>>> >>>>>>>> lorisadmin at hbp:/var/www/loris$ sudo ./node_modules/.bin/eslint >>>>>>>> --init >>>>>>>> ? How would you like to configure ESLint? Answer questions about >>>>>>>> your style >>>>>>>> ? Which version of ECMAScript do you use? ES2015 >>>>>>>> ? Are you using ES6 modules? Yes >>>>>>>> ? Where will your code run? Browser >>>>>>>> ? Do you use CommonJS? Yes >>>>>>>> ? Do you use JSX? Yes >>>>>>>> ? Do you use React? Yes >>>>>>>> ? What style of indentation do you use? Spaces >>>>>>>> ? What quotes do you use for strings? Single >>>>>>>> ? What line endings do you use? Unix >>>>>>>> ? Do you require semicolons? Yes >>>>>>>> ? What format do you want your config file to be in? JSON >>>>>>>> The config that you've selected requires the following dependencies: >>>>>>>> >>>>>>>> eslint-plugin-react at latest >>>>>>>> Successfully created .eslintrc.json file in /var/www/loris >>>>>>>> >>>>>>>> lorisadmin at hbp:/var/www/loris$ sudo make > sudo_make_output >>>>>>>> npm WARN The package prop-types is included as both a dev and >>>>>>>> production dependency. >>>>>>>> npm WARN optional SKIPPING OPTIONAL DEPENDENCY: fsevents at 1.2.4 >>>>>>>> (node_modules/fsevents): >>>>>>>> npm WARN notsup SKIPPING OPTIONAL DEPENDENCY: Unsupported platform >>>>>>>> for fsevents at 1.2.4: wanted {"os":"darwin","arch":"any"} (current: >>>>>>>> {"os":"linux","arch":"x64"}) >>>>>>>> >>>>>>>> npm ERR! code ELIFECYCLE >>>>>>>> npm ERR! errno 2 >>>>>>>> npm ERR! loris at 1.0.0 compile: `webpack` >>>>>>>> npm ERR! Exit status 2 >>>>>>>> npm ERR! >>>>>>>> npm ERR! Failed at the loris at 1.0.0 compile script. >>>>>>>> npm ERR! This is probably not a problem with npm. There is likely >>>>>>>> additional logging output above. >>>>>>>> >>>>>>>> npm ERR! A complete log of this run can be found in: >>>>>>>> npm ERR! >>>>>>>> /home/lorisadmin/.npm/_logs/2019-08-13T23_40_58_841Z-debug.log >>>>>>>> >>>>>>>> ???? ???, 14 ??? 2019 ???? 2:29 ?.?., ?/? Shen Wang < >>>>>>>> wangshen.mcin at gmail.com> ??????: >>>>>>>> >>>>>>>>> Hi Sotirios, >>>>>>>>> When you do make command, please make sure with sudo at the >>>>>>>>> beginning. [sudo make] >>>>>>>>> If it still doesn't work for you. >>>>>>>>> Then try the solutions below. >>>>>>>>> solution 1: >>>>>>>>> [image: ???? 2019-08-13 19.21.15.png] >>>>>>>>> Regards >>>>>>>>> Shen >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> On Tue, 13 Aug 2019 at 17:22, Sotirios Nikoloutsopoulos < >>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>> >>>>>>>>>> I think that the files exists although i redownloaded the >>>>>>>>>> eslintrc.json i checked others files that had similar errors. >>>>>>>>>> >>>>>>>>>> lorisadmin at hbp:/var/www/loris$ ls -l >>>>>>>>>> ./node_modules/eslint-loader/index.js >>>>>>>>>> -rw-rw-r-- 1 lorisadmin lorisadmin 6463 ??? 26 1985 >>>>>>>>>> ./node_modules/eslint-loader/index.js >>>>>>>>>> >>>>>>>>>> lorisadmin at hbp:/var/www/loris$ ls -l .eslintrc.json >>>>>>>>>> -rw-rw-r-- 1 lorisadmin lorisadmin 84530 ??? 14 00:04 >>>>>>>>>> .eslintrc.json >>>>>>>>>> >>>>>>>>>> Maybe this can help >>>>>>>>>> >>>>>>>>>> Module build failed (from ./node_modules/eslint-loader/index.js): >>>>>>>>>> SyntaxError: Cannot read config file: >>>>>>>>>> /var/www/loris/.eslintrc.json >>>>>>>>>> Error: Unexpected token < in JSON at position 6 >>>>>>>>>> at JSON.parse () >>>>>>>>>> at loadJSONConfigFile >>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config/config-file.js:114:21) >>>>>>>>>> at loadConfigFile >>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config/config-file.js:230:26) >>>>>>>>>> at loadFromDisk >>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config/config-file.js:500:18) >>>>>>>>>> at Object.load >>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config/config-file.js:564:20) >>>>>>>>>> at Config.getLocalConfigHierarchy >>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config.js:227:44) >>>>>>>>>> at Config.getConfigHierarchy >>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config.js:179:43) >>>>>>>>>> at Config.getConfigVector >>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config.js:286:21) >>>>>>>>>> at Config.getConfig >>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config.js:329:29) >>>>>>>>>> at processText >>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/cli-engine.js:162:33) >>>>>>>>>> at CLIEngine.executeOnText >>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/cli-engine.js:596:17) >>>>>>>>>> at lint >>>>>>>>>> (/var/www/loris/node_modules/eslint-loader/index.js:237:17) >>>>>>>>>> at Object.module.exports >>>>>>>>>> (/var/www/loris/node_modules/eslint-loader/index.js:232:21) >>>>>>>>>> >>>>>>>>>> ERROR in ./modules/imaging_uploader/jsx/index.js >>>>>>>>>> Module build failed (from >>>>>>>>>> ./node_modules/eslint-loader/index.js): >>>>>>>>>> SyntaxError: Cannot read config file: >>>>>>>>>> /var/www/loris/.eslintrc.json >>>>>>>>>> Error: Unexpected token < in JSON at position 6 >>>>>>>>>> at JSON.parse () >>>>>>>>>> at loadJSONConfigFile >>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config/config-file.js:114:21) >>>>>>>>>> at loadConfigFile >>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config/config-file.js:230:26) >>>>>>>>>> at loadFromDisk >>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config/config-file.js:500:18) >>>>>>>>>> at Object.load >>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config/config-file.js:564:20) >>>>>>>>>> at Config.getLocalConfigHierarchy >>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config.js:227:44) >>>>>>>>>> at Config.getConfigHierarchy >>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config.js:179:43) >>>>>>>>>> at Config.getConfigVector >>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config.js:286:21) >>>>>>>>>> at Config.getConfig >>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config.js:329:29) >>>>>>>>>> at processText >>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/cli-engine.js:162:33) >>>>>>>>>> at CLIEngine.executeOnText >>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/cli-engine.js:596:17) >>>>>>>>>> at lint >>>>>>>>>> (/var/www/loris/node_modules/eslint-loader/index.js:237:17) >>>>>>>>>> at Object.module.exports >>>>>>>>>> (/var/www/loris/node_modules/eslint-loader/index.js:232:21) >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> ???? ???, 13 ??? 2019 ???? 11:52 ?.?., ?/? John Saigle < >>>>>>>>>> john.saigle at mcin.ca> ??????: >>>>>>>>>> >>>>>>>>>>> HI Sotirios, >>>>>>>>>>> >>>>>>>>>>> The make_output.txt file shows webpack failing because it can't >>>>>>>>>>> find the ESLint config file. >>>>>>>>>>> >>>>>>>>>>> Can you confirm whether the file `.eslintrc.json` exists within >>>>>>>>>>> your loris root directory (usually `/var/www/loris/`)? When I delete my >>>>>>>>>>> file I get the same errors as you. >>>>>>>>>>> >>>>>>>>>>> If you find that it's missing, you can make a local copy with >>>>>>>>>>> the contents found here: >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> https://github.com/aces/Loris/blob/e26a6ad49a73fcffef0cd73bb600c4d17b200b62/.eslintrc.json >>>>>>>>>>> >>>>>>>>>>> Once you know it exists, try running `make` again. >>>>>>>>>>> >>>>>>>>>>> Let us know if that moves you forward. >>>>>>>>>>> >>>>>>>>>>> Best, >>>>>>>>>>> John >>>>>>>>>>> >>>>>>>>>>> On Tue, Aug 13, 2019 at 2:21 PM Sotirios Nikoloutsopoulos < >>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>> >>>>>>>>>>>> Hi, >>>>>>>>>>>> I executed the commands for the node and now i am get the >>>>>>>>>>>> followings: >>>>>>>>>>>> >>>>>>>>>>>> lorisadmin at hbp:/var/www/loris$ make > ~/make_output >>>>>>>>>>>> npm WARN The package prop-types is included as both a dev and >>>>>>>>>>>> production dependency. >>>>>>>>>>>> npm WARN optional SKIPPING OPTIONAL DEPENDENCY: fsevents at 1.2.4 >>>>>>>>>>>> (node_modules/fsevents): >>>>>>>>>>>> npm WARN notsup SKIPPING OPTIONAL DEPENDENCY: Unsupported >>>>>>>>>>>> platform for fsevents at 1.2.4: wanted >>>>>>>>>>>> {"os":"darwin","arch":"any"} (current: {"os":"linux","arch":"x64"}) >>>>>>>>>>>> >>>>>>>>>>>> npm ERR! code ELIFECYCLE >>>>>>>>>>>> npm ERR! errno 2 >>>>>>>>>>>> npm ERR! loris at 1.0.0 compile: `webpack` >>>>>>>>>>>> npm ERR! Exit status 2 >>>>>>>>>>>> npm ERR! >>>>>>>>>>>> npm ERR! Failed at the loris at 1.0.0 compile script. >>>>>>>>>>>> npm ERR! This is probably not a problem with npm. There is >>>>>>>>>>>> likely additional logging output above. >>>>>>>>>>>> >>>>>>>>>>>> npm ERR! A complete log of this run can be found in: >>>>>>>>>>>> npm ERR! >>>>>>>>>>>> /home/lorisadmin/.npm/_logs/2019-08-13T18_12_05_378Z-debug.log >>>>>>>>>>>> make: *** [javascript] Error 2 >>>>>>>>>>>> >>>>>>>>>>>> Thanks, >>>>>>>>>>>> Sotirios >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> ???? ???, 12 ??? 2019 ???? 10:19 ?.?., ?/? Christine Rogers, >>>>>>>>>>>> Ms. ??????: >>>>>>>>>>>> >>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>> >>>>>>>>>>>>> We've seen some users installing LORIS 21 or upgrading to 21 >>>>>>>>>>>>> whose version of node doesn't work well with webpack, due to updated >>>>>>>>>>>>> packages they're missing. >>>>>>>>>>>>> If so, update your node : >>>>>>>>>>>>> >>>>>>>>>>>>> curl -sL https://deb.nodesource.com/setup_8.x | sudo -E bash - >>>>>>>>>>>>> sudo apt-get install -y nodejs >>>>>>>>>>>>> >>>>>>>>>>>>> Let us know how that goes -- please send us output from the >>>>>>>>>>>>> same log if any issues. >>>>>>>>>>>>> Best, >>>>>>>>>>>>> Christine >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> On Thu, Aug 8, 2019 at 2:38 PM Sotirios Nikoloutsopoulos < >>>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>> >>>>>>>>>>>>>> It's not a disk space issue, as you can see below i have >>>>>>>>>>>>>> still 74GB available. >>>>>>>>>>>>>> >>>>>>>>>>>>>> lorisadmin at hbp:/var/www/loris$ df -h >>>>>>>>>>>>>> Filesystem Size Used Avail Use% Mounted on >>>>>>>>>>>>>> udev 2,9G 0 2,9G 0% /dev >>>>>>>>>>>>>> tmpfs 597M 8,6M 588M 2% /run >>>>>>>>>>>>>> /dev/sda1 98G 19G 74G 21% / >>>>>>>>>>>>>> >>>>>>>>>>>>>> Maybe we have to pass a flag to get into strict mode? as >>>>>>>>>>>>>> stated "SyntaxError: Block-scoped declarations (let, const, function, >>>>>>>>>>>>>> class) not yet supported outside strict mode" >>>>>>>>>>>>>> >>>>>>>>>>>>>> Thanks, >>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>> >>>>>>>>>>>>>> ???? ???, 8 ??? 2019 ???? 4:32 ?.?., ?/? Dave MacFarlane < >>>>>>>>>>>>>> dave.macfarlane at mcin.ca> ??????: >>>>>>>>>>>>>> >>>>>>>>>>>>>>> It looks like the javascript snippet shown in the error >>>>>>>>>>>>>>> message when trying to compile the js is truncated. Have you run out of >>>>>>>>>>>>>>> disk space? >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> On Thu, Aug 8, 2019 at 8:37 AM Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> I runned make and also included the file it reports at the >>>>>>>>>>>>>>>> end. >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> lorisadmin at hbp:/var/www/loris$ make >>>>>>>>>>>>>>>> npm install >>>>>>>>>>>>>>>> npm WARN optional Skipping failed optional dependency >>>>>>>>>>>>>>>> /chokidar/fsevents: >>>>>>>>>>>>>>>> npm WARN notsup Not compatible with your operating system >>>>>>>>>>>>>>>> or architecture: fsevents at 1.2.9 >>>>>>>>>>>>>>>> npm WARN optional Skipping failed optional dependency >>>>>>>>>>>>>>>> /watchpack/chokidar/fsevents: >>>>>>>>>>>>>>>> npm WARN notsup Not compatible with your operating system >>>>>>>>>>>>>>>> or architecture: fsevents at 1.2.9 >>>>>>>>>>>>>>>> npm run compile >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> > loris at 1.0.0 compile /var/www/loris >>>>>>>>>>>>>>>> > webpack >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> /var/www/loris/node_modules/webpack/bin/webpack.js:86 >>>>>>>>>>>>>>>> let notify = >>>>>>>>>>>>>>>> ^^^ >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> SyntaxError: Block-scoped declarations (let, const, >>>>>>>>>>>>>>>> function, class) not yet supported outside strict mode >>>>>>>>>>>>>>>> at exports.runInThisContext (vm.js:53:16) >>>>>>>>>>>>>>>> at Module._compile (module.js:374:25) >>>>>>>>>>>>>>>> at Object.Module._extensions..js (module.js:417:10) >>>>>>>>>>>>>>>> at Module.load (module.js:344:32) >>>>>>>>>>>>>>>> at Function.Module._load (module.js:301:12) >>>>>>>>>>>>>>>> at Function.Module.runMain (module.js:442:10) >>>>>>>>>>>>>>>> at startup (node.js:136:18) >>>>>>>>>>>>>>>> at node.js:966:3 >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> npm ERR! Linux 4.15.0-55-generic >>>>>>>>>>>>>>>> npm ERR! argv "/usr/bin/nodejs" "/usr/bin/npm" "run" >>>>>>>>>>>>>>>> "compile" >>>>>>>>>>>>>>>> npm ERR! node v4.2.6 >>>>>>>>>>>>>>>> npm ERR! npm v3.5.2 >>>>>>>>>>>>>>>> npm ERR! code ELIFECYCLE >>>>>>>>>>>>>>>> npm ERR! loris at 1.0.0 compile: `webpack` >>>>>>>>>>>>>>>> npm ERR! Exit status 1 >>>>>>>>>>>>>>>> npm ERR! >>>>>>>>>>>>>>>> npm ERR! Failed at the loris at 1.0.0 compile script >>>>>>>>>>>>>>>> 'webpack'. >>>>>>>>>>>>>>>> npm ERR! Make sure you have the latest version of node.js >>>>>>>>>>>>>>>> and npm installed. >>>>>>>>>>>>>>>> npm ERR! If you do, this is most likely a problem with the >>>>>>>>>>>>>>>> loris package, >>>>>>>>>>>>>>>> npm ERR! not with npm itself. >>>>>>>>>>>>>>>> npm ERR! Tell the author that this fails on your system: >>>>>>>>>>>>>>>> npm ERR! webpack >>>>>>>>>>>>>>>> npm ERR! You can get information on how to open an issue >>>>>>>>>>>>>>>> for this project with: >>>>>>>>>>>>>>>> npm ERR! npm bugs loris >>>>>>>>>>>>>>>> npm ERR! Or if that isn't available, you can get their info >>>>>>>>>>>>>>>> via: >>>>>>>>>>>>>>>> npm ERR! npm owner ls loris >>>>>>>>>>>>>>>> npm ERR! There is likely additional logging output above. >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> npm ERR! Please include the following file with any support >>>>>>>>>>>>>>>> request: >>>>>>>>>>>>>>>> npm ERR! /var/www/loris/npm-debug.log >>>>>>>>>>>>>>>> Makefile:14: recipe for target 'javascript' failed >>>>>>>>>>>>>>>> make: *** [javascript] Error 1 >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Thanks, >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> ???? ???, 7 ??? 2019 ???? 5:41 ?.?., ?/? Christine Rogers, >>>>>>>>>>>>>>>> Ms. ??????: >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Thanks, have you tried all of these steps? >>>>>>>>>>>>>>>>> - clear your browser cache (and refresh a few times) >>>>>>>>>>>>>>>>> - delete any files in your smarty/templates_c directory >>>>>>>>>>>>>>>>> (this will clear the template cache - do Not touch smarty/templates/) >>>>>>>>>>>>>>>>> - run `make` (per the 21 release notes, this replaces the >>>>>>>>>>>>>>>>> composer commands used in previous releases to update your dependencies) >>>>>>>>>>>>>>>>> - restart apache (doesn't hurt) >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Let us know how it goes -- let us know what difference you >>>>>>>>>>>>>>>>> see after, with your logs. A >>>>>>>>>>>>>>>>> lso please send us your Config path settings (see these >>>>>>>>>>>>>>>>> Troubleshooting Queries >>>>>>>>>>>>>>>>> ) >>>>>>>>>>>>>>>>> if you're still seeing front-end issues. >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Thanks, >>>>>>>>>>>>>>>>> Christine >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> On Wed, Aug 7, 2019 at 8:02 AM Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> lorisadmin at hbp:/var/www/loris$ sudo cat >>>>>>>>>>>>>>>>>> /var/log/apache2/error.log >>>>>>>>>>>>>>>>>> [Wed Aug 07 07:35:02.422501 2019] [mpm_prefork:notice] >>>>>>>>>>>>>>>>>> [pid 1267] AH00163: Apache/2.4.18 (Ubuntu) OpenSSL/1.0.2g configured -- >>>>>>>>>>>>>>>>>> resuming normal operations >>>>>>>>>>>>>>>>>> [Wed Aug 07 07:35:02.422514 2019] [core:notice] [pid >>>>>>>>>>>>>>>>>> 1267] AH00094: Command line: '/usr/sbin/apache2' >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> And as for the access.log the content are empty >>>>>>>>>>>>>>>>>> lorisadmin at hbp:/var/www/loris$ sudo ls -l >>>>>>>>>>>>>>>>>> /var/log/apache2/access.log >>>>>>>>>>>>>>>>>> lorisadmin at hbp:/var/www/loris$ sudo ls -l >>>>>>>>>>>>>>>>>> /var/log/apache2/access.log >>>>>>>>>>>>>>>>>> -rw-r----- 1 root adm 0 ???? 28 14:09 >>>>>>>>>>>>>>>>>> /var/log/apache2/access.log >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Also i noticed a loris_access.log. >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> The only non-blank pages are: >>>>>>>>>>>>>>>>>> mri_violations, dataquery does not exist at all, >>>>>>>>>>>>>>>>>> statistics, data_team_helper, genomic_browser, configuration and >>>>>>>>>>>>>>>>>> server_processes_manager/ prints "Required configuration settings for >>>>>>>>>>>>>>>>>> Server Processes Manager are missing. Cannot continue." >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Thanks, >>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> ???? ???, 6 ??? 2019 ???? 10:13 ?.?., ?/? Christine >>>>>>>>>>>>>>>>>> Rogers, Ms. ??????: >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Hi Sotirios and LORIS community -- >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> When upgrading to brand-new release 21 -- just a >>>>>>>>>>>>>>>>>>> reminder to follow the release notes and run the new >>>>>>>>>>>>>>>>>>> *make* file to update your dependencies (instead of >>>>>>>>>>>>>>>>>>> using *composer* commands). >>>>>>>>>>>>>>>>>>> We've also updated the Wiki page >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> to clarify that the release notes for each version will tell you what to >>>>>>>>>>>>>>>>>>> run. >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> If your current version is not the last release (20.3), >>>>>>>>>>>>>>>>>>> it's still important to upgrade to each minor release increment (e.g. 20.2, >>>>>>>>>>>>>>>>>>> 20.3) before making the leap to 21.0. >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> If you're getting blank pages, post-upgrade -- Try >>>>>>>>>>>>>>>>>>> clearing your cache. >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Got questions or feedback e.g. on the Release Notes? >>>>>>>>>>>>>>>>>>> please don't hesitate to let us know. >>>>>>>>>>>>>>>>>>> Thanks, >>>>>>>>>>>>>>>>>>> Christine >>>>>>>>>>>>>>>>>>> The LORIS team >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> On Tue, Aug 6, 2019 at 10:09 AM Christine Rogers, Ms. < >>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca> wrote: >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>> Could you also let us know -- on which pages is content >>>>>>>>>>>>>>>>>>>> visible, and on which pages/modules is content not visible for you? >>>>>>>>>>>>>>>>>>>> Thanks, >>>>>>>>>>>>>>>>>>>> Christine >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> On Tue, Aug 6, 2019 at 9:54 AM Christine Rogers, Ms. < >>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca> wrote: >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> Thanks Sotirios, >>>>>>>>>>>>>>>>>>>>> That's good to know. It sounds like you've checked >>>>>>>>>>>>>>>>>>>>> that your /var/www/loris/project/config.xml file get populated properly. >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> Please send us the last few errors you're seeing in >>>>>>>>>>>>>>>>>>>>> your apache error log file, and your config paths and we can see what's >>>>>>>>>>>>>>>>>>>>> happening with your front end -- >>>>>>>>>>>>>>>>>>>>> Run these Troubleshooting Queries >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> to get your config path settings, given your front end is not displaying >>>>>>>>>>>>>>>>>>>>> fully. >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> The Loris-MRI repo >>>>>>>>>>>>>>>>>>>>> 21 >>>>>>>>>>>>>>>>>>>>> install/upgrade would then be your next steps. >>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>> Christine >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> On Tue, Aug 6, 2019 at 7:53 AM Sotirios >>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos wrote: >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> I am using a VM. What i did was: >>>>>>>>>>>>>>>>>>>>>> 1) Download the files from >>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris and replace them to my >>>>>>>>>>>>>>>>>>>>>> existing /vaw/www/loris folder. >>>>>>>>>>>>>>>>>>>>>> 2) Execute the composer install --no-dev and then composer >>>>>>>>>>>>>>>>>>>>>> dump-autoload as mentioned here >>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris/wiki/Updating-your-LORIS >>>>>>>>>>>>>>>>>>>>>> . >>>>>>>>>>>>>>>>>>>>>> 3) Execute install.sh from /var/www/loris/tools and >>>>>>>>>>>>>>>>>>>>>> because LORIS already existed i moved a .config file, then re-executed the >>>>>>>>>>>>>>>>>>>>>> install.sh successfully >>>>>>>>>>>>>>>>>>>>>> 4 ) As for the database, i dropped the schema and i >>>>>>>>>>>>>>>>>>>>>> executed the installdb.php >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> ???? ???, 5 ??? 2019 ???? 5:22 ?.?., ?/? Christine >>>>>>>>>>>>>>>>>>>>>> Rogers, Ms. ??????: >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> Hi Sotorios, >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> Thanks - when you re-installed did you start on a >>>>>>>>>>>>>>>>>>>>>>> fresh root path / VM or might some of your old system setting still apply? >>>>>>>>>>>>>>>>>>>>>>> (And if you did any steps similar to an upgrade, did >>>>>>>>>>>>>>>>>>>>>>> you follow the Upgrade steps in the Release Notes, from both repos?) >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> About the TR_range column - it was recently split (MRI >>>>>>>>>>>>>>>>>>>>>>> pr339 ) split >>>>>>>>>>>>>>>>>>>>>>> into TR_min and _max columns. Given the code was trying to query TR_range >>>>>>>>>>>>>>>>>>>>>>> which does not exist in your mri_protocol table, double-check which version >>>>>>>>>>>>>>>>>>>>>>> of the Loris repo (tables) and the Loris-MRI repo (code) you have installed >>>>>>>>>>>>>>>>>>>>>>> to ensure they match. >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> Christine >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> On Mon, Aug 5, 2019 at 9:06 AM Sotirios >>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos wrote: >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> I reinstalled LORIS to 21 version and now the >>>>>>>>>>>>>>>>>>>>>>>> content is not visible at all at most pages. >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 5 ??? 2019 ???? 3:19 ?.?., ?/? Sotirios >>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos ??????: >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> Is it easy to upgrade to Loris 21? Also the >>>>>>>>>>>>>>>>>>>>>>>>> following fails because the line 1985 of NeuroDB/MRIProcessingUtility.pm >>>>>>>>>>>>>>>>>>>>>>>>> query mri_protocol which doesn't have TR_range >>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris/blob/21.0-release/SQL/0000-00-00-schema.sql#L556 >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> lorisadmin at hbp:/data/loris/bin/mri$ >>>>>>>>>>>>>>>>>>>>>>>>> ./batch_uploads_imageuploader -profile prod < ~/Desktop/input.txt > log.txt >>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $_ in pattern match >>>>>>>>>>>>>>>>>>>>>>>>> (m//) at ./batch_uploads_imageuploader line 147. >>>>>>>>>>>>>>>>>>>>>>>>> base is DCC0000_258024_V1 >>>>>>>>>>>>>>>>>>>>>>>>> path is /data/incoming/ >>>>>>>>>>>>>>>>>>>>>>>>> type is .tar.gz >>>>>>>>>>>>>>>>>>>>>>>>> fullpath is >>>>>>>>>>>>>>>>>>>>>>>>> /data/incoming/DCC0000_258024_V1.tar.gz >>>>>>>>>>>>>>>>>>>>>>>>> DBD::mysql::st execute failed: Unknown column >>>>>>>>>>>>>>>>>>>>>>>>> 'TR_range' in 'where clause' at >>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line 1985. >>>>>>>>>>>>>>>>>>>>>>>>> DBD::mysql::st fetchrow_array failed: fetch() >>>>>>>>>>>>>>>>>>>>>>>>> without execute() at >>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line 1986. >>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $count_mri_protocol in >>>>>>>>>>>>>>>>>>>>>>>>> numeric gt (>) at >>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line 1995. >>>>>>>>>>>>>>>>>>>>>>>>> DBD::mysql::st execute failed: Unknown column >>>>>>>>>>>>>>>>>>>>>>>>> 'TR_range' in 'field list' at >>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 562. >>>>>>>>>>>>>>>>>>>>>>>>> Can't exec "mail": No such file or directory at >>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 721. >>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 722. >>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 723. >>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 724. >>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 725. >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> No Mincs inserted >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> Thanks, >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 3 ??? 2019 ???? 1:08 ?.?., ?/? Christine >>>>>>>>>>>>>>>>>>>>>>>>> Rogers, Ms. ??????: >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> First, just a note: we've released LORIS 21 this >>>>>>>>>>>>>>>>>>>>>>>>>> week with some major new features and cleanup -- especially if you are >>>>>>>>>>>>>>>>>>>>>>>>>> early in your setup phase, check out the Release notes for both the >>>>>>>>>>>>>>>>>>>>>>>>>> LORIS >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> and Loris-MRI >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> repos. >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> Thanks for your screenshots -- your empty >>>>>>>>>>>>>>>>>>>>>>>>>> mri_protocol table should be at the root of these issues : >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> The mri_protocol table must be populated >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> in order for your scans to be registered in LORIS -- it serves as a >>>>>>>>>>>>>>>>>>>>>>>>>> whitelist for the insertion pipeline which filters out scans that aren't >>>>>>>>>>>>>>>>>>>>>>>>>> identified or matched to scan types in this table. >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> By default, this table is populated with entries >>>>>>>>>>>>>>>>>>>>>>>>>> for t1, t2, fMRI and DTI (Insert statements for >>>>>>>>>>>>>>>>>>>>>>>>>> 21 release branch are here >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> ) >>>>>>>>>>>>>>>>>>>>>>>>>> Feel free to restore our default records and >>>>>>>>>>>>>>>>>>>>>>>>>> broaden their parameters to match all your scan types. >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> re Defaced, native, selected -- these filter the >>>>>>>>>>>>>>>>>>>>>>>>>> scans displayed as you move to the next page (View Session), instead of >>>>>>>>>>>>>>>>>>>>>>>>>> viewing "all types" of scans from a given session : >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> - "defaced" means that a defacing script >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> has masked the subject's face in the volume (for patient privacy) >>>>>>>>>>>>>>>>>>>>>>>>>> - "native" means that no pre-processing has >>>>>>>>>>>>>>>>>>>>>>>>>> been performed on the scan (it's raw data), >>>>>>>>>>>>>>>>>>>>>>>>>> - "selected" will show only volumes that >>>>>>>>>>>>>>>>>>>>>>>>>> have been QC'd and "selected" as the best of their type -- used to display >>>>>>>>>>>>>>>>>>>>>>>>>> only the best quality T1 image instead of all T1s acquired in a session, >>>>>>>>>>>>>>>>>>>>>>>>>> e.g. >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> re QC Comments -- >>>>>>>>>>>>>>>>>>>>>>>>>> Once you have successfully loaded scans (matched >>>>>>>>>>>>>>>>>>>>>>>>>> to the mri_protocol table), you'll be able to use the Imaging Browser's >>>>>>>>>>>>>>>>>>>>>>>>>> View Session subpage to enter/view QC comments on each volume, or for each >>>>>>>>>>>>>>>>>>>>>>>>>> visit. >>>>>>>>>>>>>>>>>>>>>>>>>> These are stored directly in the database, and >>>>>>>>>>>>>>>>>>>>>>>>>> linked to each scan. (Table name: >>>>>>>>>>>>>>>>>>>>>>>>>> feedback_mri_comments) >>>>>>>>>>>>>>>>>>>>>>>>>> (Visit-level QC comments are linked to the >>>>>>>>>>>>>>>>>>>>>>>>>> session.) >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> For a walkthrough of the Imaging setup - please >>>>>>>>>>>>>>>>>>>>>>>>>> see the Imaging Setup guide >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> - >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> An old LORIS walkthrough video >>>>>>>>>>>>>>>>>>>>>>>>>> can >>>>>>>>>>>>>>>>>>>>>>>>>> also walk you through some of the Imaging front-end features, starting at >>>>>>>>>>>>>>>>>>>>>>>>>> 8:00 >>>>>>>>>>>>>>>>>>>>>>>>>> LORIS' imaging modules have been updated many >>>>>>>>>>>>>>>>>>>>>>>>>> times since this video, but the functionality and workflow is similar. >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> Let us know how it goes once you have entries in >>>>>>>>>>>>>>>>>>>>>>>>>> your mri_protocol table - >>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>> Christine >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> On Fri, Aug 2, 2019 at 7:58 AM Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos wrote: >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Christine, >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> In the candidate_list page i can see this patient >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> If i press the link under PSCID i get to see >>>>>>>>>>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> and if i press the link under Scan Done it >>>>>>>>>>>>>>>>>>>>>>>>>>> redirects me to imaging_browser >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> At the mri_violations page i also see No results >>>>>>>>>>>>>>>>>>>>>>>>>>> ( neither on resolved / not resolved ). >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> At the imaging_uploader i can see the record >>>>>>>>>>>>>>>>>>>>>>>>>>> that failed. >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> If i click on the tarchive info i get to see the >>>>>>>>>>>>>>>>>>>>>>>>>>> Protocol Name which i think is the acquisition we wanted? >>>>>>>>>>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> Also my mri_protocol table is empty. >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> Furthermore i would like to ask about the >>>>>>>>>>>>>>>>>>>>>>>>>>> defaced, native, selected. What exactly is native and selected? And where >>>>>>>>>>>>>>>>>>>>>>>>>>> are the qc comments stored? >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> Finally a walkthrough would be helpful. >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> Thanks, >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 30 ???? 2019 ???? 8:29 ?.?., ?/? >>>>>>>>>>>>>>>>>>>>>>>>>>> Christine Rogers, Ms. < >>>>>>>>>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>> Glad to hear you're making progress with the >>>>>>>>>>>>>>>>>>>>>>>>>>>> visit labels. To follow up on your last few emails: >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> a- The Wiki's Setup Guide contains Sample >>>>>>>>>>>>>>>>>>>>>>>>>>>> insert statements for the Visit Windows table >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> . >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> As Cecile mentioned, the consistency of visit >>>>>>>>>>>>>>>>>>>>>>>>>>>> label format is important: V01, v01, V1, 01 -- whichever you select to use >>>>>>>>>>>>>>>>>>>>>>>>>>>> is fine; we use V01 by default across all documentation. >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> b- For Password reset, there is a script in the >>>>>>>>>>>>>>>>>>>>>>>>>>>> tools/ directory so that a back-end administrator can reset any front-end >>>>>>>>>>>>>>>>>>>>>>>>>>>> user password, including Admin. (See info on setting up / resetting User >>>>>>>>>>>>>>>>>>>>>>>>>>>> passwords in the Wiki's Setup Guide >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> ) >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> c- The minc file not being registered -- due to >>>>>>>>>>>>>>>>>>>>>>>>>>>> AcquisitionProtocol unknown. >>>>>>>>>>>>>>>>>>>>>>>>>>>> This means the SeriesDescription (Acquisition >>>>>>>>>>>>>>>>>>>>>>>>>>>> Protocol) in you Dicom header was not matched to any scan listed in the >>>>>>>>>>>>>>>>>>>>>>>>>>>> mri_protocol database table. >>>>>>>>>>>>>>>>>>>>>>>>>>>> (In the online Loris-MRI Troubleshooting Guide, >>>>>>>>>>>>>>>>>>>>>>>>>>>> this >>>>>>>>>>>>>>>>>>>>>>>>>>>> is Table 3, 2nd-last item "no MINCs inserted"). >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> The MRI Violations module (Readme here) >>>>>>>>>>>>>>>>>>>>>>>>>>>> will show >>>>>>>>>>>>>>>>>>>>>>>>>>>> you the details of this mismatch -- >>>>>>>>>>>>>>>>>>>>>>>>>>>> Go to the module (under the Imaging menu), find >>>>>>>>>>>>>>>>>>>>>>>>>>>> your scan and click the link "Could not identify scan type" -- in the next >>>>>>>>>>>>>>>>>>>>>>>>>>>> subpage you can compare the scan's actual parameters against the >>>>>>>>>>>>>>>>>>>>>>>>>>>> mri_protocol table. >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> To resolve this, adjust your mri_protocol table >>>>>>>>>>>>>>>>>>>>>>>>>>>> values or perhaps ensure your DICOMs are labelled consistently. >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> Let us know if this works for you -- we can >>>>>>>>>>>>>>>>>>>>>>>>>>>> also walk you through an example of non-identified scans on >>>>>>>>>>>>>>>>>>>>>>>>>>>> Demo.loris.ca (MRI Violations module). >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>>> Christine >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> The LORIS team >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> On Tue, Jul 30, 2019 at 10:47 AM Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos wrote: >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> I hope this is sufficient as the error for the >>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit label disappeared. >>>>>>>>>>>>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Please see the attached file. Also something i >>>>>>>>>>>>>>>>>>>>>>>>>>>>> found. >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> lorisadmin at hbp:/data/loris/bin/mri$ cat >>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data//logs/TarLoad-17-39-xubBdv.log >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> ==> Loading file from disk >>>>>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-17-39-UyQcG2/dcc0000_258024_v1_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> --> mapping DICOM parameter for >>>>>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-17-39-UyQcG2/dcc0000_258024_v1_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> ==> computing md5 hash for MINC body. >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> --> md5: 6b1202fd63e29de4c9be1cd9925888a5 >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> ==> verifying acquisition protocol >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Acquisition protocol is unknown >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> --> The minc file cannot be registered since >>>>>>>>>>>>>>>>>>>>>>>>>>>>> the AcquisitionProtocol is unknown >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 30 ???? 2019 ???? 4:58 ?.?., ?/? >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Ok I fixed the login problem by using a known >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> hash and by deleting the rows from the login_history i was able to login. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 30 ???? 2019 ???? 4:50 ?.?., ?/? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> there was no visit label 01 in the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Visit_Windows table and i don't know how to insert it because the record >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> requires lots of attributes. Also the system for a reason asked me to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> update my password and now i don't remember it and my account got >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> suspended. Is there a way to reset it or set a simple password? I updated >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the password hash in the users table by using the hash from another LORIS >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> setup we had and i still couldn't login ( also the attribute password is >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> always NULL and the expiration date is 1999-01-01 for some reason ). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thanks >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 29 ???? 2019 ???? 5:21 ?.?., ?/? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Cecile Madjar >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Can you try adding the visit label v01 to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the Visit_Windows table? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> However, I noticed that in a previous >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> dataset, the label was V1. Does that refer to the same visit? If so, you >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> might want to harmonize the visit labels so they are all the same across >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> datasets for a given timepoint, meaning you will need to relabel scans when >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the visit label is different but referring to the same visit label (v01 = >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> V1 etc...). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helps, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> On Mon, Jul 29, 2019 at 10:15 AM Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> wrote: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Could you help me with the "Visit label >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> does not exist"? I had changed $subjectID{'createVisitLabel'} to 1 as you >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> had suggested but it appears that this problem hasn't been resolved yet. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> lorisadmin at hbp:/data/loris/bin/mri$ cat >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data//logs/TarLoad-14-58-9Xog7H.log >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ==> Loading file from disk >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> --> mapping DICOM parameter for >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> --> using user-defined filterParameters >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> for >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Candidate Mismatch Error is Visit label >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> does not exist >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -> WARNING: This candidate was invalid. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Logging to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> MRICandidateErrors table >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> with reason Visit label does not exist >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 26 ???? 2019 ???? 3:02 ?.?., ?/? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Cecile, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The Center error was fixed. Still the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> insertion of mincs fails. Please see the output.txt file i attached. Also >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> is there something else i need to change at the paths configuration? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 25 ???? 2019 ???? 6:55 ?.?., >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ?/? Cecile Madjar >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> We are making progress! >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I have a feeling this error comes from >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the fact that your psc table does not have the MRI_alias populated for the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DCC site. Running the following query in the mysql database should fix this: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> UPDATE psc SET MRI_alias="DCC", >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Alias="DCC" WHERE Name="Data Coordinating Center"; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Repeat the same with all your sites >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> (make sure to change the Aliases between sites, they should all be unique). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Let me know how it goes! >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> On Thu, Jul 25, 2019 at 11:43 AM >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Dear Cecile, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> You were right about your guesses. I >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> did the modifications you suggested, i still get the "no mincs inserted" >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> error, now i am getting the "No center found this candidate" error ( how do >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> i fix that? from what i see the .dcm files contains a 'Institution Name', >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> is that the center? ), so i guess that's why the validation fails, but i >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> changed the force variable of tarchiveLoader to 1, shouldn't it have >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> inserted the mincs then? Also it is optional to have a mail server, right? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ( from what i see the mail error does not affect the $valid_study, so i >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> assume we are okay with that ) >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you a lot, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 25 ???? 2019 ???? 5:48 ?.?., >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ?/? Cecile Madjar < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> cecile.madjar at mcin.ca> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> From what I understand, I believe you >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> just need to update a few config settings from the frontend in the Config >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> module (under the Admin menu). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [image: Screen Shot 2019-07-25 at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 10.31.35 AM.png] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Then go to the Paths section of the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> config module and update the "LORIS-MRI code" config setting to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri (my guess is that currently, it is set to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data) and click on the submit button. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [image: Screen Shot 2019-07-25 at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 10.32.50 AM.png] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Then, go to Imaging Pipeline section >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> of the Configuration module and update the "Loris-MRI Data Directory" to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/ (my guess is that it is empty at the moment in your >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> database which is why $data_dir is not defined when you run the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> tarchiveLoader step of the insertion pipeline). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [image: Screen Shot 2019-07-25 at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 10.40.52 AM.png] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Finally, I took a look at your >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> environment file and it might be a good idea to update your PERL5LIB >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> variable to the following (it has been added to the code a few releases ago >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> as we realized this was needed for the libraries. Not sure which version of >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> LORIS-MRI you are using but it does not hurt to update this variable to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> what I suggest below): >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> export >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PERL5LIB=/data/loris/bin/mri/uploadNeuroDB:/data/loris/bin/mri/dicom-archive:$PERL5LIB >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helps. Sorry you are >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> experiencing so much trouble setting things up. We probably need to update >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> our WIKI. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> On Thu, Jul 25, 2019 at 9:48 AM >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The "Loris-MRI Data Directory" should >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> be in the environment file? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 25 ???? 2019 ???? 12:59 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ?.?., ?/? Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The scripts are located in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/. Somewhere I might have messed something up but i >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> remember following the instructions in the wiki.For example when i tried to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> execute the batch_uploads_imageuploader perl script the line >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> my $command = >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> "$bin_dir/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl " >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> was pointing to an invalid path, for >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> example: it was repeating a pattern and had LORIS instead of loris ( i >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> think the mistake was that in the wiki it suggested to use $PROJECT for >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the name of the folder and i choosed 'loris' >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris/wiki/Imaging-Database >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ). See also the in image for the modification i did. Also i didn't find the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> section to config the $data_dir variable. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 24 ???? 2019 ???? 6:05 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ?.?., ?/? Cecile Madjar < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> cecile.madjar at mcin.ca> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> It looks like you have one Config >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> setting not set (based on the first error message you got when running it >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the first time). You need to set a value for "Loris-MRI Data Directory" in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the Config module under the Imaging pipeline section (from what I can see, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> it would be /data/loris/data/ for your setup). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The reason you got that error >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> message the second time is that the pipeline checks if the DICOM study was >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> already inserted in the tarchive table. Since you ran the study once >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> already, the study is inserted into the tarchive, hence the message. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> However, the pipeline did not complete as the MINC files were not created >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and inserted into the files/parameter_file table. In order to continue the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> insertion, you will then need to run the tarchiveLoader command suggested >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in the terminal during the second run: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -globLocation -profile prod >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive//2012/DCM_2012-12-05_ImagingUpload-17-43-ZUEFjb.tar >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -verbose >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Finally, I am a bit confused by >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> your setup. Where are the scripts located? In /data/loris/bin/mri or >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data? It feels like the Config setting "LORIS-MRI code" in the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Paths section was set to "/data/LORIS/data" but it should have been set to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the directory where the scripts are located (most probably >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helps, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> On Wed, Jul 24, 2019 at 10:55 AM >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Ok first i execute this command: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> "lorisadmin at hbp:/data/loris/bin/mri$ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ./batch_uploads_imageuploader -profile prod < ~/Desktop/input.txt > log.txt >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> $data_dir in concatenation (.) or string at ./batch_uploads_imageuploader >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> line 143. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> $data_dir in concatenation (.) or string at ./batch_uploads_imageuploader >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> line 143. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $_ in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> pattern match (m//) at ./batch_uploads_imageuploader line 147. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> base is DCC0000_258024_V01 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> path is /data/incoming/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> type is .tar.gz >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> fullpath is >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/incoming/DCC0000_258024_V01.tar.gz >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> source >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/ImagingUpload-17-43-ZUEFjb >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> targetlocation >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> $data_dir in concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 256. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> $data_dir in concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 284. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> $data_dir in concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> tarchive_validation.pl line 219. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> $data_dir in concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl line 270. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> $data_dir in concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 711. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Can't exec "mail": No such file or >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> directory at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 721. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 722. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 723. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> $data_dir in concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 724. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 724. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 725. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> $data_dir in concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 735. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> No Mincs inserted >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The tarchiveLoader insertion >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> script has failed. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Running now the following command: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl -profile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> prod -upload_id 3 /data/incoming/DCC0000_258024_V01.tar.gz -verbose" >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I inserted the VisitLabel, but >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> still the Mincs are not inserted and i am getting this error >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> "lorisadmin at hbp:/data/loris/bin/mri$ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl -profile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> prod -upload_id 3 /data/incoming/DCC0000_258024_V01.tar.gz -verbose >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> find -path >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> \/tmp\/ImagingUpload\-17\-45\-5MsWEd -name '__MACOSX' -delete >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Spool message is: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The Scan for the uploadID 3 has >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> already been run with tarchiveID: 7. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> To continue with the rest of the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> insertion pipeline, please run tarchiveLoader from a terminal as follows: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader -globLocation -profile prod >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive//2012/DCM_2012-12-05_ImagingUpload-17-43-ZUEFjb.tar >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -verbose" >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Which files should i delete? I >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> thought that deleting the files from the tarchive was enough. And i >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> executed the last proposed command to continue to rest of the insertion >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> pipeline ( check the image ). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 24 ???? 2019 ???? 5:05 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ?.?., ?/? Cecile Madjar < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> cecile.madjar at mcin.ca> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sorry I was not clear before. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Every visits of candidates are created in the session table with one entry >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> per CandID/VisitLabel. So if the imaging pipeline created visits in the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> session table (that are not attached to instruments) and you want to clean >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> your database completely, you can delete entries in that table as well. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Regarding your point 2, the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> imaging pipeline can create the visit in the session table as long as the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit label is present in the Visit_Windows table (which means the visit >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> label stored in the PatientName is a valid visit label). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> However, in your prod file, if >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the variable $subjectID{'createVisitLabel'} is set to 1 for candidates, the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit label should be created in the Visit_Windows table I believe. Here >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> is the line of the prod file you would need to change >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> . >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> In general, we prefer populating >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the Visit_Windows table and set the $subjectID{'createVisitLabel'} to 0 for >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> candidate data to avoid insertion of badly labelled MRI data that are >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> complex to relabel. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Finally, regarding the candidate >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> creation, if you execute the following steps, the pipeline should be able >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> to create candidates: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - set in the Imaging Pipeline >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> section of the config module the config setting "Upload creation of >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> candidates" to Yes >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - manually transfer the scans to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the LORIS server instead of uploading it via the imaging browser >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - run batch_imaging_upload.pl as >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> you did until now. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helps! >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> On Wed, Jul 24, 2019 at 8:47 AM >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> About my second question i >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> replaced the name of the patient in the .dcm files and now i am getting an >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> error that the visit label does not exist. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I thought it was supposed to be >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> automatically created. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> "Done adding archive info into >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> database >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -globLocation -profile prod >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive//DCM_2012-12-05_ImagingUpload-15-42-yUwQQV.tar >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -verbose >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> md5sum >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive/DCM_2012-12-05_ImagingUpload-15-42-yUwQQV.tar >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> candidate id 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> => No Visit labelVisit label >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> does not exist >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Set centerID = 1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Number of MINC files that will >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> be considered for inserting into the database: 1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> log dir is /logs and log file is >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /logs/TarLoad-15-42-L6pocU.log >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> candidate id 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> => No Visit label >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Cleaning up temp files: rm -rf >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-15-42-J2rQms/ImagingUpload-15-42-yUwQQV*" >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 24 ???? 2019 ???? 3:38 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ?.?., ?/? Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 1) What are the records in the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> session table? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 2) I tried to upload a >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> non-phantom file like this >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> input_file.txt: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/incoming/DCC0000_258024_V1.tar.gz >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> N DCC0000_258024_V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Terminal: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ./batch_uploads_imageuploader >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -profile prod < ~/Desktop/input.txt > log.txt >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and i get the following error >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in the log.txt file >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> "Running now the following >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> command: /data/loris/data/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -profile prod -upload_id 7 /data/incoming/DCC0000_258024_V1.tar.gz -verbose >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> find -path >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> \/tmp\/ImagingUpload\-14\-56\-FeLCB4 -name '__MACOSX' -delete >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Spool message is: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The PatientName read from the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DICOM header does not start with DCC0000_258024_V1 from the mri_upload table >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> " >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and the spool message is >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> repeated for each .dcm file. Should i preprocess every .dcm file and change >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the PatientName to "DCC0000_258024_V1"? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 3) As far as it concerns the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> candidate profile i have to create a new one each time before i try to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> upload a file? Is there already a way to create a candidate profile and get >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the DCCID and PSCID without the user interface? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 18 ???? 2019 ???? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 5:00 ?.?., ?/? Cecile Madjar < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> cecile.madjar at mcin.ca> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> See answers to your questions >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> below. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> About the 1st case we had a >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> dicom with a blank studyUID, maybe someone accidentally removed it. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> That is strange. Something >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> must have been done to the DICOM files. I have never seen a study with no >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> StudyUID out of the scanner. Usually, you need to manually erase it with >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> some tool. However, DICOMs never cease to surprise me... >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Some other questions: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 1) What are the steps to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> remove all of my patients and uploads?: because i want to try to reupload >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> all the testing dicoms we had with a clean database. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Release 21.0 of LORIS-MRI will >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> offer a script to remove all the entries and files specific to an upload. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> However, this release is not yet out. Hopefully in the next few weeks. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> In the meantime, since your >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> case is particular and that you just want to start with a clean database, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the following deletes should work (hopefully I won't forget any tables): >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from mri_violations_log; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> mri_protocol_violated_scans; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from MRICandidateErrors; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from parameter_file; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from files_qcstatus; # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> (if you played with the QC part of the imaging browser for testing) >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> feedback_mri_comments; # (if you played with the QC part of the imaging >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> browser for testing) >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from tarchive_series; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from tarchive_files; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from mri_upload; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from tarchive; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from mri_scanner; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from candidate where >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID="scanner"; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I don't know if you want to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> also delete entries in the session and candidate table too? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 2) We do not need to create >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the profile of a patient ( are the patients stored in the candidate table? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> because i can't see the ghosts ), because will it automatically be created >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> when importing a dicom? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I am not sure I understand >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> fully this question. All candidates are stored in the candidate table. The >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> phantom scans however are attached to a scanner candidate depending on >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> where the scan happened. It is a bit of a weird concept that we have to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> redesign eventually but never got a chance to get to it. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hopefully this answered your >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> question, otherwise, don't hesitate to let me know. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 3) What is the difference >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> between uploading a dicom as phantom instead of importing as >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCCID_DCCID_VisitLabel? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> When you upload the scan as >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID_DCCID_VisitLabel, there is a check that makes sure the candidate IDs >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and visit label are valid at the time of upload. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> When you upload a scan as >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> phantom, it expects that the DICOM field PatientName and uploaded filename >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> contains the string "phantom". We enforced this behaviour on the imaging >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> uploader side in recent releases but I can't remember which one. Probably >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the upcoming 21.0 release. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> All those verifications might >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> seem cumbersome but they are here to ensure that the files inserted are all >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> valid and labelled properly as it is a bit messy to have to delete files >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> that were wrongly labelled. At least, the delete script present in release >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 21.0 will make this process easier but it is still good practice to verify >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> those things. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> With pleasure. Hopefully the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> answers to your questions will be helpful. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PS: loris-dev mailing list: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> you will find the initial answer I gave Sotirios below. I forgot to cc the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> loris-dev in my earlier reply... >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 16 ???? 2019 ???? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 12:02 ?.?., ?/? Cecile Madjar < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> cecile.madjar at mcin.ca> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Dear Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you for reaching out. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Since your email was already organized in points, I will reply directly >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> below your questions below. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 1) What do we do when the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> StudyUID is blank on the header? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/minor/docs/AppendixA-Troubleshooting_guideline.md >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> There solution provided at the table 3 does not guide us how to find the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> information ( is possible ). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The StudyUID is the field >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> used in our pipeline at the moment to check whether a DICOM study was >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> already inserted into LORIS with that same StudyUID since it is supposed to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> be unique for every single study. Currently, we do not support insertion of >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DICOM studies if they do not have a StudyUID associated with them. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Is there a specific reason >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> why the StudyUID is blank in the DICOM headers in your DICOM files? Did >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> they go through some processes before upload to LORIS? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 2) When i am about to upload >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> a non-phanton case i need a 'Visit Label'. Is there already a script that >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> can create a new visit label for a specific Candidate, so i can provide it >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> as input afterwards to the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> batch_uploads_imageuploader ( See option 5.1.3 https://github.com/aces/Loris-MRI/blob/minor/docs/05-PipelineLaunchOptions.md ) >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I am not sure if the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> front-end allows for it but if you use batch_uploads_imageuploader, the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> insertion scripts could create the visit label for you. However, it does >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> need to be included in the patient name in order for the script to know >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> which label it should use. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> For example: you upload V02 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> for MTL0123 (DCCID: 456789) but V02 was not yet created for MTL0123; the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> insertion scripts will create a V02 visit for MTL0123 if the PatientName >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> field for the dataset is MTL0123_456789_V02 with Stage marked as "Not >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Started". >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> However, *note that for the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> script to create the visit for the candidate, you have to make sure that >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> all the visit label of your projects were inserted in the Visit_Windows >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> table* (otherwise, the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit will never be created as they were not specified as being part of the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> list of visit label to expect). So in the example above, you should have >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> one row in Visit_Windows with Visit_label="V02" set. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 3) Section 4.3 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/minor/docs/04-Scripts.md >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> What do we do when the folder contains multiple mnc files? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> This is a case by case. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Most of the time, the MINC files that failed insertion into the imaging >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> browser end up in the MRI violation module where you can see what went >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> wrong with the acquisitions not inserted. If you notice that the MINC file >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> should be inserted as a specific protocol, you can force the insertion as >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> explained in section 4.3. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> In your case, I have a >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> feeling that you want to be able to insert MINC files that did not go >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> through the whole pipeline insertion (DICOM archival, then dcm2mnc, then >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> protocol identification, then insertion...). In theory, you could call >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl on any >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> MINC file, provided you have at least the following information: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - path to the MINC file >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - uploadID associated with >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the MINC files or DICOM archive path from which those MINC files were >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> created from >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Then the minc_insertion.pl >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> script will do the subject information and protocol validation etc... >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> If all the MINC files come >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> from the same uploadID or TarchiveID, then you could run a loop in bash >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> calling the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl script >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> like this for files deriving from uploadID=1: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ls /path/to/mnc/folder/* | >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> while read f; do >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl -profile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> prod -uploadID 1 -mincPath $f; done >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helped! >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>>>>>>>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | >>>>>>>>>>>>>>>>>>>>>>>>>>>> MCIN.ca >>>>>>>>>>>>>>>>>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>>>>>>>>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>>>>>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | >>>>>>>>>>>>>>>>>>>>>>>>>> MCIN.ca >>>>>>>>>>>>>>>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>>>>>>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>>>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> -- >>>>>>>>>>>>> >>>>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>>>> >>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>> >>>>>>>>>>> _______________________________________________ >>>>>>>>>> Loris-dev mailing list >>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> -- >>>>>>>>> Shen Wang >>>>>>>>> Loris Developer >>>>>>>>> Montreal Neurological Institute >>>>>>>>> McGill University >>>>>>>>> >>>>>>>>> >>>>> >>>>> -- >>>>> Shen Wang >>>>> Loris Developer >>>>> Montreal Neurological Institute >>>>> McGill University >>>>> >>>>> -- >>>> Shen Wang >>>> Loris Developer >>>> Montreal Neurological Institute >>>> McGill University >>>> >>>> _______________________________________________ >>>> Loris-dev mailing list >>>> Loris-dev at bic.mni.mcgill.ca >>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>> >>> >>> >>> -- >>> >>> christine.rogers at mcgill.ca >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>> Montreal Neurological Institute >>> McGill University | Montreal | Canada >>> >> -- Shen Wang Loris Developer Montreal Neurological Institute McGill University -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: ???? 2019-08-13 19.21.15.png Type: image/png Size: 508603 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: ???? 2019-08-14 18.22.08.png Type: image/png Size: 227099 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: ???? 2019-08-14 18.25.14.png Type: image/png Size: 75078 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: ???? 2019-08-14 18.25.24.png Type: image/png Size: 136227 bytes Desc: not available URL: From sotirisnik at gmail.com Wed Aug 14 18:52:32 2019 From: sotirisnik at gmail.com (Sotirios Nikoloutsopoulos) Date: Thu, 15 Aug 2019 01:52:32 +0300 Subject: [Loris-dev] Upgrading to Loris 21 - new make file In-Reply-To: References: Message-ID: Hi Shen, That didn't work either. Also i had removed the git files because i was getting this error when i used make: "git describe --tags --always > VERSION fatal: Not a git repository (or any of the parent directories): .git Makefile:8: recipe for target 'VERSION' failed make: *** [VERSION] Error 128" Thanks ???? ???, 15 ??? 2019 ???? 1:36 ?.?., ?/? Shen Wang ??????: > Hi,Sotirios > In your special situation, there is a temporary fix. > step 1. sudo git stash > step 2. open webpack.config.js file > remove line 75 use: ['babel-loader', 'eslint-loader'], > save it. > step 3. sudo make > > I hope this could help you to compile the js files. > > > > On Wed, 14 Aug 2019 at 08:28, Sotirios Nikoloutsopoulos < > sotirisnik at gmail.com> wrote: > >> I forgot to mention that i had already moved my previous config file and >> re-executed the installation script. >> >> ???? ???, 14 ??? 2019 ???? 3:26 ?.?., ?/? Sotirios Nikoloutsopoulos < >> sotirisnik at gmail.com> ??????: >> >>> Hi, >>> >>> Step 1 worked and the indentation errors were fixed. About step2 i added >>> all of these( there are more to include in the list) these to .eslintignore >>> which were reported to fail at being built, but they still appear on the >>> errors at the make_output file. >>> >>> /jsx/DynamicDataTable.js >>> /jsx/StaticDataTable.js >>> /jsx/MultiSelectDropdown.js >>> /jsx/Breadcrumbs.js >>> /jsx/Form.js >>> /jsx/Markdown.js >>> /modules/media/jsx/mediaIndex.js >>> /modules/issue_tracker/jsx/issueTrackerIndex.js >>> /modules/issue_tracker/jsx/index.js >>> /modules/candidate_parameters/jsx/CandidateParameters.js >>> /modules/configuration/jsx/SubprojectRelations.js >>> /modules/conflict_resolver/jsx/conflictResolverIndex.js >>> /modules/conflict_resolver/jsx/resolvedConflictsIndex.js >>> /modules/bvl_feedback/jsx/react.behavioural_feedback_panel.js >>> /modules/dataquery/jsx/react.tabs.js >>> /modules/document_repository/jsx/docIndex.js >>> /modules/instrument_builder/jsx/react.instrument_builder.js >>> /modules/imaging_uploader/jsx/index.js >>> /modules/datadict/jsx/dataDictIndex.js >>> /modules/bvl_feedback/jsx/react.behavioural_feedback_panel.js >>> /modules/new_profile/jsx/NewProfileIndex.js >>> /modules/examiner/jsx/examinerIndex.js >>> /modules/configuration/jsx/SubprojectRelations.js >>> /modules/data_team_helper/jsx/behavioural_qc_module.js >>> /modules/acknowledgements/jsx/acknowledgementsIndex.js >>> /modules/candidate_parameters/jsx/CandidateParameters.js >>> /modules/imaging_browser/jsx/ImagePanel.js >>> /modules/mri_violations/jsx/mri_protocol_violations_columnFormatter.js >>> >>> /modules/mri_violations/jsx/mri_protocol_check_violations_columnFormatter.js >>> /modules/genomic_browser/jsx/profileColumnFormatter.js >>> /modules/dataquery/jsx/react.tabs.js >>> /jsx/MultiSelectDropdown.js >>> /modules/mri_violations/jsx/columnFormatterUnresolved.js >>> /modules/dataquery/jsx/react.sidebar.js >>> /modules/dataquery/jsx/react.fieldselector.js >>> /modules/quality_control/jsx/qualityControlIndex.js >>> /modules/dataquery/jsx/react.paginator.js >>> /modules/instrument_builder/jsx/react.questions.js >>> /modules/dataquery/jsx/react.filterBuilder.js >>> /modules/conflict_resolver/jsx/conflictResolverIndex.js >>> /jsx/PaginationLinks.js >>> /modules/conflict_resolver/jsx/resolvedConflictsIndex.js >>> /modules/dataquery/jsx/react.app.js >>> /modules/candidate_list/jsx/onLoad.js >>> /jsx/Form.js >>> /modules/publication/jsx/publicationIndex.js >>> /modules/server_processes_manager/jsx/server_processes_managerIndex.js >>> /modules/imaging_browser/jsx/imagingBrowserIndex.js >>> /modules/issue_tracker/jsx/issueTrackerIndex.js >>> /modules/survey_accounts/jsx/surveyAccountsIndex.js >>> /modules/data_integrity_flag/jsx/dataIntegrityFlagIndex.js >>> /modules/instrument_manager/jsx/instrumentManagerIndex.js >>> /modules/media/jsx/mediaIndex.js >>> /modules/user_accounts/jsx/userAccountsIndex.js >>> /modules/help_editor/jsx/help_editor.js >>> /modules/dicom_archive/jsx/dicom_archive.js >>> /modules/mri_violations/jsx/columnFormatter.js >>> /modules/brainbrowser/jsx/Brainbrowser.js >>> /node_modules/babel-loader/lib/index.js >>> /modules/document_repository/jsx/editFormIndex.js >>> >>> Thanks >>> >>> ???? ???, 14 ??? 2019 ???? 7:50 ?.?., ?/? Christine Rogers, Ms. < >>> christine.rogers at mcgill.ca> ??????: >>> >>>> Hi Shen and Sotirios - just a note, >>>> >>>> For the 21 release, it's best to run the install script without sudoing >>>> it. >>>> >>>> (Shen, I believe we discovered a minor issue with the sudo last week >>>> #5008) >>>> >>>> Best, >>>> Christine >>>> >>>> On Tue, Aug 13, 2019 at 9:22 PM Shen Wang >>>> wrote: >>>> >>>>> Does it work? If still doesn?t work, try to remove project/config.xml >>>>> file. Do sudo ./install.sh again. To reinstall Loris again. >>>>> >>>>> >>>>> Shen Wang ?2019?8?13? ????9:02??? >>>>> >>>>>> Hi Sotirios, >>>>>> step 1: >>>>>> sudo ./node_modules/.bin/eslint --fix /var/www/loris >>>>>> step 2: >>>>>> put the rest error files under this line [# Ignore until ESLint is >>>>>> run] in the .eslintignore file. >>>>>> step 3: >>>>>> sudo make >>>>>> >>>>>> >>>>>> >>>>>> On Tue, 13 Aug 2019 at 20:34, Sotirios Nikoloutsopoulos < >>>>>> sotirisnik at gmail.com> wrote: >>>>>> >>>>>>> I did the modifications, still there are errors. >>>>>>> Thanks >>>>>>> >>>>>>> >>>>>>> ???? ???, 14 ??? 2019 ???? 3:22 ?.?., ?/? Shen Wang < >>>>>>> wangshen.mcin at gmail.com> ??????: >>>>>>> >>>>>>>> Hi Sotirios, >>>>>>>> I saw your output file, the config issue is gone. >>>>>>>> you can use [sudo npm run lintfix:javascript ] to fix these indent >>>>>>>> issues. >>>>>>>> If it still has errors. >>>>>>>> Then try modify this file .eslintignore >>>>>>>> with this >>>>>>>> >>>>>>>> # Ignore until ESLint is run >>>>>>>> >>>>>>>> modules/* >>>>>>>> >>>>>>>> modules/dataquery/ >>>>>>>> >>>>>>>> node_modules/* >>>>>>>> >>>>>>>> htdocs/js/components/* >>>>>>>> >>>>>>>> jsx/* >>>>>>>> >>>>>>>> >>>>>>>> # Ignore external libs >>>>>>>> >>>>>>>> htdocs/js/flot/* >>>>>>>> >>>>>>>> htdocs/js/jquery/* >>>>>>>> >>>>>>>> htdocs/js/jszip/* >>>>>>>> >>>>>>>> htdocs/js/modernizr/* >>>>>>>> >>>>>>>> htdocs/js/modules/* >>>>>>>> >>>>>>>> htdocs/js/react/* >>>>>>>> >>>>>>>> htdocs/js/shims/* >>>>>>>> >>>>>>>> htdocs/js/c3.min.js >>>>>>>> >>>>>>>> htdocs/js/d3.min.js >>>>>>>> >>>>>>>> htdocs/js/FileSaver.min.js >>>>>>>> >>>>>>>> >>>>>>>> then do sudo make. >>>>>>>> It should work. >>>>>>>> Regards >>>>>>>> Shen >>>>>>>> >>>>>>>> >>>>>>>> Sotirios Nikoloutsopoulos ?2019?8?13? >>>>>>>> ????7:54??? >>>>>>>> >>>>>>>>> No, it didn't work, i also tried space/tabs because most of the >>>>>>>>> errors where about indentation, also there are some errors about React. >>>>>>>>> >>>>>>>>> Thanks >>>>>>>>> >>>>>>>>> lorisadmin at hbp:/var/www/loris$ sudo ./node_modules/.bin/eslint >>>>>>>>> --init >>>>>>>>> ? How would you like to configure ESLint? Answer questions about >>>>>>>>> your style >>>>>>>>> ? Which version of ECMAScript do you use? ES2015 >>>>>>>>> ? Are you using ES6 modules? Yes >>>>>>>>> ? Where will your code run? Browser >>>>>>>>> ? Do you use CommonJS? Yes >>>>>>>>> ? Do you use JSX? Yes >>>>>>>>> ? Do you use React? Yes >>>>>>>>> ? What style of indentation do you use? Spaces >>>>>>>>> ? What quotes do you use for strings? Single >>>>>>>>> ? What line endings do you use? Unix >>>>>>>>> ? Do you require semicolons? Yes >>>>>>>>> ? What format do you want your config file to be in? JSON >>>>>>>>> The config that you've selected requires the following >>>>>>>>> dependencies: >>>>>>>>> >>>>>>>>> eslint-plugin-react at latest >>>>>>>>> Successfully created .eslintrc.json file in /var/www/loris >>>>>>>>> >>>>>>>>> lorisadmin at hbp:/var/www/loris$ sudo make > sudo_make_output >>>>>>>>> npm WARN The package prop-types is included as both a dev and >>>>>>>>> production dependency. >>>>>>>>> npm WARN optional SKIPPING OPTIONAL DEPENDENCY: fsevents at 1.2.4 >>>>>>>>> (node_modules/fsevents): >>>>>>>>> npm WARN notsup SKIPPING OPTIONAL DEPENDENCY: Unsupported platform >>>>>>>>> for fsevents at 1.2.4: wanted {"os":"darwin","arch":"any"} (current: >>>>>>>>> {"os":"linux","arch":"x64"}) >>>>>>>>> >>>>>>>>> npm ERR! code ELIFECYCLE >>>>>>>>> npm ERR! errno 2 >>>>>>>>> npm ERR! loris at 1.0.0 compile: `webpack` >>>>>>>>> npm ERR! Exit status 2 >>>>>>>>> npm ERR! >>>>>>>>> npm ERR! Failed at the loris at 1.0.0 compile script. >>>>>>>>> npm ERR! This is probably not a problem with npm. There is likely >>>>>>>>> additional logging output above. >>>>>>>>> >>>>>>>>> npm ERR! A complete log of this run can be found in: >>>>>>>>> npm ERR! >>>>>>>>> /home/lorisadmin/.npm/_logs/2019-08-13T23_40_58_841Z-debug.log >>>>>>>>> >>>>>>>>> ???? ???, 14 ??? 2019 ???? 2:29 ?.?., ?/? Shen Wang < >>>>>>>>> wangshen.mcin at gmail.com> ??????: >>>>>>>>> >>>>>>>>>> Hi Sotirios, >>>>>>>>>> When you do make command, please make sure with sudo at the >>>>>>>>>> beginning. [sudo make] >>>>>>>>>> If it still doesn't work for you. >>>>>>>>>> Then try the solutions below. >>>>>>>>>> solution 1: >>>>>>>>>> [image: ???? 2019-08-13 19.21.15.png] >>>>>>>>>> Regards >>>>>>>>>> Shen >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> On Tue, 13 Aug 2019 at 17:22, Sotirios Nikoloutsopoulos < >>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>> >>>>>>>>>>> I think that the files exists although i redownloaded the >>>>>>>>>>> eslintrc.json i checked others files that had similar errors. >>>>>>>>>>> >>>>>>>>>>> lorisadmin at hbp:/var/www/loris$ ls -l >>>>>>>>>>> ./node_modules/eslint-loader/index.js >>>>>>>>>>> -rw-rw-r-- 1 lorisadmin lorisadmin 6463 ??? 26 1985 >>>>>>>>>>> ./node_modules/eslint-loader/index.js >>>>>>>>>>> >>>>>>>>>>> lorisadmin at hbp:/var/www/loris$ ls -l .eslintrc.json >>>>>>>>>>> -rw-rw-r-- 1 lorisadmin lorisadmin 84530 ??? 14 00:04 >>>>>>>>>>> .eslintrc.json >>>>>>>>>>> >>>>>>>>>>> Maybe this can help >>>>>>>>>>> >>>>>>>>>>> Module build failed (from ./node_modules/eslint-loader/index.js): >>>>>>>>>>> SyntaxError: Cannot read config file: >>>>>>>>>>> /var/www/loris/.eslintrc.json >>>>>>>>>>> Error: Unexpected token < in JSON at position 6 >>>>>>>>>>> at JSON.parse () >>>>>>>>>>> at loadJSONConfigFile >>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config/config-file.js:114:21) >>>>>>>>>>> at loadConfigFile >>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config/config-file.js:230:26) >>>>>>>>>>> at loadFromDisk >>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config/config-file.js:500:18) >>>>>>>>>>> at Object.load >>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config/config-file.js:564:20) >>>>>>>>>>> at Config.getLocalConfigHierarchy >>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config.js:227:44) >>>>>>>>>>> at Config.getConfigHierarchy >>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config.js:179:43) >>>>>>>>>>> at Config.getConfigVector >>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config.js:286:21) >>>>>>>>>>> at Config.getConfig >>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config.js:329:29) >>>>>>>>>>> at processText >>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/cli-engine.js:162:33) >>>>>>>>>>> at CLIEngine.executeOnText >>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/cli-engine.js:596:17) >>>>>>>>>>> at lint >>>>>>>>>>> (/var/www/loris/node_modules/eslint-loader/index.js:237:17) >>>>>>>>>>> at Object.module.exports >>>>>>>>>>> (/var/www/loris/node_modules/eslint-loader/index.js:232:21) >>>>>>>>>>> >>>>>>>>>>> ERROR in ./modules/imaging_uploader/jsx/index.js >>>>>>>>>>> Module build failed (from >>>>>>>>>>> ./node_modules/eslint-loader/index.js): >>>>>>>>>>> SyntaxError: Cannot read config file: >>>>>>>>>>> /var/www/loris/.eslintrc.json >>>>>>>>>>> Error: Unexpected token < in JSON at position 6 >>>>>>>>>>> at JSON.parse () >>>>>>>>>>> at loadJSONConfigFile >>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config/config-file.js:114:21) >>>>>>>>>>> at loadConfigFile >>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config/config-file.js:230:26) >>>>>>>>>>> at loadFromDisk >>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config/config-file.js:500:18) >>>>>>>>>>> at Object.load >>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config/config-file.js:564:20) >>>>>>>>>>> at Config.getLocalConfigHierarchy >>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config.js:227:44) >>>>>>>>>>> at Config.getConfigHierarchy >>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config.js:179:43) >>>>>>>>>>> at Config.getConfigVector >>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config.js:286:21) >>>>>>>>>>> at Config.getConfig >>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config.js:329:29) >>>>>>>>>>> at processText >>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/cli-engine.js:162:33) >>>>>>>>>>> at CLIEngine.executeOnText >>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/cli-engine.js:596:17) >>>>>>>>>>> at lint >>>>>>>>>>> (/var/www/loris/node_modules/eslint-loader/index.js:237:17) >>>>>>>>>>> at Object.module.exports >>>>>>>>>>> (/var/www/loris/node_modules/eslint-loader/index.js:232:21) >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> ???? ???, 13 ??? 2019 ???? 11:52 ?.?., ?/? John Saigle < >>>>>>>>>>> john.saigle at mcin.ca> ??????: >>>>>>>>>>> >>>>>>>>>>>> HI Sotirios, >>>>>>>>>>>> >>>>>>>>>>>> The make_output.txt file shows webpack failing because it can't >>>>>>>>>>>> find the ESLint config file. >>>>>>>>>>>> >>>>>>>>>>>> Can you confirm whether the file `.eslintrc.json` exists within >>>>>>>>>>>> your loris root directory (usually `/var/www/loris/`)? When I delete my >>>>>>>>>>>> file I get the same errors as you. >>>>>>>>>>>> >>>>>>>>>>>> If you find that it's missing, you can make a local copy with >>>>>>>>>>>> the contents found here: >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> https://github.com/aces/Loris/blob/e26a6ad49a73fcffef0cd73bb600c4d17b200b62/.eslintrc.json >>>>>>>>>>>> >>>>>>>>>>>> Once you know it exists, try running `make` again. >>>>>>>>>>>> >>>>>>>>>>>> Let us know if that moves you forward. >>>>>>>>>>>> >>>>>>>>>>>> Best, >>>>>>>>>>>> John >>>>>>>>>>>> >>>>>>>>>>>> On Tue, Aug 13, 2019 at 2:21 PM Sotirios Nikoloutsopoulos < >>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>> >>>>>>>>>>>>> Hi, >>>>>>>>>>>>> I executed the commands for the node and now i am get the >>>>>>>>>>>>> followings: >>>>>>>>>>>>> >>>>>>>>>>>>> lorisadmin at hbp:/var/www/loris$ make > ~/make_output >>>>>>>>>>>>> npm WARN The package prop-types is included as both a dev and >>>>>>>>>>>>> production dependency. >>>>>>>>>>>>> npm WARN optional SKIPPING OPTIONAL DEPENDENCY: fsevents at 1.2.4 >>>>>>>>>>>>> (node_modules/fsevents): >>>>>>>>>>>>> npm WARN notsup SKIPPING OPTIONAL DEPENDENCY: Unsupported >>>>>>>>>>>>> platform for fsevents at 1.2.4: wanted >>>>>>>>>>>>> {"os":"darwin","arch":"any"} (current: {"os":"linux","arch":"x64"}) >>>>>>>>>>>>> >>>>>>>>>>>>> npm ERR! code ELIFECYCLE >>>>>>>>>>>>> npm ERR! errno 2 >>>>>>>>>>>>> npm ERR! loris at 1.0.0 compile: `webpack` >>>>>>>>>>>>> npm ERR! Exit status 2 >>>>>>>>>>>>> npm ERR! >>>>>>>>>>>>> npm ERR! Failed at the loris at 1.0.0 compile script. >>>>>>>>>>>>> npm ERR! This is probably not a problem with npm. There is >>>>>>>>>>>>> likely additional logging output above. >>>>>>>>>>>>> >>>>>>>>>>>>> npm ERR! A complete log of this run can be found in: >>>>>>>>>>>>> npm ERR! >>>>>>>>>>>>> /home/lorisadmin/.npm/_logs/2019-08-13T18_12_05_378Z-debug.log >>>>>>>>>>>>> make: *** [javascript] Error 2 >>>>>>>>>>>>> >>>>>>>>>>>>> Thanks, >>>>>>>>>>>>> Sotirios >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> ???? ???, 12 ??? 2019 ???? 10:19 ?.?., ?/? Christine Rogers, >>>>>>>>>>>>> Ms. ??????: >>>>>>>>>>>>> >>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>> >>>>>>>>>>>>>> We've seen some users installing LORIS 21 or upgrading to 21 >>>>>>>>>>>>>> whose version of node doesn't work well with webpack, due to updated >>>>>>>>>>>>>> packages they're missing. >>>>>>>>>>>>>> If so, update your node : >>>>>>>>>>>>>> >>>>>>>>>>>>>> curl -sL https://deb.nodesource.com/setup_8.x | sudo -E bash - >>>>>>>>>>>>>> sudo apt-get install -y nodejs >>>>>>>>>>>>>> >>>>>>>>>>>>>> Let us know how that goes -- please send us output from the >>>>>>>>>>>>>> same log if any issues. >>>>>>>>>>>>>> Best, >>>>>>>>>>>>>> Christine >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> On Thu, Aug 8, 2019 at 2:38 PM Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>> >>>>>>>>>>>>>>> It's not a disk space issue, as you can see below i have >>>>>>>>>>>>>>> still 74GB available. >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> lorisadmin at hbp:/var/www/loris$ df -h >>>>>>>>>>>>>>> Filesystem Size Used Avail Use% Mounted on >>>>>>>>>>>>>>> udev 2,9G 0 2,9G 0% /dev >>>>>>>>>>>>>>> tmpfs 597M 8,6M 588M 2% /run >>>>>>>>>>>>>>> /dev/sda1 98G 19G 74G 21% / >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> Maybe we have to pass a flag to get into strict mode? as >>>>>>>>>>>>>>> stated "SyntaxError: Block-scoped declarations (let, const, function, >>>>>>>>>>>>>>> class) not yet supported outside strict mode" >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> Thanks, >>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> ???? ???, 8 ??? 2019 ???? 4:32 ?.?., ?/? Dave MacFarlane < >>>>>>>>>>>>>>> dave.macfarlane at mcin.ca> ??????: >>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> It looks like the javascript snippet shown in the error >>>>>>>>>>>>>>>> message when trying to compile the js is truncated. Have you run out of >>>>>>>>>>>>>>>> disk space? >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> On Thu, Aug 8, 2019 at 8:37 AM Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> I runned make and also included the file it reports at the >>>>>>>>>>>>>>>>> end. >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> lorisadmin at hbp:/var/www/loris$ make >>>>>>>>>>>>>>>>> npm install >>>>>>>>>>>>>>>>> npm WARN optional Skipping failed optional dependency >>>>>>>>>>>>>>>>> /chokidar/fsevents: >>>>>>>>>>>>>>>>> npm WARN notsup Not compatible with your operating system >>>>>>>>>>>>>>>>> or architecture: fsevents at 1.2.9 >>>>>>>>>>>>>>>>> npm WARN optional Skipping failed optional dependency >>>>>>>>>>>>>>>>> /watchpack/chokidar/fsevents: >>>>>>>>>>>>>>>>> npm WARN notsup Not compatible with your operating system >>>>>>>>>>>>>>>>> or architecture: fsevents at 1.2.9 >>>>>>>>>>>>>>>>> npm run compile >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> > loris at 1.0.0 compile /var/www/loris >>>>>>>>>>>>>>>>> > webpack >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> /var/www/loris/node_modules/webpack/bin/webpack.js:86 >>>>>>>>>>>>>>>>> let notify = >>>>>>>>>>>>>>>>> ^^^ >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> SyntaxError: Block-scoped declarations (let, const, >>>>>>>>>>>>>>>>> function, class) not yet supported outside strict mode >>>>>>>>>>>>>>>>> at exports.runInThisContext (vm.js:53:16) >>>>>>>>>>>>>>>>> at Module._compile (module.js:374:25) >>>>>>>>>>>>>>>>> at Object.Module._extensions..js (module.js:417:10) >>>>>>>>>>>>>>>>> at Module.load (module.js:344:32) >>>>>>>>>>>>>>>>> at Function.Module._load (module.js:301:12) >>>>>>>>>>>>>>>>> at Function.Module.runMain (module.js:442:10) >>>>>>>>>>>>>>>>> at startup (node.js:136:18) >>>>>>>>>>>>>>>>> at node.js:966:3 >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> npm ERR! Linux 4.15.0-55-generic >>>>>>>>>>>>>>>>> npm ERR! argv "/usr/bin/nodejs" "/usr/bin/npm" "run" >>>>>>>>>>>>>>>>> "compile" >>>>>>>>>>>>>>>>> npm ERR! node v4.2.6 >>>>>>>>>>>>>>>>> npm ERR! npm v3.5.2 >>>>>>>>>>>>>>>>> npm ERR! code ELIFECYCLE >>>>>>>>>>>>>>>>> npm ERR! loris at 1.0.0 compile: `webpack` >>>>>>>>>>>>>>>>> npm ERR! Exit status 1 >>>>>>>>>>>>>>>>> npm ERR! >>>>>>>>>>>>>>>>> npm ERR! Failed at the loris at 1.0.0 compile script >>>>>>>>>>>>>>>>> 'webpack'. >>>>>>>>>>>>>>>>> npm ERR! Make sure you have the latest version of node.js >>>>>>>>>>>>>>>>> and npm installed. >>>>>>>>>>>>>>>>> npm ERR! If you do, this is most likely a problem with the >>>>>>>>>>>>>>>>> loris package, >>>>>>>>>>>>>>>>> npm ERR! not with npm itself. >>>>>>>>>>>>>>>>> npm ERR! Tell the author that this fails on your system: >>>>>>>>>>>>>>>>> npm ERR! webpack >>>>>>>>>>>>>>>>> npm ERR! You can get information on how to open an issue >>>>>>>>>>>>>>>>> for this project with: >>>>>>>>>>>>>>>>> npm ERR! npm bugs loris >>>>>>>>>>>>>>>>> npm ERR! Or if that isn't available, you can get their >>>>>>>>>>>>>>>>> info via: >>>>>>>>>>>>>>>>> npm ERR! npm owner ls loris >>>>>>>>>>>>>>>>> npm ERR! There is likely additional logging output above. >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> npm ERR! Please include the following file with any >>>>>>>>>>>>>>>>> support request: >>>>>>>>>>>>>>>>> npm ERR! /var/www/loris/npm-debug.log >>>>>>>>>>>>>>>>> Makefile:14: recipe for target 'javascript' failed >>>>>>>>>>>>>>>>> make: *** [javascript] Error 1 >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Thanks, >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> ???? ???, 7 ??? 2019 ???? 5:41 ?.?., ?/? Christine Rogers, >>>>>>>>>>>>>>>>> Ms. ??????: >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Thanks, have you tried all of these steps? >>>>>>>>>>>>>>>>>> - clear your browser cache (and refresh a few times) >>>>>>>>>>>>>>>>>> - delete any files in your smarty/templates_c directory >>>>>>>>>>>>>>>>>> (this will clear the template cache - do Not touch smarty/templates/) >>>>>>>>>>>>>>>>>> - run `make` (per the 21 release notes, this replaces the >>>>>>>>>>>>>>>>>> composer commands used in previous releases to update your dependencies) >>>>>>>>>>>>>>>>>> - restart apache (doesn't hurt) >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Let us know how it goes -- let us know what difference >>>>>>>>>>>>>>>>>> you see after, with your logs. A >>>>>>>>>>>>>>>>>> lso please send us your Config path settings (see these >>>>>>>>>>>>>>>>>> Troubleshooting Queries >>>>>>>>>>>>>>>>>> ) >>>>>>>>>>>>>>>>>> if you're still seeing front-end issues. >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Thanks, >>>>>>>>>>>>>>>>>> Christine >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> On Wed, Aug 7, 2019 at 8:02 AM Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> lorisadmin at hbp:/var/www/loris$ sudo cat >>>>>>>>>>>>>>>>>>> /var/log/apache2/error.log >>>>>>>>>>>>>>>>>>> [Wed Aug 07 07:35:02.422501 2019] [mpm_prefork:notice] >>>>>>>>>>>>>>>>>>> [pid 1267] AH00163: Apache/2.4.18 (Ubuntu) OpenSSL/1.0.2g configured -- >>>>>>>>>>>>>>>>>>> resuming normal operations >>>>>>>>>>>>>>>>>>> [Wed Aug 07 07:35:02.422514 2019] [core:notice] [pid >>>>>>>>>>>>>>>>>>> 1267] AH00094: Command line: '/usr/sbin/apache2' >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> And as for the access.log the content are empty >>>>>>>>>>>>>>>>>>> lorisadmin at hbp:/var/www/loris$ sudo ls -l >>>>>>>>>>>>>>>>>>> /var/log/apache2/access.log >>>>>>>>>>>>>>>>>>> lorisadmin at hbp:/var/www/loris$ sudo ls -l >>>>>>>>>>>>>>>>>>> /var/log/apache2/access.log >>>>>>>>>>>>>>>>>>> -rw-r----- 1 root adm 0 ???? 28 14:09 >>>>>>>>>>>>>>>>>>> /var/log/apache2/access.log >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Also i noticed a loris_access.log. >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> The only non-blank pages are: >>>>>>>>>>>>>>>>>>> mri_violations, dataquery does not exist at all, >>>>>>>>>>>>>>>>>>> statistics, data_team_helper, genomic_browser, configuration and >>>>>>>>>>>>>>>>>>> server_processes_manager/ prints "Required configuration settings for >>>>>>>>>>>>>>>>>>> Server Processes Manager are missing. Cannot continue." >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Thanks, >>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> ???? ???, 6 ??? 2019 ???? 10:13 ?.?., ?/? Christine >>>>>>>>>>>>>>>>>>> Rogers, Ms. ??????: >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Hi Sotirios and LORIS community -- >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> When upgrading to brand-new release 21 -- just a >>>>>>>>>>>>>>>>>>>> reminder to follow the release notes and run the new >>>>>>>>>>>>>>>>>>>> *make* file to update your dependencies (instead of >>>>>>>>>>>>>>>>>>>> using *composer* commands). >>>>>>>>>>>>>>>>>>>> We've also updated the Wiki page >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> to clarify that the release notes for each version will tell you what to >>>>>>>>>>>>>>>>>>>> run. >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> If your current version is not the last release (20.3), >>>>>>>>>>>>>>>>>>>> it's still important to upgrade to each minor release increment (e.g. 20.2, >>>>>>>>>>>>>>>>>>>> 20.3) before making the leap to 21.0. >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> If you're getting blank pages, post-upgrade -- Try >>>>>>>>>>>>>>>>>>>> clearing your cache. >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Got questions or feedback e.g. on the Release Notes? >>>>>>>>>>>>>>>>>>>> please don't hesitate to let us know. >>>>>>>>>>>>>>>>>>>> Thanks, >>>>>>>>>>>>>>>>>>>> Christine >>>>>>>>>>>>>>>>>>>> The LORIS team >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> On Tue, Aug 6, 2019 at 10:09 AM Christine Rogers, Ms. < >>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca> wrote: >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>> Could you also let us know -- on which pages is >>>>>>>>>>>>>>>>>>>>> content visible, and on which pages/modules is content not visible for you? >>>>>>>>>>>>>>>>>>>>> Thanks, >>>>>>>>>>>>>>>>>>>>> Christine >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> On Tue, Aug 6, 2019 at 9:54 AM Christine Rogers, Ms. < >>>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca> wrote: >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> Thanks Sotirios, >>>>>>>>>>>>>>>>>>>>>> That's good to know. It sounds like you've checked >>>>>>>>>>>>>>>>>>>>>> that your /var/www/loris/project/config.xml file get populated properly. >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> Please send us the last few errors you're seeing in >>>>>>>>>>>>>>>>>>>>>> your apache error log file, and your config paths and we can see what's >>>>>>>>>>>>>>>>>>>>>> happening with your front end -- >>>>>>>>>>>>>>>>>>>>>> Run these Troubleshooting Queries >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> to get your config path settings, given your front end is not displaying >>>>>>>>>>>>>>>>>>>>>> fully. >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> The Loris-MRI repo >>>>>>>>>>>>>>>>>>>>>> 21 >>>>>>>>>>>>>>>>>>>>>> install/upgrade would then be your next steps. >>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>> Christine >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> On Tue, Aug 6, 2019 at 7:53 AM Sotirios >>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos wrote: >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> I am using a VM. What i did was: >>>>>>>>>>>>>>>>>>>>>>> 1) Download the files from >>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris and replace them to >>>>>>>>>>>>>>>>>>>>>>> my existing /vaw/www/loris folder. >>>>>>>>>>>>>>>>>>>>>>> 2) Execute the composer install --no-dev and then composer >>>>>>>>>>>>>>>>>>>>>>> dump-autoload as mentioned here >>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris/wiki/Updating-your-LORIS >>>>>>>>>>>>>>>>>>>>>>> . >>>>>>>>>>>>>>>>>>>>>>> 3) Execute install.sh from /var/www/loris/tools and >>>>>>>>>>>>>>>>>>>>>>> because LORIS already existed i moved a .config file, then re-executed the >>>>>>>>>>>>>>>>>>>>>>> install.sh successfully >>>>>>>>>>>>>>>>>>>>>>> 4 ) As for the database, i dropped the schema and i >>>>>>>>>>>>>>>>>>>>>>> executed the installdb.php >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> ???? ???, 5 ??? 2019 ???? 5:22 ?.?., ?/? Christine >>>>>>>>>>>>>>>>>>>>>>> Rogers, Ms. ??????: >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> Hi Sotorios, >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> Thanks - when you re-installed did you start on a >>>>>>>>>>>>>>>>>>>>>>>> fresh root path / VM or might some of your old system setting still apply? >>>>>>>>>>>>>>>>>>>>>>>> (And if you did any steps similar to an upgrade, >>>>>>>>>>>>>>>>>>>>>>>> did you follow the Upgrade steps in the Release Notes, from both repos?) >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> About the TR_range column - it was recently split (MRI >>>>>>>>>>>>>>>>>>>>>>>> pr339 ) split >>>>>>>>>>>>>>>>>>>>>>>> into TR_min and _max columns. Given the code was trying to query TR_range >>>>>>>>>>>>>>>>>>>>>>>> which does not exist in your mri_protocol table, double-check which version >>>>>>>>>>>>>>>>>>>>>>>> of the Loris repo (tables) and the Loris-MRI repo (code) you have installed >>>>>>>>>>>>>>>>>>>>>>>> to ensure they match. >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> Christine >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> On Mon, Aug 5, 2019 at 9:06 AM Sotirios >>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos wrote: >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> I reinstalled LORIS to 21 version and now the >>>>>>>>>>>>>>>>>>>>>>>>> content is not visible at all at most pages. >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 5 ??? 2019 ???? 3:19 ?.?., ?/? Sotirios >>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos ??????: >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> Is it easy to upgrade to Loris 21? Also the >>>>>>>>>>>>>>>>>>>>>>>>>> following fails because the line 1985 of NeuroDB/MRIProcessingUtility.pm >>>>>>>>>>>>>>>>>>>>>>>>>> query mri_protocol which doesn't have TR_range >>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris/blob/21.0-release/SQL/0000-00-00-schema.sql#L556 >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> lorisadmin at hbp:/data/loris/bin/mri$ >>>>>>>>>>>>>>>>>>>>>>>>>> ./batch_uploads_imageuploader -profile prod < ~/Desktop/input.txt > log.txt >>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $_ in pattern match >>>>>>>>>>>>>>>>>>>>>>>>>> (m//) at ./batch_uploads_imageuploader line 147. >>>>>>>>>>>>>>>>>>>>>>>>>> base is DCC0000_258024_V1 >>>>>>>>>>>>>>>>>>>>>>>>>> path is /data/incoming/ >>>>>>>>>>>>>>>>>>>>>>>>>> type is .tar.gz >>>>>>>>>>>>>>>>>>>>>>>>>> fullpath is >>>>>>>>>>>>>>>>>>>>>>>>>> /data/incoming/DCC0000_258024_V1.tar.gz >>>>>>>>>>>>>>>>>>>>>>>>>> DBD::mysql::st execute failed: Unknown column >>>>>>>>>>>>>>>>>>>>>>>>>> 'TR_range' in 'where clause' at >>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line 1985. >>>>>>>>>>>>>>>>>>>>>>>>>> DBD::mysql::st fetchrow_array failed: fetch() >>>>>>>>>>>>>>>>>>>>>>>>>> without execute() at >>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line 1986. >>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $count_mri_protocol in >>>>>>>>>>>>>>>>>>>>>>>>>> numeric gt (>) at >>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line 1995. >>>>>>>>>>>>>>>>>>>>>>>>>> DBD::mysql::st execute failed: Unknown column >>>>>>>>>>>>>>>>>>>>>>>>>> 'TR_range' in 'field list' at >>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 562. >>>>>>>>>>>>>>>>>>>>>>>>>> Can't exec "mail": No such file or directory at >>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 721. >>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 722. >>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 723. >>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 724. >>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 725. >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> No Mincs inserted >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> Thanks, >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 3 ??? 2019 ???? 1:08 ?.?., ?/? >>>>>>>>>>>>>>>>>>>>>>>>>> Christine Rogers, Ms. >>>>>>>>>>>>>>>>>>>>>>>>>> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> First, just a note: we've released LORIS 21 >>>>>>>>>>>>>>>>>>>>>>>>>>> this week with some major new features and cleanup -- especially if you are >>>>>>>>>>>>>>>>>>>>>>>>>>> early in your setup phase, check out the Release notes for both the >>>>>>>>>>>>>>>>>>>>>>>>>>> LORIS >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> and Loris-MRI >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> repos. >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> Thanks for your screenshots -- your empty >>>>>>>>>>>>>>>>>>>>>>>>>>> mri_protocol table should be at the root of these issues : >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> The mri_protocol table must be populated >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> in order for your scans to be registered in LORIS -- it serves as a >>>>>>>>>>>>>>>>>>>>>>>>>>> whitelist for the insertion pipeline which filters out scans that aren't >>>>>>>>>>>>>>>>>>>>>>>>>>> identified or matched to scan types in this table. >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> By default, this table is populated with entries >>>>>>>>>>>>>>>>>>>>>>>>>>> for t1, t2, fMRI and DTI (Insert statements for >>>>>>>>>>>>>>>>>>>>>>>>>>> 21 release branch are here >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> ) >>>>>>>>>>>>>>>>>>>>>>>>>>> Feel free to restore our default records and >>>>>>>>>>>>>>>>>>>>>>>>>>> broaden their parameters to match all your scan types. >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> re Defaced, native, selected -- these filter the >>>>>>>>>>>>>>>>>>>>>>>>>>> scans displayed as you move to the next page (View Session), instead of >>>>>>>>>>>>>>>>>>>>>>>>>>> viewing "all types" of scans from a given session : >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> - "defaced" means that a defacing script >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> has masked the subject's face in the volume (for patient privacy) >>>>>>>>>>>>>>>>>>>>>>>>>>> - "native" means that no pre-processing has >>>>>>>>>>>>>>>>>>>>>>>>>>> been performed on the scan (it's raw data), >>>>>>>>>>>>>>>>>>>>>>>>>>> - "selected" will show only volumes that >>>>>>>>>>>>>>>>>>>>>>>>>>> have been QC'd and "selected" as the best of their type -- used to display >>>>>>>>>>>>>>>>>>>>>>>>>>> only the best quality T1 image instead of all T1s acquired in a session, >>>>>>>>>>>>>>>>>>>>>>>>>>> e.g. >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> re QC Comments -- >>>>>>>>>>>>>>>>>>>>>>>>>>> Once you have successfully loaded scans (matched >>>>>>>>>>>>>>>>>>>>>>>>>>> to the mri_protocol table), you'll be able to use the Imaging Browser's >>>>>>>>>>>>>>>>>>>>>>>>>>> View Session subpage to enter/view QC comments on each volume, or for each >>>>>>>>>>>>>>>>>>>>>>>>>>> visit. >>>>>>>>>>>>>>>>>>>>>>>>>>> These are stored directly in the database, and >>>>>>>>>>>>>>>>>>>>>>>>>>> linked to each scan. (Table name: >>>>>>>>>>>>>>>>>>>>>>>>>>> feedback_mri_comments) >>>>>>>>>>>>>>>>>>>>>>>>>>> (Visit-level QC comments are linked to the >>>>>>>>>>>>>>>>>>>>>>>>>>> session.) >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> For a walkthrough of the Imaging setup - please >>>>>>>>>>>>>>>>>>>>>>>>>>> see the Imaging Setup guide >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> - >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> An old LORIS walkthrough video >>>>>>>>>>>>>>>>>>>>>>>>>>> can >>>>>>>>>>>>>>>>>>>>>>>>>>> also walk you through some of the Imaging front-end features, starting at >>>>>>>>>>>>>>>>>>>>>>>>>>> 8:00 >>>>>>>>>>>>>>>>>>>>>>>>>>> LORIS' imaging modules have been updated many >>>>>>>>>>>>>>>>>>>>>>>>>>> times since this video, but the functionality and workflow is similar. >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> Let us know how it goes once you have entries in >>>>>>>>>>>>>>>>>>>>>>>>>>> your mri_protocol table - >>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>> Christine >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> On Fri, Aug 2, 2019 at 7:58 AM Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos wrote: >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Christine, >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> In the candidate_list page i can see this >>>>>>>>>>>>>>>>>>>>>>>>>>>> patient >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> If i press the link under PSCID i get to see >>>>>>>>>>>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> and if i press the link under Scan Done it >>>>>>>>>>>>>>>>>>>>>>>>>>>> redirects me to imaging_browser >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> At the mri_violations page i also see No >>>>>>>>>>>>>>>>>>>>>>>>>>>> results ( neither on resolved / not resolved ). >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> At the imaging_uploader i can see the record >>>>>>>>>>>>>>>>>>>>>>>>>>>> that failed. >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> If i click on the tarchive info i get to see >>>>>>>>>>>>>>>>>>>>>>>>>>>> the Protocol Name which i think is the acquisition we wanted? >>>>>>>>>>>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> Also my mri_protocol table is empty. >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> Furthermore i would like to ask about the >>>>>>>>>>>>>>>>>>>>>>>>>>>> defaced, native, selected. What exactly is native and selected? And where >>>>>>>>>>>>>>>>>>>>>>>>>>>> are the qc comments stored? >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> Finally a walkthrough would be helpful. >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> Thanks, >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 30 ???? 2019 ???? 8:29 ?.?., ?/? >>>>>>>>>>>>>>>>>>>>>>>>>>>> Christine Rogers, Ms. < >>>>>>>>>>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Glad to hear you're making progress with the >>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit labels. To follow up on your last few emails: >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> a- The Wiki's Setup Guide contains Sample >>>>>>>>>>>>>>>>>>>>>>>>>>>>> insert statements for the Visit Windows table >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> . >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> As Cecile mentioned, the consistency of visit >>>>>>>>>>>>>>>>>>>>>>>>>>>>> label format is important: V01, v01, V1, 01 -- whichever you select to use >>>>>>>>>>>>>>>>>>>>>>>>>>>>> is fine; we use V01 by default across all documentation. >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> b- For Password reset, there is a script in >>>>>>>>>>>>>>>>>>>>>>>>>>>>> the tools/ directory so that a back-end administrator can reset any >>>>>>>>>>>>>>>>>>>>>>>>>>>>> front-end user password, including Admin. (See info on setting up / >>>>>>>>>>>>>>>>>>>>>>>>>>>>> resetting User passwords in the Wiki's Setup >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Guide >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> ) >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> c- The minc file not being registered -- due >>>>>>>>>>>>>>>>>>>>>>>>>>>>> to AcquisitionProtocol unknown. >>>>>>>>>>>>>>>>>>>>>>>>>>>>> This means the SeriesDescription (Acquisition >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Protocol) in you Dicom header was not matched to any scan listed in the >>>>>>>>>>>>>>>>>>>>>>>>>>>>> mri_protocol database table. >>>>>>>>>>>>>>>>>>>>>>>>>>>>> (In the online Loris-MRI Troubleshooting >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Guide, >>>>>>>>>>>>>>>>>>>>>>>>>>>>> this >>>>>>>>>>>>>>>>>>>>>>>>>>>>> is Table 3, 2nd-last item "no MINCs inserted" >>>>>>>>>>>>>>>>>>>>>>>>>>>>> ). >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> The MRI Violations module (Readme here) >>>>>>>>>>>>>>>>>>>>>>>>>>>>> will show >>>>>>>>>>>>>>>>>>>>>>>>>>>>> you the details of this mismatch -- >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Go to the module (under the Imaging menu), >>>>>>>>>>>>>>>>>>>>>>>>>>>>> find your scan and click the link "Could not identify scan type" -- in the >>>>>>>>>>>>>>>>>>>>>>>>>>>>> next subpage you can compare the scan's actual parameters against the >>>>>>>>>>>>>>>>>>>>>>>>>>>>> mri_protocol table. >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> To resolve this, adjust your mri_protocol >>>>>>>>>>>>>>>>>>>>>>>>>>>>> table values or perhaps ensure your DICOMs are labelled consistently. >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Let us know if this works for you -- we can >>>>>>>>>>>>>>>>>>>>>>>>>>>>> also walk you through an example of non-identified scans on >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Demo.loris.ca (MRI Violations module). >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Christine >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> The LORIS team >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> On Tue, Jul 30, 2019 at 10:47 AM Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos wrote: >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I hope this is sufficient as the error for >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the visit label disappeared. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Please see the attached file. Also something >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> i found. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> lorisadmin at hbp:/data/loris/bin/mri$ cat >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data//logs/TarLoad-17-39-xubBdv.log >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ==> Loading file from disk >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-17-39-UyQcG2/dcc0000_258024_v1_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> --> mapping DICOM parameter for >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-17-39-UyQcG2/dcc0000_258024_v1_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ==> computing md5 hash for MINC body. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> --> md5: 6b1202fd63e29de4c9be1cd9925888a5 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ==> verifying acquisition protocol >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Acquisition protocol is unknown >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> --> The minc file cannot be registered >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> since the AcquisitionProtocol is unknown >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 30 ???? 2019 ???? 4:58 ?.?., ?/? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Ok I fixed the login problem by using a >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> known hash and by deleting the rows from the login_history i was able to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> login. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 30 ???? 2019 ???? 4:50 ?.?., ?/? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> there was no visit label 01 in the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Visit_Windows table and i don't know how to insert it because the record >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> requires lots of attributes. Also the system for a reason asked me to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> update my password and now i don't remember it and my account got >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> suspended. Is there a way to reset it or set a simple password? I updated >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the password hash in the users table by using the hash from another LORIS >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> setup we had and i still couldn't login ( also the attribute password is >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> always NULL and the expiration date is 1999-01-01 for some reason ). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thanks >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 29 ???? 2019 ???? 5:21 ?.?., ?/? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Cecile Madjar >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Can you try adding the visit label v01 to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the Visit_Windows table? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> However, I noticed that in a previous >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> dataset, the label was V1. Does that refer to the same visit? If so, you >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> might want to harmonize the visit labels so they are all the same across >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> datasets for a given timepoint, meaning you will need to relabel scans when >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the visit label is different but referring to the same visit label (v01 = >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> V1 etc...). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helps, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> On Mon, Jul 29, 2019 at 10:15 AM Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> wrote: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Could you help me with the "Visit label >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> does not exist"? I had changed $subjectID{'createVisitLabel'} to 1 as you >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> had suggested but it appears that this problem hasn't been resolved yet. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> lorisadmin at hbp:/data/loris/bin/mri$ cat >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data//logs/TarLoad-14-58-9Xog7H.log >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ==> Loading file from disk >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> --> mapping DICOM parameter for >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> --> using user-defined filterParameters >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> for >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Candidate Mismatch Error is Visit label >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> does not exist >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -> WARNING: This candidate was invalid. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Logging to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> MRICandidateErrors table >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> with reason Visit label does not exist >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 26 ???? 2019 ???? 3:02 ?.?., >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ?/? Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Cecile, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The Center error was fixed. Still the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> insertion of mincs fails. Please see the output.txt file i attached. Also >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> is there something else i need to change at the paths configuration? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 25 ???? 2019 ???? 6:55 ?.?., >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ?/? Cecile Madjar >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> We are making progress! >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I have a feeling this error comes from >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the fact that your psc table does not have the MRI_alias populated for the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DCC site. Running the following query in the mysql database should fix this: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> UPDATE psc SET MRI_alias="DCC", >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Alias="DCC" WHERE Name="Data Coordinating Center"; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Repeat the same with all your sites >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> (make sure to change the Aliases between sites, they should all be unique). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Let me know how it goes! >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> On Thu, Jul 25, 2019 at 11:43 AM >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Dear Cecile, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> You were right about your guesses. I >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> did the modifications you suggested, i still get the "no mincs inserted" >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> error, now i am getting the "No center found this candidate" error ( how do >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> i fix that? from what i see the .dcm files contains a 'Institution Name', >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> is that the center? ), so i guess that's why the validation fails, but i >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> changed the force variable of tarchiveLoader to 1, shouldn't it have >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> inserted the mincs then? Also it is optional to have a mail server, right? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ( from what i see the mail error does not affect the $valid_study, so i >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> assume we are okay with that ) >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you a lot, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 25 ???? 2019 ???? 5:48 ?.?., >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ?/? Cecile Madjar < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> cecile.madjar at mcin.ca> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> From what I understand, I believe you >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> just need to update a few config settings from the frontend in the Config >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> module (under the Admin menu). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [image: Screen Shot 2019-07-25 at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 10.31.35 AM.png] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Then go to the Paths section of the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> config module and update the "LORIS-MRI code" config setting to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri (my guess is that currently, it is set to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data) and click on the submit button. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [image: Screen Shot 2019-07-25 at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 10.32.50 AM.png] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Then, go to Imaging Pipeline section >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> of the Configuration module and update the "Loris-MRI Data Directory" to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/ (my guess is that it is empty at the moment in your >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> database which is why $data_dir is not defined when you run the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> tarchiveLoader step of the insertion pipeline). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [image: Screen Shot 2019-07-25 at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 10.40.52 AM.png] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Finally, I took a look at your >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> environment file and it might be a good idea to update your PERL5LIB >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> variable to the following (it has been added to the code a few releases ago >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> as we realized this was needed for the libraries. Not sure which version of >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> LORIS-MRI you are using but it does not hurt to update this variable to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> what I suggest below): >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> export >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PERL5LIB=/data/loris/bin/mri/uploadNeuroDB:/data/loris/bin/mri/dicom-archive:$PERL5LIB >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helps. Sorry you are >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> experiencing so much trouble setting things up. We probably need to update >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> our WIKI. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> On Thu, Jul 25, 2019 at 9:48 AM >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The "Loris-MRI Data Directory" >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> should be in the environment file? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 25 ???? 2019 ???? 12:59 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ?.?., ?/? Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The scripts are located in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/. Somewhere I might have messed something up but i >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> remember following the instructions in the wiki.For example when i tried to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> execute the batch_uploads_imageuploader perl script the line >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> my $command = >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> "$bin_dir/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl " >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> was pointing to an invalid path, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> for example: it was repeating a pattern and had LORIS instead of loris ( i >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> think the mistake was that in the wiki it suggested to use $PROJECT for >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the name of the folder and i choosed 'loris' >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris/wiki/Imaging-Database >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ). See also the in image for the modification i did. Also i didn't find the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> section to config the $data_dir variable. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 24 ???? 2019 ???? 6:05 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ?.?., ?/? Cecile Madjar < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> cecile.madjar at mcin.ca> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> It looks like you have one Config >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> setting not set (based on the first error message you got when running it >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the first time). You need to set a value for "Loris-MRI Data Directory" in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the Config module under the Imaging pipeline section (from what I can see, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> it would be /data/loris/data/ for your setup). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The reason you got that error >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> message the second time is that the pipeline checks if the DICOM study was >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> already inserted in the tarchive table. Since you ran the study once >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> already, the study is inserted into the tarchive, hence the message. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> However, the pipeline did not complete as the MINC files were not created >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and inserted into the files/parameter_file table. In order to continue the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> insertion, you will then need to run the tarchiveLoader command suggested >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in the terminal during the second run: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -globLocation -profile prod >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive//2012/DCM_2012-12-05_ImagingUpload-17-43-ZUEFjb.tar >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -verbose >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Finally, I am a bit confused by >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> your setup. Where are the scripts located? In /data/loris/bin/mri or >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data? It feels like the Config setting "LORIS-MRI code" in the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Paths section was set to "/data/LORIS/data" but it should have been set to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the directory where the scripts are located (most probably >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helps, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> On Wed, Jul 24, 2019 at 10:55 AM >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Ok first i execute this command: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> "lorisadmin at hbp:/data/loris/bin/mri$ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ./batch_uploads_imageuploader -profile prod < ~/Desktop/input.txt > log.txt >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> $data_dir in concatenation (.) or string at ./batch_uploads_imageuploader >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> line 143. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> $data_dir in concatenation (.) or string at ./batch_uploads_imageuploader >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> line 143. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $_ in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> pattern match (m//) at ./batch_uploads_imageuploader line 147. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> base is DCC0000_258024_V01 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> path is /data/incoming/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> type is .tar.gz >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> fullpath is >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/incoming/DCC0000_258024_V01.tar.gz >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> source >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/ImagingUpload-17-43-ZUEFjb >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> targetlocation >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> $data_dir in concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 256. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> $data_dir in concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 284. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> $data_dir in concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> tarchive_validation.pl line 219. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> $data_dir in concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl line 270. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> $data_dir in concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 711. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Can't exec "mail": No such file >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> or directory at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 721. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 722. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 723. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> $data_dir in concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 724. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 724. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 725. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> $data_dir in concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 735. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> No Mincs inserted >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The tarchiveLoader insertion >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> script has failed. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Running now the following >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> command: /data/loris/data/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl -profile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> prod -upload_id 3 /data/incoming/DCC0000_258024_V01.tar.gz -verbose" >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I inserted the VisitLabel, but >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> still the Mincs are not inserted and i am getting this error >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> "lorisadmin at hbp:/data/loris/bin/mri$ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl -profile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> prod -upload_id 3 /data/incoming/DCC0000_258024_V01.tar.gz -verbose >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> find -path >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> \/tmp\/ImagingUpload\-17\-45\-5MsWEd -name '__MACOSX' -delete >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Spool message is: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The Scan for the uploadID 3 has >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> already been run with tarchiveID: 7. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> To continue with the rest of the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> insertion pipeline, please run tarchiveLoader from a terminal as follows: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader -globLocation -profile prod >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive//2012/DCM_2012-12-05_ImagingUpload-17-43-ZUEFjb.tar >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -verbose" >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Which files should i delete? I >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> thought that deleting the files from the tarchive was enough. And i >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> executed the last proposed command to continue to rest of the insertion >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> pipeline ( check the image ). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 24 ???? 2019 ???? 5:05 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ?.?., ?/? Cecile Madjar < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> cecile.madjar at mcin.ca> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sorry I was not clear before. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Every visits of candidates are created in the session table with one entry >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> per CandID/VisitLabel. So if the imaging pipeline created visits in the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> session table (that are not attached to instruments) and you want to clean >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> your database completely, you can delete entries in that table as well. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Regarding your point 2, the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> imaging pipeline can create the visit in the session table as long as the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit label is present in the Visit_Windows table (which means the visit >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> label stored in the PatientName is a valid visit label). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> However, in your prod file, if >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the variable $subjectID{'createVisitLabel'} is set to 1 for candidates, the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit label should be created in the Visit_Windows table I believe. Here >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> is the line of the prod file you would need to change >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> . >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> In general, we prefer populating >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the Visit_Windows table and set the $subjectID{'createVisitLabel'} to 0 for >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> candidate data to avoid insertion of badly labelled MRI data that are >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> complex to relabel. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Finally, regarding the candidate >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> creation, if you execute the following steps, the pipeline should be able >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> to create candidates: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - set in the Imaging Pipeline >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> section of the config module the config setting "Upload creation of >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> candidates" to Yes >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - manually transfer the scans to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the LORIS server instead of uploading it via the imaging browser >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - run batch_imaging_upload.pl >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> as you did until now. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helps! >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> On Wed, Jul 24, 2019 at 8:47 AM >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> About my second question i >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> replaced the name of the patient in the .dcm files and now i am getting an >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> error that the visit label does not exist. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I thought it was supposed to be >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> automatically created. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> "Done adding archive info into >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> database >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -globLocation -profile prod >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive//DCM_2012-12-05_ImagingUpload-15-42-yUwQQV.tar >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -verbose >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> md5sum >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive/DCM_2012-12-05_ImagingUpload-15-42-yUwQQV.tar >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> candidate id 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> => No Visit labelVisit label >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> does not exist >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Set centerID = 1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Number of MINC files that will >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> be considered for inserting into the database: 1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> log dir is /logs and log file >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> is /logs/TarLoad-15-42-L6pocU.log >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> candidate id 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> => No Visit label >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Cleaning up temp files: rm -rf >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-15-42-J2rQms/ImagingUpload-15-42-yUwQQV*" >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 24 ???? 2019 ???? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 3:38 ?.?., ?/? Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 1) What are the records in the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> session table? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 2) I tried to upload a >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> non-phantom file like this >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> input_file.txt: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/incoming/DCC0000_258024_V1.tar.gz >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> N DCC0000_258024_V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Terminal: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ./batch_uploads_imageuploader >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -profile prod < ~/Desktop/input.txt > log.txt >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and i get the following error >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in the log.txt file >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> "Running now the following >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> command: /data/loris/data/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -profile prod -upload_id 7 /data/incoming/DCC0000_258024_V1.tar.gz -verbose >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> find -path >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> \/tmp\/ImagingUpload\-14\-56\-FeLCB4 -name '__MACOSX' -delete >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Spool message is: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The PatientName read from the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DICOM header does not start with DCC0000_258024_V1 from the mri_upload table >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> " >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and the spool message is >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> repeated for each .dcm file. Should i preprocess every .dcm file and change >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the PatientName to "DCC0000_258024_V1"? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 3) As far as it concerns the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> candidate profile i have to create a new one each time before i try to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> upload a file? Is there already a way to create a candidate profile and get >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the DCCID and PSCID without the user interface? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 18 ???? 2019 ???? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 5:00 ?.?., ?/? Cecile Madjar < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> cecile.madjar at mcin.ca> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> See answers to your questions >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> below. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> About the 1st case we had a >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> dicom with a blank studyUID, maybe someone accidentally removed it. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> That is strange. Something >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> must have been done to the DICOM files. I have never seen a study with no >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> StudyUID out of the scanner. Usually, you need to manually erase it with >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> some tool. However, DICOMs never cease to surprise me... >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Some other questions: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 1) What are the steps to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> remove all of my patients and uploads?: because i want to try to reupload >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> all the testing dicoms we had with a clean database. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Release 21.0 of LORIS-MRI >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> will offer a script to remove all the entries and files specific to an >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> upload. However, this release is not yet out. Hopefully in the next few >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> weeks. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> In the meantime, since your >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> case is particular and that you just want to start with a clean database, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the following deletes should work (hopefully I won't forget any tables): >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> mri_violations_log; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> mri_protocol_violated_scans; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> MRICandidateErrors; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from parameter_file; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from files_qcstatus; # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> (if you played with the QC part of the imaging browser for testing) >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> feedback_mri_comments; # (if you played with the QC part of the imaging >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> browser for testing) >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from tarchive_series; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from tarchive_files; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from mri_upload; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from tarchive; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from mri_scanner; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from candidate where >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID="scanner"; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I don't know if you want to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> also delete entries in the session and candidate table too? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 2) We do not need to create >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the profile of a patient ( are the patients stored in the candidate table? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> because i can't see the ghosts ), because will it automatically be created >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> when importing a dicom? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I am not sure I understand >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> fully this question. All candidates are stored in the candidate table. The >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> phantom scans however are attached to a scanner candidate depending on >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> where the scan happened. It is a bit of a weird concept that we have to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> redesign eventually but never got a chance to get to it. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hopefully this answered your >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> question, otherwise, don't hesitate to let me know. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 3) What is the difference >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> between uploading a dicom as phantom instead of importing as >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCCID_DCCID_VisitLabel? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> When you upload the scan as >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID_DCCID_VisitLabel, there is a check that makes sure the candidate IDs >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and visit label are valid at the time of upload. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> When you upload a scan as >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> phantom, it expects that the DICOM field PatientName and uploaded filename >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> contains the string "phantom". We enforced this behaviour on the imaging >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> uploader side in recent releases but I can't remember which one. Probably >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the upcoming 21.0 release. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> All those verifications might >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> seem cumbersome but they are here to ensure that the files inserted are all >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> valid and labelled properly as it is a bit messy to have to delete files >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> that were wrongly labelled. At least, the delete script present in release >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 21.0 will make this process easier but it is still good practice to verify >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> those things. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> With pleasure. Hopefully the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> answers to your questions will be helpful. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PS: loris-dev mailing list: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> you will find the initial answer I gave Sotirios below. I forgot to cc the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> loris-dev in my earlier reply... >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 16 ???? 2019 ???? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 12:02 ?.?., ?/? Cecile Madjar < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> cecile.madjar at mcin.ca> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Dear Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you for reaching out. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Since your email was already organized in points, I will reply directly >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> below your questions below. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 1) What do we do when the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> StudyUID is blank on the header? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/minor/docs/AppendixA-Troubleshooting_guideline.md >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> There solution provided at the table 3 does not guide us how to find the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> information ( is possible ). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The StudyUID is the field >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> used in our pipeline at the moment to check whether a DICOM study was >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> already inserted into LORIS with that same StudyUID since it is supposed to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> be unique for every single study. Currently, we do not support insertion of >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DICOM studies if they do not have a StudyUID associated with them. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Is there a specific reason >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> why the StudyUID is blank in the DICOM headers in your DICOM files? Did >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> they go through some processes before upload to LORIS? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 2) When i am about to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> upload a non-phanton case i need a 'Visit Label'. Is there already a script >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> that can create a new visit label for a specific Candidate, so i can >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> provide it as input afterwards to the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> batch_uploads_imageuploader ( See option 5.1.3 https://github.com/aces/Loris-MRI/blob/minor/docs/05-PipelineLaunchOptions.md ) >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I am not sure if the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> front-end allows for it but if you use batch_uploads_imageuploader, the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> insertion scripts could create the visit label for you. However, it does >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> need to be included in the patient name in order for the script to know >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> which label it should use. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> For example: you upload V02 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> for MTL0123 (DCCID: 456789) but V02 was not yet created for MTL0123; the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> insertion scripts will create a V02 visit for MTL0123 if the PatientName >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> field for the dataset is MTL0123_456789_V02 with Stage marked as "Not >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Started". >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> However, *note that for >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the script to create the visit for the candidate, you have to make sure >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> that all the visit label of your projects were inserted in the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Visit_Windows table* >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> (otherwise, the visit will never be created as they were not specified as >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> being part of the list of visit label to expect). So in the example above, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> you should have one row in Visit_Windows with Visit_label="V02" set. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 3) Section 4.3 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/minor/docs/04-Scripts.md >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> What do we do when the folder contains multiple mnc files? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> This is a case by case. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Most of the time, the MINC files that failed insertion into the imaging >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> browser end up in the MRI violation module where you can see what went >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> wrong with the acquisitions not inserted. If you notice that the MINC file >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> should be inserted as a specific protocol, you can force the insertion as >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> explained in section 4.3. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> In your case, I have a >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> feeling that you want to be able to insert MINC files that did not go >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> through the whole pipeline insertion (DICOM archival, then dcm2mnc, then >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> protocol identification, then insertion...). In theory, you could call >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl on any >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> MINC file, provided you have at least the following information: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - path to the MINC file >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - uploadID associated with >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the MINC files or DICOM archive path from which those MINC files were >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> created from >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Then the minc_insertion.pl >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> script will do the subject information and protocol validation etc... >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> If all the MINC files come >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> from the same uploadID or TarchiveID, then you could run a loop in bash >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> calling the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl script >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> like this for files deriving from uploadID=1: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ls /path/to/mnc/folder/* | >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> while read f; do >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl -profile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> prod -uploadID 1 -mincPath $f; done >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helped! >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>>>>>>>>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | >>>>>>>>>>>>>>>>>>>>>>>>>>>>> MCIN.ca >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>>>>>>>>>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>>>>>>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | >>>>>>>>>>>>>>>>>>>>>>>>>>> MCIN.ca >>>>>>>>>>>>>>>>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>>>>>>>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>>>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>>>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>>>>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> -- >>>>>>>>>>>>>> >>>>>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>>>>> >>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>> >>>>>>>>>>>> _______________________________________________ >>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> -- >>>>>>>>>> Shen Wang >>>>>>>>>> Loris Developer >>>>>>>>>> Montreal Neurological Institute >>>>>>>>>> McGill University >>>>>>>>>> >>>>>>>>>> >>>>>> >>>>>> -- >>>>>> Shen Wang >>>>>> Loris Developer >>>>>> Montreal Neurological Institute >>>>>> McGill University >>>>>> >>>>>> -- >>>>> Shen Wang >>>>> Loris Developer >>>>> Montreal Neurological Institute >>>>> McGill University >>>>> >>>>> _______________________________________________ >>>>> Loris-dev mailing list >>>>> Loris-dev at bic.mni.mcgill.ca >>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>> >>>> >>>> >>>> -- >>>> >>>> christine.rogers at mcgill.ca >>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>> Montreal Neurological Institute >>>> McGill University | Montreal | Canada >>>> >>> > > -- > Shen Wang > Loris Developer > Montreal Neurological Institute > McGill University > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: ???? 2019-08-13 19.21.15.png Type: image/png Size: 508603 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: sudo_make_output Type: application/octet-stream Size: 36841 bytes Desc: not available URL: From wangshen.mcin at gmail.com Thu Aug 15 14:17:40 2019 From: wangshen.mcin at gmail.com (Shen Wang) Date: Thu, 15 Aug 2019 14:17:40 -0400 Subject: [Loris-dev] Upgrading to Loris 21 - new make file In-Reply-To: References: Message-ID: Hi Sotirios, It seems like you are missing this file. [ .babelrc] step 1: copy from https://github.com/aces/Loris/blob/major/.babelrc step 2: sudo vi webpack.config.js remove these lines { test: /\.js$/, exclude: /node_modules/, // use: ['babel-loader', 'eslint-loader'], }, step 3: sudo make On Wed, 14 Aug 2019 at 18:52, Sotirios Nikoloutsopoulos < sotirisnik at gmail.com> wrote: > Hi Shen, > > That didn't work either. Also i had removed the git files because i was > getting this error when i used make: > > "git describe --tags --always > VERSION > fatal: Not a git repository (or any of the parent directories): .git > Makefile:8: recipe for target 'VERSION' failed > make: *** [VERSION] Error 128" > > Thanks > > ???? ???, 15 ??? 2019 ???? 1:36 ?.?., ?/? Shen Wang < > wangshen.mcin at gmail.com> ??????: > >> Hi,Sotirios >> In your special situation, there is a temporary fix. >> step 1. sudo git stash >> step 2. open webpack.config.js file >> remove line 75 use: ['babel-loader', 'eslint-loader'], >> save it. >> step 3. sudo make >> >> I hope this could help you to compile the js files. >> >> >> >> On Wed, 14 Aug 2019 at 08:28, Sotirios Nikoloutsopoulos < >> sotirisnik at gmail.com> wrote: >> >>> I forgot to mention that i had already moved my previous config file and >>> re-executed the installation script. >>> >>> ???? ???, 14 ??? 2019 ???? 3:26 ?.?., ?/? Sotirios Nikoloutsopoulos < >>> sotirisnik at gmail.com> ??????: >>> >>>> Hi, >>>> >>>> Step 1 worked and the indentation errors were fixed. About step2 i >>>> added all of these( there are more to include in the list) these to >>>> .eslintignore which were reported to fail at being built, but they still >>>> appear on the errors at the make_output file. >>>> >>>> /jsx/DynamicDataTable.js >>>> /jsx/StaticDataTable.js >>>> /jsx/MultiSelectDropdown.js >>>> /jsx/Breadcrumbs.js >>>> /jsx/Form.js >>>> /jsx/Markdown.js >>>> /modules/media/jsx/mediaIndex.js >>>> /modules/issue_tracker/jsx/issueTrackerIndex.js >>>> /modules/issue_tracker/jsx/index.js >>>> /modules/candidate_parameters/jsx/CandidateParameters.js >>>> /modules/configuration/jsx/SubprojectRelations.js >>>> /modules/conflict_resolver/jsx/conflictResolverIndex.js >>>> /modules/conflict_resolver/jsx/resolvedConflictsIndex.js >>>> /modules/bvl_feedback/jsx/react.behavioural_feedback_panel.js >>>> /modules/dataquery/jsx/react.tabs.js >>>> /modules/document_repository/jsx/docIndex.js >>>> /modules/instrument_builder/jsx/react.instrument_builder.js >>>> /modules/imaging_uploader/jsx/index.js >>>> /modules/datadict/jsx/dataDictIndex.js >>>> /modules/bvl_feedback/jsx/react.behavioural_feedback_panel.js >>>> /modules/new_profile/jsx/NewProfileIndex.js >>>> /modules/examiner/jsx/examinerIndex.js >>>> /modules/configuration/jsx/SubprojectRelations.js >>>> /modules/data_team_helper/jsx/behavioural_qc_module.js >>>> /modules/acknowledgements/jsx/acknowledgementsIndex.js >>>> /modules/candidate_parameters/jsx/CandidateParameters.js >>>> /modules/imaging_browser/jsx/ImagePanel.js >>>> /modules/mri_violations/jsx/mri_protocol_violations_columnFormatter.js >>>> >>>> /modules/mri_violations/jsx/mri_protocol_check_violations_columnFormatter.js >>>> /modules/genomic_browser/jsx/profileColumnFormatter.js >>>> /modules/dataquery/jsx/react.tabs.js >>>> /jsx/MultiSelectDropdown.js >>>> /modules/mri_violations/jsx/columnFormatterUnresolved.js >>>> /modules/dataquery/jsx/react.sidebar.js >>>> /modules/dataquery/jsx/react.fieldselector.js >>>> /modules/quality_control/jsx/qualityControlIndex.js >>>> /modules/dataquery/jsx/react.paginator.js >>>> /modules/instrument_builder/jsx/react.questions.js >>>> /modules/dataquery/jsx/react.filterBuilder.js >>>> /modules/conflict_resolver/jsx/conflictResolverIndex.js >>>> /jsx/PaginationLinks.js >>>> /modules/conflict_resolver/jsx/resolvedConflictsIndex.js >>>> /modules/dataquery/jsx/react.app.js >>>> /modules/candidate_list/jsx/onLoad.js >>>> /jsx/Form.js >>>> /modules/publication/jsx/publicationIndex.js >>>> /modules/server_processes_manager/jsx/server_processes_managerIndex.js >>>> /modules/imaging_browser/jsx/imagingBrowserIndex.js >>>> /modules/issue_tracker/jsx/issueTrackerIndex.js >>>> /modules/survey_accounts/jsx/surveyAccountsIndex.js >>>> /modules/data_integrity_flag/jsx/dataIntegrityFlagIndex.js >>>> /modules/instrument_manager/jsx/instrumentManagerIndex.js >>>> /modules/media/jsx/mediaIndex.js >>>> /modules/user_accounts/jsx/userAccountsIndex.js >>>> /modules/help_editor/jsx/help_editor.js >>>> /modules/dicom_archive/jsx/dicom_archive.js >>>> /modules/mri_violations/jsx/columnFormatter.js >>>> /modules/brainbrowser/jsx/Brainbrowser.js >>>> /node_modules/babel-loader/lib/index.js >>>> /modules/document_repository/jsx/editFormIndex.js >>>> >>>> Thanks >>>> >>>> ???? ???, 14 ??? 2019 ???? 7:50 ?.?., ?/? Christine Rogers, Ms. < >>>> christine.rogers at mcgill.ca> ??????: >>>> >>>>> Hi Shen and Sotirios - just a note, >>>>> >>>>> For the 21 release, it's best to run the install script without >>>>> sudoing it. >>>>> >>>>> (Shen, I believe we discovered a minor issue with the sudo last week >>>>> #5008) >>>>> >>>>> Best, >>>>> Christine >>>>> >>>>> On Tue, Aug 13, 2019 at 9:22 PM Shen Wang >>>>> wrote: >>>>> >>>>>> Does it work? If still doesn?t work, try to remove project/config.xml >>>>>> file. Do sudo ./install.sh again. To reinstall Loris again. >>>>>> >>>>>> >>>>>> Shen Wang ?2019?8?13? ????9:02??? >>>>>> >>>>>>> Hi Sotirios, >>>>>>> step 1: >>>>>>> sudo ./node_modules/.bin/eslint --fix /var/www/loris >>>>>>> step 2: >>>>>>> put the rest error files under this line [# Ignore until ESLint is >>>>>>> run] in the .eslintignore file. >>>>>>> step 3: >>>>>>> sudo make >>>>>>> >>>>>>> >>>>>>> >>>>>>> On Tue, 13 Aug 2019 at 20:34, Sotirios Nikoloutsopoulos < >>>>>>> sotirisnik at gmail.com> wrote: >>>>>>> >>>>>>>> I did the modifications, still there are errors. >>>>>>>> Thanks >>>>>>>> >>>>>>>> >>>>>>>> ???? ???, 14 ??? 2019 ???? 3:22 ?.?., ?/? Shen Wang < >>>>>>>> wangshen.mcin at gmail.com> ??????: >>>>>>>> >>>>>>>>> Hi Sotirios, >>>>>>>>> I saw your output file, the config issue is gone. >>>>>>>>> you can use [sudo npm run lintfix:javascript ] to fix these >>>>>>>>> indent issues. >>>>>>>>> If it still has errors. >>>>>>>>> Then try modify this file .eslintignore >>>>>>>>> with this >>>>>>>>> >>>>>>>>> # Ignore until ESLint is run >>>>>>>>> >>>>>>>>> modules/* >>>>>>>>> >>>>>>>>> modules/dataquery/ >>>>>>>>> >>>>>>>>> node_modules/* >>>>>>>>> >>>>>>>>> htdocs/js/components/* >>>>>>>>> >>>>>>>>> jsx/* >>>>>>>>> >>>>>>>>> >>>>>>>>> # Ignore external libs >>>>>>>>> >>>>>>>>> htdocs/js/flot/* >>>>>>>>> >>>>>>>>> htdocs/js/jquery/* >>>>>>>>> >>>>>>>>> htdocs/js/jszip/* >>>>>>>>> >>>>>>>>> htdocs/js/modernizr/* >>>>>>>>> >>>>>>>>> htdocs/js/modules/* >>>>>>>>> >>>>>>>>> htdocs/js/react/* >>>>>>>>> >>>>>>>>> htdocs/js/shims/* >>>>>>>>> >>>>>>>>> htdocs/js/c3.min.js >>>>>>>>> >>>>>>>>> htdocs/js/d3.min.js >>>>>>>>> >>>>>>>>> htdocs/js/FileSaver.min.js >>>>>>>>> >>>>>>>>> >>>>>>>>> then do sudo make. >>>>>>>>> It should work. >>>>>>>>> Regards >>>>>>>>> Shen >>>>>>>>> >>>>>>>>> >>>>>>>>> Sotirios Nikoloutsopoulos ?2019?8?13? >>>>>>>>> ????7:54??? >>>>>>>>> >>>>>>>>>> No, it didn't work, i also tried space/tabs because most of the >>>>>>>>>> errors where about indentation, also there are some errors about React. >>>>>>>>>> >>>>>>>>>> Thanks >>>>>>>>>> >>>>>>>>>> lorisadmin at hbp:/var/www/loris$ sudo ./node_modules/.bin/eslint >>>>>>>>>> --init >>>>>>>>>> ? How would you like to configure ESLint? Answer questions about >>>>>>>>>> your style >>>>>>>>>> ? Which version of ECMAScript do you use? ES2015 >>>>>>>>>> ? Are you using ES6 modules? Yes >>>>>>>>>> ? Where will your code run? Browser >>>>>>>>>> ? Do you use CommonJS? Yes >>>>>>>>>> ? Do you use JSX? Yes >>>>>>>>>> ? Do you use React? Yes >>>>>>>>>> ? What style of indentation do you use? Spaces >>>>>>>>>> ? What quotes do you use for strings? Single >>>>>>>>>> ? What line endings do you use? Unix >>>>>>>>>> ? Do you require semicolons? Yes >>>>>>>>>> ? What format do you want your config file to be in? JSON >>>>>>>>>> The config that you've selected requires the following >>>>>>>>>> dependencies: >>>>>>>>>> >>>>>>>>>> eslint-plugin-react at latest >>>>>>>>>> Successfully created .eslintrc.json file in /var/www/loris >>>>>>>>>> >>>>>>>>>> lorisadmin at hbp:/var/www/loris$ sudo make > sudo_make_output >>>>>>>>>> npm WARN The package prop-types is included as both a dev and >>>>>>>>>> production dependency. >>>>>>>>>> npm WARN optional SKIPPING OPTIONAL DEPENDENCY: fsevents at 1.2.4 >>>>>>>>>> (node_modules/fsevents): >>>>>>>>>> npm WARN notsup SKIPPING OPTIONAL DEPENDENCY: Unsupported >>>>>>>>>> platform for fsevents at 1.2.4: wanted {"os":"darwin","arch":"any"} >>>>>>>>>> (current: {"os":"linux","arch":"x64"}) >>>>>>>>>> >>>>>>>>>> npm ERR! code ELIFECYCLE >>>>>>>>>> npm ERR! errno 2 >>>>>>>>>> npm ERR! loris at 1.0.0 compile: `webpack` >>>>>>>>>> npm ERR! Exit status 2 >>>>>>>>>> npm ERR! >>>>>>>>>> npm ERR! Failed at the loris at 1.0.0 compile script. >>>>>>>>>> npm ERR! This is probably not a problem with npm. There is likely >>>>>>>>>> additional logging output above. >>>>>>>>>> >>>>>>>>>> npm ERR! A complete log of this run can be found in: >>>>>>>>>> npm ERR! >>>>>>>>>> /home/lorisadmin/.npm/_logs/2019-08-13T23_40_58_841Z-debug.log >>>>>>>>>> >>>>>>>>>> ???? ???, 14 ??? 2019 ???? 2:29 ?.?., ?/? Shen Wang < >>>>>>>>>> wangshen.mcin at gmail.com> ??????: >>>>>>>>>> >>>>>>>>>>> Hi Sotirios, >>>>>>>>>>> When you do make command, please make sure with sudo at the >>>>>>>>>>> beginning. [sudo make] >>>>>>>>>>> If it still doesn't work for you. >>>>>>>>>>> Then try the solutions below. >>>>>>>>>>> solution 1: >>>>>>>>>>> [image: ???? 2019-08-13 19.21.15.png] >>>>>>>>>>> Regards >>>>>>>>>>> Shen >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> On Tue, 13 Aug 2019 at 17:22, Sotirios Nikoloutsopoulos < >>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>> >>>>>>>>>>>> I think that the files exists although i redownloaded the >>>>>>>>>>>> eslintrc.json i checked others files that had similar errors. >>>>>>>>>>>> >>>>>>>>>>>> lorisadmin at hbp:/var/www/loris$ ls -l >>>>>>>>>>>> ./node_modules/eslint-loader/index.js >>>>>>>>>>>> -rw-rw-r-- 1 lorisadmin lorisadmin 6463 ??? 26 1985 >>>>>>>>>>>> ./node_modules/eslint-loader/index.js >>>>>>>>>>>> >>>>>>>>>>>> lorisadmin at hbp:/var/www/loris$ ls -l .eslintrc.json >>>>>>>>>>>> -rw-rw-r-- 1 lorisadmin lorisadmin 84530 ??? 14 00:04 >>>>>>>>>>>> .eslintrc.json >>>>>>>>>>>> >>>>>>>>>>>> Maybe this can help >>>>>>>>>>>> >>>>>>>>>>>> Module build failed (from >>>>>>>>>>>> ./node_modules/eslint-loader/index.js): >>>>>>>>>>>> SyntaxError: Cannot read config file: >>>>>>>>>>>> /var/www/loris/.eslintrc.json >>>>>>>>>>>> Error: Unexpected token < in JSON at position 6 >>>>>>>>>>>> at JSON.parse () >>>>>>>>>>>> at loadJSONConfigFile >>>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config/config-file.js:114:21) >>>>>>>>>>>> at loadConfigFile >>>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config/config-file.js:230:26) >>>>>>>>>>>> at loadFromDisk >>>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config/config-file.js:500:18) >>>>>>>>>>>> at Object.load >>>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config/config-file.js:564:20) >>>>>>>>>>>> at Config.getLocalConfigHierarchy >>>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config.js:227:44) >>>>>>>>>>>> at Config.getConfigHierarchy >>>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config.js:179:43) >>>>>>>>>>>> at Config.getConfigVector >>>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config.js:286:21) >>>>>>>>>>>> at Config.getConfig >>>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config.js:329:29) >>>>>>>>>>>> at processText >>>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/cli-engine.js:162:33) >>>>>>>>>>>> at CLIEngine.executeOnText >>>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/cli-engine.js:596:17) >>>>>>>>>>>> at lint >>>>>>>>>>>> (/var/www/loris/node_modules/eslint-loader/index.js:237:17) >>>>>>>>>>>> at Object.module.exports >>>>>>>>>>>> (/var/www/loris/node_modules/eslint-loader/index.js:232:21) >>>>>>>>>>>> >>>>>>>>>>>> ERROR in ./modules/imaging_uploader/jsx/index.js >>>>>>>>>>>> Module build failed (from >>>>>>>>>>>> ./node_modules/eslint-loader/index.js): >>>>>>>>>>>> SyntaxError: Cannot read config file: >>>>>>>>>>>> /var/www/loris/.eslintrc.json >>>>>>>>>>>> Error: Unexpected token < in JSON at position 6 >>>>>>>>>>>> at JSON.parse () >>>>>>>>>>>> at loadJSONConfigFile >>>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config/config-file.js:114:21) >>>>>>>>>>>> at loadConfigFile >>>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config/config-file.js:230:26) >>>>>>>>>>>> at loadFromDisk >>>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config/config-file.js:500:18) >>>>>>>>>>>> at Object.load >>>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config/config-file.js:564:20) >>>>>>>>>>>> at Config.getLocalConfigHierarchy >>>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config.js:227:44) >>>>>>>>>>>> at Config.getConfigHierarchy >>>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config.js:179:43) >>>>>>>>>>>> at Config.getConfigVector >>>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config.js:286:21) >>>>>>>>>>>> at Config.getConfig >>>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config.js:329:29) >>>>>>>>>>>> at processText >>>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/cli-engine.js:162:33) >>>>>>>>>>>> at CLIEngine.executeOnText >>>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/cli-engine.js:596:17) >>>>>>>>>>>> at lint >>>>>>>>>>>> (/var/www/loris/node_modules/eslint-loader/index.js:237:17) >>>>>>>>>>>> at Object.module.exports >>>>>>>>>>>> (/var/www/loris/node_modules/eslint-loader/index.js:232:21) >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> ???? ???, 13 ??? 2019 ???? 11:52 ?.?., ?/? John Saigle < >>>>>>>>>>>> john.saigle at mcin.ca> ??????: >>>>>>>>>>>> >>>>>>>>>>>>> HI Sotirios, >>>>>>>>>>>>> >>>>>>>>>>>>> The make_output.txt file shows webpack failing because it >>>>>>>>>>>>> can't find the ESLint config file. >>>>>>>>>>>>> >>>>>>>>>>>>> Can you confirm whether the file `.eslintrc.json` exists >>>>>>>>>>>>> within your loris root directory (usually `/var/www/loris/`)? When I delete >>>>>>>>>>>>> my file I get the same errors as you. >>>>>>>>>>>>> >>>>>>>>>>>>> If you find that it's missing, you can make a local copy with >>>>>>>>>>>>> the contents found here: >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> https://github.com/aces/Loris/blob/e26a6ad49a73fcffef0cd73bb600c4d17b200b62/.eslintrc.json >>>>>>>>>>>>> >>>>>>>>>>>>> Once you know it exists, try running `make` again. >>>>>>>>>>>>> >>>>>>>>>>>>> Let us know if that moves you forward. >>>>>>>>>>>>> >>>>>>>>>>>>> Best, >>>>>>>>>>>>> John >>>>>>>>>>>>> >>>>>>>>>>>>> On Tue, Aug 13, 2019 at 2:21 PM Sotirios Nikoloutsopoulos < >>>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>> >>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>> I executed the commands for the node and now i am get the >>>>>>>>>>>>>> followings: >>>>>>>>>>>>>> >>>>>>>>>>>>>> lorisadmin at hbp:/var/www/loris$ make > ~/make_output >>>>>>>>>>>>>> npm WARN The package prop-types is included as both a dev and >>>>>>>>>>>>>> production dependency. >>>>>>>>>>>>>> npm WARN optional SKIPPING OPTIONAL DEPENDENCY: fsevents at 1.2.4 >>>>>>>>>>>>>> (node_modules/fsevents): >>>>>>>>>>>>>> npm WARN notsup SKIPPING OPTIONAL DEPENDENCY: Unsupported >>>>>>>>>>>>>> platform for fsevents at 1.2.4: wanted >>>>>>>>>>>>>> {"os":"darwin","arch":"any"} (current: {"os":"linux","arch":"x64"}) >>>>>>>>>>>>>> >>>>>>>>>>>>>> npm ERR! code ELIFECYCLE >>>>>>>>>>>>>> npm ERR! errno 2 >>>>>>>>>>>>>> npm ERR! loris at 1.0.0 compile: `webpack` >>>>>>>>>>>>>> npm ERR! Exit status 2 >>>>>>>>>>>>>> npm ERR! >>>>>>>>>>>>>> npm ERR! Failed at the loris at 1.0.0 compile script. >>>>>>>>>>>>>> npm ERR! This is probably not a problem with npm. There is >>>>>>>>>>>>>> likely additional logging output above. >>>>>>>>>>>>>> >>>>>>>>>>>>>> npm ERR! A complete log of this run can be found in: >>>>>>>>>>>>>> npm ERR! >>>>>>>>>>>>>> /home/lorisadmin/.npm/_logs/2019-08-13T18_12_05_378Z-debug.log >>>>>>>>>>>>>> make: *** [javascript] Error 2 >>>>>>>>>>>>>> >>>>>>>>>>>>>> Thanks, >>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> ???? ???, 12 ??? 2019 ???? 10:19 ?.?., ?/? Christine Rogers, >>>>>>>>>>>>>> Ms. ??????: >>>>>>>>>>>>>> >>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> We've seen some users installing LORIS 21 or upgrading to 21 >>>>>>>>>>>>>>> whose version of node doesn't work well with webpack, due to updated >>>>>>>>>>>>>>> packages they're missing. >>>>>>>>>>>>>>> If so, update your node : >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> curl -sL https://deb.nodesource.com/setup_8.x | sudo -E bash - >>>>>>>>>>>>>>> sudo apt-get install -y nodejs >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> Let us know how that goes -- please send us output from the >>>>>>>>>>>>>>> same log if any issues. >>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>> Christine >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> On Thu, Aug 8, 2019 at 2:38 PM Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> It's not a disk space issue, as you can see below i have >>>>>>>>>>>>>>>> still 74GB available. >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> lorisadmin at hbp:/var/www/loris$ df -h >>>>>>>>>>>>>>>> Filesystem Size Used Avail Use% Mounted on >>>>>>>>>>>>>>>> udev 2,9G 0 2,9G 0% /dev >>>>>>>>>>>>>>>> tmpfs 597M 8,6M 588M 2% /run >>>>>>>>>>>>>>>> /dev/sda1 98G 19G 74G 21% / >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Maybe we have to pass a flag to get into strict mode? as >>>>>>>>>>>>>>>> stated "SyntaxError: Block-scoped declarations (let, const, function, >>>>>>>>>>>>>>>> class) not yet supported outside strict mode" >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Thanks, >>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> ???? ???, 8 ??? 2019 ???? 4:32 ?.?., ?/? Dave MacFarlane < >>>>>>>>>>>>>>>> dave.macfarlane at mcin.ca> ??????: >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> It looks like the javascript snippet shown in the error >>>>>>>>>>>>>>>>> message when trying to compile the js is truncated. Have you run out of >>>>>>>>>>>>>>>>> disk space? >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> On Thu, Aug 8, 2019 at 8:37 AM Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> I runned make and also included the file it reports at >>>>>>>>>>>>>>>>>> the end. >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> lorisadmin at hbp:/var/www/loris$ make >>>>>>>>>>>>>>>>>> npm install >>>>>>>>>>>>>>>>>> npm WARN optional Skipping failed optional dependency >>>>>>>>>>>>>>>>>> /chokidar/fsevents: >>>>>>>>>>>>>>>>>> npm WARN notsup Not compatible with your operating system >>>>>>>>>>>>>>>>>> or architecture: fsevents at 1.2.9 >>>>>>>>>>>>>>>>>> npm WARN optional Skipping failed optional dependency >>>>>>>>>>>>>>>>>> /watchpack/chokidar/fsevents: >>>>>>>>>>>>>>>>>> npm WARN notsup Not compatible with your operating system >>>>>>>>>>>>>>>>>> or architecture: fsevents at 1.2.9 >>>>>>>>>>>>>>>>>> npm run compile >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> > loris at 1.0.0 compile /var/www/loris >>>>>>>>>>>>>>>>>> > webpack >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> /var/www/loris/node_modules/webpack/bin/webpack.js:86 >>>>>>>>>>>>>>>>>> let notify = >>>>>>>>>>>>>>>>>> ^^^ >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> SyntaxError: Block-scoped declarations (let, const, >>>>>>>>>>>>>>>>>> function, class) not yet supported outside strict mode >>>>>>>>>>>>>>>>>> at exports.runInThisContext (vm.js:53:16) >>>>>>>>>>>>>>>>>> at Module._compile (module.js:374:25) >>>>>>>>>>>>>>>>>> at Object.Module._extensions..js (module.js:417:10) >>>>>>>>>>>>>>>>>> at Module.load (module.js:344:32) >>>>>>>>>>>>>>>>>> at Function.Module._load (module.js:301:12) >>>>>>>>>>>>>>>>>> at Function.Module.runMain (module.js:442:10) >>>>>>>>>>>>>>>>>> at startup (node.js:136:18) >>>>>>>>>>>>>>>>>> at node.js:966:3 >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> npm ERR! Linux 4.15.0-55-generic >>>>>>>>>>>>>>>>>> npm ERR! argv "/usr/bin/nodejs" "/usr/bin/npm" "run" >>>>>>>>>>>>>>>>>> "compile" >>>>>>>>>>>>>>>>>> npm ERR! node v4.2.6 >>>>>>>>>>>>>>>>>> npm ERR! npm v3.5.2 >>>>>>>>>>>>>>>>>> npm ERR! code ELIFECYCLE >>>>>>>>>>>>>>>>>> npm ERR! loris at 1.0.0 compile: `webpack` >>>>>>>>>>>>>>>>>> npm ERR! Exit status 1 >>>>>>>>>>>>>>>>>> npm ERR! >>>>>>>>>>>>>>>>>> npm ERR! Failed at the loris at 1.0.0 compile script >>>>>>>>>>>>>>>>>> 'webpack'. >>>>>>>>>>>>>>>>>> npm ERR! Make sure you have the latest version of node.js >>>>>>>>>>>>>>>>>> and npm installed. >>>>>>>>>>>>>>>>>> npm ERR! If you do, this is most likely a problem with >>>>>>>>>>>>>>>>>> the loris package, >>>>>>>>>>>>>>>>>> npm ERR! not with npm itself. >>>>>>>>>>>>>>>>>> npm ERR! Tell the author that this fails on your system: >>>>>>>>>>>>>>>>>> npm ERR! webpack >>>>>>>>>>>>>>>>>> npm ERR! You can get information on how to open an issue >>>>>>>>>>>>>>>>>> for this project with: >>>>>>>>>>>>>>>>>> npm ERR! npm bugs loris >>>>>>>>>>>>>>>>>> npm ERR! Or if that isn't available, you can get their >>>>>>>>>>>>>>>>>> info via: >>>>>>>>>>>>>>>>>> npm ERR! npm owner ls loris >>>>>>>>>>>>>>>>>> npm ERR! There is likely additional logging output above. >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> npm ERR! Please include the following file with any >>>>>>>>>>>>>>>>>> support request: >>>>>>>>>>>>>>>>>> npm ERR! /var/www/loris/npm-debug.log >>>>>>>>>>>>>>>>>> Makefile:14: recipe for target 'javascript' failed >>>>>>>>>>>>>>>>>> make: *** [javascript] Error 1 >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Thanks, >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> ???? ???, 7 ??? 2019 ???? 5:41 ?.?., ?/? Christine >>>>>>>>>>>>>>>>>> Rogers, Ms. ??????: >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Thanks, have you tried all of these steps? >>>>>>>>>>>>>>>>>>> - clear your browser cache (and refresh a few times) >>>>>>>>>>>>>>>>>>> - delete any files in your smarty/templates_c directory >>>>>>>>>>>>>>>>>>> (this will clear the template cache - do Not touch smarty/templates/) >>>>>>>>>>>>>>>>>>> - run `make` (per the 21 release notes, this replaces >>>>>>>>>>>>>>>>>>> the composer commands used in previous releases to update your dependencies) >>>>>>>>>>>>>>>>>>> - restart apache (doesn't hurt) >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Let us know how it goes -- let us know what difference >>>>>>>>>>>>>>>>>>> you see after, with your logs. A >>>>>>>>>>>>>>>>>>> lso please send us your Config path settings (see these >>>>>>>>>>>>>>>>>>> Troubleshooting Queries >>>>>>>>>>>>>>>>>>> ) >>>>>>>>>>>>>>>>>>> if you're still seeing front-end issues. >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Thanks, >>>>>>>>>>>>>>>>>>> Christine >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> On Wed, Aug 7, 2019 at 8:02 AM Sotirios Nikoloutsopoulos >>>>>>>>>>>>>>>>>>> wrote: >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> lorisadmin at hbp:/var/www/loris$ sudo cat >>>>>>>>>>>>>>>>>>>> /var/log/apache2/error.log >>>>>>>>>>>>>>>>>>>> [Wed Aug 07 07:35:02.422501 2019] [mpm_prefork:notice] >>>>>>>>>>>>>>>>>>>> [pid 1267] AH00163: Apache/2.4.18 (Ubuntu) OpenSSL/1.0.2g configured -- >>>>>>>>>>>>>>>>>>>> resuming normal operations >>>>>>>>>>>>>>>>>>>> [Wed Aug 07 07:35:02.422514 2019] [core:notice] [pid >>>>>>>>>>>>>>>>>>>> 1267] AH00094: Command line: '/usr/sbin/apache2' >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> And as for the access.log the content are empty >>>>>>>>>>>>>>>>>>>> lorisadmin at hbp:/var/www/loris$ sudo ls -l >>>>>>>>>>>>>>>>>>>> /var/log/apache2/access.log >>>>>>>>>>>>>>>>>>>> lorisadmin at hbp:/var/www/loris$ sudo ls -l >>>>>>>>>>>>>>>>>>>> /var/log/apache2/access.log >>>>>>>>>>>>>>>>>>>> -rw-r----- 1 root adm 0 ???? 28 14:09 >>>>>>>>>>>>>>>>>>>> /var/log/apache2/access.log >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Also i noticed a loris_access.log. >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> The only non-blank pages are: >>>>>>>>>>>>>>>>>>>> mri_violations, dataquery does not exist at all, >>>>>>>>>>>>>>>>>>>> statistics, data_team_helper, genomic_browser, configuration and >>>>>>>>>>>>>>>>>>>> server_processes_manager/ prints "Required configuration settings for >>>>>>>>>>>>>>>>>>>> Server Processes Manager are missing. Cannot continue." >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Thanks, >>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> ???? ???, 6 ??? 2019 ???? 10:13 ?.?., ?/? Christine >>>>>>>>>>>>>>>>>>>> Rogers, Ms. ??????: >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> Hi Sotirios and LORIS community -- >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> When upgrading to brand-new release 21 -- just a >>>>>>>>>>>>>>>>>>>>> reminder to follow the release notes and run the new >>>>>>>>>>>>>>>>>>>>> *make* file to update your dependencies (instead of >>>>>>>>>>>>>>>>>>>>> using *composer* commands). >>>>>>>>>>>>>>>>>>>>> We've also updated the Wiki page >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> to clarify that the release notes for each version will tell you what to >>>>>>>>>>>>>>>>>>>>> run. >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> If your current version is not the last release >>>>>>>>>>>>>>>>>>>>> (20.3), it's still important to upgrade to each minor release increment >>>>>>>>>>>>>>>>>>>>> (e.g. 20.2, 20.3) before making the leap to 21.0. >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> If you're getting blank pages, post-upgrade -- Try >>>>>>>>>>>>>>>>>>>>> clearing your cache. >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> Got questions or feedback e.g. on the Release Notes? >>>>>>>>>>>>>>>>>>>>> please don't hesitate to let us know. >>>>>>>>>>>>>>>>>>>>> Thanks, >>>>>>>>>>>>>>>>>>>>> Christine >>>>>>>>>>>>>>>>>>>>> The LORIS team >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> On Tue, Aug 6, 2019 at 10:09 AM Christine Rogers, Ms. < >>>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca> wrote: >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>> Could you also let us know -- on which pages is >>>>>>>>>>>>>>>>>>>>>> content visible, and on which pages/modules is content not visible for you? >>>>>>>>>>>>>>>>>>>>>> Thanks, >>>>>>>>>>>>>>>>>>>>>> Christine >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> On Tue, Aug 6, 2019 at 9:54 AM Christine Rogers, Ms. < >>>>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca> wrote: >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> Thanks Sotirios, >>>>>>>>>>>>>>>>>>>>>>> That's good to know. It sounds like you've checked >>>>>>>>>>>>>>>>>>>>>>> that your /var/www/loris/project/config.xml file get populated properly. >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> Please send us the last few errors you're seeing in >>>>>>>>>>>>>>>>>>>>>>> your apache error log file, and your config paths and we can see what's >>>>>>>>>>>>>>>>>>>>>>> happening with your front end -- >>>>>>>>>>>>>>>>>>>>>>> Run these Troubleshooting Queries >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> to get your config path settings, given your front end is not displaying >>>>>>>>>>>>>>>>>>>>>>> fully. >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> The Loris-MRI repo >>>>>>>>>>>>>>>>>>>>>>> 21 >>>>>>>>>>>>>>>>>>>>>>> install/upgrade would then be your next steps. >>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>> Christine >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> On Tue, Aug 6, 2019 at 7:53 AM Sotirios >>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos wrote: >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> I am using a VM. What i did was: >>>>>>>>>>>>>>>>>>>>>>>> 1) Download the files from >>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris and replace them to >>>>>>>>>>>>>>>>>>>>>>>> my existing /vaw/www/loris folder. >>>>>>>>>>>>>>>>>>>>>>>> 2) Execute the composer install --no-dev and then composer >>>>>>>>>>>>>>>>>>>>>>>> dump-autoload as mentioned here >>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris/wiki/Updating-your-LORIS >>>>>>>>>>>>>>>>>>>>>>>> . >>>>>>>>>>>>>>>>>>>>>>>> 3) Execute install.sh from /var/www/loris/tools >>>>>>>>>>>>>>>>>>>>>>>> and because LORIS already existed i moved a .config file, then re-executed >>>>>>>>>>>>>>>>>>>>>>>> the install.sh successfully >>>>>>>>>>>>>>>>>>>>>>>> 4 ) As for the database, i dropped the schema and i >>>>>>>>>>>>>>>>>>>>>>>> executed the installdb.php >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 5 ??? 2019 ???? 5:22 ?.?., ?/? Christine >>>>>>>>>>>>>>>>>>>>>>>> Rogers, Ms. ??????: >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotorios, >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> Thanks - when you re-installed did you start on a >>>>>>>>>>>>>>>>>>>>>>>>> fresh root path / VM or might some of your old system setting still apply? >>>>>>>>>>>>>>>>>>>>>>>>> (And if you did any steps similar to an upgrade, >>>>>>>>>>>>>>>>>>>>>>>>> did you follow the Upgrade steps in the Release Notes, from both repos?) >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> About the TR_range column - it was recently split (MRI >>>>>>>>>>>>>>>>>>>>>>>>> pr339 ) split >>>>>>>>>>>>>>>>>>>>>>>>> into TR_min and _max columns. Given the code was trying to query TR_range >>>>>>>>>>>>>>>>>>>>>>>>> which does not exist in your mri_protocol table, double-check which version >>>>>>>>>>>>>>>>>>>>>>>>> of the Loris repo (tables) and the Loris-MRI repo (code) you have installed >>>>>>>>>>>>>>>>>>>>>>>>> to ensure they match. >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> Christine >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> On Mon, Aug 5, 2019 at 9:06 AM Sotirios >>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos wrote: >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> I reinstalled LORIS to 21 version and now the >>>>>>>>>>>>>>>>>>>>>>>>>> content is not visible at all at most pages. >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 5 ??? 2019 ???? 3:19 ?.?., ?/? Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos ??????: >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> Is it easy to upgrade to Loris 21? Also the >>>>>>>>>>>>>>>>>>>>>>>>>>> following fails because the line 1985 of NeuroDB/MRIProcessingUtility.pm >>>>>>>>>>>>>>>>>>>>>>>>>>> query mri_protocol which doesn't have TR_range >>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris/blob/21.0-release/SQL/0000-00-00-schema.sql#L556 >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> lorisadmin at hbp:/data/loris/bin/mri$ >>>>>>>>>>>>>>>>>>>>>>>>>>> ./batch_uploads_imageuploader -profile prod < ~/Desktop/input.txt > log.txt >>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $_ in pattern match >>>>>>>>>>>>>>>>>>>>>>>>>>> (m//) at ./batch_uploads_imageuploader line 147. >>>>>>>>>>>>>>>>>>>>>>>>>>> base is DCC0000_258024_V1 >>>>>>>>>>>>>>>>>>>>>>>>>>> path is /data/incoming/ >>>>>>>>>>>>>>>>>>>>>>>>>>> type is .tar.gz >>>>>>>>>>>>>>>>>>>>>>>>>>> fullpath is >>>>>>>>>>>>>>>>>>>>>>>>>>> /data/incoming/DCC0000_258024_V1.tar.gz >>>>>>>>>>>>>>>>>>>>>>>>>>> DBD::mysql::st execute failed: Unknown column >>>>>>>>>>>>>>>>>>>>>>>>>>> 'TR_range' in 'where clause' at >>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line 1985. >>>>>>>>>>>>>>>>>>>>>>>>>>> DBD::mysql::st fetchrow_array failed: fetch() >>>>>>>>>>>>>>>>>>>>>>>>>>> without execute() at >>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line 1986. >>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $count_mri_protocol >>>>>>>>>>>>>>>>>>>>>>>>>>> in numeric gt (>) at >>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line 1995. >>>>>>>>>>>>>>>>>>>>>>>>>>> DBD::mysql::st execute failed: Unknown column >>>>>>>>>>>>>>>>>>>>>>>>>>> 'TR_range' in 'field list' at >>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 562. >>>>>>>>>>>>>>>>>>>>>>>>>>> Can't exec "mail": No such file or directory at >>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 721. >>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 722. >>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 723. >>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 724. >>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 725. >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> No Mincs inserted >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> Thanks, >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 3 ??? 2019 ???? 1:08 ?.?., ?/? >>>>>>>>>>>>>>>>>>>>>>>>>>> Christine Rogers, Ms. < >>>>>>>>>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> First, just a note: we've released LORIS 21 >>>>>>>>>>>>>>>>>>>>>>>>>>>> this week with some major new features and cleanup -- especially if you are >>>>>>>>>>>>>>>>>>>>>>>>>>>> early in your setup phase, check out the Release notes for both the >>>>>>>>>>>>>>>>>>>>>>>>>>>> LORIS >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> and Loris-MRI >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> repos. >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> Thanks for your screenshots -- your empty >>>>>>>>>>>>>>>>>>>>>>>>>>>> mri_protocol table should be at the root of these issues : >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> The mri_protocol table must be populated >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> in order for your scans to be registered in LORIS -- it serves as a >>>>>>>>>>>>>>>>>>>>>>>>>>>> whitelist for the insertion pipeline which filters out scans that aren't >>>>>>>>>>>>>>>>>>>>>>>>>>>> identified or matched to scan types in this table. >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> By default, this table is populated with >>>>>>>>>>>>>>>>>>>>>>>>>>>> entries for t1, t2, fMRI and DTI (Insert >>>>>>>>>>>>>>>>>>>>>>>>>>>> statements for 21 release branch are here >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> ) >>>>>>>>>>>>>>>>>>>>>>>>>>>> Feel free to restore our default records and >>>>>>>>>>>>>>>>>>>>>>>>>>>> broaden their parameters to match all your scan types. >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> re Defaced, native, selected -- these filter >>>>>>>>>>>>>>>>>>>>>>>>>>>> the scans displayed as you move to the next page (View Session), instead of >>>>>>>>>>>>>>>>>>>>>>>>>>>> viewing "all types" of scans from a given session : >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> - "defaced" means that a defacing script >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> has masked the subject's face in the volume (for patient privacy) >>>>>>>>>>>>>>>>>>>>>>>>>>>> - "native" means that no pre-processing has >>>>>>>>>>>>>>>>>>>>>>>>>>>> been performed on the scan (it's raw data), >>>>>>>>>>>>>>>>>>>>>>>>>>>> - "selected" will show only volumes that >>>>>>>>>>>>>>>>>>>>>>>>>>>> have been QC'd and "selected" as the best of their type -- used to display >>>>>>>>>>>>>>>>>>>>>>>>>>>> only the best quality T1 image instead of all T1s acquired in a session, >>>>>>>>>>>>>>>>>>>>>>>>>>>> e.g. >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> re QC Comments -- >>>>>>>>>>>>>>>>>>>>>>>>>>>> Once you have successfully loaded scans >>>>>>>>>>>>>>>>>>>>>>>>>>>> (matched to the mri_protocol table), you'll be able to use the Imaging >>>>>>>>>>>>>>>>>>>>>>>>>>>> Browser's View Session subpage to enter/view QC comments on each volume, or >>>>>>>>>>>>>>>>>>>>>>>>>>>> for each visit. >>>>>>>>>>>>>>>>>>>>>>>>>>>> These are stored directly in the database, and >>>>>>>>>>>>>>>>>>>>>>>>>>>> linked to each scan. (Table name: >>>>>>>>>>>>>>>>>>>>>>>>>>>> feedback_mri_comments) >>>>>>>>>>>>>>>>>>>>>>>>>>>> (Visit-level QC comments are linked to the >>>>>>>>>>>>>>>>>>>>>>>>>>>> session.) >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> For a walkthrough of the Imaging setup - please >>>>>>>>>>>>>>>>>>>>>>>>>>>> see the Imaging Setup guide >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> - >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> An old LORIS walkthrough video >>>>>>>>>>>>>>>>>>>>>>>>>>>> can >>>>>>>>>>>>>>>>>>>>>>>>>>>> also walk you through some of the Imaging front-end features, starting at >>>>>>>>>>>>>>>>>>>>>>>>>>>> 8:00 >>>>>>>>>>>>>>>>>>>>>>>>>>>> LORIS' imaging modules have been updated many >>>>>>>>>>>>>>>>>>>>>>>>>>>> times since this video, but the functionality and workflow is similar. >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> Let us know how it goes once you have entries >>>>>>>>>>>>>>>>>>>>>>>>>>>> in your mri_protocol table - >>>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>>> Christine >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> On Fri, Aug 2, 2019 at 7:58 AM Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos wrote: >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Christine, >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> In the candidate_list page i can see this >>>>>>>>>>>>>>>>>>>>>>>>>>>>> patient >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> If i press the link under PSCID i get to see >>>>>>>>>>>>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> and if i press the link under Scan Done it >>>>>>>>>>>>>>>>>>>>>>>>>>>>> redirects me to imaging_browser >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> At the mri_violations page i also see No >>>>>>>>>>>>>>>>>>>>>>>>>>>>> results ( neither on resolved / not resolved ). >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> At the imaging_uploader i can see the record >>>>>>>>>>>>>>>>>>>>>>>>>>>>> that failed. >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> If i click on the tarchive info i get to see >>>>>>>>>>>>>>>>>>>>>>>>>>>>> the Protocol Name which i think is the acquisition we wanted? >>>>>>>>>>>>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Also my mri_protocol table is empty. >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Furthermore i would like to ask about the >>>>>>>>>>>>>>>>>>>>>>>>>>>>> defaced, native, selected. What exactly is native and selected? And where >>>>>>>>>>>>>>>>>>>>>>>>>>>>> are the qc comments stored? >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Finally a walkthrough would be helpful. >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thanks, >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 30 ???? 2019 ???? 8:29 ?.?., ?/? >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Christine Rogers, Ms. < >>>>>>>>>>>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Glad to hear you're making progress with the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit labels. To follow up on your last few emails: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> a- The Wiki's Setup Guide contains Sample >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> insert statements for the Visit Windows table >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> . >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> As Cecile mentioned, the consistency of visit >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> label format is important: V01, v01, V1, 01 -- whichever you select to use >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> is fine; we use V01 by default across all documentation. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> b- For Password reset, there is a script in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the tools/ directory so that a back-end administrator can reset any >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> front-end user password, including Admin. (See info on setting up / >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> resetting User passwords in the Wiki's Setup >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Guide >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ) >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> c- The minc file not being registered -- due >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> to AcquisitionProtocol unknown. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> This means the SeriesDescription (Acquisition >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Protocol) in you Dicom header was not matched to any scan listed in the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> mri_protocol database table. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> (In the online Loris-MRI Troubleshooting >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Guide, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> this >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> is Table 3, 2nd-last item "no MINCs inserted" >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The MRI Violations module (Readme here) >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> will show >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> you the details of this mismatch -- >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Go to the module (under the Imaging menu), >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> find your scan and click the link "Could not identify scan type" -- in the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> next subpage you can compare the scan's actual parameters against the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> mri_protocol table. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> To resolve this, adjust your mri_protocol >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> table values or perhaps ensure your DICOMs are labelled consistently. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Let us know if this works for you -- we can >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> also walk you through an example of non-identified scans on >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Demo.loris.ca (MRI Violations module). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Christine >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The LORIS team >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> On Tue, Jul 30, 2019 at 10:47 AM Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> wrote: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I hope this is sufficient as the error for >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the visit label disappeared. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Please see the attached file. Also something >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> i found. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> lorisadmin at hbp:/data/loris/bin/mri$ cat >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data//logs/TarLoad-17-39-xubBdv.log >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ==> Loading file from disk >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-17-39-UyQcG2/dcc0000_258024_v1_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> --> mapping DICOM parameter for >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-17-39-UyQcG2/dcc0000_258024_v1_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ==> computing md5 hash for MINC body. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> --> md5: 6b1202fd63e29de4c9be1cd9925888a5 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ==> verifying acquisition protocol >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Acquisition protocol is unknown >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> --> The minc file cannot be registered >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> since the AcquisitionProtocol is unknown >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 30 ???? 2019 ???? 4:58 ?.?., ?/? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Ok I fixed the login problem by using a >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> known hash and by deleting the rows from the login_history i was able to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> login. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 30 ???? 2019 ???? 4:50 ?.?., ?/? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> there was no visit label 01 in the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Visit_Windows table and i don't know how to insert it because the record >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> requires lots of attributes. Also the system for a reason asked me to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> update my password and now i don't remember it and my account got >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> suspended. Is there a way to reset it or set a simple password? I updated >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the password hash in the users table by using the hash from another LORIS >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> setup we had and i still couldn't login ( also the attribute password is >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> always NULL and the expiration date is 1999-01-01 for some reason ). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thanks >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 29 ???? 2019 ???? 5:21 ?.?., ?/? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Cecile Madjar >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Can you try adding the visit label v01 to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the Visit_Windows table? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> However, I noticed that in a previous >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> dataset, the label was V1. Does that refer to the same visit? If so, you >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> might want to harmonize the visit labels so they are all the same across >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> datasets for a given timepoint, meaning you will need to relabel scans when >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the visit label is different but referring to the same visit label (v01 = >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> V1 etc...). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helps, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> On Mon, Jul 29, 2019 at 10:15 AM Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> wrote: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Could you help me with the "Visit label >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> does not exist"? I had changed $subjectID{'createVisitLabel'} to 1 as you >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> had suggested but it appears that this problem hasn't been resolved yet. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> lorisadmin at hbp:/data/loris/bin/mri$ cat >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data//logs/TarLoad-14-58-9Xog7H.log >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ==> Loading file from disk >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> --> mapping DICOM parameter for >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> --> using user-defined filterParameters >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> for >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Candidate Mismatch Error is Visit label >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> does not exist >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -> WARNING: This candidate was invalid. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Logging to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> MRICandidateErrors table >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> with reason Visit label does not exist >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 26 ???? 2019 ???? 3:02 ?.?., >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ?/? Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Cecile, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The Center error was fixed. Still the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> insertion of mincs fails. Please see the output.txt file i attached. Also >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> is there something else i need to change at the paths configuration? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 25 ???? 2019 ???? 6:55 ?.?., >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ?/? Cecile Madjar < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> cecile.madjar at mcin.ca> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> We are making progress! >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I have a feeling this error comes from >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the fact that your psc table does not have the MRI_alias populated for the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DCC site. Running the following query in the mysql database should fix this: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> UPDATE psc SET MRI_alias="DCC", >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Alias="DCC" WHERE Name="Data Coordinating Center"; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Repeat the same with all your sites >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> (make sure to change the Aliases between sites, they should all be unique). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Let me know how it goes! >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> On Thu, Jul 25, 2019 at 11:43 AM >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Dear Cecile, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> You were right about your guesses. I >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> did the modifications you suggested, i still get the "no mincs inserted" >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> error, now i am getting the "No center found this candidate" error ( how do >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> i fix that? from what i see the .dcm files contains a 'Institution Name', >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> is that the center? ), so i guess that's why the validation fails, but i >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> changed the force variable of tarchiveLoader to 1, shouldn't it have >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> inserted the mincs then? Also it is optional to have a mail server, right? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ( from what i see the mail error does not affect the $valid_study, so i >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> assume we are okay with that ) >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you a lot, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 25 ???? 2019 ???? 5:48 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ?.?., ?/? Cecile Madjar < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> cecile.madjar at mcin.ca> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> From what I understand, I believe >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> you just need to update a few config settings from the frontend in the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Config module (under the Admin menu). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [image: Screen Shot 2019-07-25 at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 10.31.35 AM.png] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Then go to the Paths section of the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> config module and update the "LORIS-MRI code" config setting to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri (my guess is that currently, it is set to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data) and click on the submit button. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [image: Screen Shot 2019-07-25 at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 10.32.50 AM.png] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Then, go to Imaging Pipeline section >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> of the Configuration module and update the "Loris-MRI Data Directory" to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/ (my guess is that it is empty at the moment in your >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> database which is why $data_dir is not defined when you run the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> tarchiveLoader step of the insertion pipeline). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [image: Screen Shot 2019-07-25 at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 10.40.52 AM.png] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Finally, I took a look at your >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> environment file and it might be a good idea to update your PERL5LIB >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> variable to the following (it has been added to the code a few releases ago >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> as we realized this was needed for the libraries. Not sure which version of >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> LORIS-MRI you are using but it does not hurt to update this variable to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> what I suggest below): >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> export >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PERL5LIB=/data/loris/bin/mri/uploadNeuroDB:/data/loris/bin/mri/dicom-archive:$PERL5LIB >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helps. Sorry you are >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> experiencing so much trouble setting things up. We probably need to update >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> our WIKI. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> On Thu, Jul 25, 2019 at 9:48 AM >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The "Loris-MRI Data Directory" >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> should be in the environment file? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 25 ???? 2019 ???? 12:59 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ?.?., ?/? Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The scripts are located in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/. Somewhere I might have messed something up but i >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> remember following the instructions in the wiki.For example when i tried to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> execute the batch_uploads_imageuploader perl script the line >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> my $command = >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> "$bin_dir/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl " >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> was pointing to an invalid path, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> for example: it was repeating a pattern and had LORIS instead of loris ( i >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> think the mistake was that in the wiki it suggested to use $PROJECT for >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the name of the folder and i choosed 'loris' >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris/wiki/Imaging-Database >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ). See also the in image for the modification i did. Also i didn't find the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> section to config the $data_dir variable. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 24 ???? 2019 ???? 6:05 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ?.?., ?/? Cecile Madjar < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> cecile.madjar at mcin.ca> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> It looks like you have one Config >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> setting not set (based on the first error message you got when running it >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the first time). You need to set a value for "Loris-MRI Data Directory" in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the Config module under the Imaging pipeline section (from what I can see, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> it would be /data/loris/data/ for your setup). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The reason you got that error >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> message the second time is that the pipeline checks if the DICOM study was >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> already inserted in the tarchive table. Since you ran the study once >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> already, the study is inserted into the tarchive, hence the message. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> However, the pipeline did not complete as the MINC files were not created >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and inserted into the files/parameter_file table. In order to continue the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> insertion, you will then need to run the tarchiveLoader command suggested >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in the terminal during the second run: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -globLocation -profile prod >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive//2012/DCM_2012-12-05_ImagingUpload-17-43-ZUEFjb.tar >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -verbose >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Finally, I am a bit confused by >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> your setup. Where are the scripts located? In /data/loris/bin/mri or >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data? It feels like the Config setting "LORIS-MRI code" in the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Paths section was set to "/data/LORIS/data" but it should have been set to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the directory where the scripts are located (most probably >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helps, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> On Wed, Jul 24, 2019 at 10:55 AM >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Ok first i execute this command: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> "lorisadmin at hbp:/data/loris/bin/mri$ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ./batch_uploads_imageuploader -profile prod < ~/Desktop/input.txt > log.txt >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> $data_dir in concatenation (.) or string at ./batch_uploads_imageuploader >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> line 143. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> $data_dir in concatenation (.) or string at ./batch_uploads_imageuploader >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> line 143. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $_ in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> pattern match (m//) at ./batch_uploads_imageuploader line 147. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> base is DCC0000_258024_V01 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> path is /data/incoming/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> type is .tar.gz >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> fullpath is >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/incoming/DCC0000_258024_V01.tar.gz >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> source >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/ImagingUpload-17-43-ZUEFjb >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> targetlocation >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> $data_dir in concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 256. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> $data_dir in concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 284. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> $data_dir in concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> tarchive_validation.pl line 219. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> $data_dir in concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl line 270. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> $data_dir in concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 711. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Can't exec "mail": No such file >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> or directory at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 721. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> MAIL at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 722. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> MAIL at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 723. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> $data_dir in concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 724. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> MAIL at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 724. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> MAIL at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 725. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> $data_dir in concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 735. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> No Mincs inserted >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The tarchiveLoader insertion >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> script has failed. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Running now the following >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> command: /data/loris/data/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl -profile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> prod -upload_id 3 /data/incoming/DCC0000_258024_V01.tar.gz -verbose" >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I inserted the VisitLabel, but >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> still the Mincs are not inserted and i am getting this error >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> "lorisadmin at hbp:/data/loris/bin/mri$ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl -profile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> prod -upload_id 3 /data/incoming/DCC0000_258024_V01.tar.gz -verbose >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> find -path >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> \/tmp\/ImagingUpload\-17\-45\-5MsWEd -name '__MACOSX' -delete >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Spool message is: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The Scan for the uploadID 3 has >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> already been run with tarchiveID: 7. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> To continue with the rest of the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> insertion pipeline, please run tarchiveLoader from a terminal as follows: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader -globLocation -profile prod >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive//2012/DCM_2012-12-05_ImagingUpload-17-43-ZUEFjb.tar >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -verbose" >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Which files should i delete? I >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> thought that deleting the files from the tarchive was enough. And i >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> executed the last proposed command to continue to rest of the insertion >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> pipeline ( check the image ). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 24 ???? 2019 ???? 5:05 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ?.?., ?/? Cecile Madjar < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> cecile.madjar at mcin.ca> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sorry I was not clear before. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Every visits of candidates are created in the session table with one entry >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> per CandID/VisitLabel. So if the imaging pipeline created visits in the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> session table (that are not attached to instruments) and you want to clean >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> your database completely, you can delete entries in that table as well. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Regarding your point 2, the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> imaging pipeline can create the visit in the session table as long as the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit label is present in the Visit_Windows table (which means the visit >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> label stored in the PatientName is a valid visit label). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> However, in your prod file, if >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the variable $subjectID{'createVisitLabel'} is set to 1 for candidates, the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit label should be created in the Visit_Windows table I believe. Here >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> is the line of the prod file you would need to change >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> . >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> In general, we prefer >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> populating the Visit_Windows table and set the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> $subjectID{'createVisitLabel'} to 0 for candidate data to avoid insertion >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> of badly labelled MRI data that are complex to relabel. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Finally, regarding the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> candidate creation, if you execute the following steps, the pipeline should >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> be able to create candidates: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - set in the Imaging Pipeline >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> section of the config module the config setting "Upload creation of >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> candidates" to Yes >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - manually transfer the scans >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> to the LORIS server instead of uploading it via the imaging browser >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - run batch_imaging_upload.pl >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> as you did until now. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helps! >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> On Wed, Jul 24, 2019 at 8:47 AM >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> About my second question i >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> replaced the name of the patient in the .dcm files and now i am getting an >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> error that the visit label does not exist. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I thought it was supposed to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> be automatically created. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> "Done adding archive info into >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> database >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -globLocation -profile prod >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive//DCM_2012-12-05_ImagingUpload-15-42-yUwQQV.tar >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -verbose >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> md5sum >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive/DCM_2012-12-05_ImagingUpload-15-42-yUwQQV.tar >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> candidate id 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> => No Visit labelVisit label >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> does not exist >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Set centerID = 1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Number of MINC files that will >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> be considered for inserting into the database: 1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> log dir is /logs and log file >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> is /logs/TarLoad-15-42-L6pocU.log >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> candidate id 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> => No Visit label >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Cleaning up temp files: rm -rf >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-15-42-J2rQms/ImagingUpload-15-42-yUwQQV*" >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 24 ???? 2019 ???? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 3:38 ?.?., ?/? Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 1) What are the records in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the session table? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 2) I tried to upload a >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> non-phantom file like this >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> input_file.txt: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/incoming/DCC0000_258024_V1.tar.gz >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> N DCC0000_258024_V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Terminal: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ./batch_uploads_imageuploader >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -profile prod < ~/Desktop/input.txt > log.txt >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and i get the following error >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in the log.txt file >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> "Running now the following >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> command: /data/loris/data/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -profile prod -upload_id 7 /data/incoming/DCC0000_258024_V1.tar.gz -verbose >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> find -path >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> \/tmp\/ImagingUpload\-14\-56\-FeLCB4 -name '__MACOSX' -delete >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Spool message is: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The PatientName read from the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DICOM header does not start with DCC0000_258024_V1 from the mri_upload table >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> " >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and the spool message is >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> repeated for each .dcm file. Should i preprocess every .dcm file and change >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the PatientName to "DCC0000_258024_V1"? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 3) As far as it concerns the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> candidate profile i have to create a new one each time before i try to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> upload a file? Is there already a way to create a candidate profile and get >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the DCCID and PSCID without the user interface? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 18 ???? 2019 ???? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 5:00 ?.?., ?/? Cecile Madjar < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> cecile.madjar at mcin.ca> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> See answers to your >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> questions below. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> About the 1st case we had a >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> dicom with a blank studyUID, maybe someone accidentally removed it. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> That is strange. Something >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> must have been done to the DICOM files. I have never seen a study with no >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> StudyUID out of the scanner. Usually, you need to manually erase it with >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> some tool. However, DICOMs never cease to surprise me... >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Some other questions: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 1) What are the steps to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> remove all of my patients and uploads?: because i want to try to reupload >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> all the testing dicoms we had with a clean database. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Release 21.0 of LORIS-MRI >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> will offer a script to remove all the entries and files specific to an >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> upload. However, this release is not yet out. Hopefully in the next few >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> weeks. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> In the meantime, since your >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> case is particular and that you just want to start with a clean database, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the following deletes should work (hopefully I won't forget any tables): >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> mri_violations_log; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> mri_protocol_violated_scans; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> MRICandidateErrors; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from parameter_file; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from files_qcstatus; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> # (if you played with the QC part of the imaging browser for testing) >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> feedback_mri_comments; # (if you played with the QC part of the imaging >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> browser for testing) >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from tarchive_series; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from tarchive_files; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from mri_upload; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from tarchive; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from mri_scanner; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from candidate where >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID="scanner"; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I don't know if you want to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> also delete entries in the session and candidate table too? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 2) We do not need to create >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the profile of a patient ( are the patients stored in the candidate table? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> because i can't see the ghosts ), because will it automatically be created >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> when importing a dicom? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I am not sure I understand >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> fully this question. All candidates are stored in the candidate table. The >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> phantom scans however are attached to a scanner candidate depending on >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> where the scan happened. It is a bit of a weird concept that we have to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> redesign eventually but never got a chance to get to it. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hopefully this answered your >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> question, otherwise, don't hesitate to let me know. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 3) What is the difference >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> between uploading a dicom as phantom instead of importing as >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCCID_DCCID_VisitLabel? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> When you upload the scan as >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID_DCCID_VisitLabel, there is a check that makes sure the candidate IDs >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and visit label are valid at the time of upload. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> When you upload a scan as >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> phantom, it expects that the DICOM field PatientName and uploaded filename >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> contains the string "phantom". We enforced this behaviour on the imaging >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> uploader side in recent releases but I can't remember which one. Probably >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the upcoming 21.0 release. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> All those verifications >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> might seem cumbersome but they are here to ensure that the files inserted >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> are all valid and labelled properly as it is a bit messy to have to delete >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> files that were wrongly labelled. At least, the delete script present in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> release 21.0 will make this process easier but it is still good practice to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> verify those things. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> With pleasure. Hopefully the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> answers to your questions will be helpful. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PS: loris-dev mailing list: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> you will find the initial answer I gave Sotirios below. I forgot to cc the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> loris-dev in my earlier reply... >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 16 ???? 2019 ???? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 12:02 ?.?., ?/? Cecile Madjar < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> cecile.madjar at mcin.ca> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Dear Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you for reaching >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> out. Since your email was already organized in points, I will reply >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> directly below your questions below. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 1) What do we do when the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> StudyUID is blank on the header? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/minor/docs/AppendixA-Troubleshooting_guideline.md >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> There solution provided at the table 3 does not guide us how to find the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> information ( is possible ). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The StudyUID is the field >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> used in our pipeline at the moment to check whether a DICOM study was >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> already inserted into LORIS with that same StudyUID since it is supposed to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> be unique for every single study. Currently, we do not support insertion of >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DICOM studies if they do not have a StudyUID associated with them. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Is there a specific reason >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> why the StudyUID is blank in the DICOM headers in your DICOM files? Did >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> they go through some processes before upload to LORIS? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 2) When i am about to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> upload a non-phanton case i need a 'Visit Label'. Is there already a script >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> that can create a new visit label for a specific Candidate, so i can >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> provide it as input afterwards to the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> batch_uploads_imageuploader ( See option 5.1.3 https://github.com/aces/Loris-MRI/blob/minor/docs/05-PipelineLaunchOptions.md ) >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I am not sure if the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> front-end allows for it but if you use batch_uploads_imageuploader, the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> insertion scripts could create the visit label for you. However, it does >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> need to be included in the patient name in order for the script to know >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> which label it should use. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> For example: you upload >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> V02 for MTL0123 (DCCID: 456789) but V02 was not yet created for MTL0123; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the insertion scripts will create a V02 visit for MTL0123 if the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PatientName field for the dataset is MTL0123_456789_V02 with Stage marked >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> as "Not Started". >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> However, *note that for >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the script to create the visit for the candidate, you have to make sure >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> that all the visit label of your projects were inserted in the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Visit_Windows table* >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> (otherwise, the visit will never be created as they were not specified as >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> being part of the list of visit label to expect). So in the example above, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> you should have one row in Visit_Windows with Visit_label="V02" set. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 3) Section 4.3 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/minor/docs/04-Scripts.md >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> What do we do when the folder contains multiple mnc files? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> This is a case by case. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Most of the time, the MINC files that failed insertion into the imaging >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> browser end up in the MRI violation module where you can see what went >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> wrong with the acquisitions not inserted. If you notice that the MINC file >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> should be inserted as a specific protocol, you can force the insertion as >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> explained in section 4.3. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> In your case, I have a >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> feeling that you want to be able to insert MINC files that did not go >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> through the whole pipeline insertion (DICOM archival, then dcm2mnc, then >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> protocol identification, then insertion...). In theory, you could call >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl on any >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> MINC file, provided you have at least the following information: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - path to the MINC file >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - uploadID associated with >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the MINC files or DICOM archive path from which those MINC files were >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> created from >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Then the minc_insertion.pl >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> script will do the subject information and protocol validation etc... >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> If all the MINC files come >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> from the same uploadID or TarchiveID, then you could run a loop in bash >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> calling the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl script >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> like this for files deriving from uploadID=1: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ls /path/to/mnc/folder/* | >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> while read f; do >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -profile prod -uploadID 1 -mincPath $f; done >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helped! >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> MCIN.ca >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>>>>>>>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | >>>>>>>>>>>>>>>>>>>>>>>>>>>> MCIN.ca >>>>>>>>>>>>>>>>>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>>>>>>>>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>>>>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | >>>>>>>>>>>>>>>>>>>>>>>>> MCIN.ca >>>>>>>>>>>>>>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>>>>>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>>>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>>>>>> >>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>> >>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> -- >>>>>>>>>>> Shen Wang >>>>>>>>>>> Loris Developer >>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>> McGill University >>>>>>>>>>> >>>>>>>>>>> >>>>>>> >>>>>>> -- >>>>>>> Shen Wang >>>>>>> Loris Developer >>>>>>> Montreal Neurological Institute >>>>>>> McGill University >>>>>>> >>>>>>> -- >>>>>> Shen Wang >>>>>> Loris Developer >>>>>> Montreal Neurological Institute >>>>>> McGill University >>>>>> >>>>>> _______________________________________________ >>>>>> Loris-dev mailing list >>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>> >>>>> >>>>> >>>>> -- >>>>> >>>>> christine.rogers at mcgill.ca >>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>> Montreal Neurological Institute >>>>> McGill University | Montreal | Canada >>>>> >>>> >> >> -- >> Shen Wang >> Loris 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URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: ???? 2019-08-13 19.21.15.png Type: image/png Size: 508603 bytes Desc: not available URL: From sotirisnik at gmail.com Thu Aug 15 14:28:35 2019 From: sotirisnik at gmail.com (Sotirios Nikoloutsopoulos) Date: Thu, 15 Aug 2019 21:28:35 +0300 Subject: [Loris-dev] Upgrading to Loris 21 - new make file In-Reply-To: References: Message-ID: Hi, should i try to redownload the files from https://github.com/aces/Loris/tree/major and execute the install.sh? I find it weird that i am missing some files. Thanks ???? ???, 15 ??? 2019 ???? 9:17 ?.?., ?/? Shen Wang ??????: > Hi Sotirios, > It seems like you are missing this file. [ .babelrc] > step 1: copy from https://github.com/aces/Loris/blob/major/.babelrc > step 2: sudo vi webpack.config.js > remove these lines > > { test: /\.js$/, > > exclude: /node_modules/, > > // use: ['babel-loader', 'eslint-loader'], > > }, > > step 3: sudo make > > > > On Wed, 14 Aug 2019 at 18:52, Sotirios Nikoloutsopoulos < > sotirisnik at gmail.com> wrote: > >> Hi Shen, >> >> That didn't work either. Also i had removed the git files because i was >> getting this error when i used make: >> >> "git describe --tags --always > VERSION >> fatal: Not a git repository (or any of the parent directories): .git >> Makefile:8: recipe for target 'VERSION' failed >> make: *** [VERSION] Error 128" >> >> Thanks >> >> ???? ???, 15 ??? 2019 ???? 1:36 ?.?., ?/? Shen Wang < >> wangshen.mcin at gmail.com> ??????: >> >>> Hi,Sotirios >>> In your special situation, there is a temporary fix. >>> step 1. sudo git stash >>> step 2. open webpack.config.js file >>> remove line 75 use: ['babel-loader', 'eslint-loader'], >>> save it. >>> step 3. sudo make >>> >>> I hope this could help you to compile the js files. >>> >>> >>> >>> On Wed, 14 Aug 2019 at 08:28, Sotirios Nikoloutsopoulos < >>> sotirisnik at gmail.com> wrote: >>> >>>> I forgot to mention that i had already moved my previous config file >>>> and re-executed the installation script. >>>> >>>> ???? ???, 14 ??? 2019 ???? 3:26 ?.?., ?/? Sotirios Nikoloutsopoulos < >>>> sotirisnik at gmail.com> ??????: >>>> >>>>> Hi, >>>>> >>>>> Step 1 worked and the indentation errors were fixed. About step2 i >>>>> added all of these( there are more to include in the list) these to >>>>> .eslintignore which were reported to fail at being built, but they still >>>>> appear on the errors at the make_output file. >>>>> >>>>> /jsx/DynamicDataTable.js >>>>> /jsx/StaticDataTable.js >>>>> /jsx/MultiSelectDropdown.js >>>>> /jsx/Breadcrumbs.js >>>>> /jsx/Form.js >>>>> /jsx/Markdown.js >>>>> /modules/media/jsx/mediaIndex.js >>>>> /modules/issue_tracker/jsx/issueTrackerIndex.js >>>>> /modules/issue_tracker/jsx/index.js >>>>> /modules/candidate_parameters/jsx/CandidateParameters.js >>>>> /modules/configuration/jsx/SubprojectRelations.js >>>>> /modules/conflict_resolver/jsx/conflictResolverIndex.js >>>>> /modules/conflict_resolver/jsx/resolvedConflictsIndex.js >>>>> /modules/bvl_feedback/jsx/react.behavioural_feedback_panel.js >>>>> /modules/dataquery/jsx/react.tabs.js >>>>> /modules/document_repository/jsx/docIndex.js >>>>> /modules/instrument_builder/jsx/react.instrument_builder.js >>>>> /modules/imaging_uploader/jsx/index.js >>>>> /modules/datadict/jsx/dataDictIndex.js >>>>> /modules/bvl_feedback/jsx/react.behavioural_feedback_panel.js >>>>> /modules/new_profile/jsx/NewProfileIndex.js >>>>> /modules/examiner/jsx/examinerIndex.js >>>>> /modules/configuration/jsx/SubprojectRelations.js >>>>> /modules/data_team_helper/jsx/behavioural_qc_module.js >>>>> /modules/acknowledgements/jsx/acknowledgementsIndex.js >>>>> /modules/candidate_parameters/jsx/CandidateParameters.js >>>>> /modules/imaging_browser/jsx/ImagePanel.js >>>>> /modules/mri_violations/jsx/mri_protocol_violations_columnFormatter.js >>>>> >>>>> /modules/mri_violations/jsx/mri_protocol_check_violations_columnFormatter.js >>>>> /modules/genomic_browser/jsx/profileColumnFormatter.js >>>>> /modules/dataquery/jsx/react.tabs.js >>>>> /jsx/MultiSelectDropdown.js >>>>> /modules/mri_violations/jsx/columnFormatterUnresolved.js >>>>> /modules/dataquery/jsx/react.sidebar.js >>>>> /modules/dataquery/jsx/react.fieldselector.js >>>>> /modules/quality_control/jsx/qualityControlIndex.js >>>>> /modules/dataquery/jsx/react.paginator.js >>>>> /modules/instrument_builder/jsx/react.questions.js >>>>> /modules/dataquery/jsx/react.filterBuilder.js >>>>> /modules/conflict_resolver/jsx/conflictResolverIndex.js >>>>> /jsx/PaginationLinks.js >>>>> /modules/conflict_resolver/jsx/resolvedConflictsIndex.js >>>>> /modules/dataquery/jsx/react.app.js >>>>> /modules/candidate_list/jsx/onLoad.js >>>>> /jsx/Form.js >>>>> /modules/publication/jsx/publicationIndex.js >>>>> /modules/server_processes_manager/jsx/server_processes_managerIndex.js >>>>> /modules/imaging_browser/jsx/imagingBrowserIndex.js >>>>> /modules/issue_tracker/jsx/issueTrackerIndex.js >>>>> /modules/survey_accounts/jsx/surveyAccountsIndex.js >>>>> /modules/data_integrity_flag/jsx/dataIntegrityFlagIndex.js >>>>> /modules/instrument_manager/jsx/instrumentManagerIndex.js >>>>> /modules/media/jsx/mediaIndex.js >>>>> /modules/user_accounts/jsx/userAccountsIndex.js >>>>> /modules/help_editor/jsx/help_editor.js >>>>> /modules/dicom_archive/jsx/dicom_archive.js >>>>> /modules/mri_violations/jsx/columnFormatter.js >>>>> /modules/brainbrowser/jsx/Brainbrowser.js >>>>> /node_modules/babel-loader/lib/index.js >>>>> /modules/document_repository/jsx/editFormIndex.js >>>>> >>>>> Thanks >>>>> >>>>> ???? ???, 14 ??? 2019 ???? 7:50 ?.?., ?/? Christine Rogers, Ms. < >>>>> christine.rogers at mcgill.ca> ??????: >>>>> >>>>>> Hi Shen and Sotirios - just a note, >>>>>> >>>>>> For the 21 release, it's best to run the install script without >>>>>> sudoing it. >>>>>> >>>>>> (Shen, I believe we discovered a minor issue with the sudo last week >>>>>> #5008) >>>>>> >>>>>> Best, >>>>>> Christine >>>>>> >>>>>> On Tue, Aug 13, 2019 at 9:22 PM Shen Wang >>>>>> wrote: >>>>>> >>>>>>> Does it work? If still doesn?t work, try to remove >>>>>>> project/config.xml file. Do sudo ./install.sh again. To reinstall Loris >>>>>>> again. >>>>>>> >>>>>>> >>>>>>> Shen Wang ?2019?8?13? ????9:02??? >>>>>>> >>>>>>>> Hi Sotirios, >>>>>>>> step 1: >>>>>>>> sudo ./node_modules/.bin/eslint --fix /var/www/loris >>>>>>>> step 2: >>>>>>>> put the rest error files under this line [# Ignore until ESLint is >>>>>>>> run] in the .eslintignore file. >>>>>>>> step 3: >>>>>>>> sudo make >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> On Tue, 13 Aug 2019 at 20:34, Sotirios Nikoloutsopoulos < >>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>> >>>>>>>>> I did the modifications, still there are errors. >>>>>>>>> Thanks >>>>>>>>> >>>>>>>>> >>>>>>>>> ???? ???, 14 ??? 2019 ???? 3:22 ?.?., ?/? Shen Wang < >>>>>>>>> wangshen.mcin at gmail.com> ??????: >>>>>>>>> >>>>>>>>>> Hi Sotirios, >>>>>>>>>> I saw your output file, the config issue is gone. >>>>>>>>>> you can use [sudo npm run lintfix:javascript ] to fix these >>>>>>>>>> indent issues. >>>>>>>>>> If it still has errors. >>>>>>>>>> Then try modify this file .eslintignore >>>>>>>>>> with this >>>>>>>>>> >>>>>>>>>> # Ignore until ESLint is run >>>>>>>>>> >>>>>>>>>> modules/* >>>>>>>>>> >>>>>>>>>> modules/dataquery/ >>>>>>>>>> >>>>>>>>>> node_modules/* >>>>>>>>>> >>>>>>>>>> htdocs/js/components/* >>>>>>>>>> >>>>>>>>>> jsx/* >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> # Ignore external libs >>>>>>>>>> >>>>>>>>>> htdocs/js/flot/* >>>>>>>>>> >>>>>>>>>> htdocs/js/jquery/* >>>>>>>>>> >>>>>>>>>> htdocs/js/jszip/* >>>>>>>>>> >>>>>>>>>> htdocs/js/modernizr/* >>>>>>>>>> >>>>>>>>>> htdocs/js/modules/* >>>>>>>>>> >>>>>>>>>> htdocs/js/react/* >>>>>>>>>> >>>>>>>>>> htdocs/js/shims/* >>>>>>>>>> >>>>>>>>>> htdocs/js/c3.min.js >>>>>>>>>> >>>>>>>>>> htdocs/js/d3.min.js >>>>>>>>>> >>>>>>>>>> htdocs/js/FileSaver.min.js >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> then do sudo make. >>>>>>>>>> It should work. >>>>>>>>>> Regards >>>>>>>>>> Shen >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> Sotirios Nikoloutsopoulos ?2019?8?13? >>>>>>>>>> ????7:54??? >>>>>>>>>> >>>>>>>>>>> No, it didn't work, i also tried space/tabs because most of the >>>>>>>>>>> errors where about indentation, also there are some errors about React. >>>>>>>>>>> >>>>>>>>>>> Thanks >>>>>>>>>>> >>>>>>>>>>> lorisadmin at hbp:/var/www/loris$ sudo ./node_modules/.bin/eslint >>>>>>>>>>> --init >>>>>>>>>>> ? How would you like to configure ESLint? Answer questions about >>>>>>>>>>> your style >>>>>>>>>>> ? Which version of ECMAScript do you use? ES2015 >>>>>>>>>>> ? Are you using ES6 modules? Yes >>>>>>>>>>> ? Where will your code run? Browser >>>>>>>>>>> ? Do you use CommonJS? Yes >>>>>>>>>>> ? Do you use JSX? Yes >>>>>>>>>>> ? Do you use React? Yes >>>>>>>>>>> ? What style of indentation do you use? Spaces >>>>>>>>>>> ? What quotes do you use for strings? Single >>>>>>>>>>> ? What line endings do you use? Unix >>>>>>>>>>> ? Do you require semicolons? Yes >>>>>>>>>>> ? What format do you want your config file to be in? JSON >>>>>>>>>>> The config that you've selected requires the following >>>>>>>>>>> dependencies: >>>>>>>>>>> >>>>>>>>>>> eslint-plugin-react at latest >>>>>>>>>>> Successfully created .eslintrc.json file in /var/www/loris >>>>>>>>>>> >>>>>>>>>>> lorisadmin at hbp:/var/www/loris$ sudo make > sudo_make_output >>>>>>>>>>> npm WARN The package prop-types is included as both a dev and >>>>>>>>>>> production dependency. >>>>>>>>>>> npm WARN optional SKIPPING OPTIONAL DEPENDENCY: fsevents at 1.2.4 >>>>>>>>>>> (node_modules/fsevents): >>>>>>>>>>> npm WARN notsup SKIPPING OPTIONAL DEPENDENCY: Unsupported >>>>>>>>>>> platform for fsevents at 1.2.4: wanted >>>>>>>>>>> {"os":"darwin","arch":"any"} (current: {"os":"linux","arch":"x64"}) >>>>>>>>>>> >>>>>>>>>>> npm ERR! code ELIFECYCLE >>>>>>>>>>> npm ERR! errno 2 >>>>>>>>>>> npm ERR! loris at 1.0.0 compile: `webpack` >>>>>>>>>>> npm ERR! Exit status 2 >>>>>>>>>>> npm ERR! >>>>>>>>>>> npm ERR! Failed at the loris at 1.0.0 compile script. >>>>>>>>>>> npm ERR! This is probably not a problem with npm. There is >>>>>>>>>>> likely additional logging output above. >>>>>>>>>>> >>>>>>>>>>> npm ERR! A complete log of this run can be found in: >>>>>>>>>>> npm ERR! >>>>>>>>>>> /home/lorisadmin/.npm/_logs/2019-08-13T23_40_58_841Z-debug.log >>>>>>>>>>> >>>>>>>>>>> ???? ???, 14 ??? 2019 ???? 2:29 ?.?., ?/? Shen Wang < >>>>>>>>>>> wangshen.mcin at gmail.com> ??????: >>>>>>>>>>> >>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>> When you do make command, please make sure with sudo at the >>>>>>>>>>>> beginning. [sudo make] >>>>>>>>>>>> If it still doesn't work for you. >>>>>>>>>>>> Then try the solutions below. >>>>>>>>>>>> solution 1: >>>>>>>>>>>> [image: ???? 2019-08-13 19.21.15.png] >>>>>>>>>>>> Regards >>>>>>>>>>>> Shen >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> On Tue, 13 Aug 2019 at 17:22, Sotirios Nikoloutsopoulos < >>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>> >>>>>>>>>>>>> I think that the files exists although i redownloaded the >>>>>>>>>>>>> eslintrc.json i checked others files that had similar errors. >>>>>>>>>>>>> >>>>>>>>>>>>> lorisadmin at hbp:/var/www/loris$ ls -l >>>>>>>>>>>>> ./node_modules/eslint-loader/index.js >>>>>>>>>>>>> -rw-rw-r-- 1 lorisadmin lorisadmin 6463 ??? 26 1985 >>>>>>>>>>>>> ./node_modules/eslint-loader/index.js >>>>>>>>>>>>> >>>>>>>>>>>>> lorisadmin at hbp:/var/www/loris$ ls -l .eslintrc.json >>>>>>>>>>>>> -rw-rw-r-- 1 lorisadmin lorisadmin 84530 ??? 14 00:04 >>>>>>>>>>>>> .eslintrc.json >>>>>>>>>>>>> >>>>>>>>>>>>> Maybe this can help >>>>>>>>>>>>> >>>>>>>>>>>>> Module build failed (from >>>>>>>>>>>>> ./node_modules/eslint-loader/index.js): >>>>>>>>>>>>> SyntaxError: Cannot read config file: >>>>>>>>>>>>> /var/www/loris/.eslintrc.json >>>>>>>>>>>>> Error: Unexpected token < in JSON at position 6 >>>>>>>>>>>>> at JSON.parse () >>>>>>>>>>>>> at loadJSONConfigFile >>>>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config/config-file.js:114:21) >>>>>>>>>>>>> at loadConfigFile >>>>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config/config-file.js:230:26) >>>>>>>>>>>>> at loadFromDisk >>>>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config/config-file.js:500:18) >>>>>>>>>>>>> at Object.load >>>>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config/config-file.js:564:20) >>>>>>>>>>>>> at Config.getLocalConfigHierarchy >>>>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config.js:227:44) >>>>>>>>>>>>> at Config.getConfigHierarchy >>>>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config.js:179:43) >>>>>>>>>>>>> at Config.getConfigVector >>>>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config.js:286:21) >>>>>>>>>>>>> at Config.getConfig >>>>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config.js:329:29) >>>>>>>>>>>>> at processText >>>>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/cli-engine.js:162:33) >>>>>>>>>>>>> at CLIEngine.executeOnText >>>>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/cli-engine.js:596:17) >>>>>>>>>>>>> at lint >>>>>>>>>>>>> (/var/www/loris/node_modules/eslint-loader/index.js:237:17) >>>>>>>>>>>>> at Object.module.exports >>>>>>>>>>>>> (/var/www/loris/node_modules/eslint-loader/index.js:232:21) >>>>>>>>>>>>> >>>>>>>>>>>>> ERROR in ./modules/imaging_uploader/jsx/index.js >>>>>>>>>>>>> Module build failed (from >>>>>>>>>>>>> ./node_modules/eslint-loader/index.js): >>>>>>>>>>>>> SyntaxError: Cannot read config file: >>>>>>>>>>>>> /var/www/loris/.eslintrc.json >>>>>>>>>>>>> Error: Unexpected token < in JSON at position 6 >>>>>>>>>>>>> at JSON.parse () >>>>>>>>>>>>> at loadJSONConfigFile >>>>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config/config-file.js:114:21) >>>>>>>>>>>>> at loadConfigFile >>>>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config/config-file.js:230:26) >>>>>>>>>>>>> at loadFromDisk >>>>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config/config-file.js:500:18) >>>>>>>>>>>>> at Object.load >>>>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config/config-file.js:564:20) >>>>>>>>>>>>> at Config.getLocalConfigHierarchy >>>>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config.js:227:44) >>>>>>>>>>>>> at Config.getConfigHierarchy >>>>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config.js:179:43) >>>>>>>>>>>>> at Config.getConfigVector >>>>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config.js:286:21) >>>>>>>>>>>>> at Config.getConfig >>>>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config.js:329:29) >>>>>>>>>>>>> at processText >>>>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/cli-engine.js:162:33) >>>>>>>>>>>>> at CLIEngine.executeOnText >>>>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/cli-engine.js:596:17) >>>>>>>>>>>>> at lint >>>>>>>>>>>>> (/var/www/loris/node_modules/eslint-loader/index.js:237:17) >>>>>>>>>>>>> at Object.module.exports >>>>>>>>>>>>> (/var/www/loris/node_modules/eslint-loader/index.js:232:21) >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> ???? ???, 13 ??? 2019 ???? 11:52 ?.?., ?/? John Saigle < >>>>>>>>>>>>> john.saigle at mcin.ca> ??????: >>>>>>>>>>>>> >>>>>>>>>>>>>> HI Sotirios, >>>>>>>>>>>>>> >>>>>>>>>>>>>> The make_output.txt file shows webpack failing because it >>>>>>>>>>>>>> can't find the ESLint config file. >>>>>>>>>>>>>> >>>>>>>>>>>>>> Can you confirm whether the file `.eslintrc.json` exists >>>>>>>>>>>>>> within your loris root directory (usually `/var/www/loris/`)? When I delete >>>>>>>>>>>>>> my file I get the same errors as you. >>>>>>>>>>>>>> >>>>>>>>>>>>>> If you find that it's missing, you can make a local copy with >>>>>>>>>>>>>> the contents found here: >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> https://github.com/aces/Loris/blob/e26a6ad49a73fcffef0cd73bb600c4d17b200b62/.eslintrc.json >>>>>>>>>>>>>> >>>>>>>>>>>>>> Once you know it exists, try running `make` again. >>>>>>>>>>>>>> >>>>>>>>>>>>>> Let us know if that moves you forward. >>>>>>>>>>>>>> >>>>>>>>>>>>>> Best, >>>>>>>>>>>>>> John >>>>>>>>>>>>>> >>>>>>>>>>>>>> On Tue, Aug 13, 2019 at 2:21 PM Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>> >>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>> I executed the commands for the node and now i am get the >>>>>>>>>>>>>>> followings: >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> lorisadmin at hbp:/var/www/loris$ make > ~/make_output >>>>>>>>>>>>>>> npm WARN The package prop-types is included as both a dev >>>>>>>>>>>>>>> and production dependency. >>>>>>>>>>>>>>> npm WARN optional SKIPPING OPTIONAL DEPENDENCY: >>>>>>>>>>>>>>> fsevents at 1.2.4 (node_modules/fsevents): >>>>>>>>>>>>>>> npm WARN notsup SKIPPING OPTIONAL DEPENDENCY: Unsupported >>>>>>>>>>>>>>> platform for fsevents at 1.2.4: wanted >>>>>>>>>>>>>>> {"os":"darwin","arch":"any"} (current: {"os":"linux","arch":"x64"}) >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> npm ERR! code ELIFECYCLE >>>>>>>>>>>>>>> npm ERR! errno 2 >>>>>>>>>>>>>>> npm ERR! loris at 1.0.0 compile: `webpack` >>>>>>>>>>>>>>> npm ERR! Exit status 2 >>>>>>>>>>>>>>> npm ERR! >>>>>>>>>>>>>>> npm ERR! Failed at the loris at 1.0.0 compile script. >>>>>>>>>>>>>>> npm ERR! This is probably not a problem with npm. There is >>>>>>>>>>>>>>> likely additional logging output above. >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> npm ERR! A complete log of this run can be found in: >>>>>>>>>>>>>>> npm ERR! >>>>>>>>>>>>>>> /home/lorisadmin/.npm/_logs/2019-08-13T18_12_05_378Z-debug.log >>>>>>>>>>>>>>> make: *** [javascript] Error 2 >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> Thanks, >>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> ???? ???, 12 ??? 2019 ???? 10:19 ?.?., ?/? Christine Rogers, >>>>>>>>>>>>>>> Ms. ??????: >>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> We've seen some users installing LORIS 21 or upgrading to >>>>>>>>>>>>>>>> 21 whose version of node doesn't work well with webpack, due to updated >>>>>>>>>>>>>>>> packages they're missing. >>>>>>>>>>>>>>>> If so, update your node : >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> curl -sL https://deb.nodesource.com/setup_8.x | sudo -E bash - >>>>>>>>>>>>>>>> sudo apt-get install -y nodejs >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Let us know how that goes -- please send us output from the >>>>>>>>>>>>>>>> same log if any issues. >>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>> Christine >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> On Thu, Aug 8, 2019 at 2:38 PM Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> It's not a disk space issue, as you can see below i have >>>>>>>>>>>>>>>>> still 74GB available. >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> lorisadmin at hbp:/var/www/loris$ df -h >>>>>>>>>>>>>>>>> Filesystem Size Used Avail Use% Mounted on >>>>>>>>>>>>>>>>> udev 2,9G 0 2,9G 0% /dev >>>>>>>>>>>>>>>>> tmpfs 597M 8,6M 588M 2% /run >>>>>>>>>>>>>>>>> /dev/sda1 98G 19G 74G 21% / >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Maybe we have to pass a flag to get into strict mode? as >>>>>>>>>>>>>>>>> stated "SyntaxError: Block-scoped declarations (let, const, function, >>>>>>>>>>>>>>>>> class) not yet supported outside strict mode" >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Thanks, >>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> ???? ???, 8 ??? 2019 ???? 4:32 ?.?., ?/? Dave MacFarlane < >>>>>>>>>>>>>>>>> dave.macfarlane at mcin.ca> ??????: >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> It looks like the javascript snippet shown in the error >>>>>>>>>>>>>>>>>> message when trying to compile the js is truncated. Have you run out of >>>>>>>>>>>>>>>>>> disk space? >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> On Thu, Aug 8, 2019 at 8:37 AM Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> I runned make and also included the file it reports at >>>>>>>>>>>>>>>>>>> the end. >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> lorisadmin at hbp:/var/www/loris$ make >>>>>>>>>>>>>>>>>>> npm install >>>>>>>>>>>>>>>>>>> npm WARN optional Skipping failed optional dependency >>>>>>>>>>>>>>>>>>> /chokidar/fsevents: >>>>>>>>>>>>>>>>>>> npm WARN notsup Not compatible with your operating >>>>>>>>>>>>>>>>>>> system or architecture: fsevents at 1.2.9 >>>>>>>>>>>>>>>>>>> npm WARN optional Skipping failed optional dependency >>>>>>>>>>>>>>>>>>> /watchpack/chokidar/fsevents: >>>>>>>>>>>>>>>>>>> npm WARN notsup Not compatible with your operating >>>>>>>>>>>>>>>>>>> system or architecture: fsevents at 1.2.9 >>>>>>>>>>>>>>>>>>> npm run compile >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> > loris at 1.0.0 compile /var/www/loris >>>>>>>>>>>>>>>>>>> > webpack >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> /var/www/loris/node_modules/webpack/bin/webpack.js:86 >>>>>>>>>>>>>>>>>>> let notify = >>>>>>>>>>>>>>>>>>> ^^^ >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> SyntaxError: Block-scoped declarations (let, const, >>>>>>>>>>>>>>>>>>> function, class) not yet supported outside strict mode >>>>>>>>>>>>>>>>>>> at exports.runInThisContext (vm.js:53:16) >>>>>>>>>>>>>>>>>>> at Module._compile (module.js:374:25) >>>>>>>>>>>>>>>>>>> at Object.Module._extensions..js (module.js:417:10) >>>>>>>>>>>>>>>>>>> at Module.load (module.js:344:32) >>>>>>>>>>>>>>>>>>> at Function.Module._load (module.js:301:12) >>>>>>>>>>>>>>>>>>> at Function.Module.runMain (module.js:442:10) >>>>>>>>>>>>>>>>>>> at startup (node.js:136:18) >>>>>>>>>>>>>>>>>>> at node.js:966:3 >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> npm ERR! Linux 4.15.0-55-generic >>>>>>>>>>>>>>>>>>> npm ERR! argv "/usr/bin/nodejs" "/usr/bin/npm" "run" >>>>>>>>>>>>>>>>>>> "compile" >>>>>>>>>>>>>>>>>>> npm ERR! node v4.2.6 >>>>>>>>>>>>>>>>>>> npm ERR! npm v3.5.2 >>>>>>>>>>>>>>>>>>> npm ERR! code ELIFECYCLE >>>>>>>>>>>>>>>>>>> npm ERR! loris at 1.0.0 compile: `webpack` >>>>>>>>>>>>>>>>>>> npm ERR! Exit status 1 >>>>>>>>>>>>>>>>>>> npm ERR! >>>>>>>>>>>>>>>>>>> npm ERR! Failed at the loris at 1.0.0 compile script >>>>>>>>>>>>>>>>>>> 'webpack'. >>>>>>>>>>>>>>>>>>> npm ERR! Make sure you have the latest version of >>>>>>>>>>>>>>>>>>> node.js and npm installed. >>>>>>>>>>>>>>>>>>> npm ERR! If you do, this is most likely a problem with >>>>>>>>>>>>>>>>>>> the loris package, >>>>>>>>>>>>>>>>>>> npm ERR! not with npm itself. >>>>>>>>>>>>>>>>>>> npm ERR! Tell the author that this fails on your system: >>>>>>>>>>>>>>>>>>> npm ERR! webpack >>>>>>>>>>>>>>>>>>> npm ERR! You can get information on how to open an issue >>>>>>>>>>>>>>>>>>> for this project with: >>>>>>>>>>>>>>>>>>> npm ERR! npm bugs loris >>>>>>>>>>>>>>>>>>> npm ERR! Or if that isn't available, you can get their >>>>>>>>>>>>>>>>>>> info via: >>>>>>>>>>>>>>>>>>> npm ERR! npm owner ls loris >>>>>>>>>>>>>>>>>>> npm ERR! There is likely additional logging output above. >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> npm ERR! Please include the following file with any >>>>>>>>>>>>>>>>>>> support request: >>>>>>>>>>>>>>>>>>> npm ERR! /var/www/loris/npm-debug.log >>>>>>>>>>>>>>>>>>> Makefile:14: recipe for target 'javascript' failed >>>>>>>>>>>>>>>>>>> make: *** [javascript] Error 1 >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Thanks, >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> ???? ???, 7 ??? 2019 ???? 5:41 ?.?., ?/? Christine >>>>>>>>>>>>>>>>>>> Rogers, Ms. ??????: >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Thanks, have you tried all of these steps? >>>>>>>>>>>>>>>>>>>> - clear your browser cache (and refresh a few times) >>>>>>>>>>>>>>>>>>>> - delete any files in your smarty/templates_c directory >>>>>>>>>>>>>>>>>>>> (this will clear the template cache - do Not touch smarty/templates/) >>>>>>>>>>>>>>>>>>>> - run `make` (per the 21 release notes, this replaces >>>>>>>>>>>>>>>>>>>> the composer commands used in previous releases to update your dependencies) >>>>>>>>>>>>>>>>>>>> - restart apache (doesn't hurt) >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Let us know how it goes -- let us know what difference >>>>>>>>>>>>>>>>>>>> you see after, with your logs. A >>>>>>>>>>>>>>>>>>>> lso please send us your Config path settings (see these >>>>>>>>>>>>>>>>>>>> Troubleshooting Queries >>>>>>>>>>>>>>>>>>>> ) >>>>>>>>>>>>>>>>>>>> if you're still seeing front-end issues. >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Thanks, >>>>>>>>>>>>>>>>>>>> Christine >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> On Wed, Aug 7, 2019 at 8:02 AM Sotirios >>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos wrote: >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> lorisadmin at hbp:/var/www/loris$ sudo cat >>>>>>>>>>>>>>>>>>>>> /var/log/apache2/error.log >>>>>>>>>>>>>>>>>>>>> [Wed Aug 07 07:35:02.422501 2019] [mpm_prefork:notice] >>>>>>>>>>>>>>>>>>>>> [pid 1267] AH00163: Apache/2.4.18 (Ubuntu) OpenSSL/1.0.2g configured -- >>>>>>>>>>>>>>>>>>>>> resuming normal operations >>>>>>>>>>>>>>>>>>>>> [Wed Aug 07 07:35:02.422514 2019] [core:notice] [pid >>>>>>>>>>>>>>>>>>>>> 1267] AH00094: Command line: '/usr/sbin/apache2' >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> And as for the access.log the content are empty >>>>>>>>>>>>>>>>>>>>> lorisadmin at hbp:/var/www/loris$ sudo ls -l >>>>>>>>>>>>>>>>>>>>> /var/log/apache2/access.log >>>>>>>>>>>>>>>>>>>>> lorisadmin at hbp:/var/www/loris$ sudo ls -l >>>>>>>>>>>>>>>>>>>>> /var/log/apache2/access.log >>>>>>>>>>>>>>>>>>>>> -rw-r----- 1 root adm 0 ???? 28 14:09 >>>>>>>>>>>>>>>>>>>>> /var/log/apache2/access.log >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> Also i noticed a loris_access.log. >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> The only non-blank pages are: >>>>>>>>>>>>>>>>>>>>> mri_violations, dataquery does not exist at all, >>>>>>>>>>>>>>>>>>>>> statistics, data_team_helper, genomic_browser, configuration and >>>>>>>>>>>>>>>>>>>>> server_processes_manager/ prints "Required configuration settings for >>>>>>>>>>>>>>>>>>>>> Server Processes Manager are missing. Cannot continue." >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> Thanks, >>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> ???? ???, 6 ??? 2019 ???? 10:13 ?.?., ?/? Christine >>>>>>>>>>>>>>>>>>>>> Rogers, Ms. ??????: >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> Hi Sotirios and LORIS community -- >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> When upgrading to brand-new release 21 -- just a >>>>>>>>>>>>>>>>>>>>>> reminder to follow the release notes and run the new >>>>>>>>>>>>>>>>>>>>>> *make* file to update your dependencies (instead of >>>>>>>>>>>>>>>>>>>>>> using *composer* commands). >>>>>>>>>>>>>>>>>>>>>> We've also updated the Wiki page >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> to clarify that the release notes for each version will tell you what to >>>>>>>>>>>>>>>>>>>>>> run. >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> If your current version is not the last release >>>>>>>>>>>>>>>>>>>>>> (20.3), it's still important to upgrade to each minor release increment >>>>>>>>>>>>>>>>>>>>>> (e.g. 20.2, 20.3) before making the leap to 21.0. >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> If you're getting blank pages, post-upgrade -- Try >>>>>>>>>>>>>>>>>>>>>> clearing your cache. >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> Got questions or feedback e.g. on the Release Notes? >>>>>>>>>>>>>>>>>>>>>> please don't hesitate to let us know. >>>>>>>>>>>>>>>>>>>>>> Thanks, >>>>>>>>>>>>>>>>>>>>>> Christine >>>>>>>>>>>>>>>>>>>>>> The LORIS team >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> On Tue, Aug 6, 2019 at 10:09 AM Christine Rogers, Ms. >>>>>>>>>>>>>>>>>>>>>> wrote: >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>> Could you also let us know -- on which pages is >>>>>>>>>>>>>>>>>>>>>>> content visible, and on which pages/modules is content not visible for you? >>>>>>>>>>>>>>>>>>>>>>> Thanks, >>>>>>>>>>>>>>>>>>>>>>> Christine >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> On Tue, Aug 6, 2019 at 9:54 AM Christine Rogers, Ms. >>>>>>>>>>>>>>>>>>>>>>> wrote: >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> Thanks Sotirios, >>>>>>>>>>>>>>>>>>>>>>>> That's good to know. It sounds like you've checked >>>>>>>>>>>>>>>>>>>>>>>> that your /var/www/loris/project/config.xml file get populated properly. >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> Please send us the last few errors you're seeing in >>>>>>>>>>>>>>>>>>>>>>>> your apache error log file, and your config paths and we can see what's >>>>>>>>>>>>>>>>>>>>>>>> happening with your front end -- >>>>>>>>>>>>>>>>>>>>>>>> Run these Troubleshooting Queries >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> to get your config path settings, given your front end is not displaying >>>>>>>>>>>>>>>>>>>>>>>> fully. >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> The Loris-MRI repo >>>>>>>>>>>>>>>>>>>>>>>> 21 >>>>>>>>>>>>>>>>>>>>>>>> install/upgrade would then be your next steps. >>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>> Christine >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> On Tue, Aug 6, 2019 at 7:53 AM Sotirios >>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos wrote: >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> I am using a VM. What i did was: >>>>>>>>>>>>>>>>>>>>>>>>> 1) Download the files from >>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris and replace them to >>>>>>>>>>>>>>>>>>>>>>>>> my existing /vaw/www/loris folder. >>>>>>>>>>>>>>>>>>>>>>>>> 2) Execute the composer install --no-dev and then composer >>>>>>>>>>>>>>>>>>>>>>>>> dump-autoload as mentioned here >>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris/wiki/Updating-your-LORIS >>>>>>>>>>>>>>>>>>>>>>>>> . >>>>>>>>>>>>>>>>>>>>>>>>> 3) Execute install.sh from /var/www/loris/tools >>>>>>>>>>>>>>>>>>>>>>>>> and because LORIS already existed i moved a .config file, then re-executed >>>>>>>>>>>>>>>>>>>>>>>>> the install.sh successfully >>>>>>>>>>>>>>>>>>>>>>>>> 4 ) As for the database, i dropped the schema and >>>>>>>>>>>>>>>>>>>>>>>>> i executed the installdb.php >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 5 ??? 2019 ???? 5:22 ?.?., ?/? Christine >>>>>>>>>>>>>>>>>>>>>>>>> Rogers, Ms. ??????: >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotorios, >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> Thanks - when you re-installed did you start on a >>>>>>>>>>>>>>>>>>>>>>>>>> fresh root path / VM or might some of your old system setting still apply? >>>>>>>>>>>>>>>>>>>>>>>>>> (And if you did any steps similar to an upgrade, >>>>>>>>>>>>>>>>>>>>>>>>>> did you follow the Upgrade steps in the Release Notes, from both repos?) >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> About the TR_range column - it was recently split >>>>>>>>>>>>>>>>>>>>>>>>>> (MRI pr339 >>>>>>>>>>>>>>>>>>>>>>>>>> ) split >>>>>>>>>>>>>>>>>>>>>>>>>> into TR_min and _max columns. Given the code was trying to query TR_range >>>>>>>>>>>>>>>>>>>>>>>>>> which does not exist in your mri_protocol table, double-check which version >>>>>>>>>>>>>>>>>>>>>>>>>> of the Loris repo (tables) and the Loris-MRI repo (code) you have installed >>>>>>>>>>>>>>>>>>>>>>>>>> to ensure they match. >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> Christine >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> On Mon, Aug 5, 2019 at 9:06 AM Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos wrote: >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> I reinstalled LORIS to 21 version and now the >>>>>>>>>>>>>>>>>>>>>>>>>>> content is not visible at all at most pages. >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 5 ??? 2019 ???? 3:19 ?.?., ?/? >>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos >>>>>>>>>>>>>>>>>>>>>>>>>>> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> Is it easy to upgrade to Loris 21? Also the >>>>>>>>>>>>>>>>>>>>>>>>>>>> following fails because the line 1985 of NeuroDB/MRIProcessingUtility.pm >>>>>>>>>>>>>>>>>>>>>>>>>>>> query mri_protocol which doesn't have TR_range >>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris/blob/21.0-release/SQL/0000-00-00-schema.sql#L556 >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> lorisadmin at hbp:/data/loris/bin/mri$ >>>>>>>>>>>>>>>>>>>>>>>>>>>> ./batch_uploads_imageuploader -profile prod < ~/Desktop/input.txt > log.txt >>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $_ in pattern match >>>>>>>>>>>>>>>>>>>>>>>>>>>> (m//) at ./batch_uploads_imageuploader line 147. >>>>>>>>>>>>>>>>>>>>>>>>>>>> base is DCC0000_258024_V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>> path is /data/incoming/ >>>>>>>>>>>>>>>>>>>>>>>>>>>> type is .tar.gz >>>>>>>>>>>>>>>>>>>>>>>>>>>> fullpath is >>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/incoming/DCC0000_258024_V1.tar.gz >>>>>>>>>>>>>>>>>>>>>>>>>>>> DBD::mysql::st execute failed: Unknown column >>>>>>>>>>>>>>>>>>>>>>>>>>>> 'TR_range' in 'where clause' at >>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line 1985. >>>>>>>>>>>>>>>>>>>>>>>>>>>> DBD::mysql::st fetchrow_array failed: fetch() >>>>>>>>>>>>>>>>>>>>>>>>>>>> without execute() at >>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line 1986. >>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $count_mri_protocol >>>>>>>>>>>>>>>>>>>>>>>>>>>> in numeric gt (>) at >>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line 1995. >>>>>>>>>>>>>>>>>>>>>>>>>>>> DBD::mysql::st execute failed: Unknown column >>>>>>>>>>>>>>>>>>>>>>>>>>>> 'TR_range' in 'field list' at >>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 562. >>>>>>>>>>>>>>>>>>>>>>>>>>>> Can't exec "mail": No such file or directory at >>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 721. >>>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 722. >>>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 723. >>>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 724. >>>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 725. >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> No Mincs inserted >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> Thanks, >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 3 ??? 2019 ???? 1:08 ?.?., ?/? >>>>>>>>>>>>>>>>>>>>>>>>>>>> Christine Rogers, Ms. < >>>>>>>>>>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> First, just a note: we've released LORIS 21 >>>>>>>>>>>>>>>>>>>>>>>>>>>>> this week with some major new features and cleanup -- especially if you are >>>>>>>>>>>>>>>>>>>>>>>>>>>>> early in your setup phase, check out the Release notes for both the >>>>>>>>>>>>>>>>>>>>>>>>>>>>> LORIS >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> and Loris-MRI >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> repos. >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thanks for your screenshots -- your empty >>>>>>>>>>>>>>>>>>>>>>>>>>>>> mri_protocol table should be at the root of these issues : >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> The mri_protocol table must be populated >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> in order for your scans to be registered in LORIS -- it serves as a >>>>>>>>>>>>>>>>>>>>>>>>>>>>> whitelist for the insertion pipeline which filters out scans that aren't >>>>>>>>>>>>>>>>>>>>>>>>>>>>> identified or matched to scan types in this table. >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> By default, this table is populated with >>>>>>>>>>>>>>>>>>>>>>>>>>>>> entries for t1, t2, fMRI and DTI (Insert >>>>>>>>>>>>>>>>>>>>>>>>>>>>> statements for 21 release branch are here >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> ) >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Feel free to restore our default records and >>>>>>>>>>>>>>>>>>>>>>>>>>>>> broaden their parameters to match all your scan types. >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> re Defaced, native, selected -- these filter >>>>>>>>>>>>>>>>>>>>>>>>>>>>> the scans displayed as you move to the next page (View Session), instead of >>>>>>>>>>>>>>>>>>>>>>>>>>>>> viewing "all types" of scans from a given session : >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> - "defaced" means that a defacing script >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> has masked the subject's face in the volume (for patient privacy) >>>>>>>>>>>>>>>>>>>>>>>>>>>>> - "native" means that no pre-processing >>>>>>>>>>>>>>>>>>>>>>>>>>>>> has been performed on the scan (it's raw data), >>>>>>>>>>>>>>>>>>>>>>>>>>>>> - "selected" will show only volumes that >>>>>>>>>>>>>>>>>>>>>>>>>>>>> have been QC'd and "selected" as the best of their type -- used to display >>>>>>>>>>>>>>>>>>>>>>>>>>>>> only the best quality T1 image instead of all T1s acquired in a session, >>>>>>>>>>>>>>>>>>>>>>>>>>>>> e.g. >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> re QC Comments -- >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Once you have successfully loaded scans >>>>>>>>>>>>>>>>>>>>>>>>>>>>> (matched to the mri_protocol table), you'll be able to use the Imaging >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Browser's View Session subpage to enter/view QC comments on each volume, or >>>>>>>>>>>>>>>>>>>>>>>>>>>>> for each visit. >>>>>>>>>>>>>>>>>>>>>>>>>>>>> These are stored directly in the database, and >>>>>>>>>>>>>>>>>>>>>>>>>>>>> linked to each scan. (Table name: >>>>>>>>>>>>>>>>>>>>>>>>>>>>> feedback_mri_comments) >>>>>>>>>>>>>>>>>>>>>>>>>>>>> (Visit-level QC comments are linked to the >>>>>>>>>>>>>>>>>>>>>>>>>>>>> session.) >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> For a walkthrough of the Imaging setup - >>>>>>>>>>>>>>>>>>>>>>>>>>>>> please see the Imaging Setup guide >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> - >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> An old LORIS walkthrough video >>>>>>>>>>>>>>>>>>>>>>>>>>>>> can >>>>>>>>>>>>>>>>>>>>>>>>>>>>> also walk you through some of the Imaging front-end features, starting at >>>>>>>>>>>>>>>>>>>>>>>>>>>>> 8:00 >>>>>>>>>>>>>>>>>>>>>>>>>>>>> LORIS' imaging modules have been updated many >>>>>>>>>>>>>>>>>>>>>>>>>>>>> times since this video, but the functionality and workflow is similar. >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Let us know how it goes once you have entries >>>>>>>>>>>>>>>>>>>>>>>>>>>>> in your mri_protocol table - >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Christine >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> On Fri, Aug 2, 2019 at 7:58 AM Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos wrote: >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Christine, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> In the candidate_list page i can see this >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> patient >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> If i press the link under PSCID i get to see >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and if i press the link under Scan Done it >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> redirects me to imaging_browser >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> At the mri_violations page i also see No >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> results ( neither on resolved / not resolved ). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> At the imaging_uploader i can see the record >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> that failed. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> If i click on the tarchive info i get to see >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the Protocol Name which i think is the acquisition we wanted? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Also my mri_protocol table is empty. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Furthermore i would like to ask about the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> defaced, native, selected. What exactly is native and selected? And where >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> are the qc comments stored? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Finally a walkthrough would be helpful. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thanks, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 30 ???? 2019 ???? 8:29 ?.?., ?/? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Christine Rogers, Ms. < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Glad to hear you're making progress with the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit labels. To follow up on your last few emails: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> a- The Wiki's Setup Guide contains Sample >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> insert statements for the Visit Windows table >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> . >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> As Cecile mentioned, the consistency of >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit label format is important: V01, v01, V1, 01 -- whichever you select >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> to use is fine; we use V01 by default across all documentation. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> b- For Password reset, there is a script in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the tools/ directory so that a back-end administrator can reset any >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> front-end user password, including Admin. (See info on setting up / >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> resetting User passwords in the Wiki's >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Setup Guide >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ) >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> c- The minc file not being registered -- due >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> to AcquisitionProtocol unknown. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> This means the SeriesDescription >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> (Acquisition Protocol) in you Dicom header was not matched to any scan >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> listed in the mri_protocol database table. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> (In the online Loris-MRI Troubleshooting >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Guide, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> this >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> is Table 3, 2nd-last item "no MINCs >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> inserted"). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The MRI Violations module (Readme here) >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> will show >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> you the details of this mismatch -- >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Go to the module (under the Imaging menu), >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> find your scan and click the link "Could not identify scan type" -- in the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> next subpage you can compare the scan's actual parameters against the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> mri_protocol table. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> To resolve this, adjust your mri_protocol >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> table values or perhaps ensure your DICOMs are labelled consistently. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Let us know if this works for you -- we can >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> also walk you through an example of non-identified scans on >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Demo.loris.ca (MRI Violations module). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Christine >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The LORIS team >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> On Tue, Jul 30, 2019 at 10:47 AM Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> wrote: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I hope this is sufficient as the error for >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the visit label disappeared. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Please see the attached file. Also >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> something i found. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> lorisadmin at hbp:/data/loris/bin/mri$ cat >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data//logs/TarLoad-17-39-xubBdv.log >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ==> Loading file from disk >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-17-39-UyQcG2/dcc0000_258024_v1_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> --> mapping DICOM parameter for >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-17-39-UyQcG2/dcc0000_258024_v1_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ==> computing md5 hash for MINC body. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> --> md5: 6b1202fd63e29de4c9be1cd9925888a5 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ==> verifying acquisition protocol >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Acquisition protocol is unknown >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> --> The minc file cannot be registered >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> since the AcquisitionProtocol is unknown >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 30 ???? 2019 ???? 4:58 ?.?., ?/? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Ok I fixed the login problem by using a >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> known hash and by deleting the rows from the login_history i was able to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> login. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 30 ???? 2019 ???? 4:50 ?.?., ?/? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> there was no visit label 01 in the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Visit_Windows table and i don't know how to insert it because the record >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> requires lots of attributes. Also the system for a reason asked me to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> update my password and now i don't remember it and my account got >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> suspended. Is there a way to reset it or set a simple password? I updated >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the password hash in the users table by using the hash from another LORIS >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> setup we had and i still couldn't login ( also the attribute password is >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> always NULL and the expiration date is 1999-01-01 for some reason ). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thanks >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 29 ???? 2019 ???? 5:21 ?.?., >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ?/? Cecile Madjar >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Can you try adding the visit label v01 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> to the Visit_Windows table? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> However, I noticed that in a previous >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> dataset, the label was V1. Does that refer to the same visit? If so, you >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> might want to harmonize the visit labels so they are all the same across >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> datasets for a given timepoint, meaning you will need to relabel scans when >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the visit label is different but referring to the same visit label (v01 = >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> V1 etc...). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helps, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> On Mon, Jul 29, 2019 at 10:15 AM >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Could you help me with the "Visit label >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> does not exist"? I had changed $subjectID{'createVisitLabel'} to 1 as you >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> had suggested but it appears that this problem hasn't been resolved yet. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> lorisadmin at hbp:/data/loris/bin/mri$ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> cat /data/loris/data//logs/TarLoad-14-58-9Xog7H.log >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ==> Loading file from disk >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> --> mapping DICOM parameter for >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> --> using user-defined filterParameters >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> for >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Candidate Mismatch Error is Visit label >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> does not exist >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -> WARNING: This candidate was >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> invalid. Logging to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> MRICandidateErrors table >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> with reason Visit label does not exist >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 26 ???? 2019 ???? 3:02 ?.?., >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ?/? Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Cecile, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The Center error was fixed. Still the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> insertion of mincs fails. Please see the output.txt file i attached. Also >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> is there something else i need to change at the paths configuration? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 25 ???? 2019 ???? 6:55 ?.?., >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ?/? Cecile Madjar < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> cecile.madjar at mcin.ca> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> We are making progress! >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I have a feeling this error comes >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> from the fact that your psc table does not have the MRI_alias populated for >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the DCC site. Running the following query in the mysql database should fix >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> this: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> UPDATE psc SET MRI_alias="DCC", >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Alias="DCC" WHERE Name="Data Coordinating Center"; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Repeat the same with all your sites >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> (make sure to change the Aliases between sites, they should all be unique). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Let me know how it goes! >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> On Thu, Jul 25, 2019 at 11:43 AM >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Dear Cecile, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> You were right about your guesses. I >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> did the modifications you suggested, i still get the "no mincs inserted" >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> error, now i am getting the "No center found this candidate" error ( how do >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> i fix that? from what i see the .dcm files contains a 'Institution Name', >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> is that the center? ), so i guess that's why the validation fails, but i >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> changed the force variable of tarchiveLoader to 1, shouldn't it have >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> inserted the mincs then? Also it is optional to have a mail server, right? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ( from what i see the mail error does not affect the $valid_study, so i >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> assume we are okay with that ) >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you a lot, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 25 ???? 2019 ???? 5:48 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ?.?., ?/? Cecile Madjar < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> cecile.madjar at mcin.ca> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> From what I understand, I believe >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> you just need to update a few config settings from the frontend in the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Config module (under the Admin menu). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [image: Screen Shot 2019-07-25 at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 10.31.35 AM.png] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Then go to the Paths section of the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> config module and update the "LORIS-MRI code" config setting to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri (my guess is that currently, it is set to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data) and click on the submit button. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [image: Screen Shot 2019-07-25 at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 10.32.50 AM.png] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Then, go to Imaging Pipeline >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> section of the Configuration module and update the "Loris-MRI Data >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Directory" to /data/loris/data/ (my guess is that it is empty at the moment >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in your database which is why $data_dir is not defined when you run the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> tarchiveLoader step of the insertion pipeline). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [image: Screen Shot 2019-07-25 at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 10.40.52 AM.png] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Finally, I took a look at your >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> environment file and it might be a good idea to update your PERL5LIB >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> variable to the following (it has been added to the code a few releases ago >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> as we realized this was needed for the libraries. Not sure which version of >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> LORIS-MRI you are using but it does not hurt to update this variable to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> what I suggest below): >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> export >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PERL5LIB=/data/loris/bin/mri/uploadNeuroDB:/data/loris/bin/mri/dicom-archive:$PERL5LIB >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helps. Sorry you are >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> experiencing so much trouble setting things up. We probably need to update >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> our WIKI. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> On Thu, Jul 25, 2019 at 9:48 AM >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The "Loris-MRI Data Directory" >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> should be in the environment file? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 25 ???? 2019 ???? 12:59 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ?.?., ?/? Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The scripts are located in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/. Somewhere I might have messed something up but i >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> remember following the instructions in the wiki.For example when i tried to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> execute the batch_uploads_imageuploader perl script the line >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> my $command = >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> "$bin_dir/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl " >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> was pointing to an invalid path, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> for example: it was repeating a pattern and had LORIS instead of loris ( i >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> think the mistake was that in the wiki it suggested to use $PROJECT for >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the name of the folder and i choosed 'loris' >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris/wiki/Imaging-Database >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ). See also the in image for the modification i did. Also i didn't find the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> section to config the $data_dir variable. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 24 ???? 2019 ???? 6:05 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ?.?., ?/? Cecile Madjar < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> cecile.madjar at mcin.ca> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> It looks like you have one >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Config setting not set (based on the first error message you got when >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> running it the first time). You need to set a value for "Loris-MRI Data >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Directory" in the Config module under the Imaging pipeline section (from >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> what I can see, it would be /data/loris/data/ for your setup). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The reason you got that error >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> message the second time is that the pipeline checks if the DICOM study was >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> already inserted in the tarchive table. Since you ran the study once >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> already, the study is inserted into the tarchive, hence the message. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> However, the pipeline did not complete as the MINC files were not created >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and inserted into the files/parameter_file table. In order to continue the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> insertion, you will then need to run the tarchiveLoader command suggested >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in the terminal during the second run: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -globLocation -profile prod >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive//2012/DCM_2012-12-05_ImagingUpload-17-43-ZUEFjb.tar >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -verbose >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Finally, I am a bit confused by >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> your setup. Where are the scripts located? In /data/loris/bin/mri or >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data? It feels like the Config setting "LORIS-MRI code" in the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Paths section was set to "/data/LORIS/data" but it should have been set to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the directory where the scripts are located (most probably >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helps, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> On Wed, Jul 24, 2019 at 10:55 AM >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Ok first i execute this command: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> "lorisadmin at hbp:/data/loris/bin/mri$ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ./batch_uploads_imageuploader -profile prod < ~/Desktop/input.txt > log.txt >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> $data_dir in concatenation (.) or string at ./batch_uploads_imageuploader >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> line 143. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> $data_dir in concatenation (.) or string at ./batch_uploads_imageuploader >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> line 143. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $_ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in pattern match (m//) at ./batch_uploads_imageuploader line 147. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> base is DCC0000_258024_V01 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> path is /data/incoming/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> type is .tar.gz >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> fullpath is >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/incoming/DCC0000_258024_V01.tar.gz >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> source >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/ImagingUpload-17-43-ZUEFjb >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> targetlocation >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> $data_dir in concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 256. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> $data_dir in concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 284. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> $data_dir in concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> tarchive_validation.pl line >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 219. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> $data_dir in concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl line 270. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> $data_dir in concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 711. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Can't exec "mail": No such file >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> or directory at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 721. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> MAIL at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 722. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> MAIL at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 723. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> $data_dir in concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 724. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> MAIL at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 724. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> MAIL at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 725. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> $data_dir in concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 735. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> No Mincs inserted >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The tarchiveLoader insertion >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> script has failed. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Running now the following >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> command: /data/loris/data/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -profile prod -upload_id 3 /data/incoming/DCC0000_258024_V01.tar.gz >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -verbose" >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I inserted the VisitLabel, but >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> still the Mincs are not inserted and i am getting this error >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> "lorisadmin at hbp:/data/loris/bin/mri$ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -profile prod -upload_id 3 /data/incoming/DCC0000_258024_V01.tar.gz -verbose >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> find -path >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> \/tmp\/ImagingUpload\-17\-45\-5MsWEd -name '__MACOSX' -delete >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Spool message is: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The Scan for the uploadID 3 has >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> already been run with tarchiveID: 7. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> To continue with the rest of >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the insertion pipeline, please run tarchiveLoader from a terminal as >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> follows: /data/LORIS/data//uploadNeuroDB/tarchiveLoader -globLocation >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -profile prod >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive//2012/DCM_2012-12-05_ImagingUpload-17-43-ZUEFjb.tar >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -verbose" >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Which files should i delete? I >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> thought that deleting the files from the tarchive was enough. And i >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> executed the last proposed command to continue to rest of the insertion >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> pipeline ( check the image ). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 24 ???? 2019 ???? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 5:05 ?.?., ?/? Cecile Madjar < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> cecile.madjar at mcin.ca> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sorry I was not clear before. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Every visits of candidates are created in the session table with one entry >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> per CandID/VisitLabel. So if the imaging pipeline created visits in the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> session table (that are not attached to instruments) and you want to clean >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> your database completely, you can delete entries in that table as well. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Regarding your point 2, the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> imaging pipeline can create the visit in the session table as long as the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit label is present in the Visit_Windows table (which means the visit >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> label stored in the PatientName is a valid visit label). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> However, in your prod file, if >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the variable $subjectID{'createVisitLabel'} is set to 1 for candidates, the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit label should be created in the Visit_Windows table I believe. Here >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> is the line of the prod file you would need to change >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> . >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> In general, we prefer >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> populating the Visit_Windows table and set the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> $subjectID{'createVisitLabel'} to 0 for candidate data to avoid insertion >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> of badly labelled MRI data that are complex to relabel. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Finally, regarding the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> candidate creation, if you execute the following steps, the pipeline should >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> be able to create candidates: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - set in the Imaging Pipeline >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> section of the config module the config setting "Upload creation of >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> candidates" to Yes >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - manually transfer the scans >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> to the LORIS server instead of uploading it via the imaging browser >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - run batch_imaging_upload.pl >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> as you did until now. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helps! >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> On Wed, Jul 24, 2019 at 8:47 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> AM Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> About my second question i >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> replaced the name of the patient in the .dcm files and now i am getting an >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> error that the visit label does not exist. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I thought it was supposed to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> be automatically created. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> "Done adding archive info >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> into database >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -globLocation -profile prod >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive//DCM_2012-12-05_ImagingUpload-15-42-yUwQQV.tar >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -verbose >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> md5sum >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive/DCM_2012-12-05_ImagingUpload-15-42-yUwQQV.tar >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> candidate id 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> => No Visit labelVisit label >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> does not exist >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Set centerID = 1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Number of MINC files that >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> will be considered for inserting into the database: 1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> log dir is /logs and log file >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> is /logs/TarLoad-15-42-L6pocU.log >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> candidate id 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> => No Visit label >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Cleaning up temp files: rm >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -rf /tmp/TarLoad-15-42-J2rQms/ImagingUpload-15-42-yUwQQV*" >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 24 ???? 2019 ???? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 3:38 ?.?., ?/? Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 1) What are the records in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the session table? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 2) I tried to upload a >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> non-phantom file like this >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> input_file.txt: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/incoming/DCC0000_258024_V1.tar.gz >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> N DCC0000_258024_V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Terminal: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ./batch_uploads_imageuploader >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -profile prod < ~/Desktop/input.txt > log.txt >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and i get the following >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> error in the log.txt file >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> "Running now the following >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> command: /data/loris/data/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -profile prod -upload_id 7 /data/incoming/DCC0000_258024_V1.tar.gz -verbose >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> find -path >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> \/tmp\/ImagingUpload\-14\-56\-FeLCB4 -name '__MACOSX' -delete >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Spool message is: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The PatientName read from >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the DICOM header does not start with DCC0000_258024_V1 from the mri_upload >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> table >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> " >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and the spool message is >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> repeated for each .dcm file. Should i preprocess every .dcm file and change >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the PatientName to "DCC0000_258024_V1"? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 3) As far as it concerns the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> candidate profile i have to create a new one each time before i try to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> upload a file? Is there already a way to create a candidate profile and get >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the DCCID and PSCID without the user interface? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 18 ???? 2019 ???? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 5:00 ?.?., ?/? Cecile Madjar < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> cecile.madjar at mcin.ca> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> See answers to your >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> questions below. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> About the 1st case we had a >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> dicom with a blank studyUID, maybe someone accidentally removed it. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> That is strange. Something >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> must have been done to the DICOM files. I have never seen a study with no >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> StudyUID out of the scanner. Usually, you need to manually erase it with >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> some tool. However, DICOMs never cease to surprise me... >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Some other questions: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 1) What are the steps to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> remove all of my patients and uploads?: because i want to try to reupload >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> all the testing dicoms we had with a clean database. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Release 21.0 of LORIS-MRI >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> will offer a script to remove all the entries and files specific to an >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> upload. However, this release is not yet out. Hopefully in the next few >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> weeks. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> In the meantime, since your >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> case is particular and that you just want to start with a clean database, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the following deletes should work (hopefully I won't forget any tables): >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> mri_violations_log; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> mri_protocol_violated_scans; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> MRICandidateErrors; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from parameter_file; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from files_qcstatus; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> # (if you played with the QC part of the imaging browser for testing) >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> feedback_mri_comments; # (if you played with the QC part of the imaging >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> browser for testing) >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from tarchive_series; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from tarchive_files; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from mri_upload; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from tarchive; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from mri_scanner; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from candidate where >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID="scanner"; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I don't know if you want to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> also delete entries in the session and candidate table too? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 2) We do not need to create >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the profile of a patient ( are the patients stored in the candidate table? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> because i can't see the ghosts ), because will it automatically be created >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> when importing a dicom? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I am not sure I understand >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> fully this question. All candidates are stored in the candidate table. The >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> phantom scans however are attached to a scanner candidate depending on >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> where the scan happened. It is a bit of a weird concept that we have to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> redesign eventually but never got a chance to get to it. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hopefully this answered >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> your question, otherwise, don't hesitate to let me know. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 3) What is the difference >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> between uploading a dicom as phantom instead of importing as >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCCID_DCCID_VisitLabel? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> When you upload the scan as >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID_DCCID_VisitLabel, there is a check that makes sure the candidate IDs >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and visit label are valid at the time of upload. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> When you upload a scan as >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> phantom, it expects that the DICOM field PatientName and uploaded filename >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> contains the string "phantom". We enforced this behaviour on the imaging >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> uploader side in recent releases but I can't remember which one. Probably >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the upcoming 21.0 release. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> All those verifications >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> might seem cumbersome but they are here to ensure that the files inserted >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> are all valid and labelled properly as it is a bit messy to have to delete >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> files that were wrongly labelled. At least, the delete script present in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> release 21.0 will make this process easier but it is still good practice to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> verify those things. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> With pleasure. Hopefully >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the answers to your questions will be helpful. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PS: loris-dev mailing list: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> you will find the initial answer I gave Sotirios below. I forgot to cc the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> loris-dev in my earlier reply... >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 16 ???? 2019 ???? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 12:02 ?.?., ?/? Cecile Madjar < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> cecile.madjar at mcin.ca> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Dear Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you for reaching >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> out. Since your email was already organized in points, I will reply >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> directly below your questions below. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 1) What do we do when the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> StudyUID is blank on the header? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/minor/docs/AppendixA-Troubleshooting_guideline.md >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> There solution provided at the table 3 does not guide us how to find the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> information ( is possible ). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The StudyUID is the field >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> used in our pipeline at the moment to check whether a DICOM study was >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> already inserted into LORIS with that same StudyUID since it is supposed to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> be unique for every single study. Currently, we do not support insertion of >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DICOM studies if they do not have a StudyUID associated with them. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Is there a specific >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> reason why the StudyUID is blank in the DICOM headers in your DICOM files? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Did they go through some processes before upload to LORIS? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 2) When i am about to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> upload a non-phanton case i need a 'Visit Label'. Is there already a script >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> that can create a new visit label for a specific Candidate, so i can >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> provide it as input afterwards to the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> batch_uploads_imageuploader ( See option 5.1.3 https://github.com/aces/Loris-MRI/blob/minor/docs/05-PipelineLaunchOptions.md ) >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I am not sure if the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> front-end allows for it but if you use batch_uploads_imageuploader, the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> insertion scripts could create the visit label for you. However, it does >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> need to be included in the patient name in order for the script to know >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> which label it should use. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> For example: you upload >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> V02 for MTL0123 (DCCID: 456789) but V02 was not yet created for MTL0123; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the insertion scripts will create a V02 visit for MTL0123 if the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PatientName field for the dataset is MTL0123_456789_V02 with Stage marked >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> as "Not Started". >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> However, *note that for >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the script to create the visit for the candidate, you have to make sure >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> that all the visit label of your projects were inserted in the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Visit_Windows table* >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> (otherwise, the visit will never be created as they were not specified as >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> being part of the list of visit label to expect). So in the example above, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> you should have one row in Visit_Windows with Visit_label="V02" set. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 3) Section 4.3 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/minor/docs/04-Scripts.md >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> What do we do when the folder contains multiple mnc files? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> This is a case by case. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Most of the time, the MINC files that failed insertion into the imaging >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> browser end up in the MRI violation module where you can see what went >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> wrong with the acquisitions not inserted. If you notice that the MINC file >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> should be inserted as a specific protocol, you can force the insertion as >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> explained in section 4.3. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> In your case, I have a >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> feeling that you want to be able to insert MINC files that did not go >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> through the whole pipeline insertion (DICOM archival, then dcm2mnc, then >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> protocol identification, then insertion...). In theory, you could call >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl on any >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> MINC file, provided you have at least the following information: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - path to the MINC file >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - uploadID associated >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> with the MINC files or DICOM archive path from which those MINC files were >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> created from >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Then the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl script >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> will do the subject information and protocol validation etc... >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> If all the MINC files >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> come from the same uploadID or TarchiveID, then you could run a loop in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> bash calling the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl script >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> like this for files deriving from uploadID=1: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ls /path/to/mnc/folder/* >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> | while read f; do >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -profile prod -uploadID 1 -mincPath $f; done >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helped! >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> MCIN.ca >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>>>>>>>>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | >>>>>>>>>>>>>>>>>>>>>>>>>>>>> MCIN.ca >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>>>>>>>>>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>>>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>>>>>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | >>>>>>>>>>>>>>>>>>>>>>>>>> MCIN.ca >>>>>>>>>>>>>>>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>>>>>>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>>>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>>>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>>>>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>>>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>>> >>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> -- >>>>>>>>>>>> Shen Wang >>>>>>>>>>>> Loris Developer >>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>> McGill University >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>> >>>>>>>> -- >>>>>>>> Shen Wang >>>>>>>> Loris Developer >>>>>>>> Montreal Neurological Institute >>>>>>>> McGill University >>>>>>>> >>>>>>>> -- >>>>>>> Shen Wang >>>>>>> Loris Developer >>>>>>> Montreal Neurological Institute >>>>>>> McGill University >>>>>>> >>>>>>> _______________________________________________ >>>>>>> Loris-dev mailing list >>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>> >>>>>> >>>>>> >>>>>> -- >>>>>> >>>>>> christine.rogers at mcgill.ca >>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>> Montreal Neurological Institute >>>>>> McGill University | Montreal | Canada >>>>>> >>>>> >>> >>> -- >>> Shen Wang >>> Loris Developer >>> Montreal Neurological Institute >>> McGill University >>> >>> > > -- > Shen Wang > Loris Developer > Montreal Neurological Institute > McGill University > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: ???? 2019-08-13 19.21.15.png Type: image/png Size: 508603 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: sudo_make_output Type: application/octet-stream Size: 97247 bytes Desc: not available URL: From wangshen.mcin at gmail.com Thu Aug 15 14:36:27 2019 From: wangshen.mcin at gmail.com (Shen Wang) Date: Thu, 15 Aug 2019 14:36:27 -0400 Subject: [Loris-dev] Upgrading to Loris 21 - new make file In-Reply-To: References: Message-ID: Hi, You don't need to run install.sh this time. Redownload the missing file, then do sudo make. If it still have indent and no-def errors, then remove the lines which I told you from webpack.config.js, then try do sudo make again. On Thu, 15 Aug 2019 at 14:28, Sotirios Nikoloutsopoulos < sotirisnik at gmail.com> wrote: > Hi, > > should i try to redownload the files from > https://github.com/aces/Loris/tree/major and execute the install.sh? I > find it weird that i am missing some files. > > Thanks > > ???? ???, 15 ??? 2019 ???? 9:17 ?.?., ?/? Shen Wang < > wangshen.mcin at gmail.com> ??????: > >> Hi Sotirios, >> It seems like you are missing this file. [ .babelrc] >> step 1: copy from https://github.com/aces/Loris/blob/major/.babelrc >> step 2: sudo vi webpack.config.js >> remove these lines >> >> { test: /\.js$/, >> >> exclude: /node_modules/, >> >> // use: ['babel-loader', 'eslint-loader'], >> >> }, >> >> step 3: sudo make >> >> >> >> On Wed, 14 Aug 2019 at 18:52, Sotirios Nikoloutsopoulos < >> sotirisnik at gmail.com> wrote: >> >>> Hi Shen, >>> >>> That didn't work either. Also i had removed the git files because i was >>> getting this error when i used make: >>> >>> "git describe --tags --always > VERSION >>> fatal: Not a git repository (or any of the parent directories): .git >>> Makefile:8: recipe for target 'VERSION' failed >>> make: *** [VERSION] Error 128" >>> >>> Thanks >>> >>> ???? ???, 15 ??? 2019 ???? 1:36 ?.?., ?/? Shen Wang < >>> wangshen.mcin at gmail.com> ??????: >>> >>>> Hi,Sotirios >>>> In your special situation, there is a temporary fix. >>>> step 1. sudo git stash >>>> step 2. open webpack.config.js file >>>> remove line 75 use: ['babel-loader', 'eslint-loader'], >>>> save it. >>>> step 3. sudo make >>>> >>>> I hope this could help you to compile the js files. >>>> >>>> >>>> >>>> On Wed, 14 Aug 2019 at 08:28, Sotirios Nikoloutsopoulos < >>>> sotirisnik at gmail.com> wrote: >>>> >>>>> I forgot to mention that i had already moved my previous config file >>>>> and re-executed the installation script. >>>>> >>>>> ???? ???, 14 ??? 2019 ???? 3:26 ?.?., ?/? Sotirios Nikoloutsopoulos < >>>>> sotirisnik at gmail.com> ??????: >>>>> >>>>>> Hi, >>>>>> >>>>>> Step 1 worked and the indentation errors were fixed. About step2 i >>>>>> added all of these( there are more to include in the list) these to >>>>>> .eslintignore which were reported to fail at being built, but they still >>>>>> appear on the errors at the make_output file. >>>>>> >>>>>> /jsx/DynamicDataTable.js >>>>>> /jsx/StaticDataTable.js >>>>>> /jsx/MultiSelectDropdown.js >>>>>> /jsx/Breadcrumbs.js >>>>>> /jsx/Form.js >>>>>> /jsx/Markdown.js >>>>>> /modules/media/jsx/mediaIndex.js >>>>>> /modules/issue_tracker/jsx/issueTrackerIndex.js >>>>>> /modules/issue_tracker/jsx/index.js >>>>>> /modules/candidate_parameters/jsx/CandidateParameters.js >>>>>> /modules/configuration/jsx/SubprojectRelations.js >>>>>> /modules/conflict_resolver/jsx/conflictResolverIndex.js >>>>>> /modules/conflict_resolver/jsx/resolvedConflictsIndex.js >>>>>> /modules/bvl_feedback/jsx/react.behavioural_feedback_panel.js >>>>>> /modules/dataquery/jsx/react.tabs.js >>>>>> /modules/document_repository/jsx/docIndex.js >>>>>> /modules/instrument_builder/jsx/react.instrument_builder.js >>>>>> /modules/imaging_uploader/jsx/index.js >>>>>> /modules/datadict/jsx/dataDictIndex.js >>>>>> /modules/bvl_feedback/jsx/react.behavioural_feedback_panel.js >>>>>> /modules/new_profile/jsx/NewProfileIndex.js >>>>>> /modules/examiner/jsx/examinerIndex.js >>>>>> /modules/configuration/jsx/SubprojectRelations.js >>>>>> /modules/data_team_helper/jsx/behavioural_qc_module.js >>>>>> /modules/acknowledgements/jsx/acknowledgementsIndex.js >>>>>> /modules/candidate_parameters/jsx/CandidateParameters.js >>>>>> /modules/imaging_browser/jsx/ImagePanel.js >>>>>> /modules/mri_violations/jsx/mri_protocol_violations_columnFormatter.js >>>>>> >>>>>> /modules/mri_violations/jsx/mri_protocol_check_violations_columnFormatter.js >>>>>> /modules/genomic_browser/jsx/profileColumnFormatter.js >>>>>> /modules/dataquery/jsx/react.tabs.js >>>>>> /jsx/MultiSelectDropdown.js >>>>>> /modules/mri_violations/jsx/columnFormatterUnresolved.js >>>>>> /modules/dataquery/jsx/react.sidebar.js >>>>>> /modules/dataquery/jsx/react.fieldselector.js >>>>>> /modules/quality_control/jsx/qualityControlIndex.js >>>>>> /modules/dataquery/jsx/react.paginator.js >>>>>> /modules/instrument_builder/jsx/react.questions.js >>>>>> /modules/dataquery/jsx/react.filterBuilder.js >>>>>> /modules/conflict_resolver/jsx/conflictResolverIndex.js >>>>>> /jsx/PaginationLinks.js >>>>>> /modules/conflict_resolver/jsx/resolvedConflictsIndex.js >>>>>> /modules/dataquery/jsx/react.app.js >>>>>> /modules/candidate_list/jsx/onLoad.js >>>>>> /jsx/Form.js >>>>>> /modules/publication/jsx/publicationIndex.js >>>>>> /modules/server_processes_manager/jsx/server_processes_managerIndex.js >>>>>> /modules/imaging_browser/jsx/imagingBrowserIndex.js >>>>>> /modules/issue_tracker/jsx/issueTrackerIndex.js >>>>>> /modules/survey_accounts/jsx/surveyAccountsIndex.js >>>>>> /modules/data_integrity_flag/jsx/dataIntegrityFlagIndex.js >>>>>> /modules/instrument_manager/jsx/instrumentManagerIndex.js >>>>>> /modules/media/jsx/mediaIndex.js >>>>>> /modules/user_accounts/jsx/userAccountsIndex.js >>>>>> /modules/help_editor/jsx/help_editor.js >>>>>> /modules/dicom_archive/jsx/dicom_archive.js >>>>>> /modules/mri_violations/jsx/columnFormatter.js >>>>>> /modules/brainbrowser/jsx/Brainbrowser.js >>>>>> /node_modules/babel-loader/lib/index.js >>>>>> /modules/document_repository/jsx/editFormIndex.js >>>>>> >>>>>> Thanks >>>>>> >>>>>> ???? ???, 14 ??? 2019 ???? 7:50 ?.?., ?/? Christine Rogers, Ms. < >>>>>> christine.rogers at mcgill.ca> ??????: >>>>>> >>>>>>> Hi Shen and Sotirios - just a note, >>>>>>> >>>>>>> For the 21 release, it's best to run the install script without >>>>>>> sudoing it. >>>>>>> >>>>>>> (Shen, I believe we discovered a minor issue with the sudo last week >>>>>>> #5008) >>>>>>> >>>>>>> Best, >>>>>>> Christine >>>>>>> >>>>>>> On Tue, Aug 13, 2019 at 9:22 PM Shen Wang >>>>>>> wrote: >>>>>>> >>>>>>>> Does it work? If still doesn?t work, try to remove >>>>>>>> project/config.xml file. Do sudo ./install.sh again. To reinstall Loris >>>>>>>> again. >>>>>>>> >>>>>>>> >>>>>>>> Shen Wang ?2019?8?13? ????9:02??? >>>>>>>> >>>>>>>>> Hi Sotirios, >>>>>>>>> step 1: >>>>>>>>> sudo ./node_modules/.bin/eslint --fix /var/www/loris >>>>>>>>> step 2: >>>>>>>>> put the rest error files under this line [# Ignore until ESLint >>>>>>>>> is run] in the .eslintignore file. >>>>>>>>> step 3: >>>>>>>>> sudo make >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> On Tue, 13 Aug 2019 at 20:34, Sotirios Nikoloutsopoulos < >>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>> >>>>>>>>>> I did the modifications, still there are errors. >>>>>>>>>> Thanks >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> ???? ???, 14 ??? 2019 ???? 3:22 ?.?., ?/? Shen Wang < >>>>>>>>>> wangshen.mcin at gmail.com> ??????: >>>>>>>>>> >>>>>>>>>>> Hi Sotirios, >>>>>>>>>>> I saw your output file, the config issue is gone. >>>>>>>>>>> you can use [sudo npm run lintfix:javascript ] to fix these >>>>>>>>>>> indent issues. >>>>>>>>>>> If it still has errors. >>>>>>>>>>> Then try modify this file .eslintignore >>>>>>>>>>> with this >>>>>>>>>>> >>>>>>>>>>> # Ignore until ESLint is run >>>>>>>>>>> >>>>>>>>>>> modules/* >>>>>>>>>>> >>>>>>>>>>> modules/dataquery/ >>>>>>>>>>> >>>>>>>>>>> node_modules/* >>>>>>>>>>> >>>>>>>>>>> htdocs/js/components/* >>>>>>>>>>> >>>>>>>>>>> jsx/* >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> # Ignore external libs >>>>>>>>>>> >>>>>>>>>>> htdocs/js/flot/* >>>>>>>>>>> >>>>>>>>>>> htdocs/js/jquery/* >>>>>>>>>>> >>>>>>>>>>> htdocs/js/jszip/* >>>>>>>>>>> >>>>>>>>>>> htdocs/js/modernizr/* >>>>>>>>>>> >>>>>>>>>>> htdocs/js/modules/* >>>>>>>>>>> >>>>>>>>>>> htdocs/js/react/* >>>>>>>>>>> >>>>>>>>>>> htdocs/js/shims/* >>>>>>>>>>> >>>>>>>>>>> htdocs/js/c3.min.js >>>>>>>>>>> >>>>>>>>>>> htdocs/js/d3.min.js >>>>>>>>>>> >>>>>>>>>>> htdocs/js/FileSaver.min.js >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> then do sudo make. >>>>>>>>>>> It should work. >>>>>>>>>>> Regards >>>>>>>>>>> Shen >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> Sotirios Nikoloutsopoulos ?2019?8?13? >>>>>>>>>>> ????7:54??? >>>>>>>>>>> >>>>>>>>>>>> No, it didn't work, i also tried space/tabs because most of the >>>>>>>>>>>> errors where about indentation, also there are some errors about React. >>>>>>>>>>>> >>>>>>>>>>>> Thanks >>>>>>>>>>>> >>>>>>>>>>>> lorisadmin at hbp:/var/www/loris$ sudo ./node_modules/.bin/eslint >>>>>>>>>>>> --init >>>>>>>>>>>> ? How would you like to configure ESLint? Answer questions >>>>>>>>>>>> about your style >>>>>>>>>>>> ? Which version of ECMAScript do you use? ES2015 >>>>>>>>>>>> ? Are you using ES6 modules? Yes >>>>>>>>>>>> ? Where will your code run? Browser >>>>>>>>>>>> ? Do you use CommonJS? Yes >>>>>>>>>>>> ? Do you use JSX? Yes >>>>>>>>>>>> ? Do you use React? Yes >>>>>>>>>>>> ? What style of indentation do you use? Spaces >>>>>>>>>>>> ? What quotes do you use for strings? Single >>>>>>>>>>>> ? What line endings do you use? Unix >>>>>>>>>>>> ? Do you require semicolons? Yes >>>>>>>>>>>> ? What format do you want your config file to be in? JSON >>>>>>>>>>>> The config that you've selected requires the following >>>>>>>>>>>> dependencies: >>>>>>>>>>>> >>>>>>>>>>>> eslint-plugin-react at latest >>>>>>>>>>>> Successfully created .eslintrc.json file in /var/www/loris >>>>>>>>>>>> >>>>>>>>>>>> lorisadmin at hbp:/var/www/loris$ sudo make > sudo_make_output >>>>>>>>>>>> npm WARN The package prop-types is included as both a dev and >>>>>>>>>>>> production dependency. >>>>>>>>>>>> npm WARN optional SKIPPING OPTIONAL DEPENDENCY: fsevents at 1.2.4 >>>>>>>>>>>> (node_modules/fsevents): >>>>>>>>>>>> npm WARN notsup SKIPPING OPTIONAL DEPENDENCY: Unsupported >>>>>>>>>>>> platform for fsevents at 1.2.4: wanted >>>>>>>>>>>> {"os":"darwin","arch":"any"} (current: {"os":"linux","arch":"x64"}) >>>>>>>>>>>> >>>>>>>>>>>> npm ERR! code ELIFECYCLE >>>>>>>>>>>> npm ERR! errno 2 >>>>>>>>>>>> npm ERR! loris at 1.0.0 compile: `webpack` >>>>>>>>>>>> npm ERR! Exit status 2 >>>>>>>>>>>> npm ERR! >>>>>>>>>>>> npm ERR! Failed at the loris at 1.0.0 compile script. >>>>>>>>>>>> npm ERR! This is probably not a problem with npm. There is >>>>>>>>>>>> likely additional logging output above. >>>>>>>>>>>> >>>>>>>>>>>> npm ERR! A complete log of this run can be found in: >>>>>>>>>>>> npm ERR! >>>>>>>>>>>> /home/lorisadmin/.npm/_logs/2019-08-13T23_40_58_841Z-debug.log >>>>>>>>>>>> >>>>>>>>>>>> ???? ???, 14 ??? 2019 ???? 2:29 ?.?., ?/? Shen Wang < >>>>>>>>>>>> wangshen.mcin at gmail.com> ??????: >>>>>>>>>>>> >>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>> When you do make command, please make sure with sudo at the >>>>>>>>>>>>> beginning. [sudo make] >>>>>>>>>>>>> If it still doesn't work for you. >>>>>>>>>>>>> Then try the solutions below. >>>>>>>>>>>>> solution 1: >>>>>>>>>>>>> [image: ???? 2019-08-13 19.21.15.png] >>>>>>>>>>>>> Regards >>>>>>>>>>>>> Shen >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> On Tue, 13 Aug 2019 at 17:22, Sotirios Nikoloutsopoulos < >>>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>> >>>>>>>>>>>>>> I think that the files exists although i redownloaded the >>>>>>>>>>>>>> eslintrc.json i checked others files that had similar errors. >>>>>>>>>>>>>> >>>>>>>>>>>>>> lorisadmin at hbp:/var/www/loris$ ls -l >>>>>>>>>>>>>> ./node_modules/eslint-loader/index.js >>>>>>>>>>>>>> -rw-rw-r-- 1 lorisadmin lorisadmin 6463 ??? 26 1985 >>>>>>>>>>>>>> ./node_modules/eslint-loader/index.js >>>>>>>>>>>>>> >>>>>>>>>>>>>> lorisadmin at hbp:/var/www/loris$ ls -l .eslintrc.json >>>>>>>>>>>>>> -rw-rw-r-- 1 lorisadmin lorisadmin 84530 ??? 14 00:04 >>>>>>>>>>>>>> .eslintrc.json >>>>>>>>>>>>>> >>>>>>>>>>>>>> Maybe this can help >>>>>>>>>>>>>> >>>>>>>>>>>>>> Module build failed (from >>>>>>>>>>>>>> ./node_modules/eslint-loader/index.js): >>>>>>>>>>>>>> SyntaxError: Cannot read config file: >>>>>>>>>>>>>> /var/www/loris/.eslintrc.json >>>>>>>>>>>>>> Error: Unexpected token < in JSON at position 6 >>>>>>>>>>>>>> at JSON.parse () >>>>>>>>>>>>>> at loadJSONConfigFile >>>>>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config/config-file.js:114:21) >>>>>>>>>>>>>> at loadConfigFile >>>>>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config/config-file.js:230:26) >>>>>>>>>>>>>> at loadFromDisk >>>>>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config/config-file.js:500:18) >>>>>>>>>>>>>> at Object.load >>>>>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config/config-file.js:564:20) >>>>>>>>>>>>>> at Config.getLocalConfigHierarchy >>>>>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config.js:227:44) >>>>>>>>>>>>>> at Config.getConfigHierarchy >>>>>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config.js:179:43) >>>>>>>>>>>>>> at Config.getConfigVector >>>>>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config.js:286:21) >>>>>>>>>>>>>> at Config.getConfig >>>>>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config.js:329:29) >>>>>>>>>>>>>> at processText >>>>>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/cli-engine.js:162:33) >>>>>>>>>>>>>> at CLIEngine.executeOnText >>>>>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/cli-engine.js:596:17) >>>>>>>>>>>>>> at lint >>>>>>>>>>>>>> (/var/www/loris/node_modules/eslint-loader/index.js:237:17) >>>>>>>>>>>>>> at Object.module.exports >>>>>>>>>>>>>> (/var/www/loris/node_modules/eslint-loader/index.js:232:21) >>>>>>>>>>>>>> >>>>>>>>>>>>>> ERROR in ./modules/imaging_uploader/jsx/index.js >>>>>>>>>>>>>> Module build failed (from >>>>>>>>>>>>>> ./node_modules/eslint-loader/index.js): >>>>>>>>>>>>>> SyntaxError: Cannot read config file: >>>>>>>>>>>>>> /var/www/loris/.eslintrc.json >>>>>>>>>>>>>> Error: Unexpected token < in JSON at position 6 >>>>>>>>>>>>>> at JSON.parse () >>>>>>>>>>>>>> at loadJSONConfigFile >>>>>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config/config-file.js:114:21) >>>>>>>>>>>>>> at loadConfigFile >>>>>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config/config-file.js:230:26) >>>>>>>>>>>>>> at loadFromDisk >>>>>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config/config-file.js:500:18) >>>>>>>>>>>>>> at Object.load >>>>>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config/config-file.js:564:20) >>>>>>>>>>>>>> at Config.getLocalConfigHierarchy >>>>>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config.js:227:44) >>>>>>>>>>>>>> at Config.getConfigHierarchy >>>>>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config.js:179:43) >>>>>>>>>>>>>> at Config.getConfigVector >>>>>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config.js:286:21) >>>>>>>>>>>>>> at Config.getConfig >>>>>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config.js:329:29) >>>>>>>>>>>>>> at processText >>>>>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/cli-engine.js:162:33) >>>>>>>>>>>>>> at CLIEngine.executeOnText >>>>>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/cli-engine.js:596:17) >>>>>>>>>>>>>> at lint >>>>>>>>>>>>>> (/var/www/loris/node_modules/eslint-loader/index.js:237:17) >>>>>>>>>>>>>> at Object.module.exports >>>>>>>>>>>>>> (/var/www/loris/node_modules/eslint-loader/index.js:232:21) >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> ???? ???, 13 ??? 2019 ???? 11:52 ?.?., ?/? John Saigle < >>>>>>>>>>>>>> john.saigle at mcin.ca> ??????: >>>>>>>>>>>>>> >>>>>>>>>>>>>>> HI Sotirios, >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> The make_output.txt file shows webpack failing because it >>>>>>>>>>>>>>> can't find the ESLint config file. >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> Can you confirm whether the file `.eslintrc.json` exists >>>>>>>>>>>>>>> within your loris root directory (usually `/var/www/loris/`)? When I delete >>>>>>>>>>>>>>> my file I get the same errors as you. >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> If you find that it's missing, you can make a local copy >>>>>>>>>>>>>>> with the contents found here: >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> https://github.com/aces/Loris/blob/e26a6ad49a73fcffef0cd73bb600c4d17b200b62/.eslintrc.json >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> Once you know it exists, try running `make` again. >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> Let us know if that moves you forward. >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>> John >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> On Tue, Aug 13, 2019 at 2:21 PM Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>> I executed the commands for the node and now i am get the >>>>>>>>>>>>>>>> followings: >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> lorisadmin at hbp:/var/www/loris$ make > ~/make_output >>>>>>>>>>>>>>>> npm WARN The package prop-types is included as both a dev >>>>>>>>>>>>>>>> and production dependency. >>>>>>>>>>>>>>>> npm WARN optional SKIPPING OPTIONAL DEPENDENCY: >>>>>>>>>>>>>>>> fsevents at 1.2.4 (node_modules/fsevents): >>>>>>>>>>>>>>>> npm WARN notsup SKIPPING OPTIONAL DEPENDENCY: Unsupported >>>>>>>>>>>>>>>> platform for fsevents at 1.2.4: wanted >>>>>>>>>>>>>>>> {"os":"darwin","arch":"any"} (current: {"os":"linux","arch":"x64"}) >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> npm ERR! code ELIFECYCLE >>>>>>>>>>>>>>>> npm ERR! errno 2 >>>>>>>>>>>>>>>> npm ERR! loris at 1.0.0 compile: `webpack` >>>>>>>>>>>>>>>> npm ERR! Exit status 2 >>>>>>>>>>>>>>>> npm ERR! >>>>>>>>>>>>>>>> npm ERR! Failed at the loris at 1.0.0 compile script. >>>>>>>>>>>>>>>> npm ERR! This is probably not a problem with npm. There is >>>>>>>>>>>>>>>> likely additional logging output above. >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> npm ERR! A complete log of this run can be found in: >>>>>>>>>>>>>>>> npm ERR! >>>>>>>>>>>>>>>> /home/lorisadmin/.npm/_logs/2019-08-13T18_12_05_378Z-debug.log >>>>>>>>>>>>>>>> make: *** [javascript] Error 2 >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Thanks, >>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> ???? ???, 12 ??? 2019 ???? 10:19 ?.?., ?/? Christine >>>>>>>>>>>>>>>> Rogers, Ms. ??????: >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> We've seen some users installing LORIS 21 or upgrading to >>>>>>>>>>>>>>>>> 21 whose version of node doesn't work well with webpack, due to updated >>>>>>>>>>>>>>>>> packages they're missing. >>>>>>>>>>>>>>>>> If so, update your node : >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> curl -sL https://deb.nodesource.com/setup_8.x | sudo -E bash - >>>>>>>>>>>>>>>>> sudo apt-get install -y nodejs >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Let us know how that goes -- please send us output from >>>>>>>>>>>>>>>>> the same log if any issues. >>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>> Christine >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> On Thu, Aug 8, 2019 at 2:38 PM Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> It's not a disk space issue, as you can see below i have >>>>>>>>>>>>>>>>>> still 74GB available. >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> lorisadmin at hbp:/var/www/loris$ df -h >>>>>>>>>>>>>>>>>> Filesystem Size Used Avail Use% Mounted on >>>>>>>>>>>>>>>>>> udev 2,9G 0 2,9G 0% /dev >>>>>>>>>>>>>>>>>> tmpfs 597M 8,6M 588M 2% /run >>>>>>>>>>>>>>>>>> /dev/sda1 98G 19G 74G 21% / >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Maybe we have to pass a flag to get into strict mode? as >>>>>>>>>>>>>>>>>> stated "SyntaxError: Block-scoped declarations (let, const, function, >>>>>>>>>>>>>>>>>> class) not yet supported outside strict mode" >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Thanks, >>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> ???? ???, 8 ??? 2019 ???? 4:32 ?.?., ?/? Dave MacFarlane < >>>>>>>>>>>>>>>>>> dave.macfarlane at mcin.ca> ??????: >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> It looks like the javascript snippet shown in the error >>>>>>>>>>>>>>>>>>> message when trying to compile the js is truncated. Have you run out of >>>>>>>>>>>>>>>>>>> disk space? >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> On Thu, Aug 8, 2019 at 8:37 AM Sotirios Nikoloutsopoulos >>>>>>>>>>>>>>>>>>> wrote: >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> I runned make and also included the file it reports at >>>>>>>>>>>>>>>>>>>> the end. >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> lorisadmin at hbp:/var/www/loris$ make >>>>>>>>>>>>>>>>>>>> npm install >>>>>>>>>>>>>>>>>>>> npm WARN optional Skipping failed optional dependency >>>>>>>>>>>>>>>>>>>> /chokidar/fsevents: >>>>>>>>>>>>>>>>>>>> npm WARN notsup Not compatible with your operating >>>>>>>>>>>>>>>>>>>> system or architecture: fsevents at 1.2.9 >>>>>>>>>>>>>>>>>>>> npm WARN optional Skipping failed optional dependency >>>>>>>>>>>>>>>>>>>> /watchpack/chokidar/fsevents: >>>>>>>>>>>>>>>>>>>> npm WARN notsup Not compatible with your operating >>>>>>>>>>>>>>>>>>>> system or architecture: fsevents at 1.2.9 >>>>>>>>>>>>>>>>>>>> npm run compile >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> > loris at 1.0.0 compile /var/www/loris >>>>>>>>>>>>>>>>>>>> > webpack >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> /var/www/loris/node_modules/webpack/bin/webpack.js:86 >>>>>>>>>>>>>>>>>>>> let notify = >>>>>>>>>>>>>>>>>>>> ^^^ >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> SyntaxError: Block-scoped declarations (let, const, >>>>>>>>>>>>>>>>>>>> function, class) not yet supported outside strict mode >>>>>>>>>>>>>>>>>>>> at exports.runInThisContext (vm.js:53:16) >>>>>>>>>>>>>>>>>>>> at Module._compile (module.js:374:25) >>>>>>>>>>>>>>>>>>>> at Object.Module._extensions..js (module.js:417:10) >>>>>>>>>>>>>>>>>>>> at Module.load (module.js:344:32) >>>>>>>>>>>>>>>>>>>> at Function.Module._load (module.js:301:12) >>>>>>>>>>>>>>>>>>>> at Function.Module.runMain (module.js:442:10) >>>>>>>>>>>>>>>>>>>> at startup (node.js:136:18) >>>>>>>>>>>>>>>>>>>> at node.js:966:3 >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> npm ERR! Linux 4.15.0-55-generic >>>>>>>>>>>>>>>>>>>> npm ERR! argv "/usr/bin/nodejs" "/usr/bin/npm" "run" >>>>>>>>>>>>>>>>>>>> "compile" >>>>>>>>>>>>>>>>>>>> npm ERR! node v4.2.6 >>>>>>>>>>>>>>>>>>>> npm ERR! npm v3.5.2 >>>>>>>>>>>>>>>>>>>> npm ERR! code ELIFECYCLE >>>>>>>>>>>>>>>>>>>> npm ERR! loris at 1.0.0 compile: `webpack` >>>>>>>>>>>>>>>>>>>> npm ERR! Exit status 1 >>>>>>>>>>>>>>>>>>>> npm ERR! >>>>>>>>>>>>>>>>>>>> npm ERR! Failed at the loris at 1.0.0 compile script >>>>>>>>>>>>>>>>>>>> 'webpack'. >>>>>>>>>>>>>>>>>>>> npm ERR! Make sure you have the latest version of >>>>>>>>>>>>>>>>>>>> node.js and npm installed. >>>>>>>>>>>>>>>>>>>> npm ERR! If you do, this is most likely a problem with >>>>>>>>>>>>>>>>>>>> the loris package, >>>>>>>>>>>>>>>>>>>> npm ERR! not with npm itself. >>>>>>>>>>>>>>>>>>>> npm ERR! Tell the author that this fails on your system: >>>>>>>>>>>>>>>>>>>> npm ERR! webpack >>>>>>>>>>>>>>>>>>>> npm ERR! You can get information on how to open an >>>>>>>>>>>>>>>>>>>> issue for this project with: >>>>>>>>>>>>>>>>>>>> npm ERR! npm bugs loris >>>>>>>>>>>>>>>>>>>> npm ERR! Or if that isn't available, you can get their >>>>>>>>>>>>>>>>>>>> info via: >>>>>>>>>>>>>>>>>>>> npm ERR! npm owner ls loris >>>>>>>>>>>>>>>>>>>> npm ERR! There is likely additional logging output >>>>>>>>>>>>>>>>>>>> above. >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> npm ERR! Please include the following file with any >>>>>>>>>>>>>>>>>>>> support request: >>>>>>>>>>>>>>>>>>>> npm ERR! /var/www/loris/npm-debug.log >>>>>>>>>>>>>>>>>>>> Makefile:14: recipe for target 'javascript' failed >>>>>>>>>>>>>>>>>>>> make: *** [javascript] Error 1 >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Thanks, >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> ???? ???, 7 ??? 2019 ???? 5:41 ?.?., ?/? Christine >>>>>>>>>>>>>>>>>>>> Rogers, Ms. ??????: >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> Thanks, have you tried all of these steps? >>>>>>>>>>>>>>>>>>>>> - clear your browser cache (and refresh a few times) >>>>>>>>>>>>>>>>>>>>> - delete any files in your smarty/templates_c >>>>>>>>>>>>>>>>>>>>> directory (this will clear the template cache - do Not touch >>>>>>>>>>>>>>>>>>>>> smarty/templates/) >>>>>>>>>>>>>>>>>>>>> - run `make` (per the 21 release notes, this replaces >>>>>>>>>>>>>>>>>>>>> the composer commands used in previous releases to update your dependencies) >>>>>>>>>>>>>>>>>>>>> - restart apache (doesn't hurt) >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> Let us know how it goes -- let us know what difference >>>>>>>>>>>>>>>>>>>>> you see after, with your logs. A >>>>>>>>>>>>>>>>>>>>> lso please send us your Config path settings (see these >>>>>>>>>>>>>>>>>>>>> Troubleshooting Queries >>>>>>>>>>>>>>>>>>>>> ) >>>>>>>>>>>>>>>>>>>>> if you're still seeing front-end issues. >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> Thanks, >>>>>>>>>>>>>>>>>>>>> Christine >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> On Wed, Aug 7, 2019 at 8:02 AM Sotirios >>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos wrote: >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> lorisadmin at hbp:/var/www/loris$ sudo cat >>>>>>>>>>>>>>>>>>>>>> /var/log/apache2/error.log >>>>>>>>>>>>>>>>>>>>>> [Wed Aug 07 07:35:02.422501 2019] >>>>>>>>>>>>>>>>>>>>>> [mpm_prefork:notice] [pid 1267] AH00163: Apache/2.4.18 (Ubuntu) >>>>>>>>>>>>>>>>>>>>>> OpenSSL/1.0.2g configured -- resuming normal operations >>>>>>>>>>>>>>>>>>>>>> [Wed Aug 07 07:35:02.422514 2019] [core:notice] [pid >>>>>>>>>>>>>>>>>>>>>> 1267] AH00094: Command line: '/usr/sbin/apache2' >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> And as for the access.log the content are empty >>>>>>>>>>>>>>>>>>>>>> lorisadmin at hbp:/var/www/loris$ sudo ls -l >>>>>>>>>>>>>>>>>>>>>> /var/log/apache2/access.log >>>>>>>>>>>>>>>>>>>>>> lorisadmin at hbp:/var/www/loris$ sudo ls -l >>>>>>>>>>>>>>>>>>>>>> /var/log/apache2/access.log >>>>>>>>>>>>>>>>>>>>>> -rw-r----- 1 root adm 0 ???? 28 14:09 >>>>>>>>>>>>>>>>>>>>>> /var/log/apache2/access.log >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> Also i noticed a loris_access.log. >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> The only non-blank pages are: >>>>>>>>>>>>>>>>>>>>>> mri_violations, dataquery does not exist at all, >>>>>>>>>>>>>>>>>>>>>> statistics, data_team_helper, genomic_browser, configuration and >>>>>>>>>>>>>>>>>>>>>> server_processes_manager/ prints "Required configuration settings for >>>>>>>>>>>>>>>>>>>>>> Server Processes Manager are missing. Cannot continue." >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> Thanks, >>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> ???? ???, 6 ??? 2019 ???? 10:13 ?.?., ?/? Christine >>>>>>>>>>>>>>>>>>>>>> Rogers, Ms. ??????: >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios and LORIS community -- >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> When upgrading to brand-new release 21 -- just a >>>>>>>>>>>>>>>>>>>>>>> reminder to follow the release notes and run the new >>>>>>>>>>>>>>>>>>>>>>> *make* file to update your dependencies (instead of >>>>>>>>>>>>>>>>>>>>>>> using *composer* commands). >>>>>>>>>>>>>>>>>>>>>>> We've also updated the Wiki page >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> to clarify that the release notes for each version will tell you what to >>>>>>>>>>>>>>>>>>>>>>> run. >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> If your current version is not the last release >>>>>>>>>>>>>>>>>>>>>>> (20.3), it's still important to upgrade to each minor release increment >>>>>>>>>>>>>>>>>>>>>>> (e.g. 20.2, 20.3) before making the leap to 21.0. >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> If you're getting blank pages, post-upgrade -- Try >>>>>>>>>>>>>>>>>>>>>>> clearing your cache. >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> Got questions or feedback e.g. on the Release Notes? >>>>>>>>>>>>>>>>>>>>>>> please don't hesitate to let us know. >>>>>>>>>>>>>>>>>>>>>>> Thanks, >>>>>>>>>>>>>>>>>>>>>>> Christine >>>>>>>>>>>>>>>>>>>>>>> The LORIS team >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> On Tue, Aug 6, 2019 at 10:09 AM Christine Rogers, >>>>>>>>>>>>>>>>>>>>>>> Ms. wrote: >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>> Could you also let us know -- on which pages is >>>>>>>>>>>>>>>>>>>>>>>> content visible, and on which pages/modules is content not visible for you? >>>>>>>>>>>>>>>>>>>>>>>> Thanks, >>>>>>>>>>>>>>>>>>>>>>>> Christine >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> On Tue, Aug 6, 2019 at 9:54 AM Christine Rogers, >>>>>>>>>>>>>>>>>>>>>>>> Ms. wrote: >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> Thanks Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>> That's good to know. It sounds like you've >>>>>>>>>>>>>>>>>>>>>>>>> checked that your /var/www/loris/project/config.xml file get populated >>>>>>>>>>>>>>>>>>>>>>>>> properly. >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> Please send us the last few errors you're seeing >>>>>>>>>>>>>>>>>>>>>>>>> in your apache error log file, and your config paths and we can see what's >>>>>>>>>>>>>>>>>>>>>>>>> happening with your front end -- >>>>>>>>>>>>>>>>>>>>>>>>> Run these Troubleshooting Queries >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> to get your config path settings, given your front end is not displaying >>>>>>>>>>>>>>>>>>>>>>>>> fully. >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> The Loris-MRI repo >>>>>>>>>>>>>>>>>>>>>>>>> 21 >>>>>>>>>>>>>>>>>>>>>>>>> install/upgrade would then be your next steps. >>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>> Christine >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> On Tue, Aug 6, 2019 at 7:53 AM Sotirios >>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos wrote: >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> I am using a VM. What i did was: >>>>>>>>>>>>>>>>>>>>>>>>>> 1) Download the files from >>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris and replace them >>>>>>>>>>>>>>>>>>>>>>>>>> to my existing /vaw/www/loris folder. >>>>>>>>>>>>>>>>>>>>>>>>>> 2) Execute the composer install --no-dev and >>>>>>>>>>>>>>>>>>>>>>>>>> then composer dump-autoload as mentioned here >>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris/wiki/Updating-your-LORIS >>>>>>>>>>>>>>>>>>>>>>>>>> . >>>>>>>>>>>>>>>>>>>>>>>>>> 3) Execute install.sh from /var/www/loris/tools >>>>>>>>>>>>>>>>>>>>>>>>>> and because LORIS already existed i moved a .config file, then re-executed >>>>>>>>>>>>>>>>>>>>>>>>>> the install.sh successfully >>>>>>>>>>>>>>>>>>>>>>>>>> 4 ) As for the database, i dropped the schema and >>>>>>>>>>>>>>>>>>>>>>>>>> i executed the installdb.php >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 5 ??? 2019 ???? 5:22 ?.?., ?/? >>>>>>>>>>>>>>>>>>>>>>>>>> Christine Rogers, Ms. >>>>>>>>>>>>>>>>>>>>>>>>>> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotorios, >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> Thanks - when you re-installed did you start on >>>>>>>>>>>>>>>>>>>>>>>>>>> a fresh root path / VM or might some of your old system setting still >>>>>>>>>>>>>>>>>>>>>>>>>>> apply? >>>>>>>>>>>>>>>>>>>>>>>>>>> (And if you did any steps similar to an upgrade, >>>>>>>>>>>>>>>>>>>>>>>>>>> did you follow the Upgrade steps in the Release Notes, from both repos?) >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> About the TR_range column - it was recently >>>>>>>>>>>>>>>>>>>>>>>>>>> split (MRI pr339 >>>>>>>>>>>>>>>>>>>>>>>>>>> ) split >>>>>>>>>>>>>>>>>>>>>>>>>>> into TR_min and _max columns. Given the code was trying to query TR_range >>>>>>>>>>>>>>>>>>>>>>>>>>> which does not exist in your mri_protocol table, double-check which version >>>>>>>>>>>>>>>>>>>>>>>>>>> of the Loris repo (tables) and the Loris-MRI repo (code) you have installed >>>>>>>>>>>>>>>>>>>>>>>>>>> to ensure they match. >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> Christine >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> On Mon, Aug 5, 2019 at 9:06 AM Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos wrote: >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> I reinstalled LORIS to 21 version and now the >>>>>>>>>>>>>>>>>>>>>>>>>>>> content is not visible at all at most pages. >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 5 ??? 2019 ???? 3:19 ?.?., ?/? >>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos >>>>>>>>>>>>>>>>>>>>>>>>>>>> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Is it easy to upgrade to Loris 21? Also the >>>>>>>>>>>>>>>>>>>>>>>>>>>>> following fails because the line 1985 of NeuroDB/MRIProcessingUtility.pm >>>>>>>>>>>>>>>>>>>>>>>>>>>>> query mri_protocol which doesn't have TR_range >>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris/blob/21.0-release/SQL/0000-00-00-schema.sql#L556 >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> lorisadmin at hbp:/data/loris/bin/mri$ >>>>>>>>>>>>>>>>>>>>>>>>>>>>> ./batch_uploads_imageuploader -profile prod < ~/Desktop/input.txt > log.txt >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $_ in pattern match >>>>>>>>>>>>>>>>>>>>>>>>>>>>> (m//) at ./batch_uploads_imageuploader line 147. >>>>>>>>>>>>>>>>>>>>>>>>>>>>> base is DCC0000_258024_V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>> path is /data/incoming/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>> type is .tar.gz >>>>>>>>>>>>>>>>>>>>>>>>>>>>> fullpath is >>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/incoming/DCC0000_258024_V1.tar.gz >>>>>>>>>>>>>>>>>>>>>>>>>>>>> DBD::mysql::st execute failed: Unknown column >>>>>>>>>>>>>>>>>>>>>>>>>>>>> 'TR_range' in 'where clause' at >>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line 1985. >>>>>>>>>>>>>>>>>>>>>>>>>>>>> DBD::mysql::st fetchrow_array failed: fetch() >>>>>>>>>>>>>>>>>>>>>>>>>>>>> without execute() at >>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line 1986. >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $count_mri_protocol >>>>>>>>>>>>>>>>>>>>>>>>>>>>> in numeric gt (>) at >>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line 1995. >>>>>>>>>>>>>>>>>>>>>>>>>>>>> DBD::mysql::st execute failed: Unknown column >>>>>>>>>>>>>>>>>>>>>>>>>>>>> 'TR_range' in 'field list' at >>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 562. >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Can't exec "mail": No such file or directory >>>>>>>>>>>>>>>>>>>>>>>>>>>>> at /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 721. >>>>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 722. >>>>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 723. >>>>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 724. >>>>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 725. >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> No Mincs inserted >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thanks, >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 3 ??? 2019 ???? 1:08 ?.?., ?/? >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Christine Rogers, Ms. < >>>>>>>>>>>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> First, just a note: we've released LORIS 21 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> this week with some major new features and cleanup -- especially if you are >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> early in your setup phase, check out the Release notes for both the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> LORIS >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and Loris-MRI >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> repos. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thanks for your screenshots -- your empty >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> mri_protocol table should be at the root of these issues : >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The mri_protocol table must be populated >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in order for your scans to be registered in LORIS -- it serves as a >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> whitelist for the insertion pipeline which filters out scans that aren't >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> identified or matched to scan types in this table. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> By default, this table is populated with >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> entries for t1, t2, fMRI and DTI (Insert >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> statements for 21 release branch are here >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ) >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Feel free to restore our default records and >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> broaden their parameters to match all your scan types. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> re Defaced, native, selected -- these filter >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the scans displayed as you move to the next page (View Session), instead of >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> viewing "all types" of scans from a given session : >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - "defaced" means that a defacing script >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> has masked the subject's face in the volume (for patient privacy) >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - "native" means that no pre-processing >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> has been performed on the scan (it's raw data), >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - "selected" will show only volumes that >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> have been QC'd and "selected" as the best of their type -- used to display >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> only the best quality T1 image instead of all T1s acquired in a session, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> e.g. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> re QC Comments -- >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Once you have successfully loaded scans >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> (matched to the mri_protocol table), you'll be able to use the Imaging >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Browser's View Session subpage to enter/view QC comments on each volume, or >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> for each visit. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> These are stored directly in the database, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and linked to each scan. (Table name: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> feedback_mri_comments) >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> (Visit-level QC comments are linked to the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> session.) >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> For a walkthrough of the Imaging setup - >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> please see the Imaging Setup guide >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> An old LORIS walkthrough video >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> can >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> also walk you through some of the Imaging front-end features, starting at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 8:00 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> LORIS' imaging modules have been updated many >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> times since this video, but the functionality and workflow is similar. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Let us know how it goes once you have entries >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in your mri_protocol table - >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Christine >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> On Fri, Aug 2, 2019 at 7:58 AM Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> wrote: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Christine, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> In the candidate_list page i can see this >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> patient >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> If i press the link under PSCID i get to see >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and if i press the link under Scan Done it >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> redirects me to imaging_browser >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> At the mri_violations page i also see No >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> results ( neither on resolved / not resolved ). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> At the imaging_uploader i can see the record >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> that failed. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> If i click on the tarchive info i get to see >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the Protocol Name which i think is the acquisition we wanted? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Also my mri_protocol table is empty. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Furthermore i would like to ask about the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> defaced, native, selected. What exactly is native and selected? And where >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> are the qc comments stored? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Finally a walkthrough would be helpful. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thanks, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 30 ???? 2019 ???? 8:29 ?.?., ?/? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Christine Rogers, Ms. < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Glad to hear you're making progress with >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the visit labels. To follow up on your last few emails: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> a- The Wiki's Setup Guide contains Sample >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> insert statements for the Visit Windows table >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> . >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> As Cecile mentioned, the consistency of >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit label format is important: V01, v01, V1, 01 -- whichever you select >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> to use is fine; we use V01 by default across all documentation. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> b- For Password reset, there is a script in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the tools/ directory so that a back-end administrator can reset any >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> front-end user password, including Admin. (See info on setting up / >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> resetting User passwords in the Wiki's >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Setup Guide >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ) >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> c- The minc file not being registered -- >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> due to AcquisitionProtocol unknown. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> This means the SeriesDescription >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> (Acquisition Protocol) in you Dicom header was not matched to any scan >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> listed in the mri_protocol database table. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> (In the online Loris-MRI Troubleshooting >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Guide, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> this >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> is Table 3, 2nd-last item "no MINCs >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> inserted"). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The MRI Violations module (Readme here) >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> will show >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> you the details of this mismatch -- >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Go to the module (under the Imaging menu), >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> find your scan and click the link "Could not identify scan type" -- in the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> next subpage you can compare the scan's actual parameters against the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> mri_protocol table. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> To resolve this, adjust your mri_protocol >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> table values or perhaps ensure your DICOMs are labelled consistently. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Let us know if this works for you -- we can >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> also walk you through an example of non-identified scans on >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Demo.loris.ca (MRI Violations module). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Christine >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The LORIS team >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> On Tue, Jul 30, 2019 at 10:47 AM Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> wrote: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I hope this is sufficient as the error for >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the visit label disappeared. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Please see the attached file. Also >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> something i found. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> lorisadmin at hbp:/data/loris/bin/mri$ cat >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data//logs/TarLoad-17-39-xubBdv.log >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ==> Loading file from disk >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-17-39-UyQcG2/dcc0000_258024_v1_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> --> mapping DICOM parameter for >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-17-39-UyQcG2/dcc0000_258024_v1_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ==> computing md5 hash for MINC body. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> --> md5: 6b1202fd63e29de4c9be1cd9925888a5 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ==> verifying acquisition protocol >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Acquisition protocol is unknown >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> --> The minc file cannot be registered >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> since the AcquisitionProtocol is unknown >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 30 ???? 2019 ???? 4:58 ?.?., ?/? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Ok I fixed the login problem by using a >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> known hash and by deleting the rows from the login_history i was able to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> login. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 30 ???? 2019 ???? 4:50 ?.?., >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ?/? Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> there was no visit label 01 in the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Visit_Windows table and i don't know how to insert it because the record >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> requires lots of attributes. Also the system for a reason asked me to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> update my password and now i don't remember it and my account got >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> suspended. Is there a way to reset it or set a simple password? I updated >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the password hash in the users table by using the hash from another LORIS >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> setup we had and i still couldn't login ( also the attribute password is >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> always NULL and the expiration date is 1999-01-01 for some reason ). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thanks >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 29 ???? 2019 ???? 5:21 ?.?., >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ?/? Cecile Madjar >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Can you try adding the visit label v01 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> to the Visit_Windows table? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> However, I noticed that in a previous >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> dataset, the label was V1. Does that refer to the same visit? If so, you >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> might want to harmonize the visit labels so they are all the same across >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> datasets for a given timepoint, meaning you will need to relabel scans when >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the visit label is different but referring to the same visit label (v01 = >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> V1 etc...). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helps, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> On Mon, Jul 29, 2019 at 10:15 AM >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Could you help me with the "Visit >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> label does not exist"? I had changed $subjectID{'createVisitLabel'} to 1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> as you had suggested but it appears that this problem hasn't been resolved >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> yet. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> lorisadmin at hbp:/data/loris/bin/mri$ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> cat /data/loris/data//logs/TarLoad-14-58-9Xog7H.log >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ==> Loading file from disk >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> --> mapping DICOM parameter for >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> --> using user-defined >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> filterParameters for >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Candidate Mismatch Error is Visit >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> label does not exist >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -> WARNING: This candidate was >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> invalid. Logging to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> MRICandidateErrors table >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> with reason Visit label does not exist >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 26 ???? 2019 ???? 3:02 ?.?., >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ?/? Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Cecile, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The Center error was fixed. Still the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> insertion of mincs fails. Please see the output.txt file i attached. Also >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> is there something else i need to change at the paths configuration? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 25 ???? 2019 ???? 6:55 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ?.?., ?/? Cecile Madjar < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> cecile.madjar at mcin.ca> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> We are making progress! >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I have a feeling this error comes >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> from the fact that your psc table does not have the MRI_alias populated for >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the DCC site. Running the following query in the mysql database should fix >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> this: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> UPDATE psc SET MRI_alias="DCC", >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Alias="DCC" WHERE Name="Data Coordinating Center"; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Repeat the same with all your sites >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> (make sure to change the Aliases between sites, they should all be unique). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Let me know how it goes! >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> On Thu, Jul 25, 2019 at 11:43 AM >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Dear Cecile, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> You were right about your guesses. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I did the modifications you suggested, i still get the "no mincs inserted" >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> error, now i am getting the "No center found this candidate" error ( how do >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> i fix that? from what i see the .dcm files contains a 'Institution Name', >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> is that the center? ), so i guess that's why the validation fails, but i >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> changed the force variable of tarchiveLoader to 1, shouldn't it have >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> inserted the mincs then? Also it is optional to have a mail server, right? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ( from what i see the mail error does not affect the $valid_study, so i >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> assume we are okay with that ) >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you a lot, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 25 ???? 2019 ???? 5:48 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ?.?., ?/? Cecile Madjar < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> cecile.madjar at mcin.ca> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> From what I understand, I believe >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> you just need to update a few config settings from the frontend in the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Config module (under the Admin menu). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [image: Screen Shot 2019-07-25 at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 10.31.35 AM.png] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Then go to the Paths section of >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the config module and update the "LORIS-MRI code" config setting to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri (my guess is that currently, it is set to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data) and click on the submit button. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [image: Screen Shot 2019-07-25 at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 10.32.50 AM.png] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Then, go to Imaging Pipeline >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> section of the Configuration module and update the "Loris-MRI Data >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Directory" to /data/loris/data/ (my guess is that it is empty at the moment >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in your database which is why $data_dir is not defined when you run the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> tarchiveLoader step of the insertion pipeline). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [image: Screen Shot 2019-07-25 at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 10.40.52 AM.png] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Finally, I took a look at your >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> environment file and it might be a good idea to update your PERL5LIB >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> variable to the following (it has been added to the code a few releases ago >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> as we realized this was needed for the libraries. Not sure which version of >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> LORIS-MRI you are using but it does not hurt to update this variable to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> what I suggest below): >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> export >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PERL5LIB=/data/loris/bin/mri/uploadNeuroDB:/data/loris/bin/mri/dicom-archive:$PERL5LIB >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helps. Sorry you are >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> experiencing so much trouble setting things up. We probably need to update >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> our WIKI. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> On Thu, Jul 25, 2019 at 9:48 AM >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The "Loris-MRI Data Directory" >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> should be in the environment file? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 25 ???? 2019 ???? 12:59 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ?.?., ?/? Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The scripts are located in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/. Somewhere I might have messed something up but i >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> remember following the instructions in the wiki.For example when i tried to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> execute the batch_uploads_imageuploader perl script the line >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> my $command = >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> "$bin_dir/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl " >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> was pointing to an invalid path, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> for example: it was repeating a pattern and had LORIS instead of loris ( i >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> think the mistake was that in the wiki it suggested to use $PROJECT for >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the name of the folder and i choosed 'loris' >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris/wiki/Imaging-Database >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ). See also the in image for the modification i did. Also i didn't find the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> section to config the $data_dir variable. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 24 ???? 2019 ???? 6:05 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ?.?., ?/? Cecile Madjar < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> cecile.madjar at mcin.ca> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> It looks like you have one >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Config setting not set (based on the first error message you got when >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> running it the first time). You need to set a value for "Loris-MRI Data >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Directory" in the Config module under the Imaging pipeline section (from >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> what I can see, it would be /data/loris/data/ for your setup). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The reason you got that error >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> message the second time is that the pipeline checks if the DICOM study was >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> already inserted in the tarchive table. Since you ran the study once >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> already, the study is inserted into the tarchive, hence the message. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> However, the pipeline did not complete as the MINC files were not created >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and inserted into the files/parameter_file table. In order to continue the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> insertion, you will then need to run the tarchiveLoader command suggested >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in the terminal during the second run: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -globLocation -profile prod >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive//2012/DCM_2012-12-05_ImagingUpload-17-43-ZUEFjb.tar >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -verbose >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Finally, I am a bit confused by >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> your setup. Where are the scripts located? In /data/loris/bin/mri or >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data? It feels like the Config setting "LORIS-MRI code" in the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Paths section was set to "/data/LORIS/data" but it should have been set to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the directory where the scripts are located (most probably >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helps, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> On Wed, Jul 24, 2019 at 10:55 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> AM Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Ok first i execute this >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> command: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> "lorisadmin at hbp:/data/loris/bin/mri$ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ./batch_uploads_imageuploader -profile prod < ~/Desktop/input.txt > log.txt >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> $data_dir in concatenation (.) or string at ./batch_uploads_imageuploader >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> line 143. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> $data_dir in concatenation (.) or string at ./batch_uploads_imageuploader >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> line 143. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $_ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in pattern match (m//) at ./batch_uploads_imageuploader line 147. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> base is DCC0000_258024_V01 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> path is /data/incoming/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> type is .tar.gz >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> fullpath is >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/incoming/DCC0000_258024_V01.tar.gz >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> source >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/ImagingUpload-17-43-ZUEFjb >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> targetlocation >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> $data_dir in concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 256. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> $data_dir in concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 284. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> $data_dir in concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> tarchive_validation.pl line >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 219. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> $data_dir in concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl line 270. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> $data_dir in concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 711. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Can't exec "mail": No such >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> file or directory at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 721. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> MAIL at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 722. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> MAIL at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 723. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> $data_dir in concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 724. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> MAIL at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 724. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> MAIL at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 725. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> $data_dir in concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 735. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> No Mincs inserted >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The tarchiveLoader insertion >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> script has failed. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Running now the following >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> command: /data/loris/data/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -profile prod -upload_id 3 /data/incoming/DCC0000_258024_V01.tar.gz >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -verbose" >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I inserted the VisitLabel, but >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> still the Mincs are not inserted and i am getting this error >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> "lorisadmin at hbp:/data/loris/bin/mri$ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -profile prod -upload_id 3 /data/incoming/DCC0000_258024_V01.tar.gz -verbose >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> find -path >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> \/tmp\/ImagingUpload\-17\-45\-5MsWEd -name '__MACOSX' -delete >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Spool message is: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The Scan for the uploadID 3 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> has already been run with tarchiveID: 7. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> To continue with the rest of >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the insertion pipeline, please run tarchiveLoader from a terminal as >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> follows: /data/LORIS/data//uploadNeuroDB/tarchiveLoader -globLocation >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -profile prod >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive//2012/DCM_2012-12-05_ImagingUpload-17-43-ZUEFjb.tar >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -verbose" >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Which files should i delete? I >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> thought that deleting the files from the tarchive was enough. And i >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> executed the last proposed command to continue to rest of the insertion >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> pipeline ( check the image ). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 24 ???? 2019 ???? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 5:05 ?.?., ?/? Cecile Madjar < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> cecile.madjar at mcin.ca> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sorry I was not clear before. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Every visits of candidates are created in the session table with one entry >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> per CandID/VisitLabel. So if the imaging pipeline created visits in the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> session table (that are not attached to instruments) and you want to clean >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> your database completely, you can delete entries in that table as well. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Regarding your point 2, the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> imaging pipeline can create the visit in the session table as long as the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit label is present in the Visit_Windows table (which means the visit >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> label stored in the PatientName is a valid visit label). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> However, in your prod file, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> if the variable $subjectID{'createVisitLabel'} is set to 1 for candidates, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the visit label should be created in the Visit_Windows table I believe. Here >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> is the line of the prod file you would need to change >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> . >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> In general, we prefer >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> populating the Visit_Windows table and set the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> $subjectID{'createVisitLabel'} to 0 for candidate data to avoid insertion >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> of badly labelled MRI data that are complex to relabel. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Finally, regarding the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> candidate creation, if you execute the following steps, the pipeline should >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> be able to create candidates: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - set in the Imaging Pipeline >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> section of the config module the config setting "Upload creation of >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> candidates" to Yes >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - manually transfer the scans >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> to the LORIS server instead of uploading it via the imaging browser >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - run batch_imaging_upload.pl >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> as you did until now. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helps! >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> On Wed, Jul 24, 2019 at 8:47 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> AM Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> About my second question i >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> replaced the name of the patient in the .dcm files and now i am getting an >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> error that the visit label does not exist. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I thought it was supposed to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> be automatically created. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> "Done adding archive info >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> into database >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -globLocation -profile prod >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive//DCM_2012-12-05_ImagingUpload-15-42-yUwQQV.tar >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -verbose >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> md5sum >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive/DCM_2012-12-05_ImagingUpload-15-42-yUwQQV.tar >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> candidate id 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> => No Visit labelVisit label >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> does not exist >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Set centerID = 1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Number of MINC files that >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> will be considered for inserting into the database: 1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> log dir is /logs and log >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> file is /logs/TarLoad-15-42-L6pocU.log >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> candidate id 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> => No Visit label >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Cleaning up temp files: rm >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -rf /tmp/TarLoad-15-42-J2rQms/ImagingUpload-15-42-yUwQQV*" >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 24 ???? 2019 ???? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 3:38 ?.?., ?/? Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 1) What are the records in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the session table? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 2) I tried to upload a >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> non-phantom file like this >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> input_file.txt: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/incoming/DCC0000_258024_V1.tar.gz >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> N DCC0000_258024_V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Terminal: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ./batch_uploads_imageuploader >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -profile prod < ~/Desktop/input.txt > log.txt >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and i get the following >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> error in the log.txt file >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> "Running now the following >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> command: /data/loris/data/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -profile prod -upload_id 7 /data/incoming/DCC0000_258024_V1.tar.gz -verbose >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> find -path >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> \/tmp\/ImagingUpload\-14\-56\-FeLCB4 -name '__MACOSX' -delete >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Spool message is: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The PatientName read from >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the DICOM header does not start with DCC0000_258024_V1 from the mri_upload >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> table >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> " >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and the spool message is >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> repeated for each .dcm file. Should i preprocess every .dcm file and change >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the PatientName to "DCC0000_258024_V1"? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 3) As far as it concerns >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the candidate profile i have to create a new one each time before i try to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> upload a file? Is there already a way to create a candidate profile and get >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the DCCID and PSCID without the user interface? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 18 ???? 2019 ???? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 5:00 ?.?., ?/? Cecile Madjar < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> cecile.madjar at mcin.ca> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> See answers to your >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> questions below. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> About the 1st case we had >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> a dicom with a blank studyUID, maybe someone accidentally removed it. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> That is strange. Something >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> must have been done to the DICOM files. I have never seen a study with no >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> StudyUID out of the scanner. Usually, you need to manually erase it with >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> some tool. However, DICOMs never cease to surprise me... >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Some other questions: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 1) What are the steps to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> remove all of my patients and uploads?: because i want to try to reupload >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> all the testing dicoms we had with a clean database. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Release 21.0 of LORIS-MRI >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> will offer a script to remove all the entries and files specific to an >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> upload. However, this release is not yet out. Hopefully in the next few >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> weeks. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> In the meantime, since >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> your case is particular and that you just want to start with a clean >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> database, the following deletes should work (hopefully I won't forget any >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> tables): >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> mri_violations_log; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> mri_protocol_violated_scans; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> MRICandidateErrors; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from parameter_file; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> files_qcstatus; # (if you played with the QC part of the imaging browser >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> for testing) >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> feedback_mri_comments; # (if you played with the QC part of the imaging >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> browser for testing) >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> tarchive_series; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from tarchive_files; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from mri_upload; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from tarchive; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from mri_scanner; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from candidate >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> where PSCID="scanner"; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I don't know if you want >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> to also delete entries in the session and candidate table too? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 2) We do not need to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> create the profile of a patient ( are the patients stored in the candidate >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> table? because i can't see the ghosts ), because will it automatically be >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> created when importing a dicom? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I am not sure I understand >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> fully this question. All candidates are stored in the candidate table. The >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> phantom scans however are attached to a scanner candidate depending on >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> where the scan happened. It is a bit of a weird concept that we have to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> redesign eventually but never got a chance to get to it. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hopefully this answered >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> your question, otherwise, don't hesitate to let me know. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 3) What is the difference >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> between uploading a dicom as phantom instead of importing as >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCCID_DCCID_VisitLabel? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> When you upload the scan >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> as PSCID_DCCID_VisitLabel, there is a check that makes sure the candidate >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> IDs and visit label are valid at the time of upload. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> When you upload a scan as >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> phantom, it expects that the DICOM field PatientName and uploaded filename >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> contains the string "phantom". We enforced this behaviour on the imaging >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> uploader side in recent releases but I can't remember which one. Probably >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the upcoming 21.0 release. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> All those verifications >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> might seem cumbersome but they are here to ensure that the files inserted >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> are all valid and labelled properly as it is a bit messy to have to delete >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> files that were wrongly labelled. At least, the delete script present in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> release 21.0 will make this process easier but it is still good practice to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> verify those things. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> With pleasure. Hopefully >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the answers to your questions will be helpful. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PS: loris-dev mailing >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> list: you will find the initial answer I gave Sotirios below. I forgot to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> cc the loris-dev in my earlier reply... >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 16 ???? 2019 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? 12:02 ?.?., ?/? Cecile Madjar < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> cecile.madjar at mcin.ca> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Dear Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you for reaching >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> out. Since your email was already organized in points, I will reply >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> directly below your questions below. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 1) What do we do when >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the StudyUID is blank on the header? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/minor/docs/AppendixA-Troubleshooting_guideline.md >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> There solution provided at the table 3 does not guide us how to find the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> information ( is possible ). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The StudyUID is the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> field used in our pipeline at the moment to check whether a DICOM study was >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> already inserted into LORIS with that same StudyUID since it is supposed to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> be unique for every single study. Currently, we do not support insertion of >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DICOM studies if they do not have a StudyUID associated with them. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Is there a specific >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> reason why the StudyUID is blank in the DICOM headers in your DICOM files? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Did they go through some processes before upload to LORIS? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 2) When i am about to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> upload a non-phanton case i need a 'Visit Label'. Is there already a script >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> that can create a new visit label for a specific Candidate, so i can >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> provide it as input afterwards to the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> batch_uploads_imageuploader ( See option 5.1.3 https://github.com/aces/Loris-MRI/blob/minor/docs/05-PipelineLaunchOptions.md ) >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I am not sure if the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> front-end allows for it but if you use batch_uploads_imageuploader, the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> insertion scripts could create the visit label for you. However, it does >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> need to be included in the patient name in order for the script to know >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> which label it should use. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> For example: you upload >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> V02 for MTL0123 (DCCID: 456789) but V02 was not yet created for MTL0123; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the insertion scripts will create a V02 visit for MTL0123 if the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PatientName field for the dataset is MTL0123_456789_V02 with Stage marked >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> as "Not Started". >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> However, *note that for >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the script to create the visit for the candidate, you have to make sure >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> that all the visit label of your projects were inserted in the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Visit_Windows table* >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> (otherwise, the visit will never be created as they were not specified as >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> being part of the list of visit label to expect). So in the example above, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> you should have one row in Visit_Windows with Visit_label="V02" set. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 3) Section 4.3 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/minor/docs/04-Scripts.md >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> What do we do when the folder contains multiple mnc files? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> This is a case by case. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Most of the time, the MINC files that failed insertion into the imaging >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> browser end up in the MRI violation module where you can see what went >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> wrong with the acquisitions not inserted. If you notice that the MINC file >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> should be inserted as a specific protocol, you can force the insertion as >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> explained in section 4.3. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> In your case, I have a >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> feeling that you want to be able to insert MINC files that did not go >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> through the whole pipeline insertion (DICOM archival, then dcm2mnc, then >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> protocol identification, then insertion...). In theory, you could call >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl on >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> any MINC file, provided you have at least the following information: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - path to the MINC file >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - uploadID associated >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> with the MINC files or DICOM archive path from which those MINC files were >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> created from >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Then the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> script will do the subject information and protocol validation etc... >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> If all the MINC files >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> come from the same uploadID or TarchiveID, then you could run a loop in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> bash calling the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> script like this for files deriving from uploadID=1: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ls /path/to/mnc/folder/* >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> | while read f; do >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -profile prod -uploadID 1 -mincPath $f; done >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helped! >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> | MCIN.ca >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> MCIN.ca >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>>>>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>>>>>>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | >>>>>>>>>>>>>>>>>>>>>>>>>>> MCIN.ca >>>>>>>>>>>>>>>>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>>>>>>>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>>>>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | >>>>>>>>>>>>>>>>>>>>>>>>> MCIN.ca >>>>>>>>>>>>>>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>>>>>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>>>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>>>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>>>>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>>>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> -- >>>>>>>>>>>>> Shen Wang >>>>>>>>>>>>> Loris Developer >>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>> McGill University >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>> >>>>>>>>> -- >>>>>>>>> Shen Wang >>>>>>>>> Loris Developer >>>>>>>>> Montreal Neurological Institute >>>>>>>>> McGill University >>>>>>>>> >>>>>>>>> -- >>>>>>>> Shen Wang >>>>>>>> Loris Developer >>>>>>>> Montreal Neurological Institute >>>>>>>> McGill University >>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> Loris-dev mailing list >>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>> >>>>>>> >>>>>>> >>>>>>> -- >>>>>>> >>>>>>> christine.rogers at mcgill.ca >>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>> Montreal Neurological Institute >>>>>>> McGill University | Montreal | Canada >>>>>>> >>>>>> >>>> >>>> -- >>>> Shen Wang >>>> Loris Developer >>>> Montreal Neurological Institute >>>> McGill University >>>> >>>> >> >> -- >> Shen Wang >> Loris Developer >> Montreal Neurological Institute >> McGill University >> >> -- Shen Wang Loris Developer Montreal Neurological Institute McGill University -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: ???? 2019-08-13 19.21.15.png Type: image/png Size: 508603 bytes Desc: not available URL: From sotirisnik at gmail.com Thu Aug 15 14:45:17 2019 From: sotirisnik at gmail.com (Sotirios Nikoloutsopoulos) Date: Thu, 15 Aug 2019 21:45:17 +0300 Subject: [Loris-dev] Upgrading to Loris 21 - new make file In-Reply-To: References: Message-ID: I attached the sudo make output. ???? ???, 15 ??? 2019 ???? 9:36 ?.?., ?/? Shen Wang ??????: > Hi, > You don't need to run install.sh this time. Redownload the missing file, > then do sudo make. > If it still have indent and no-def errors, then remove the lines which I > told you from webpack.config.js, then try do > sudo make again. > > > On Thu, 15 Aug 2019 at 14:28, Sotirios Nikoloutsopoulos < > sotirisnik at gmail.com> wrote: > >> Hi, >> >> should i try to redownload the files from >> https://github.com/aces/Loris/tree/major and execute the install.sh? I >> find it weird that i am missing some files. >> >> Thanks >> >> ???? ???, 15 ??? 2019 ???? 9:17 ?.?., ?/? Shen Wang < >> wangshen.mcin at gmail.com> ??????: >> >>> Hi Sotirios, >>> It seems like you are missing this file. [ .babelrc] >>> step 1: copy from https://github.com/aces/Loris/blob/major/.babelrc >>> step 2: sudo vi webpack.config.js >>> remove these lines >>> >>> { test: /\.js$/, >>> >>> exclude: /node_modules/, >>> >>> // use: ['babel-loader', 'eslint-loader'], >>> >>> }, >>> >>> step 3: sudo make >>> >>> >>> >>> On Wed, 14 Aug 2019 at 18:52, Sotirios Nikoloutsopoulos < >>> sotirisnik at gmail.com> wrote: >>> >>>> Hi Shen, >>>> >>>> That didn't work either. Also i had removed the git files because i was >>>> getting this error when i used make: >>>> >>>> "git describe --tags --always > VERSION >>>> fatal: Not a git repository (or any of the parent directories): .git >>>> Makefile:8: recipe for target 'VERSION' failed >>>> make: *** [VERSION] Error 128" >>>> >>>> Thanks >>>> >>>> ???? ???, 15 ??? 2019 ???? 1:36 ?.?., ?/? Shen Wang < >>>> wangshen.mcin at gmail.com> ??????: >>>> >>>>> Hi,Sotirios >>>>> In your special situation, there is a temporary fix. >>>>> step 1. sudo git stash >>>>> step 2. open webpack.config.js file >>>>> remove line 75 use: ['babel-loader', 'eslint-loader'], >>>>> save it. >>>>> step 3. sudo make >>>>> >>>>> I hope this could help you to compile the js files. >>>>> >>>>> >>>>> >>>>> On Wed, 14 Aug 2019 at 08:28, Sotirios Nikoloutsopoulos < >>>>> sotirisnik at gmail.com> wrote: >>>>> >>>>>> I forgot to mention that i had already moved my previous config file >>>>>> and re-executed the installation script. >>>>>> >>>>>> ???? ???, 14 ??? 2019 ???? 3:26 ?.?., ?/? Sotirios Nikoloutsopoulos < >>>>>> sotirisnik at gmail.com> ??????: >>>>>> >>>>>>> Hi, >>>>>>> >>>>>>> Step 1 worked and the indentation errors were fixed. About step2 i >>>>>>> added all of these( there are more to include in the list) these to >>>>>>> .eslintignore which were reported to fail at being built, but they still >>>>>>> appear on the errors at the make_output file. >>>>>>> >>>>>>> /jsx/DynamicDataTable.js >>>>>>> /jsx/StaticDataTable.js >>>>>>> /jsx/MultiSelectDropdown.js >>>>>>> /jsx/Breadcrumbs.js >>>>>>> /jsx/Form.js >>>>>>> /jsx/Markdown.js >>>>>>> /modules/media/jsx/mediaIndex.js >>>>>>> /modules/issue_tracker/jsx/issueTrackerIndex.js >>>>>>> /modules/issue_tracker/jsx/index.js >>>>>>> /modules/candidate_parameters/jsx/CandidateParameters.js >>>>>>> /modules/configuration/jsx/SubprojectRelations.js >>>>>>> /modules/conflict_resolver/jsx/conflictResolverIndex.js >>>>>>> /modules/conflict_resolver/jsx/resolvedConflictsIndex.js >>>>>>> /modules/bvl_feedback/jsx/react.behavioural_feedback_panel.js >>>>>>> /modules/dataquery/jsx/react.tabs.js >>>>>>> /modules/document_repository/jsx/docIndex.js >>>>>>> /modules/instrument_builder/jsx/react.instrument_builder.js >>>>>>> /modules/imaging_uploader/jsx/index.js >>>>>>> /modules/datadict/jsx/dataDictIndex.js >>>>>>> /modules/bvl_feedback/jsx/react.behavioural_feedback_panel.js >>>>>>> /modules/new_profile/jsx/NewProfileIndex.js >>>>>>> /modules/examiner/jsx/examinerIndex.js >>>>>>> /modules/configuration/jsx/SubprojectRelations.js >>>>>>> /modules/data_team_helper/jsx/behavioural_qc_module.js >>>>>>> /modules/acknowledgements/jsx/acknowledgementsIndex.js >>>>>>> /modules/candidate_parameters/jsx/CandidateParameters.js >>>>>>> /modules/imaging_browser/jsx/ImagePanel.js >>>>>>> >>>>>>> /modules/mri_violations/jsx/mri_protocol_violations_columnFormatter.js >>>>>>> >>>>>>> /modules/mri_violations/jsx/mri_protocol_check_violations_columnFormatter.js >>>>>>> /modules/genomic_browser/jsx/profileColumnFormatter.js >>>>>>> /modules/dataquery/jsx/react.tabs.js >>>>>>> /jsx/MultiSelectDropdown.js >>>>>>> /modules/mri_violations/jsx/columnFormatterUnresolved.js >>>>>>> /modules/dataquery/jsx/react.sidebar.js >>>>>>> /modules/dataquery/jsx/react.fieldselector.js >>>>>>> /modules/quality_control/jsx/qualityControlIndex.js >>>>>>> /modules/dataquery/jsx/react.paginator.js >>>>>>> /modules/instrument_builder/jsx/react.questions.js >>>>>>> /modules/dataquery/jsx/react.filterBuilder.js >>>>>>> /modules/conflict_resolver/jsx/conflictResolverIndex.js >>>>>>> /jsx/PaginationLinks.js >>>>>>> /modules/conflict_resolver/jsx/resolvedConflictsIndex.js >>>>>>> /modules/dataquery/jsx/react.app.js >>>>>>> /modules/candidate_list/jsx/onLoad.js >>>>>>> /jsx/Form.js >>>>>>> /modules/publication/jsx/publicationIndex.js >>>>>>> >>>>>>> /modules/server_processes_manager/jsx/server_processes_managerIndex.js >>>>>>> /modules/imaging_browser/jsx/imagingBrowserIndex.js >>>>>>> /modules/issue_tracker/jsx/issueTrackerIndex.js >>>>>>> /modules/survey_accounts/jsx/surveyAccountsIndex.js >>>>>>> /modules/data_integrity_flag/jsx/dataIntegrityFlagIndex.js >>>>>>> /modules/instrument_manager/jsx/instrumentManagerIndex.js >>>>>>> /modules/media/jsx/mediaIndex.js >>>>>>> /modules/user_accounts/jsx/userAccountsIndex.js >>>>>>> /modules/help_editor/jsx/help_editor.js >>>>>>> /modules/dicom_archive/jsx/dicom_archive.js >>>>>>> /modules/mri_violations/jsx/columnFormatter.js >>>>>>> /modules/brainbrowser/jsx/Brainbrowser.js >>>>>>> /node_modules/babel-loader/lib/index.js >>>>>>> /modules/document_repository/jsx/editFormIndex.js >>>>>>> >>>>>>> Thanks >>>>>>> >>>>>>> ???? ???, 14 ??? 2019 ???? 7:50 ?.?., ?/? Christine Rogers, Ms. < >>>>>>> christine.rogers at mcgill.ca> ??????: >>>>>>> >>>>>>>> Hi Shen and Sotirios - just a note, >>>>>>>> >>>>>>>> For the 21 release, it's best to run the install script without >>>>>>>> sudoing it. >>>>>>>> >>>>>>>> (Shen, I believe we discovered a minor issue with the sudo last >>>>>>>> week #5008) >>>>>>>> >>>>>>>> Best, >>>>>>>> Christine >>>>>>>> >>>>>>>> On Tue, Aug 13, 2019 at 9:22 PM Shen Wang >>>>>>>> wrote: >>>>>>>> >>>>>>>>> Does it work? If still doesn?t work, try to remove >>>>>>>>> project/config.xml file. Do sudo ./install.sh again. To reinstall Loris >>>>>>>>> again. >>>>>>>>> >>>>>>>>> >>>>>>>>> Shen Wang ?2019?8?13? ????9:02??? >>>>>>>>> >>>>>>>>>> Hi Sotirios, >>>>>>>>>> step 1: >>>>>>>>>> sudo ./node_modules/.bin/eslint --fix /var/www/loris >>>>>>>>>> step 2: >>>>>>>>>> put the rest error files under this line [# Ignore until ESLint >>>>>>>>>> is run] in the .eslintignore file. >>>>>>>>>> step 3: >>>>>>>>>> sudo make >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> On Tue, 13 Aug 2019 at 20:34, Sotirios Nikoloutsopoulos < >>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>> >>>>>>>>>>> I did the modifications, still there are errors. >>>>>>>>>>> Thanks >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> ???? ???, 14 ??? 2019 ???? 3:22 ?.?., ?/? Shen Wang < >>>>>>>>>>> wangshen.mcin at gmail.com> ??????: >>>>>>>>>>> >>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>> I saw your output file, the config issue is gone. >>>>>>>>>>>> you can use [sudo npm run lintfix:javascript ] to fix these >>>>>>>>>>>> indent issues. >>>>>>>>>>>> If it still has errors. >>>>>>>>>>>> Then try modify this file .eslintignore >>>>>>>>>>>> with this >>>>>>>>>>>> >>>>>>>>>>>> # Ignore until ESLint is run >>>>>>>>>>>> >>>>>>>>>>>> modules/* >>>>>>>>>>>> >>>>>>>>>>>> modules/dataquery/ >>>>>>>>>>>> >>>>>>>>>>>> node_modules/* >>>>>>>>>>>> >>>>>>>>>>>> htdocs/js/components/* >>>>>>>>>>>> >>>>>>>>>>>> jsx/* >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> # Ignore external libs >>>>>>>>>>>> >>>>>>>>>>>> htdocs/js/flot/* >>>>>>>>>>>> >>>>>>>>>>>> htdocs/js/jquery/* >>>>>>>>>>>> >>>>>>>>>>>> htdocs/js/jszip/* >>>>>>>>>>>> >>>>>>>>>>>> htdocs/js/modernizr/* >>>>>>>>>>>> >>>>>>>>>>>> htdocs/js/modules/* >>>>>>>>>>>> >>>>>>>>>>>> htdocs/js/react/* >>>>>>>>>>>> >>>>>>>>>>>> htdocs/js/shims/* >>>>>>>>>>>> >>>>>>>>>>>> htdocs/js/c3.min.js >>>>>>>>>>>> >>>>>>>>>>>> htdocs/js/d3.min.js >>>>>>>>>>>> >>>>>>>>>>>> htdocs/js/FileSaver.min.js >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> then do sudo make. >>>>>>>>>>>> It should work. >>>>>>>>>>>> Regards >>>>>>>>>>>> Shen >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> Sotirios Nikoloutsopoulos ?2019?8?13? >>>>>>>>>>>> ????7:54??? >>>>>>>>>>>> >>>>>>>>>>>>> No, it didn't work, i also tried space/tabs because most of >>>>>>>>>>>>> the errors where about indentation, also there are some errors about React. >>>>>>>>>>>>> >>>>>>>>>>>>> Thanks >>>>>>>>>>>>> >>>>>>>>>>>>> lorisadmin at hbp:/var/www/loris$ sudo >>>>>>>>>>>>> ./node_modules/.bin/eslint --init >>>>>>>>>>>>> ? How would you like to configure ESLint? Answer questions >>>>>>>>>>>>> about your style >>>>>>>>>>>>> ? Which version of ECMAScript do you use? ES2015 >>>>>>>>>>>>> ? Are you using ES6 modules? Yes >>>>>>>>>>>>> ? Where will your code run? Browser >>>>>>>>>>>>> ? Do you use CommonJS? Yes >>>>>>>>>>>>> ? Do you use JSX? Yes >>>>>>>>>>>>> ? Do you use React? Yes >>>>>>>>>>>>> ? What style of indentation do you use? Spaces >>>>>>>>>>>>> ? What quotes do you use for strings? Single >>>>>>>>>>>>> ? What line endings do you use? Unix >>>>>>>>>>>>> ? Do you require semicolons? Yes >>>>>>>>>>>>> ? What format do you want your config file to be in? JSON >>>>>>>>>>>>> The config that you've selected requires the following >>>>>>>>>>>>> dependencies: >>>>>>>>>>>>> >>>>>>>>>>>>> eslint-plugin-react at latest >>>>>>>>>>>>> Successfully created .eslintrc.json file in /var/www/loris >>>>>>>>>>>>> >>>>>>>>>>>>> lorisadmin at hbp:/var/www/loris$ sudo make > sudo_make_output >>>>>>>>>>>>> npm WARN The package prop-types is included as both a dev and >>>>>>>>>>>>> production dependency. >>>>>>>>>>>>> npm WARN optional SKIPPING OPTIONAL DEPENDENCY: fsevents at 1.2.4 >>>>>>>>>>>>> (node_modules/fsevents): >>>>>>>>>>>>> npm WARN notsup SKIPPING OPTIONAL DEPENDENCY: Unsupported >>>>>>>>>>>>> platform for fsevents at 1.2.4: wanted >>>>>>>>>>>>> {"os":"darwin","arch":"any"} (current: {"os":"linux","arch":"x64"}) >>>>>>>>>>>>> >>>>>>>>>>>>> npm ERR! code ELIFECYCLE >>>>>>>>>>>>> npm ERR! errno 2 >>>>>>>>>>>>> npm ERR! loris at 1.0.0 compile: `webpack` >>>>>>>>>>>>> npm ERR! Exit status 2 >>>>>>>>>>>>> npm ERR! >>>>>>>>>>>>> npm ERR! Failed at the loris at 1.0.0 compile script. >>>>>>>>>>>>> npm ERR! This is probably not a problem with npm. There is >>>>>>>>>>>>> likely additional logging output above. >>>>>>>>>>>>> >>>>>>>>>>>>> npm ERR! A complete log of this run can be found in: >>>>>>>>>>>>> npm ERR! >>>>>>>>>>>>> /home/lorisadmin/.npm/_logs/2019-08-13T23_40_58_841Z-debug.log >>>>>>>>>>>>> >>>>>>>>>>>>> ???? ???, 14 ??? 2019 ???? 2:29 ?.?., ?/? Shen Wang < >>>>>>>>>>>>> wangshen.mcin at gmail.com> ??????: >>>>>>>>>>>>> >>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>> When you do make command, please make sure with sudo at the >>>>>>>>>>>>>> beginning. [sudo make] >>>>>>>>>>>>>> If it still doesn't work for you. >>>>>>>>>>>>>> Then try the solutions below. >>>>>>>>>>>>>> solution 1: >>>>>>>>>>>>>> [image: ???? 2019-08-13 19.21.15.png] >>>>>>>>>>>>>> Regards >>>>>>>>>>>>>> Shen >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> On Tue, 13 Aug 2019 at 17:22, Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>> >>>>>>>>>>>>>>> I think that the files exists although i redownloaded the >>>>>>>>>>>>>>> eslintrc.json i checked others files that had similar errors. >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> lorisadmin at hbp:/var/www/loris$ ls -l >>>>>>>>>>>>>>> ./node_modules/eslint-loader/index.js >>>>>>>>>>>>>>> -rw-rw-r-- 1 lorisadmin lorisadmin 6463 ??? 26 1985 >>>>>>>>>>>>>>> ./node_modules/eslint-loader/index.js >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> lorisadmin at hbp:/var/www/loris$ ls -l .eslintrc.json >>>>>>>>>>>>>>> -rw-rw-r-- 1 lorisadmin lorisadmin 84530 ??? 14 00:04 >>>>>>>>>>>>>>> .eslintrc.json >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> Maybe this can help >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> Module build failed (from >>>>>>>>>>>>>>> ./node_modules/eslint-loader/index.js): >>>>>>>>>>>>>>> SyntaxError: Cannot read config file: >>>>>>>>>>>>>>> /var/www/loris/.eslintrc.json >>>>>>>>>>>>>>> Error: Unexpected token < in JSON at position 6 >>>>>>>>>>>>>>> at JSON.parse () >>>>>>>>>>>>>>> at loadJSONConfigFile >>>>>>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config/config-file.js:114:21) >>>>>>>>>>>>>>> at loadConfigFile >>>>>>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config/config-file.js:230:26) >>>>>>>>>>>>>>> at loadFromDisk >>>>>>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config/config-file.js:500:18) >>>>>>>>>>>>>>> at Object.load >>>>>>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config/config-file.js:564:20) >>>>>>>>>>>>>>> at Config.getLocalConfigHierarchy >>>>>>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config.js:227:44) >>>>>>>>>>>>>>> at Config.getConfigHierarchy >>>>>>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config.js:179:43) >>>>>>>>>>>>>>> at Config.getConfigVector >>>>>>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config.js:286:21) >>>>>>>>>>>>>>> at Config.getConfig >>>>>>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config.js:329:29) >>>>>>>>>>>>>>> at processText >>>>>>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/cli-engine.js:162:33) >>>>>>>>>>>>>>> at CLIEngine.executeOnText >>>>>>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/cli-engine.js:596:17) >>>>>>>>>>>>>>> at lint >>>>>>>>>>>>>>> (/var/www/loris/node_modules/eslint-loader/index.js:237:17) >>>>>>>>>>>>>>> at Object.module.exports >>>>>>>>>>>>>>> (/var/www/loris/node_modules/eslint-loader/index.js:232:21) >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> ERROR in ./modules/imaging_uploader/jsx/index.js >>>>>>>>>>>>>>> Module build failed (from >>>>>>>>>>>>>>> ./node_modules/eslint-loader/index.js): >>>>>>>>>>>>>>> SyntaxError: Cannot read config file: >>>>>>>>>>>>>>> /var/www/loris/.eslintrc.json >>>>>>>>>>>>>>> Error: Unexpected token < in JSON at position 6 >>>>>>>>>>>>>>> at JSON.parse () >>>>>>>>>>>>>>> at loadJSONConfigFile >>>>>>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config/config-file.js:114:21) >>>>>>>>>>>>>>> at loadConfigFile >>>>>>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config/config-file.js:230:26) >>>>>>>>>>>>>>> at loadFromDisk >>>>>>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config/config-file.js:500:18) >>>>>>>>>>>>>>> at Object.load >>>>>>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config/config-file.js:564:20) >>>>>>>>>>>>>>> at Config.getLocalConfigHierarchy >>>>>>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config.js:227:44) >>>>>>>>>>>>>>> at Config.getConfigHierarchy >>>>>>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config.js:179:43) >>>>>>>>>>>>>>> at Config.getConfigVector >>>>>>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config.js:286:21) >>>>>>>>>>>>>>> at Config.getConfig >>>>>>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config.js:329:29) >>>>>>>>>>>>>>> at processText >>>>>>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/cli-engine.js:162:33) >>>>>>>>>>>>>>> at CLIEngine.executeOnText >>>>>>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/cli-engine.js:596:17) >>>>>>>>>>>>>>> at lint >>>>>>>>>>>>>>> (/var/www/loris/node_modules/eslint-loader/index.js:237:17) >>>>>>>>>>>>>>> at Object.module.exports >>>>>>>>>>>>>>> (/var/www/loris/node_modules/eslint-loader/index.js:232:21) >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> ???? ???, 13 ??? 2019 ???? 11:52 ?.?., ?/? John Saigle < >>>>>>>>>>>>>>> john.saigle at mcin.ca> ??????: >>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> HI Sotirios, >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> The make_output.txt file shows webpack failing because it >>>>>>>>>>>>>>>> can't find the ESLint config file. >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Can you confirm whether the file `.eslintrc.json` exists >>>>>>>>>>>>>>>> within your loris root directory (usually `/var/www/loris/`)? When I delete >>>>>>>>>>>>>>>> my file I get the same errors as you. >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> If you find that it's missing, you can make a local copy >>>>>>>>>>>>>>>> with the contents found here: >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> https://github.com/aces/Loris/blob/e26a6ad49a73fcffef0cd73bb600c4d17b200b62/.eslintrc.json >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Once you know it exists, try running `make` again. >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Let us know if that moves you forward. >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>> John >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> On Tue, Aug 13, 2019 at 2:21 PM Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>> I executed the commands for the node and now i am get the >>>>>>>>>>>>>>>>> followings: >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> lorisadmin at hbp:/var/www/loris$ make > ~/make_output >>>>>>>>>>>>>>>>> npm WARN The package prop-types is included as both a dev >>>>>>>>>>>>>>>>> and production dependency. >>>>>>>>>>>>>>>>> npm WARN optional SKIPPING OPTIONAL DEPENDENCY: >>>>>>>>>>>>>>>>> fsevents at 1.2.4 (node_modules/fsevents): >>>>>>>>>>>>>>>>> npm WARN notsup SKIPPING OPTIONAL DEPENDENCY: Unsupported >>>>>>>>>>>>>>>>> platform for fsevents at 1.2.4: wanted >>>>>>>>>>>>>>>>> {"os":"darwin","arch":"any"} (current: {"os":"linux","arch":"x64"}) >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> npm ERR! code ELIFECYCLE >>>>>>>>>>>>>>>>> npm ERR! errno 2 >>>>>>>>>>>>>>>>> npm ERR! loris at 1.0.0 compile: `webpack` >>>>>>>>>>>>>>>>> npm ERR! Exit status 2 >>>>>>>>>>>>>>>>> npm ERR! >>>>>>>>>>>>>>>>> npm ERR! Failed at the loris at 1.0.0 compile script. >>>>>>>>>>>>>>>>> npm ERR! This is probably not a problem with npm. There is >>>>>>>>>>>>>>>>> likely additional logging output above. >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> npm ERR! A complete log of this run can be found in: >>>>>>>>>>>>>>>>> npm ERR! >>>>>>>>>>>>>>>>> /home/lorisadmin/.npm/_logs/2019-08-13T18_12_05_378Z-debug.log >>>>>>>>>>>>>>>>> make: *** [javascript] Error 2 >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Thanks, >>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> ???? ???, 12 ??? 2019 ???? 10:19 ?.?., ?/? Christine >>>>>>>>>>>>>>>>> Rogers, Ms. ??????: >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> We've seen some users installing LORIS 21 or upgrading to >>>>>>>>>>>>>>>>>> 21 whose version of node doesn't work well with webpack, due to updated >>>>>>>>>>>>>>>>>> packages they're missing. >>>>>>>>>>>>>>>>>> If so, update your node : >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> curl -sL https://deb.nodesource.com/setup_8.x | sudo -E bash - >>>>>>>>>>>>>>>>>> sudo apt-get install -y nodejs >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Let us know how that goes -- please send us output from >>>>>>>>>>>>>>>>>> the same log if any issues. >>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>> Christine >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> On Thu, Aug 8, 2019 at 2:38 PM Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> It's not a disk space issue, as you can see below i have >>>>>>>>>>>>>>>>>>> still 74GB available. >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> lorisadmin at hbp:/var/www/loris$ df -h >>>>>>>>>>>>>>>>>>> Filesystem Size Used Avail Use% Mounted on >>>>>>>>>>>>>>>>>>> udev 2,9G 0 2,9G 0% /dev >>>>>>>>>>>>>>>>>>> tmpfs 597M 8,6M 588M 2% /run >>>>>>>>>>>>>>>>>>> /dev/sda1 98G 19G 74G 21% / >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Maybe we have to pass a flag to get into strict mode? as >>>>>>>>>>>>>>>>>>> stated "SyntaxError: Block-scoped declarations (let, const, function, >>>>>>>>>>>>>>>>>>> class) not yet supported outside strict mode" >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Thanks, >>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> ???? ???, 8 ??? 2019 ???? 4:32 ?.?., ?/? Dave MacFarlane >>>>>>>>>>>>>>>>>>> ??????: >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> It looks like the javascript snippet shown in the error >>>>>>>>>>>>>>>>>>>> message when trying to compile the js is truncated. Have you run out of >>>>>>>>>>>>>>>>>>>> disk space? >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> On Thu, Aug 8, 2019 at 8:37 AM Sotirios >>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos wrote: >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> I runned make and also included the file it reports at >>>>>>>>>>>>>>>>>>>>> the end. >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> lorisadmin at hbp:/var/www/loris$ make >>>>>>>>>>>>>>>>>>>>> npm install >>>>>>>>>>>>>>>>>>>>> npm WARN optional Skipping failed optional dependency >>>>>>>>>>>>>>>>>>>>> /chokidar/fsevents: >>>>>>>>>>>>>>>>>>>>> npm WARN notsup Not compatible with your operating >>>>>>>>>>>>>>>>>>>>> system or architecture: fsevents at 1.2.9 >>>>>>>>>>>>>>>>>>>>> npm WARN optional Skipping failed optional dependency >>>>>>>>>>>>>>>>>>>>> /watchpack/chokidar/fsevents: >>>>>>>>>>>>>>>>>>>>> npm WARN notsup Not compatible with your operating >>>>>>>>>>>>>>>>>>>>> system or architecture: fsevents at 1.2.9 >>>>>>>>>>>>>>>>>>>>> npm run compile >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> > loris at 1.0.0 compile /var/www/loris >>>>>>>>>>>>>>>>>>>>> > webpack >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> /var/www/loris/node_modules/webpack/bin/webpack.js:86 >>>>>>>>>>>>>>>>>>>>> let notify = >>>>>>>>>>>>>>>>>>>>> ^^^ >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> SyntaxError: Block-scoped declarations (let, const, >>>>>>>>>>>>>>>>>>>>> function, class) not yet supported outside strict mode >>>>>>>>>>>>>>>>>>>>> at exports.runInThisContext (vm.js:53:16) >>>>>>>>>>>>>>>>>>>>> at Module._compile (module.js:374:25) >>>>>>>>>>>>>>>>>>>>> at Object.Module._extensions..js (module.js:417:10) >>>>>>>>>>>>>>>>>>>>> at Module.load (module.js:344:32) >>>>>>>>>>>>>>>>>>>>> at Function.Module._load (module.js:301:12) >>>>>>>>>>>>>>>>>>>>> at Function.Module.runMain (module.js:442:10) >>>>>>>>>>>>>>>>>>>>> at startup (node.js:136:18) >>>>>>>>>>>>>>>>>>>>> at node.js:966:3 >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> npm ERR! Linux 4.15.0-55-generic >>>>>>>>>>>>>>>>>>>>> npm ERR! argv "/usr/bin/nodejs" "/usr/bin/npm" "run" >>>>>>>>>>>>>>>>>>>>> "compile" >>>>>>>>>>>>>>>>>>>>> npm ERR! node v4.2.6 >>>>>>>>>>>>>>>>>>>>> npm ERR! npm v3.5.2 >>>>>>>>>>>>>>>>>>>>> npm ERR! code ELIFECYCLE >>>>>>>>>>>>>>>>>>>>> npm ERR! loris at 1.0.0 compile: `webpack` >>>>>>>>>>>>>>>>>>>>> npm ERR! Exit status 1 >>>>>>>>>>>>>>>>>>>>> npm ERR! >>>>>>>>>>>>>>>>>>>>> npm ERR! Failed at the loris at 1.0.0 compile script >>>>>>>>>>>>>>>>>>>>> 'webpack'. >>>>>>>>>>>>>>>>>>>>> npm ERR! Make sure you have the latest version of >>>>>>>>>>>>>>>>>>>>> node.js and npm installed. >>>>>>>>>>>>>>>>>>>>> npm ERR! If you do, this is most likely a problem with >>>>>>>>>>>>>>>>>>>>> the loris package, >>>>>>>>>>>>>>>>>>>>> npm ERR! not with npm itself. >>>>>>>>>>>>>>>>>>>>> npm ERR! Tell the author that this fails on your >>>>>>>>>>>>>>>>>>>>> system: >>>>>>>>>>>>>>>>>>>>> npm ERR! webpack >>>>>>>>>>>>>>>>>>>>> npm ERR! You can get information on how to open an >>>>>>>>>>>>>>>>>>>>> issue for this project with: >>>>>>>>>>>>>>>>>>>>> npm ERR! npm bugs loris >>>>>>>>>>>>>>>>>>>>> npm ERR! Or if that isn't available, you can get their >>>>>>>>>>>>>>>>>>>>> info via: >>>>>>>>>>>>>>>>>>>>> npm ERR! npm owner ls loris >>>>>>>>>>>>>>>>>>>>> npm ERR! There is likely additional logging output >>>>>>>>>>>>>>>>>>>>> above. >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> npm ERR! Please include the following file with any >>>>>>>>>>>>>>>>>>>>> support request: >>>>>>>>>>>>>>>>>>>>> npm ERR! /var/www/loris/npm-debug.log >>>>>>>>>>>>>>>>>>>>> Makefile:14: recipe for target 'javascript' failed >>>>>>>>>>>>>>>>>>>>> make: *** [javascript] Error 1 >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> Thanks, >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> ???? ???, 7 ??? 2019 ???? 5:41 ?.?., ?/? Christine >>>>>>>>>>>>>>>>>>>>> Rogers, Ms. ??????: >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> Thanks, have you tried all of these steps? >>>>>>>>>>>>>>>>>>>>>> - clear your browser cache (and refresh a few times) >>>>>>>>>>>>>>>>>>>>>> - delete any files in your smarty/templates_c >>>>>>>>>>>>>>>>>>>>>> directory (this will clear the template cache - do Not touch >>>>>>>>>>>>>>>>>>>>>> smarty/templates/) >>>>>>>>>>>>>>>>>>>>>> - run `make` (per the 21 release notes, this replaces >>>>>>>>>>>>>>>>>>>>>> the composer commands used in previous releases to update your dependencies) >>>>>>>>>>>>>>>>>>>>>> - restart apache (doesn't hurt) >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> Let us know how it goes -- let us know what >>>>>>>>>>>>>>>>>>>>>> difference you see after, with your logs. A >>>>>>>>>>>>>>>>>>>>>> lso please send us your Config path settings (see these >>>>>>>>>>>>>>>>>>>>>> Troubleshooting Queries >>>>>>>>>>>>>>>>>>>>>> ) >>>>>>>>>>>>>>>>>>>>>> if you're still seeing front-end issues. >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> Thanks, >>>>>>>>>>>>>>>>>>>>>> Christine >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> On Wed, Aug 7, 2019 at 8:02 AM Sotirios >>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos wrote: >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> lorisadmin at hbp:/var/www/loris$ sudo cat >>>>>>>>>>>>>>>>>>>>>>> /var/log/apache2/error.log >>>>>>>>>>>>>>>>>>>>>>> [Wed Aug 07 07:35:02.422501 2019] >>>>>>>>>>>>>>>>>>>>>>> [mpm_prefork:notice] [pid 1267] AH00163: Apache/2.4.18 (Ubuntu) >>>>>>>>>>>>>>>>>>>>>>> OpenSSL/1.0.2g configured -- resuming normal operations >>>>>>>>>>>>>>>>>>>>>>> [Wed Aug 07 07:35:02.422514 2019] [core:notice] [pid >>>>>>>>>>>>>>>>>>>>>>> 1267] AH00094: Command line: '/usr/sbin/apache2' >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> And as for the access.log the content are empty >>>>>>>>>>>>>>>>>>>>>>> lorisadmin at hbp:/var/www/loris$ sudo ls -l >>>>>>>>>>>>>>>>>>>>>>> /var/log/apache2/access.log >>>>>>>>>>>>>>>>>>>>>>> lorisadmin at hbp:/var/www/loris$ sudo ls -l >>>>>>>>>>>>>>>>>>>>>>> /var/log/apache2/access.log >>>>>>>>>>>>>>>>>>>>>>> -rw-r----- 1 root adm 0 ???? 28 14:09 >>>>>>>>>>>>>>>>>>>>>>> /var/log/apache2/access.log >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> Also i noticed a loris_access.log. >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> The only non-blank pages are: >>>>>>>>>>>>>>>>>>>>>>> mri_violations, dataquery does not exist at all, >>>>>>>>>>>>>>>>>>>>>>> statistics, data_team_helper, genomic_browser, configuration and >>>>>>>>>>>>>>>>>>>>>>> server_processes_manager/ prints "Required configuration settings for >>>>>>>>>>>>>>>>>>>>>>> Server Processes Manager are missing. Cannot continue." >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> Thanks, >>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> ???? ???, 6 ??? 2019 ???? 10:13 ?.?., ?/? Christine >>>>>>>>>>>>>>>>>>>>>>> Rogers, Ms. ??????: >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios and LORIS community -- >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> When upgrading to brand-new release 21 -- just a >>>>>>>>>>>>>>>>>>>>>>>> reminder to follow the release notes and run the new >>>>>>>>>>>>>>>>>>>>>>>> *make* file to update your dependencies (instead >>>>>>>>>>>>>>>>>>>>>>>> of using *composer* commands). >>>>>>>>>>>>>>>>>>>>>>>> We've also updated the Wiki page >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> to clarify that the release notes for each version will tell you what to >>>>>>>>>>>>>>>>>>>>>>>> run. >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> If your current version is not the last release >>>>>>>>>>>>>>>>>>>>>>>> (20.3), it's still important to upgrade to each minor release increment >>>>>>>>>>>>>>>>>>>>>>>> (e.g. 20.2, 20.3) before making the leap to 21.0. >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> If you're getting blank pages, post-upgrade -- Try >>>>>>>>>>>>>>>>>>>>>>>> clearing your cache. >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> Got questions or feedback e.g. on the Release >>>>>>>>>>>>>>>>>>>>>>>> Notes? please don't hesitate to let us know. >>>>>>>>>>>>>>>>>>>>>>>> Thanks, >>>>>>>>>>>>>>>>>>>>>>>> Christine >>>>>>>>>>>>>>>>>>>>>>>> The LORIS team >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> On Tue, Aug 6, 2019 at 10:09 AM Christine Rogers, >>>>>>>>>>>>>>>>>>>>>>>> Ms. wrote: >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>> Could you also let us know -- on which pages is >>>>>>>>>>>>>>>>>>>>>>>>> content visible, and on which pages/modules is content not visible for you? >>>>>>>>>>>>>>>>>>>>>>>>> Thanks, >>>>>>>>>>>>>>>>>>>>>>>>> Christine >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> On Tue, Aug 6, 2019 at 9:54 AM Christine Rogers, >>>>>>>>>>>>>>>>>>>>>>>>> Ms. wrote: >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> Thanks Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>> That's good to know. It sounds like you've >>>>>>>>>>>>>>>>>>>>>>>>>> checked that your /var/www/loris/project/config.xml file get populated >>>>>>>>>>>>>>>>>>>>>>>>>> properly. >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> Please send us the last few errors you're seeing >>>>>>>>>>>>>>>>>>>>>>>>>> in your apache error log file, and your config paths and we can see what's >>>>>>>>>>>>>>>>>>>>>>>>>> happening with your front end -- >>>>>>>>>>>>>>>>>>>>>>>>>> Run these Troubleshooting Queries >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> to get your config path settings, given your front end is not displaying >>>>>>>>>>>>>>>>>>>>>>>>>> fully. >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> The Loris-MRI repo >>>>>>>>>>>>>>>>>>>>>>>>>> 21 >>>>>>>>>>>>>>>>>>>>>>>>>> install/upgrade would then be your next steps. >>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>> Christine >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> On Tue, Aug 6, 2019 at 7:53 AM Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos wrote: >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> I am using a VM. What i did was: >>>>>>>>>>>>>>>>>>>>>>>>>>> 1) Download the files from >>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris and replace them >>>>>>>>>>>>>>>>>>>>>>>>>>> to my existing /vaw/www/loris folder. >>>>>>>>>>>>>>>>>>>>>>>>>>> 2) Execute the composer install --no-dev and >>>>>>>>>>>>>>>>>>>>>>>>>>> then composer dump-autoload as mentioned here >>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris/wiki/Updating-your-LORIS >>>>>>>>>>>>>>>>>>>>>>>>>>> . >>>>>>>>>>>>>>>>>>>>>>>>>>> 3) Execute install.sh from /var/www/loris/tools >>>>>>>>>>>>>>>>>>>>>>>>>>> and because LORIS already existed i moved a .config file, then re-executed >>>>>>>>>>>>>>>>>>>>>>>>>>> the install.sh successfully >>>>>>>>>>>>>>>>>>>>>>>>>>> 4 ) As for the database, i dropped the schema >>>>>>>>>>>>>>>>>>>>>>>>>>> and i executed the installdb.php >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 5 ??? 2019 ???? 5:22 ?.?., ?/? >>>>>>>>>>>>>>>>>>>>>>>>>>> Christine Rogers, Ms. < >>>>>>>>>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotorios, >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> Thanks - when you re-installed did you start on >>>>>>>>>>>>>>>>>>>>>>>>>>>> a fresh root path / VM or might some of your old system setting still >>>>>>>>>>>>>>>>>>>>>>>>>>>> apply? >>>>>>>>>>>>>>>>>>>>>>>>>>>> (And if you did any steps similar to an >>>>>>>>>>>>>>>>>>>>>>>>>>>> upgrade, did you follow the Upgrade steps in the Release Notes, from both >>>>>>>>>>>>>>>>>>>>>>>>>>>> repos?) >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> About the TR_range column - it was recently >>>>>>>>>>>>>>>>>>>>>>>>>>>> split (MRI pr339 >>>>>>>>>>>>>>>>>>>>>>>>>>>> ) split >>>>>>>>>>>>>>>>>>>>>>>>>>>> into TR_min and _max columns. Given the code was trying to query TR_range >>>>>>>>>>>>>>>>>>>>>>>>>>>> which does not exist in your mri_protocol table, double-check which version >>>>>>>>>>>>>>>>>>>>>>>>>>>> of the Loris repo (tables) and the Loris-MRI repo (code) you have installed >>>>>>>>>>>>>>>>>>>>>>>>>>>> to ensure they match. >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> Christine >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> On Mon, Aug 5, 2019 at 9:06 AM Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos wrote: >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> I reinstalled LORIS to 21 version and now the >>>>>>>>>>>>>>>>>>>>>>>>>>>>> content is not visible at all at most pages. >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 5 ??? 2019 ???? 3:19 ?.?., ?/? >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Is it easy to upgrade to Loris 21? Also the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> following fails because the line 1985 of NeuroDB/MRIProcessingUtility.pm >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> query mri_protocol which doesn't have TR_range >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris/blob/21.0-release/SQL/0000-00-00-schema.sql#L556 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> lorisadmin at hbp:/data/loris/bin/mri$ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ./batch_uploads_imageuploader -profile prod < ~/Desktop/input.txt > log.txt >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $_ in pattern >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> match (m//) at ./batch_uploads_imageuploader line 147. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> base is DCC0000_258024_V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> path is /data/incoming/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> type is .tar.gz >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> fullpath is >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/incoming/DCC0000_258024_V1.tar.gz >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DBD::mysql::st execute failed: Unknown column >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 'TR_range' in 'where clause' at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line 1985. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DBD::mysql::st fetchrow_array failed: fetch() >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> without execute() at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line 1986. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> $count_mri_protocol in numeric gt (>) at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line 1995. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DBD::mysql::st execute failed: Unknown column >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 'TR_range' in 'field list' at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 562. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Can't exec "mail": No such file or directory >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> at /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 721. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 722. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 723. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 724. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 725. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> No Mincs inserted >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thanks, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 3 ??? 2019 ???? 1:08 ?.?., ?/? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Christine Rogers, Ms. < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> First, just a note: we've released LORIS 21 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> this week with some major new features and cleanup -- especially if you are >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> early in your setup phase, check out the Release notes for both the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> LORIS >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and Loris-MRI >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> repos. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thanks for your screenshots -- your empty >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> mri_protocol table should be at the root of these issues : >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The mri_protocol table must be populated >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in order for your scans to be registered in LORIS -- it serves as a >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> whitelist for the insertion pipeline which filters out scans that aren't >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> identified or matched to scan types in this table. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> By default, this table is populated with >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> entries for t1, t2, fMRI and DTI (Insert >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> statements for 21 release branch are here >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ) >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Feel free to restore our default records and >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> broaden their parameters to match all your scan types. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> re Defaced, native, selected -- these filter >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the scans displayed as you move to the next page (View Session), instead of >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> viewing "all types" of scans from a given session : >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - "defaced" means that a defacing script >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> has masked the subject's face in the volume (for patient privacy) >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - "native" means that no pre-processing >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> has been performed on the scan (it's raw data), >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - "selected" will show only volumes >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> that have been QC'd and "selected" as the best of their type -- used to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> display only the best quality T1 image instead of all T1s acquired in a >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> session, e.g. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> re QC Comments -- >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Once you have successfully loaded scans >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> (matched to the mri_protocol table), you'll be able to use the Imaging >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Browser's View Session subpage to enter/view QC comments on each volume, or >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> for each visit. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> These are stored directly in the database, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and linked to each scan. (Table name: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> feedback_mri_comments) >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> (Visit-level QC comments are linked to the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> session.) >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> For a walkthrough of the Imaging setup - >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> please see the Imaging Setup guide >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> An old LORIS walkthrough video >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> can >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> also walk you through some of the Imaging front-end features, starting at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 8:00 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> LORIS' imaging modules have been updated >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> many times since this video, but the functionality and workflow is similar. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Let us know how it goes once you have >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> entries in your mri_protocol table - >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Christine >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> On Fri, Aug 2, 2019 at 7:58 AM Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> wrote: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Christine, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> In the candidate_list page i can see this >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> patient >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> If i press the link under PSCID i get to see >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and if i press the link under Scan Done it >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> redirects me to imaging_browser >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> At the mri_violations page i also see No >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> results ( neither on resolved / not resolved ). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> At the imaging_uploader i can see the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> record that failed. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> If i click on the tarchive info i get to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> see the Protocol Name which i think is the acquisition we wanted? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Also my mri_protocol table is empty. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Furthermore i would like to ask about the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> defaced, native, selected. What exactly is native and selected? And where >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> are the qc comments stored? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Finally a walkthrough would be helpful. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thanks, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 30 ???? 2019 ???? 8:29 ?.?., ?/? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Christine Rogers, Ms. < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Glad to hear you're making progress with >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the visit labels. To follow up on your last few emails: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> a- The Wiki's Setup Guide contains Sample >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> insert statements for the Visit Windows table >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> . >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> As Cecile mentioned, the consistency of >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit label format is important: V01, v01, V1, 01 -- whichever you select >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> to use is fine; we use V01 by default across all documentation. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> b- For Password reset, there is a script >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in the tools/ directory so that a back-end administrator can reset any >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> front-end user password, including Admin. (See info on setting up / >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> resetting User passwords in the Wiki's >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Setup Guide >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ) >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> c- The minc file not being registered -- >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> due to AcquisitionProtocol unknown. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> This means the SeriesDescription >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> (Acquisition Protocol) in you Dicom header was not matched to any scan >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> listed in the mri_protocol database table. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> (In the online Loris-MRI Troubleshooting >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Guide, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> this >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> is Table 3, 2nd-last item "no MINCs >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> inserted"). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The MRI Violations module (Readme here) >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> will show >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> you the details of this mismatch -- >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Go to the module (under the Imaging menu), >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> find your scan and click the link "Could not identify scan type" -- in the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> next subpage you can compare the scan's actual parameters against the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> mri_protocol table. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> To resolve this, adjust your mri_protocol >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> table values or perhaps ensure your DICOMs are labelled consistently. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Let us know if this works for you -- we >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> can also walk you through an example of non-identified scans on >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Demo.loris.ca (MRI Violations module). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Christine >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The LORIS team >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> On Tue, Jul 30, 2019 at 10:47 AM Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> wrote: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I hope this is sufficient as the error >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> for the visit label disappeared. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Please see the attached file. Also >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> something i found. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> lorisadmin at hbp:/data/loris/bin/mri$ cat >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data//logs/TarLoad-17-39-xubBdv.log >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ==> Loading file from disk >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-17-39-UyQcG2/dcc0000_258024_v1_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> --> mapping DICOM parameter for >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-17-39-UyQcG2/dcc0000_258024_v1_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ==> computing md5 hash for MINC body. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> --> md5: 6b1202fd63e29de4c9be1cd9925888a5 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ==> verifying acquisition protocol >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Acquisition protocol is unknown >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> --> The minc file cannot be registered >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> since the AcquisitionProtocol is unknown >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 30 ???? 2019 ???? 4:58 ?.?., >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ?/? Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Ok I fixed the login problem by using a >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> known hash and by deleting the rows from the login_history i was able to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> login. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 30 ???? 2019 ???? 4:50 ?.?., >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ?/? Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> there was no visit label 01 in the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Visit_Windows table and i don't know how to insert it because the record >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> requires lots of attributes. Also the system for a reason asked me to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> update my password and now i don't remember it and my account got >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> suspended. Is there a way to reset it or set a simple password? I updated >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the password hash in the users table by using the hash from another LORIS >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> setup we had and i still couldn't login ( also the attribute password is >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> always NULL and the expiration date is 1999-01-01 for some reason ). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thanks >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 29 ???? 2019 ???? 5:21 ?.?., >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ?/? Cecile Madjar < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> cecile.madjar at mcin.ca> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Can you try adding the visit label v01 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> to the Visit_Windows table? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> However, I noticed that in a previous >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> dataset, the label was V1. Does that refer to the same visit? If so, you >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> might want to harmonize the visit labels so they are all the same across >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> datasets for a given timepoint, meaning you will need to relabel scans when >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the visit label is different but referring to the same visit label (v01 = >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> V1 etc...). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helps, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> On Mon, Jul 29, 2019 at 10:15 AM >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Could you help me with the "Visit >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> label does not exist"? I had changed $subjectID{'createVisitLabel'} to 1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> as you had suggested but it appears that this problem hasn't been resolved >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> yet. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> lorisadmin at hbp:/data/loris/bin/mri$ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> cat /data/loris/data//logs/TarLoad-14-58-9Xog7H.log >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ==> Loading file from disk >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> --> mapping DICOM parameter for >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> --> using user-defined >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> filterParameters for >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Candidate Mismatch Error is Visit >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> label does not exist >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -> WARNING: This candidate was >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> invalid. Logging to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> MRICandidateErrors >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> table with reason Visit label does not exist >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 26 ???? 2019 ???? 3:02 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ?.?., ?/? Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Cecile, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The Center error was fixed. Still >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the insertion of mincs fails. Please see the output.txt file i attached. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Also is there something else i need to change at the paths configuration? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 25 ???? 2019 ???? 6:55 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ?.?., ?/? Cecile Madjar < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> cecile.madjar at mcin.ca> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> We are making progress! >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I have a feeling this error comes >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> from the fact that your psc table does not have the MRI_alias populated for >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the DCC site. Running the following query in the mysql database should fix >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> this: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> UPDATE psc SET MRI_alias="DCC", >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Alias="DCC" WHERE Name="Data Coordinating Center"; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Repeat the same with all your sites >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> (make sure to change the Aliases between sites, they should all be unique). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Let me know how it goes! >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> On Thu, Jul 25, 2019 at 11:43 AM >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Dear Cecile, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> You were right about your guesses. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I did the modifications you suggested, i still get the "no mincs inserted" >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> error, now i am getting the "No center found this candidate" error ( how do >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> i fix that? from what i see the .dcm files contains a 'Institution Name', >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> is that the center? ), so i guess that's why the validation fails, but i >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> changed the force variable of tarchiveLoader to 1, shouldn't it have >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> inserted the mincs then? Also it is optional to have a mail server, right? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ( from what i see the mail error does not affect the $valid_study, so i >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> assume we are okay with that ) >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you a lot, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 25 ???? 2019 ???? 5:48 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ?.?., ?/? Cecile Madjar < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> cecile.madjar at mcin.ca> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> From what I understand, I believe >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> you just need to update a few config settings from the frontend in the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Config module (under the Admin menu). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [image: Screen Shot 2019-07-25 at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 10.31.35 AM.png] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Then go to the Paths section of >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the config module and update the "LORIS-MRI code" config setting to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri (my guess is that currently, it is set to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data) and click on the submit button. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [image: Screen Shot 2019-07-25 at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 10.32.50 AM.png] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Then, go to Imaging Pipeline >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> section of the Configuration module and update the "Loris-MRI Data >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Directory" to /data/loris/data/ (my guess is that it is empty at the moment >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in your database which is why $data_dir is not defined when you run the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> tarchiveLoader step of the insertion pipeline). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [image: Screen Shot 2019-07-25 at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 10.40.52 AM.png] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Finally, I took a look at your >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> environment file and it might be a good idea to update your PERL5LIB >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> variable to the following (it has been added to the code a few releases ago >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> as we realized this was needed for the libraries. Not sure which version of >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> LORIS-MRI you are using but it does not hurt to update this variable to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> what I suggest below): >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> export >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PERL5LIB=/data/loris/bin/mri/uploadNeuroDB:/data/loris/bin/mri/dicom-archive:$PERL5LIB >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helps. Sorry you are >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> experiencing so much trouble setting things up. We probably need to update >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> our WIKI. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> On Thu, Jul 25, 2019 at 9:48 AM >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The "Loris-MRI Data Directory" >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> should be in the environment file? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 25 ???? 2019 ???? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 12:59 ?.?., ?/? Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The scripts are located in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/. Somewhere I might have messed something up but i >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> remember following the instructions in the wiki.For example when i tried to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> execute the batch_uploads_imageuploader perl script the line >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> my $command = >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> "$bin_dir/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl " >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> was pointing to an invalid >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> path, for example: it was repeating a pattern and had LORIS instead of >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> loris ( i think the mistake was that in the wiki it suggested to use >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> $PROJECT for the name of the folder and i choosed 'loris' >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris/wiki/Imaging-Database >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ). See also the in image for the modification i did. Also i didn't find the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> section to config the $data_dir variable. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 24 ???? 2019 ???? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 6:05 ?.?., ?/? Cecile Madjar < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> cecile.madjar at mcin.ca> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> It looks like you have one >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Config setting not set (based on the first error message you got when >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> running it the first time). You need to set a value for "Loris-MRI Data >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Directory" in the Config module under the Imaging pipeline section (from >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> what I can see, it would be /data/loris/data/ for your setup). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The reason you got that error >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> message the second time is that the pipeline checks if the DICOM study was >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> already inserted in the tarchive table. Since you ran the study once >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> already, the study is inserted into the tarchive, hence the message. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> However, the pipeline did not complete as the MINC files were not created >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and inserted into the files/parameter_file table. In order to continue the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> insertion, you will then need to run the tarchiveLoader command suggested >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in the terminal during the second run: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -globLocation -profile prod >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive//2012/DCM_2012-12-05_ImagingUpload-17-43-ZUEFjb.tar >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -verbose >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Finally, I am a bit confused >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> by your setup. Where are the scripts located? In /data/loris/bin/mri or >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data? It feels like the Config setting "LORIS-MRI code" in the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Paths section was set to "/data/LORIS/data" but it should have been set to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the directory where the scripts are located (most probably >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helps, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> On Wed, Jul 24, 2019 at 10:55 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> AM Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Ok first i execute this >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> command: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> "lorisadmin at hbp:/data/loris/bin/mri$ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ./batch_uploads_imageuploader -profile prod < ~/Desktop/input.txt > log.txt >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> $data_dir in concatenation (.) or string at ./batch_uploads_imageuploader >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> line 143. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> $data_dir in concatenation (.) or string at ./batch_uploads_imageuploader >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> line 143. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $_ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in pattern match (m//) at ./batch_uploads_imageuploader line 147. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> base is DCC0000_258024_V01 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> path is /data/incoming/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> type is .tar.gz >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> fullpath is >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/incoming/DCC0000_258024_V01.tar.gz >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> source >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/ImagingUpload-17-43-ZUEFjb >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> targetlocation >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> $data_dir in concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 256. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> $data_dir in concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 284. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> $data_dir in concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> tarchive_validation.pl line >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 219. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> $data_dir in concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl line 270. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> $data_dir in concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 711. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Can't exec "mail": No such >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> file or directory at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 721. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> MAIL at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 722. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> MAIL at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 723. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> $data_dir in concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 724. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> MAIL at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 724. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> MAIL at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 725. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> $data_dir in concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 735. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> No Mincs inserted >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The tarchiveLoader insertion >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> script has failed. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Running now the following >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> command: /data/loris/data/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -profile prod -upload_id 3 /data/incoming/DCC0000_258024_V01.tar.gz >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -verbose" >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I inserted the VisitLabel, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> but still the Mincs are not inserted and i am getting this error >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> "lorisadmin at hbp:/data/loris/bin/mri$ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -profile prod -upload_id 3 /data/incoming/DCC0000_258024_V01.tar.gz -verbose >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> find -path >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> \/tmp\/ImagingUpload\-17\-45\-5MsWEd -name '__MACOSX' -delete >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Spool message is: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The Scan for the uploadID 3 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> has already been run with tarchiveID: 7. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> To continue with the rest of >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the insertion pipeline, please run tarchiveLoader from a terminal as >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> follows: /data/LORIS/data//uploadNeuroDB/tarchiveLoader -globLocation >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -profile prod >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive//2012/DCM_2012-12-05_ImagingUpload-17-43-ZUEFjb.tar >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -verbose" >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Which files should i delete? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I thought that deleting the files from the tarchive was enough. And i >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> executed the last proposed command to continue to rest of the insertion >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> pipeline ( check the image ). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 24 ???? 2019 ???? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 5:05 ?.?., ?/? Cecile Madjar < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> cecile.madjar at mcin.ca> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sorry I was not clear >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> before. Every visits of candidates are created in the session table with >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> one entry per CandID/VisitLabel. So if the imaging pipeline created visits >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in the session table (that are not attached to instruments) and you want to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> clean your database completely, you can delete entries in that table as >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> well. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Regarding your point 2, the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> imaging pipeline can create the visit in the session table as long as the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit label is present in the Visit_Windows table (which means the visit >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> label stored in the PatientName is a valid visit label). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> However, in your prod file, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> if the variable $subjectID{'createVisitLabel'} is set to 1 for candidates, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the visit label should be created in the Visit_Windows table I believe. Here >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> is the line of the prod file you would need to change >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> . >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> In general, we prefer >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> populating the Visit_Windows table and set the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> $subjectID{'createVisitLabel'} to 0 for candidate data to avoid insertion >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> of badly labelled MRI data that are complex to relabel. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Finally, regarding the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> candidate creation, if you execute the following steps, the pipeline should >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> be able to create candidates: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - set in the Imaging >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Pipeline section of the config module the config setting "Upload creation >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> of candidates" to Yes >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - manually transfer the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> scans to the LORIS server instead of uploading it via the imaging browser >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - run >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> batch_imaging_upload.pl as >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> you did until now. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helps! >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> On Wed, Jul 24, 2019 at 8:47 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> AM Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> About my second question i >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> replaced the name of the patient in the .dcm files and now i am getting an >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> error that the visit label does not exist. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I thought it was supposed >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> to be automatically created. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> "Done adding archive info >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> into database >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -globLocation -profile prod >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive//DCM_2012-12-05_ImagingUpload-15-42-yUwQQV.tar >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -verbose >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> md5sum >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive/DCM_2012-12-05_ImagingUpload-15-42-yUwQQV.tar >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> candidate id 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> => No Visit labelVisit >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> label does not exist >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Set centerID = 1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Number of MINC files that >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> will be considered for inserting into the database: 1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> log dir is /logs and log >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> file is /logs/TarLoad-15-42-L6pocU.log >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> candidate id 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> => No Visit label >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Cleaning up temp files: rm >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -rf /tmp/TarLoad-15-42-J2rQms/ImagingUpload-15-42-yUwQQV*" >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 24 ???? 2019 ???? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 3:38 ?.?., ?/? Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 1) What are the records in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the session table? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 2) I tried to upload a >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> non-phantom file like this >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> input_file.txt: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/incoming/DCC0000_258024_V1.tar.gz >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> N DCC0000_258024_V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Terminal: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ./batch_uploads_imageuploader >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -profile prod < ~/Desktop/input.txt > log.txt >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and i get the following >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> error in the log.txt file >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> "Running now the following >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> command: /data/loris/data/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -profile prod -upload_id 7 /data/incoming/DCC0000_258024_V1.tar.gz -verbose >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> find -path >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> \/tmp\/ImagingUpload\-14\-56\-FeLCB4 -name '__MACOSX' -delete >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Spool message is: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The PatientName read from >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the DICOM header does not start with DCC0000_258024_V1 from the mri_upload >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> table >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> " >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and the spool message is >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> repeated for each .dcm file. Should i preprocess every .dcm file and change >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the PatientName to "DCC0000_258024_V1"? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 3) As far as it concerns >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the candidate profile i have to create a new one each time before i try to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> upload a file? Is there already a way to create a candidate profile and get >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the DCCID and PSCID without the user interface? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 18 ???? 2019 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? 5:00 ?.?., ?/? Cecile Madjar < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> cecile.madjar at mcin.ca> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> See answers to your >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> questions below. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> About the 1st case we had >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> a dicom with a blank studyUID, maybe someone accidentally removed it. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> That is strange. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Something must have been done to the DICOM files. I have never seen a study >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> with no StudyUID out of the scanner. Usually, you need to manually erase it >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> with some tool. However, DICOMs never cease to surprise me... >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Some other questions: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 1) What are the steps to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> remove all of my patients and uploads?: because i want to try to reupload >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> all the testing dicoms we had with a clean database. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Release 21.0 of LORIS-MRI >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> will offer a script to remove all the entries and files specific to an >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> upload. However, this release is not yet out. Hopefully in the next few >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> weeks. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> In the meantime, since >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> your case is particular and that you just want to start with a clean >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> database, the following deletes should work (hopefully I won't forget any >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> tables): >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> mri_violations_log; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> mri_protocol_violated_scans; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> MRICandidateErrors; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> parameter_file; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> files_qcstatus; # (if you played with the QC part of the imaging browser >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> for testing) >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> feedback_mri_comments; # (if you played with the QC part of the imaging >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> browser for testing) >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> tarchive_series; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> tarchive_files; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from mri_upload; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from tarchive; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from mri_scanner; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from candidate >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> where PSCID="scanner"; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I don't know if you want >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> to also delete entries in the session and candidate table too? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 2) We do not need to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> create the profile of a patient ( are the patients stored in the candidate >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> table? because i can't see the ghosts ), because will it automatically be >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> created when importing a dicom? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I am not sure I >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> understand fully this question. All candidates are stored in the candidate >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> table. The phantom scans however are attached to a scanner candidate >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> depending on where the scan happened. It is a bit of a weird concept that >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> we have to redesign eventually but never got a chance to get to it. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hopefully this answered >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> your question, otherwise, don't hesitate to let me know. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 3) What is the difference >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> between uploading a dicom as phantom instead of importing as >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCCID_DCCID_VisitLabel? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> When you upload the scan >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> as PSCID_DCCID_VisitLabel, there is a check that makes sure the candidate >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> IDs and visit label are valid at the time of upload. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> When you upload a scan as >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> phantom, it expects that the DICOM field PatientName and uploaded filename >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> contains the string "phantom". We enforced this behaviour on the imaging >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> uploader side in recent releases but I can't remember which one. Probably >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the upcoming 21.0 release. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> All those verifications >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> might seem cumbersome but they are here to ensure that the files inserted >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> are all valid and labelled properly as it is a bit messy to have to delete >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> files that were wrongly labelled. At least, the delete script present in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> release 21.0 will make this process easier but it is still good practice to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> verify those things. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> With pleasure. Hopefully >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the answers to your questions will be helpful. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PS: loris-dev mailing >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> list: you will find the initial answer I gave Sotirios below. I forgot to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> cc the loris-dev in my earlier reply... >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 16 ???? 2019 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? 12:02 ?.?., ?/? Cecile Madjar < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> cecile.madjar at mcin.ca> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Dear Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you for reaching >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> out. Since your email was already organized in points, I will reply >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> directly below your questions below. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 1) What do we do when >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the StudyUID is blank on the header? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/minor/docs/AppendixA-Troubleshooting_guideline.md >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> There solution provided at the table 3 does not guide us how to find the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> information ( is possible ). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The StudyUID is the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> field used in our pipeline at the moment to check whether a DICOM study was >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> already inserted into LORIS with that same StudyUID since it is supposed to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> be unique for every single study. Currently, we do not support insertion of >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DICOM studies if they do not have a StudyUID associated with them. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Is there a specific >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> reason why the StudyUID is blank in the DICOM headers in your DICOM files? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Did they go through some processes before upload to LORIS? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 2) When i am about to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> upload a non-phanton case i need a 'Visit Label'. Is there already a script >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> that can create a new visit label for a specific Candidate, so i can >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> provide it as input afterwards to the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> batch_uploads_imageuploader ( See option 5.1.3 https://github.com/aces/Loris-MRI/blob/minor/docs/05-PipelineLaunchOptions.md ) >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I am not sure if the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> front-end allows for it but if you use batch_uploads_imageuploader, the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> insertion scripts could create the visit label for you. However, it does >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> need to be included in the patient name in order for the script to know >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> which label it should use. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> For example: you upload >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> V02 for MTL0123 (DCCID: 456789) but V02 was not yet created for MTL0123; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the insertion scripts will create a V02 visit for MTL0123 if the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PatientName field for the dataset is MTL0123_456789_V02 with Stage marked >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> as "Not Started". >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> However, *note that >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> for the script to create the visit for the candidate, you have to make sure >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> that all the visit label of your projects were inserted in the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Visit_Windows table* >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> (otherwise, the visit will never be created as they were not specified as >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> being part of the list of visit label to expect). So in the example above, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> you should have one row in Visit_Windows with Visit_label="V02" set. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 3) Section 4.3 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/minor/docs/04-Scripts.md >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> What do we do when the folder contains multiple mnc files? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> This is a case by >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> case. Most of the time, the MINC files that failed insertion into the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> imaging browser end up in the MRI violation module where you can see what >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> went wrong with the acquisitions not inserted. If you notice that the MINC >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> file should be inserted as a specific protocol, you can force the insertion >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> as explained in section 4.3. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> In your case, I have a >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> feeling that you want to be able to insert MINC files that did not go >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> through the whole pipeline insertion (DICOM archival, then dcm2mnc, then >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> protocol identification, then insertion...). In theory, you could call >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl on >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> any MINC file, provided you have at least the following information: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - path to the MINC file >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - uploadID associated >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> with the MINC files or DICOM archive path from which those MINC files were >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> created from >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Then the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> script will do the subject information and protocol validation etc... >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> If all the MINC files >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> come from the same uploadID or TarchiveID, then you could run a loop in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> bash calling the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> script like this for files deriving from uploadID=1: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ls >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /path/to/mnc/folder/* | while read f; do >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -profile prod -uploadID 1 -mincPath $f; done >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helped! >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> | MCIN.ca >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> MCIN.ca >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>>>>>>>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | >>>>>>>>>>>>>>>>>>>>>>>>>>>> MCIN.ca >>>>>>>>>>>>>>>>>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>>>>>>>>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>>>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>>>>>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | >>>>>>>>>>>>>>>>>>>>>>>>>> MCIN.ca >>>>>>>>>>>>>>>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>>>>>>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>>>>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | >>>>>>>>>>>>>>>>>>>>>>>>> MCIN.ca >>>>>>>>>>>>>>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>>>>>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>>>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>>>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>>>>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> -- >>>>>>>>>>>>>> Shen Wang >>>>>>>>>>>>>> Loris Developer >>>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>>> McGill University >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>> >>>>>>>>>> -- >>>>>>>>>> Shen Wang >>>>>>>>>> Loris Developer >>>>>>>>>> Montreal Neurological Institute >>>>>>>>>> McGill University >>>>>>>>>> >>>>>>>>>> -- >>>>>>>>> Shen Wang >>>>>>>>> Loris Developer >>>>>>>>> Montreal Neurological Institute >>>>>>>>> McGill University >>>>>>>>> >>>>>>>>> _______________________________________________ >>>>>>>>> Loris-dev mailing list >>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> -- >>>>>>>> >>>>>>>> christine.rogers at mcgill.ca >>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>> Montreal Neurological Institute >>>>>>>> McGill University | Montreal | Canada >>>>>>>> >>>>>>> >>>>> >>>>> -- >>>>> Shen Wang >>>>> Loris Developer >>>>> Montreal Neurological Institute >>>>> McGill University >>>>> >>>>> >>> >>> -- >>> Shen Wang >>> Loris Developer >>> Montreal Neurological Institute >>> McGill University >>> >>> > > -- > Shen Wang > Loris Developer > Montreal Neurological Institute > McGill University > > 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URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: ???? 2019-08-13 19.21.15.png Type: image/png Size: 508603 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: sudo_make_output Type: application/octet-stream Size: 97247 bytes Desc: not available URL: From waveflux at gmail.com Thu Aug 15 15:03:20 2019 From: waveflux at gmail.com (Tom Beaudry) Date: Thu, 15 Aug 2019 15:03:20 -0400 Subject: [Loris-dev] Upgrading to Loris 21 - new make file In-Reply-To: References: Message-ID: Any reason why you are using "sudo make" instead of just "make" ? On Thu, Aug 15, 2019 at 2:45 PM Sotirios Nikoloutsopoulos < sotirisnik at gmail.com> wrote: > I attached the sudo make output. > > ???? ???, 15 ??? 2019 ???? 9:36 ?.?., ?/? Shen Wang < > wangshen.mcin at gmail.com> ??????: > >> Hi, >> You don't need to run install.sh this time. Redownload the missing file, >> then do sudo make. >> If it still have indent and no-def errors, then remove the lines which I >> told you from webpack.config.js, then try do >> sudo make again. >> >> >> On Thu, 15 Aug 2019 at 14:28, Sotirios Nikoloutsopoulos < >> sotirisnik at gmail.com> wrote: >> >>> Hi, >>> >>> should i try to redownload the files from >>> https://github.com/aces/Loris/tree/major and execute the install.sh? I >>> find it weird that i am missing some files. >>> >>> Thanks >>> >>> ???? ???, 15 ??? 2019 ???? 9:17 ?.?., ?/? Shen Wang < >>> wangshen.mcin at gmail.com> ??????: >>> >>>> Hi Sotirios, >>>> It seems like you are missing this file. [ .babelrc] >>>> step 1: copy from https://github.com/aces/Loris/blob/major/.babelrc >>>> step 2: sudo vi webpack.config.js >>>> remove these lines >>>> >>>> { test: /\.js$/, >>>> >>>> exclude: /node_modules/, >>>> >>>> // use: ['babel-loader', 'eslint-loader'], >>>> >>>> }, >>>> >>>> step 3: sudo make >>>> >>>> >>>> >>>> On Wed, 14 Aug 2019 at 18:52, Sotirios Nikoloutsopoulos < >>>> sotirisnik at gmail.com> wrote: >>>> >>>>> Hi Shen, >>>>> >>>>> That didn't work either. Also i had removed the git files because i >>>>> was getting this error when i used make: >>>>> >>>>> "git describe --tags --always > VERSION >>>>> fatal: Not a git repository (or any of the parent directories): .git >>>>> Makefile:8: recipe for target 'VERSION' failed >>>>> make: *** [VERSION] Error 128" >>>>> >>>>> Thanks >>>>> >>>>> ???? ???, 15 ??? 2019 ???? 1:36 ?.?., ?/? Shen Wang < >>>>> wangshen.mcin at gmail.com> ??????: >>>>> >>>>>> Hi,Sotirios >>>>>> In your special situation, there is a temporary fix. >>>>>> step 1. sudo git stash >>>>>> step 2. open webpack.config.js file >>>>>> remove line 75 use: ['babel-loader', 'eslint-loader'], >>>>>> save it. >>>>>> step 3. sudo make >>>>>> >>>>>> I hope this could help you to compile the js files. >>>>>> >>>>>> >>>>>> >>>>>> On Wed, 14 Aug 2019 at 08:28, Sotirios Nikoloutsopoulos < >>>>>> sotirisnik at gmail.com> wrote: >>>>>> >>>>>>> I forgot to mention that i had already moved my previous config file >>>>>>> and re-executed the installation script. >>>>>>> >>>>>>> ???? ???, 14 ??? 2019 ???? 3:26 ?.?., ?/? Sotirios Nikoloutsopoulos < >>>>>>> sotirisnik at gmail.com> ??????: >>>>>>> >>>>>>>> Hi, >>>>>>>> >>>>>>>> Step 1 worked and the indentation errors were fixed. About step2 i >>>>>>>> added all of these( there are more to include in the list) these to >>>>>>>> .eslintignore which were reported to fail at being built, but they still >>>>>>>> appear on the errors at the make_output file. >>>>>>>> >>>>>>>> /jsx/DynamicDataTable.js >>>>>>>> /jsx/StaticDataTable.js >>>>>>>> /jsx/MultiSelectDropdown.js >>>>>>>> /jsx/Breadcrumbs.js >>>>>>>> /jsx/Form.js >>>>>>>> /jsx/Markdown.js >>>>>>>> /modules/media/jsx/mediaIndex.js >>>>>>>> /modules/issue_tracker/jsx/issueTrackerIndex.js >>>>>>>> /modules/issue_tracker/jsx/index.js >>>>>>>> /modules/candidate_parameters/jsx/CandidateParameters.js >>>>>>>> /modules/configuration/jsx/SubprojectRelations.js >>>>>>>> /modules/conflict_resolver/jsx/conflictResolverIndex.js >>>>>>>> /modules/conflict_resolver/jsx/resolvedConflictsIndex.js >>>>>>>> /modules/bvl_feedback/jsx/react.behavioural_feedback_panel.js >>>>>>>> /modules/dataquery/jsx/react.tabs.js >>>>>>>> /modules/document_repository/jsx/docIndex.js >>>>>>>> /modules/instrument_builder/jsx/react.instrument_builder.js >>>>>>>> /modules/imaging_uploader/jsx/index.js >>>>>>>> /modules/datadict/jsx/dataDictIndex.js >>>>>>>> /modules/bvl_feedback/jsx/react.behavioural_feedback_panel.js >>>>>>>> /modules/new_profile/jsx/NewProfileIndex.js >>>>>>>> /modules/examiner/jsx/examinerIndex.js >>>>>>>> /modules/configuration/jsx/SubprojectRelations.js >>>>>>>> /modules/data_team_helper/jsx/behavioural_qc_module.js >>>>>>>> /modules/acknowledgements/jsx/acknowledgementsIndex.js >>>>>>>> /modules/candidate_parameters/jsx/CandidateParameters.js >>>>>>>> /modules/imaging_browser/jsx/ImagePanel.js >>>>>>>> >>>>>>>> /modules/mri_violations/jsx/mri_protocol_violations_columnFormatter.js >>>>>>>> >>>>>>>> /modules/mri_violations/jsx/mri_protocol_check_violations_columnFormatter.js >>>>>>>> /modules/genomic_browser/jsx/profileColumnFormatter.js >>>>>>>> /modules/dataquery/jsx/react.tabs.js >>>>>>>> /jsx/MultiSelectDropdown.js >>>>>>>> /modules/mri_violations/jsx/columnFormatterUnresolved.js >>>>>>>> /modules/dataquery/jsx/react.sidebar.js >>>>>>>> /modules/dataquery/jsx/react.fieldselector.js >>>>>>>> /modules/quality_control/jsx/qualityControlIndex.js >>>>>>>> /modules/dataquery/jsx/react.paginator.js >>>>>>>> /modules/instrument_builder/jsx/react.questions.js >>>>>>>> /modules/dataquery/jsx/react.filterBuilder.js >>>>>>>> /modules/conflict_resolver/jsx/conflictResolverIndex.js >>>>>>>> /jsx/PaginationLinks.js >>>>>>>> /modules/conflict_resolver/jsx/resolvedConflictsIndex.js >>>>>>>> /modules/dataquery/jsx/react.app.js >>>>>>>> /modules/candidate_list/jsx/onLoad.js >>>>>>>> /jsx/Form.js >>>>>>>> /modules/publication/jsx/publicationIndex.js >>>>>>>> >>>>>>>> /modules/server_processes_manager/jsx/server_processes_managerIndex.js >>>>>>>> /modules/imaging_browser/jsx/imagingBrowserIndex.js >>>>>>>> /modules/issue_tracker/jsx/issueTrackerIndex.js >>>>>>>> /modules/survey_accounts/jsx/surveyAccountsIndex.js >>>>>>>> /modules/data_integrity_flag/jsx/dataIntegrityFlagIndex.js >>>>>>>> /modules/instrument_manager/jsx/instrumentManagerIndex.js >>>>>>>> /modules/media/jsx/mediaIndex.js >>>>>>>> /modules/user_accounts/jsx/userAccountsIndex.js >>>>>>>> /modules/help_editor/jsx/help_editor.js >>>>>>>> /modules/dicom_archive/jsx/dicom_archive.js >>>>>>>> /modules/mri_violations/jsx/columnFormatter.js >>>>>>>> /modules/brainbrowser/jsx/Brainbrowser.js >>>>>>>> /node_modules/babel-loader/lib/index.js >>>>>>>> /modules/document_repository/jsx/editFormIndex.js >>>>>>>> >>>>>>>> Thanks >>>>>>>> >>>>>>>> ???? ???, 14 ??? 2019 ???? 7:50 ?.?., ?/? Christine Rogers, Ms. < >>>>>>>> christine.rogers at mcgill.ca> ??????: >>>>>>>> >>>>>>>>> Hi Shen and Sotirios - just a note, >>>>>>>>> >>>>>>>>> For the 21 release, it's best to run the install script without >>>>>>>>> sudoing it. >>>>>>>>> >>>>>>>>> (Shen, I believe we discovered a minor issue with the sudo last >>>>>>>>> week #5008) >>>>>>>>> >>>>>>>>> Best, >>>>>>>>> Christine >>>>>>>>> >>>>>>>>> On Tue, Aug 13, 2019 at 9:22 PM Shen Wang >>>>>>>>> wrote: >>>>>>>>> >>>>>>>>>> Does it work? If still doesn?t work, try to remove >>>>>>>>>> project/config.xml file. Do sudo ./install.sh again. To reinstall Loris >>>>>>>>>> again. >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> Shen Wang ?2019?8?13? ????9:02??? >>>>>>>>>> >>>>>>>>>>> Hi Sotirios, >>>>>>>>>>> step 1: >>>>>>>>>>> sudo ./node_modules/.bin/eslint --fix /var/www/loris >>>>>>>>>>> step 2: >>>>>>>>>>> put the rest error files under this line [# Ignore until ESLint >>>>>>>>>>> is run] in the .eslintignore file. >>>>>>>>>>> step 3: >>>>>>>>>>> sudo make >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> On Tue, 13 Aug 2019 at 20:34, Sotirios Nikoloutsopoulos < >>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>> >>>>>>>>>>>> I did the modifications, still there are errors. >>>>>>>>>>>> Thanks >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> ???? ???, 14 ??? 2019 ???? 3:22 ?.?., ?/? Shen Wang < >>>>>>>>>>>> wangshen.mcin at gmail.com> ??????: >>>>>>>>>>>> >>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>> I saw your output file, the config issue is gone. >>>>>>>>>>>>> you can use [sudo npm run lintfix:javascript ] to fix these >>>>>>>>>>>>> indent issues. >>>>>>>>>>>>> If it still has errors. >>>>>>>>>>>>> Then try modify this file .eslintignore >>>>>>>>>>>>> with this >>>>>>>>>>>>> >>>>>>>>>>>>> # Ignore until ESLint is run >>>>>>>>>>>>> >>>>>>>>>>>>> modules/* >>>>>>>>>>>>> >>>>>>>>>>>>> modules/dataquery/ >>>>>>>>>>>>> >>>>>>>>>>>>> node_modules/* >>>>>>>>>>>>> >>>>>>>>>>>>> htdocs/js/components/* >>>>>>>>>>>>> >>>>>>>>>>>>> jsx/* >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> # Ignore external libs >>>>>>>>>>>>> >>>>>>>>>>>>> htdocs/js/flot/* >>>>>>>>>>>>> >>>>>>>>>>>>> htdocs/js/jquery/* >>>>>>>>>>>>> >>>>>>>>>>>>> htdocs/js/jszip/* >>>>>>>>>>>>> >>>>>>>>>>>>> htdocs/js/modernizr/* >>>>>>>>>>>>> >>>>>>>>>>>>> htdocs/js/modules/* >>>>>>>>>>>>> >>>>>>>>>>>>> htdocs/js/react/* >>>>>>>>>>>>> >>>>>>>>>>>>> htdocs/js/shims/* >>>>>>>>>>>>> >>>>>>>>>>>>> htdocs/js/c3.min.js >>>>>>>>>>>>> >>>>>>>>>>>>> htdocs/js/d3.min.js >>>>>>>>>>>>> >>>>>>>>>>>>> htdocs/js/FileSaver.min.js >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> then do sudo make. >>>>>>>>>>>>> It should work. >>>>>>>>>>>>> Regards >>>>>>>>>>>>> Shen >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> Sotirios Nikoloutsopoulos ?2019?8?13? >>>>>>>>>>>>> ????7:54??? >>>>>>>>>>>>> >>>>>>>>>>>>>> No, it didn't work, i also tried space/tabs because most of >>>>>>>>>>>>>> the errors where about indentation, also there are some errors about React. >>>>>>>>>>>>>> >>>>>>>>>>>>>> Thanks >>>>>>>>>>>>>> >>>>>>>>>>>>>> lorisadmin at hbp:/var/www/loris$ sudo >>>>>>>>>>>>>> ./node_modules/.bin/eslint --init >>>>>>>>>>>>>> ? How would you like to configure ESLint? Answer questions >>>>>>>>>>>>>> about your style >>>>>>>>>>>>>> ? Which version of ECMAScript do you use? ES2015 >>>>>>>>>>>>>> ? Are you using ES6 modules? Yes >>>>>>>>>>>>>> ? Where will your code run? Browser >>>>>>>>>>>>>> ? Do you use CommonJS? Yes >>>>>>>>>>>>>> ? Do you use JSX? Yes >>>>>>>>>>>>>> ? Do you use React? Yes >>>>>>>>>>>>>> ? What style of indentation do you use? Spaces >>>>>>>>>>>>>> ? What quotes do you use for strings? Single >>>>>>>>>>>>>> ? What line endings do you use? Unix >>>>>>>>>>>>>> ? Do you require semicolons? Yes >>>>>>>>>>>>>> ? What format do you want your config file to be in? JSON >>>>>>>>>>>>>> The config that you've selected requires the following >>>>>>>>>>>>>> dependencies: >>>>>>>>>>>>>> >>>>>>>>>>>>>> eslint-plugin-react at latest >>>>>>>>>>>>>> Successfully created .eslintrc.json file in /var/www/loris >>>>>>>>>>>>>> >>>>>>>>>>>>>> lorisadmin at hbp:/var/www/loris$ sudo make > sudo_make_output >>>>>>>>>>>>>> npm WARN The package prop-types is included as both a dev and >>>>>>>>>>>>>> production dependency. >>>>>>>>>>>>>> npm WARN optional SKIPPING OPTIONAL DEPENDENCY: fsevents at 1.2.4 >>>>>>>>>>>>>> (node_modules/fsevents): >>>>>>>>>>>>>> npm WARN notsup SKIPPING OPTIONAL DEPENDENCY: Unsupported >>>>>>>>>>>>>> platform for fsevents at 1.2.4: wanted >>>>>>>>>>>>>> {"os":"darwin","arch":"any"} (current: {"os":"linux","arch":"x64"}) >>>>>>>>>>>>>> >>>>>>>>>>>>>> npm ERR! code ELIFECYCLE >>>>>>>>>>>>>> npm ERR! errno 2 >>>>>>>>>>>>>> npm ERR! loris at 1.0.0 compile: `webpack` >>>>>>>>>>>>>> npm ERR! Exit status 2 >>>>>>>>>>>>>> npm ERR! >>>>>>>>>>>>>> npm ERR! Failed at the loris at 1.0.0 compile script. >>>>>>>>>>>>>> npm ERR! This is probably not a problem with npm. There is >>>>>>>>>>>>>> likely additional logging output above. >>>>>>>>>>>>>> >>>>>>>>>>>>>> npm ERR! A complete log of this run can be found in: >>>>>>>>>>>>>> npm ERR! >>>>>>>>>>>>>> /home/lorisadmin/.npm/_logs/2019-08-13T23_40_58_841Z-debug.log >>>>>>>>>>>>>> >>>>>>>>>>>>>> ???? ???, 14 ??? 2019 ???? 2:29 ?.?., ?/? Shen Wang < >>>>>>>>>>>>>> wangshen.mcin at gmail.com> ??????: >>>>>>>>>>>>>> >>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>> When you do make command, please make sure with sudo at the >>>>>>>>>>>>>>> beginning. [sudo make] >>>>>>>>>>>>>>> If it still doesn't work for you. >>>>>>>>>>>>>>> Then try the solutions below. >>>>>>>>>>>>>>> solution 1: >>>>>>>>>>>>>>> [image: ???? 2019-08-13 19.21.15.png] >>>>>>>>>>>>>>> Regards >>>>>>>>>>>>>>> Shen >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> On Tue, 13 Aug 2019 at 17:22, Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> I think that the files exists although i redownloaded the >>>>>>>>>>>>>>>> eslintrc.json i checked others files that had similar errors. >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> lorisadmin at hbp:/var/www/loris$ ls -l >>>>>>>>>>>>>>>> ./node_modules/eslint-loader/index.js >>>>>>>>>>>>>>>> -rw-rw-r-- 1 lorisadmin lorisadmin 6463 ??? 26 1985 >>>>>>>>>>>>>>>> ./node_modules/eslint-loader/index.js >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> lorisadmin at hbp:/var/www/loris$ ls -l .eslintrc.json >>>>>>>>>>>>>>>> -rw-rw-r-- 1 lorisadmin lorisadmin 84530 ??? 14 00:04 >>>>>>>>>>>>>>>> .eslintrc.json >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Maybe this can help >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Module build failed (from >>>>>>>>>>>>>>>> ./node_modules/eslint-loader/index.js): >>>>>>>>>>>>>>>> SyntaxError: Cannot read config file: >>>>>>>>>>>>>>>> /var/www/loris/.eslintrc.json >>>>>>>>>>>>>>>> Error: Unexpected token < in JSON at position 6 >>>>>>>>>>>>>>>> at JSON.parse () >>>>>>>>>>>>>>>> at loadJSONConfigFile >>>>>>>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config/config-file.js:114:21) >>>>>>>>>>>>>>>> at loadConfigFile >>>>>>>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config/config-file.js:230:26) >>>>>>>>>>>>>>>> at loadFromDisk >>>>>>>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config/config-file.js:500:18) >>>>>>>>>>>>>>>> at Object.load >>>>>>>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config/config-file.js:564:20) >>>>>>>>>>>>>>>> at Config.getLocalConfigHierarchy >>>>>>>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config.js:227:44) >>>>>>>>>>>>>>>> at Config.getConfigHierarchy >>>>>>>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config.js:179:43) >>>>>>>>>>>>>>>> at Config.getConfigVector >>>>>>>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config.js:286:21) >>>>>>>>>>>>>>>> at Config.getConfig >>>>>>>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config.js:329:29) >>>>>>>>>>>>>>>> at processText >>>>>>>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/cli-engine.js:162:33) >>>>>>>>>>>>>>>> at CLIEngine.executeOnText >>>>>>>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/cli-engine.js:596:17) >>>>>>>>>>>>>>>> at lint >>>>>>>>>>>>>>>> (/var/www/loris/node_modules/eslint-loader/index.js:237:17) >>>>>>>>>>>>>>>> at Object.module.exports >>>>>>>>>>>>>>>> (/var/www/loris/node_modules/eslint-loader/index.js:232:21) >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> ERROR in ./modules/imaging_uploader/jsx/index.js >>>>>>>>>>>>>>>> Module build failed (from >>>>>>>>>>>>>>>> ./node_modules/eslint-loader/index.js): >>>>>>>>>>>>>>>> SyntaxError: Cannot read config file: >>>>>>>>>>>>>>>> /var/www/loris/.eslintrc.json >>>>>>>>>>>>>>>> Error: Unexpected token < in JSON at position 6 >>>>>>>>>>>>>>>> at JSON.parse () >>>>>>>>>>>>>>>> at loadJSONConfigFile >>>>>>>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config/config-file.js:114:21) >>>>>>>>>>>>>>>> at loadConfigFile >>>>>>>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config/config-file.js:230:26) >>>>>>>>>>>>>>>> at loadFromDisk >>>>>>>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config/config-file.js:500:18) >>>>>>>>>>>>>>>> at Object.load >>>>>>>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config/config-file.js:564:20) >>>>>>>>>>>>>>>> at Config.getLocalConfigHierarchy >>>>>>>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config.js:227:44) >>>>>>>>>>>>>>>> at Config.getConfigHierarchy >>>>>>>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config.js:179:43) >>>>>>>>>>>>>>>> at Config.getConfigVector >>>>>>>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config.js:286:21) >>>>>>>>>>>>>>>> at Config.getConfig >>>>>>>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config.js:329:29) >>>>>>>>>>>>>>>> at processText >>>>>>>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/cli-engine.js:162:33) >>>>>>>>>>>>>>>> at CLIEngine.executeOnText >>>>>>>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/cli-engine.js:596:17) >>>>>>>>>>>>>>>> at lint >>>>>>>>>>>>>>>> (/var/www/loris/node_modules/eslint-loader/index.js:237:17) >>>>>>>>>>>>>>>> at Object.module.exports >>>>>>>>>>>>>>>> (/var/www/loris/node_modules/eslint-loader/index.js:232:21) >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> ???? ???, 13 ??? 2019 ???? 11:52 ?.?., ?/? John Saigle < >>>>>>>>>>>>>>>> john.saigle at mcin.ca> ??????: >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> HI Sotirios, >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> The make_output.txt file shows webpack failing because it >>>>>>>>>>>>>>>>> can't find the ESLint config file. >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Can you confirm whether the file `.eslintrc.json` exists >>>>>>>>>>>>>>>>> within your loris root directory (usually `/var/www/loris/`)? When I delete >>>>>>>>>>>>>>>>> my file I get the same errors as you. >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> If you find that it's missing, you can make a local copy >>>>>>>>>>>>>>>>> with the contents found here: >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> https://github.com/aces/Loris/blob/e26a6ad49a73fcffef0cd73bb600c4d17b200b62/.eslintrc.json >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Once you know it exists, try running `make` again. >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Let us know if that moves you forward. >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>> John >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> On Tue, Aug 13, 2019 at 2:21 PM Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>>> I executed the commands for the node and now i am get >>>>>>>>>>>>>>>>>> the followings: >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> lorisadmin at hbp:/var/www/loris$ make > ~/make_output >>>>>>>>>>>>>>>>>> npm WARN The package prop-types is included as both a dev >>>>>>>>>>>>>>>>>> and production dependency. >>>>>>>>>>>>>>>>>> npm WARN optional SKIPPING OPTIONAL DEPENDENCY: >>>>>>>>>>>>>>>>>> fsevents at 1.2.4 (node_modules/fsevents): >>>>>>>>>>>>>>>>>> npm WARN notsup SKIPPING OPTIONAL DEPENDENCY: Unsupported >>>>>>>>>>>>>>>>>> platform for fsevents at 1.2.4: wanted >>>>>>>>>>>>>>>>>> {"os":"darwin","arch":"any"} (current: {"os":"linux","arch":"x64"}) >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> npm ERR! code ELIFECYCLE >>>>>>>>>>>>>>>>>> npm ERR! errno 2 >>>>>>>>>>>>>>>>>> npm ERR! loris at 1.0.0 compile: `webpack` >>>>>>>>>>>>>>>>>> npm ERR! Exit status 2 >>>>>>>>>>>>>>>>>> npm ERR! >>>>>>>>>>>>>>>>>> npm ERR! Failed at the loris at 1.0.0 compile script. >>>>>>>>>>>>>>>>>> npm ERR! This is probably not a problem with npm. There >>>>>>>>>>>>>>>>>> is likely additional logging output above. >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> npm ERR! A complete log of this run can be found in: >>>>>>>>>>>>>>>>>> npm ERR! >>>>>>>>>>>>>>>>>> /home/lorisadmin/.npm/_logs/2019-08-13T18_12_05_378Z-debug.log >>>>>>>>>>>>>>>>>> make: *** [javascript] Error 2 >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Thanks, >>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> ???? ???, 12 ??? 2019 ???? 10:19 ?.?., ?/? Christine >>>>>>>>>>>>>>>>>> Rogers, Ms. ??????: >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> We've seen some users installing LORIS 21 or upgrading >>>>>>>>>>>>>>>>>>> to 21 whose version of node doesn't work well with webpack, due to updated >>>>>>>>>>>>>>>>>>> packages they're missing. >>>>>>>>>>>>>>>>>>> If so, update your node : >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> curl -sL https://deb.nodesource.com/setup_8.x | sudo -E bash - >>>>>>>>>>>>>>>>>>> sudo apt-get install -y nodejs >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Let us know how that goes -- please send us output from >>>>>>>>>>>>>>>>>>> the same log if any issues. >>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>> Christine >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> On Thu, Aug 8, 2019 at 2:38 PM Sotirios Nikoloutsopoulos >>>>>>>>>>>>>>>>>>> wrote: >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> It's not a disk space issue, as you can see below i >>>>>>>>>>>>>>>>>>>> have still 74GB available. >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> lorisadmin at hbp:/var/www/loris$ df -h >>>>>>>>>>>>>>>>>>>> Filesystem Size Used Avail Use% Mounted on >>>>>>>>>>>>>>>>>>>> udev 2,9G 0 2,9G 0% /dev >>>>>>>>>>>>>>>>>>>> tmpfs 597M 8,6M 588M 2% /run >>>>>>>>>>>>>>>>>>>> /dev/sda1 98G 19G 74G 21% / >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Maybe we have to pass a flag to get into strict mode? >>>>>>>>>>>>>>>>>>>> as stated "SyntaxError: Block-scoped declarations (let, const, function, >>>>>>>>>>>>>>>>>>>> class) not yet supported outside strict mode" >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Thanks, >>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> ???? ???, 8 ??? 2019 ???? 4:32 ?.?., ?/? Dave >>>>>>>>>>>>>>>>>>>> MacFarlane ??????: >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> It looks like the javascript snippet shown in the >>>>>>>>>>>>>>>>>>>>> error message when trying to compile the js is truncated. Have you run out >>>>>>>>>>>>>>>>>>>>> of disk space? >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> On Thu, Aug 8, 2019 at 8:37 AM Sotirios >>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos wrote: >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> I runned make and also included the file it reports >>>>>>>>>>>>>>>>>>>>>> at the end. >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> lorisadmin at hbp:/var/www/loris$ make >>>>>>>>>>>>>>>>>>>>>> npm install >>>>>>>>>>>>>>>>>>>>>> npm WARN optional Skipping failed optional dependency >>>>>>>>>>>>>>>>>>>>>> /chokidar/fsevents: >>>>>>>>>>>>>>>>>>>>>> npm WARN notsup Not compatible with your operating >>>>>>>>>>>>>>>>>>>>>> system or architecture: fsevents at 1.2.9 >>>>>>>>>>>>>>>>>>>>>> npm WARN optional Skipping failed optional dependency >>>>>>>>>>>>>>>>>>>>>> /watchpack/chokidar/fsevents: >>>>>>>>>>>>>>>>>>>>>> npm WARN notsup Not compatible with your operating >>>>>>>>>>>>>>>>>>>>>> system or architecture: fsevents at 1.2.9 >>>>>>>>>>>>>>>>>>>>>> npm run compile >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> > loris at 1.0.0 compile /var/www/loris >>>>>>>>>>>>>>>>>>>>>> > webpack >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> /var/www/loris/node_modules/webpack/bin/webpack.js:86 >>>>>>>>>>>>>>>>>>>>>> let notify = >>>>>>>>>>>>>>>>>>>>>> ^^^ >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> SyntaxError: Block-scoped declarations (let, const, >>>>>>>>>>>>>>>>>>>>>> function, class) not yet supported outside strict mode >>>>>>>>>>>>>>>>>>>>>> at exports.runInThisContext (vm.js:53:16) >>>>>>>>>>>>>>>>>>>>>> at Module._compile (module.js:374:25) >>>>>>>>>>>>>>>>>>>>>> at Object.Module._extensions..js >>>>>>>>>>>>>>>>>>>>>> (module.js:417:10) >>>>>>>>>>>>>>>>>>>>>> at Module.load (module.js:344:32) >>>>>>>>>>>>>>>>>>>>>> at Function.Module._load (module.js:301:12) >>>>>>>>>>>>>>>>>>>>>> at Function.Module.runMain (module.js:442:10) >>>>>>>>>>>>>>>>>>>>>> at startup (node.js:136:18) >>>>>>>>>>>>>>>>>>>>>> at node.js:966:3 >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> npm ERR! Linux 4.15.0-55-generic >>>>>>>>>>>>>>>>>>>>>> npm ERR! argv "/usr/bin/nodejs" "/usr/bin/npm" "run" >>>>>>>>>>>>>>>>>>>>>> "compile" >>>>>>>>>>>>>>>>>>>>>> npm ERR! node v4.2.6 >>>>>>>>>>>>>>>>>>>>>> npm ERR! npm v3.5.2 >>>>>>>>>>>>>>>>>>>>>> npm ERR! code ELIFECYCLE >>>>>>>>>>>>>>>>>>>>>> npm ERR! loris at 1.0.0 compile: `webpack` >>>>>>>>>>>>>>>>>>>>>> npm ERR! Exit status 1 >>>>>>>>>>>>>>>>>>>>>> npm ERR! >>>>>>>>>>>>>>>>>>>>>> npm ERR! Failed at the loris at 1.0.0 compile script >>>>>>>>>>>>>>>>>>>>>> 'webpack'. >>>>>>>>>>>>>>>>>>>>>> npm ERR! Make sure you have the latest version of >>>>>>>>>>>>>>>>>>>>>> node.js and npm installed. >>>>>>>>>>>>>>>>>>>>>> npm ERR! If you do, this is most likely a problem >>>>>>>>>>>>>>>>>>>>>> with the loris package, >>>>>>>>>>>>>>>>>>>>>> npm ERR! not with npm itself. >>>>>>>>>>>>>>>>>>>>>> npm ERR! Tell the author that this fails on your >>>>>>>>>>>>>>>>>>>>>> system: >>>>>>>>>>>>>>>>>>>>>> npm ERR! webpack >>>>>>>>>>>>>>>>>>>>>> npm ERR! You can get information on how to open an >>>>>>>>>>>>>>>>>>>>>> issue for this project with: >>>>>>>>>>>>>>>>>>>>>> npm ERR! npm bugs loris >>>>>>>>>>>>>>>>>>>>>> npm ERR! Or if that isn't available, you can get >>>>>>>>>>>>>>>>>>>>>> their info via: >>>>>>>>>>>>>>>>>>>>>> npm ERR! npm owner ls loris >>>>>>>>>>>>>>>>>>>>>> npm ERR! There is likely additional logging output >>>>>>>>>>>>>>>>>>>>>> above. >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> npm ERR! Please include the following file with any >>>>>>>>>>>>>>>>>>>>>> support request: >>>>>>>>>>>>>>>>>>>>>> npm ERR! /var/www/loris/npm-debug.log >>>>>>>>>>>>>>>>>>>>>> Makefile:14: recipe for target 'javascript' failed >>>>>>>>>>>>>>>>>>>>>> make: *** [javascript] Error 1 >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> Thanks, >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> ???? ???, 7 ??? 2019 ???? 5:41 ?.?., ?/? Christine >>>>>>>>>>>>>>>>>>>>>> Rogers, Ms. ??????: >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> Thanks, have you tried all of these steps? >>>>>>>>>>>>>>>>>>>>>>> - clear your browser cache (and refresh a few times) >>>>>>>>>>>>>>>>>>>>>>> - delete any files in your smarty/templates_c >>>>>>>>>>>>>>>>>>>>>>> directory (this will clear the template cache - do Not touch >>>>>>>>>>>>>>>>>>>>>>> smarty/templates/) >>>>>>>>>>>>>>>>>>>>>>> - run `make` (per the 21 release notes, this >>>>>>>>>>>>>>>>>>>>>>> replaces the composer commands used in previous releases to update your >>>>>>>>>>>>>>>>>>>>>>> dependencies) >>>>>>>>>>>>>>>>>>>>>>> - restart apache (doesn't hurt) >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> Let us know how it goes -- let us know what >>>>>>>>>>>>>>>>>>>>>>> difference you see after, with your logs. A >>>>>>>>>>>>>>>>>>>>>>> lso please send us your Config path settings (see these >>>>>>>>>>>>>>>>>>>>>>> Troubleshooting Queries >>>>>>>>>>>>>>>>>>>>>>> ) >>>>>>>>>>>>>>>>>>>>>>> if you're still seeing front-end issues. >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> Thanks, >>>>>>>>>>>>>>>>>>>>>>> Christine >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> On Wed, Aug 7, 2019 at 8:02 AM Sotirios >>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos wrote: >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> lorisadmin at hbp:/var/www/loris$ sudo cat >>>>>>>>>>>>>>>>>>>>>>>> /var/log/apache2/error.log >>>>>>>>>>>>>>>>>>>>>>>> [Wed Aug 07 07:35:02.422501 2019] >>>>>>>>>>>>>>>>>>>>>>>> [mpm_prefork:notice] [pid 1267] AH00163: Apache/2.4.18 (Ubuntu) >>>>>>>>>>>>>>>>>>>>>>>> OpenSSL/1.0.2g configured -- resuming normal operations >>>>>>>>>>>>>>>>>>>>>>>> [Wed Aug 07 07:35:02.422514 2019] [core:notice] >>>>>>>>>>>>>>>>>>>>>>>> [pid 1267] AH00094: Command line: '/usr/sbin/apache2' >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> And as for the access.log the content are empty >>>>>>>>>>>>>>>>>>>>>>>> lorisadmin at hbp:/var/www/loris$ sudo ls -l >>>>>>>>>>>>>>>>>>>>>>>> /var/log/apache2/access.log >>>>>>>>>>>>>>>>>>>>>>>> lorisadmin at hbp:/var/www/loris$ sudo ls -l >>>>>>>>>>>>>>>>>>>>>>>> /var/log/apache2/access.log >>>>>>>>>>>>>>>>>>>>>>>> -rw-r----- 1 root adm 0 ???? 28 14:09 >>>>>>>>>>>>>>>>>>>>>>>> /var/log/apache2/access.log >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> Also i noticed a loris_access.log. >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> The only non-blank pages are: >>>>>>>>>>>>>>>>>>>>>>>> mri_violations, dataquery does not exist at all, >>>>>>>>>>>>>>>>>>>>>>>> statistics, data_team_helper, genomic_browser, configuration and >>>>>>>>>>>>>>>>>>>>>>>> server_processes_manager/ prints "Required configuration settings for >>>>>>>>>>>>>>>>>>>>>>>> Server Processes Manager are missing. Cannot continue." >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> Thanks, >>>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 6 ??? 2019 ???? 10:13 ?.?., ?/? Christine >>>>>>>>>>>>>>>>>>>>>>>> Rogers, Ms. ??????: >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios and LORIS community -- >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> When upgrading to brand-new release 21 -- just a >>>>>>>>>>>>>>>>>>>>>>>>> reminder to follow the release notes and run the new >>>>>>>>>>>>>>>>>>>>>>>>> *make* file to update your dependencies (instead >>>>>>>>>>>>>>>>>>>>>>>>> of using *composer* commands). >>>>>>>>>>>>>>>>>>>>>>>>> We've also updated the Wiki page >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> to clarify that the release notes for each version will tell you what to >>>>>>>>>>>>>>>>>>>>>>>>> run. >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> If your current version is not the last release >>>>>>>>>>>>>>>>>>>>>>>>> (20.3), it's still important to upgrade to each minor release increment >>>>>>>>>>>>>>>>>>>>>>>>> (e.g. 20.2, 20.3) before making the leap to 21.0. >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> If you're getting blank pages, post-upgrade -- Try >>>>>>>>>>>>>>>>>>>>>>>>> clearing your cache. >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> Got questions or feedback e.g. on the Release >>>>>>>>>>>>>>>>>>>>>>>>> Notes? please don't hesitate to let us know. >>>>>>>>>>>>>>>>>>>>>>>>> Thanks, >>>>>>>>>>>>>>>>>>>>>>>>> Christine >>>>>>>>>>>>>>>>>>>>>>>>> The LORIS team >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> On Tue, Aug 6, 2019 at 10:09 AM Christine Rogers, >>>>>>>>>>>>>>>>>>>>>>>>> Ms. wrote: >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>> Could you also let us know -- on which pages is >>>>>>>>>>>>>>>>>>>>>>>>>> content visible, and on which pages/modules is content not visible for you? >>>>>>>>>>>>>>>>>>>>>>>>>> Thanks, >>>>>>>>>>>>>>>>>>>>>>>>>> Christine >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> On Tue, Aug 6, 2019 at 9:54 AM Christine Rogers, >>>>>>>>>>>>>>>>>>>>>>>>>> Ms. wrote: >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> Thanks Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>> That's good to know. It sounds like you've >>>>>>>>>>>>>>>>>>>>>>>>>>> checked that your /var/www/loris/project/config.xml file get populated >>>>>>>>>>>>>>>>>>>>>>>>>>> properly. >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> Please send us the last few errors you're seeing >>>>>>>>>>>>>>>>>>>>>>>>>>> in your apache error log file, and your config paths and we can see what's >>>>>>>>>>>>>>>>>>>>>>>>>>> happening with your front end -- >>>>>>>>>>>>>>>>>>>>>>>>>>> Run these Troubleshooting Queries >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> to get your config path settings, given your front end is not displaying >>>>>>>>>>>>>>>>>>>>>>>>>>> fully. >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> The Loris-MRI repo >>>>>>>>>>>>>>>>>>>>>>>>>>> 21 >>>>>>>>>>>>>>>>>>>>>>>>>>> install/upgrade would then be your next steps. >>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>> Christine >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> On Tue, Aug 6, 2019 at 7:53 AM Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos wrote: >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> I am using a VM. What i did was: >>>>>>>>>>>>>>>>>>>>>>>>>>>> 1) Download the files from >>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris and replace them >>>>>>>>>>>>>>>>>>>>>>>>>>>> to my existing /vaw/www/loris folder. >>>>>>>>>>>>>>>>>>>>>>>>>>>> 2) Execute the composer install --no-dev and >>>>>>>>>>>>>>>>>>>>>>>>>>>> then composer dump-autoload as mentioned here >>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris/wiki/Updating-your-LORIS >>>>>>>>>>>>>>>>>>>>>>>>>>>> . >>>>>>>>>>>>>>>>>>>>>>>>>>>> 3) Execute install.sh from /var/www/loris/tools >>>>>>>>>>>>>>>>>>>>>>>>>>>> and because LORIS already existed i moved a .config file, then re-executed >>>>>>>>>>>>>>>>>>>>>>>>>>>> the install.sh successfully >>>>>>>>>>>>>>>>>>>>>>>>>>>> 4 ) As for the database, i dropped the schema >>>>>>>>>>>>>>>>>>>>>>>>>>>> and i executed the installdb.php >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 5 ??? 2019 ???? 5:22 ?.?., ?/? >>>>>>>>>>>>>>>>>>>>>>>>>>>> Christine Rogers, Ms. < >>>>>>>>>>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotorios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thanks - when you re-installed did you start >>>>>>>>>>>>>>>>>>>>>>>>>>>>> on a fresh root path / VM or might some of your old system setting still >>>>>>>>>>>>>>>>>>>>>>>>>>>>> apply? >>>>>>>>>>>>>>>>>>>>>>>>>>>>> (And if you did any steps similar to an >>>>>>>>>>>>>>>>>>>>>>>>>>>>> upgrade, did you follow the Upgrade steps in the Release Notes, from both >>>>>>>>>>>>>>>>>>>>>>>>>>>>> repos?) >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> About the TR_range column - it was recently >>>>>>>>>>>>>>>>>>>>>>>>>>>>> split (MRI pr339 >>>>>>>>>>>>>>>>>>>>>>>>>>>>> ) split >>>>>>>>>>>>>>>>>>>>>>>>>>>>> into TR_min and _max columns. Given the code was trying to query TR_range >>>>>>>>>>>>>>>>>>>>>>>>>>>>> which does not exist in your mri_protocol table, double-check which version >>>>>>>>>>>>>>>>>>>>>>>>>>>>> of the Loris repo (tables) and the Loris-MRI repo (code) you have installed >>>>>>>>>>>>>>>>>>>>>>>>>>>>> to ensure they match. >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Christine >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> On Mon, Aug 5, 2019 at 9:06 AM Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos wrote: >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I reinstalled LORIS to 21 version and now the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> content is not visible at all at most pages. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 5 ??? 2019 ???? 3:19 ?.?., ?/? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Is it easy to upgrade to Loris 21? Also the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> following fails because the line 1985 of NeuroDB/MRIProcessingUtility.pm >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> query mri_protocol which doesn't have TR_range >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris/blob/21.0-release/SQL/0000-00-00-schema.sql#L556 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> lorisadmin at hbp:/data/loris/bin/mri$ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ./batch_uploads_imageuploader -profile prod < ~/Desktop/input.txt > log.txt >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $_ in pattern >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> match (m//) at ./batch_uploads_imageuploader line 147. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> base is DCC0000_258024_V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> path is /data/incoming/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> type is .tar.gz >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> fullpath is >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/incoming/DCC0000_258024_V1.tar.gz >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DBD::mysql::st execute failed: Unknown >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> column 'TR_range' in 'where clause' at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line 1985. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DBD::mysql::st fetchrow_array failed: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> fetch() without execute() at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line 1986. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> $count_mri_protocol in numeric gt (>) at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line 1995. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DBD::mysql::st execute failed: Unknown >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> column 'TR_range' in 'field list' at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 562. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Can't exec "mail": No such file or directory >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> at /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 721. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 722. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 723. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 724. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 725. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> No Mincs inserted >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thanks, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 3 ??? 2019 ???? 1:08 ?.?., ?/? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Christine Rogers, Ms. < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> First, just a note: we've released LORIS >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 21 this week with some major new features and cleanup -- especially if you >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> are early in your setup phase, check out the Release notes for both the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> LORIS >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and Loris-MRI >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> repos. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thanks for your screenshots -- your empty >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> mri_protocol table should be at the root of these issues : >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The mri_protocol table must be populated >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in order for your scans to be registered in LORIS -- it serves as a >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> whitelist for the insertion pipeline which filters out scans that aren't >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> identified or matched to scan types in this table. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> By default, this table is populated with >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> entries for t1, t2, fMRI and DTI (Insert >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> statements for 21 release branch are here >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ) >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Feel free to restore our default records >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and broaden their parameters to match all your scan types. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> re Defaced, native, selected -- these >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> filter the scans displayed as you move to the next page (View Session), >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> instead of viewing "all types" of scans from a given session : >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - "defaced" means that a defacing script >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> has masked the subject's face in the volume (for patient privacy) >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - "native" means that no pre-processing >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> has been performed on the scan (it's raw data), >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - "selected" will show only volumes >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> that have been QC'd and "selected" as the best of their type -- used to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> display only the best quality T1 image instead of all T1s acquired in a >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> session, e.g. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> re QC Comments -- >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Once you have successfully loaded scans >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> (matched to the mri_protocol table), you'll be able to use the Imaging >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Browser's View Session subpage to enter/view QC comments on each volume, or >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> for each visit. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> These are stored directly in the database, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and linked to each scan. (Table name: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> feedback_mri_comments) >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> (Visit-level QC comments are linked to the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> session.) >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> For a walkthrough of the Imaging setup - >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> please see the Imaging Setup guide >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> An old LORIS walkthrough video >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> can >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> also walk you through some of the Imaging front-end features, starting at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 8:00 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> LORIS' imaging modules have been updated >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> many times since this video, but the functionality and workflow is similar. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Let us know how it goes once you have >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> entries in your mri_protocol table - >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Christine >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> On Fri, Aug 2, 2019 at 7:58 AM Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> wrote: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Christine, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> In the candidate_list page i can see this >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> patient >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> If i press the link under PSCID i get to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> see >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and if i press the link under Scan Done it >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> redirects me to imaging_browser >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> At the mri_violations page i also see No >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> results ( neither on resolved / not resolved ). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> At the imaging_uploader i can see the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> record that failed. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> If i click on the tarchive info i get to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> see the Protocol Name which i think is the acquisition we wanted? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Also my mri_protocol table is empty. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Furthermore i would like to ask about the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> defaced, native, selected. What exactly is native and selected? And where >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> are the qc comments stored? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Finally a walkthrough would be helpful. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thanks, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 30 ???? 2019 ???? 8:29 ?.?., ?/? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Christine Rogers, Ms. < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Glad to hear you're making progress with >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the visit labels. To follow up on your last few emails: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> a- The Wiki's Setup Guide contains Sample >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> insert statements for the Visit Windows table >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> . >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> As Cecile mentioned, the consistency of >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit label format is important: V01, v01, V1, 01 -- whichever you select >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> to use is fine; we use V01 by default across all documentation. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> b- For Password reset, there is a script >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in the tools/ directory so that a back-end administrator can reset any >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> front-end user password, including Admin. (See info on setting up / >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> resetting User passwords in the Wiki's >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Setup Guide >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ) >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> c- The minc file not being registered -- >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> due to AcquisitionProtocol unknown. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> This means the SeriesDescription >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> (Acquisition Protocol) in you Dicom header was not matched to any scan >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> listed in the mri_protocol database table. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> (In the online Loris-MRI Troubleshooting >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Guide, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> this >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> is Table 3, 2nd-last item "no MINCs >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> inserted"). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The MRI Violations module (Readme here) >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> will show >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> you the details of this mismatch -- >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Go to the module (under the Imaging >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> menu), find your scan and click the link "Could not identify scan type" -- >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in the next subpage you can compare the scan's actual parameters against >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the mri_protocol table. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> To resolve this, adjust your mri_protocol >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> table values or perhaps ensure your DICOMs are labelled consistently. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Let us know if this works for you -- we >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> can also walk you through an example of non-identified scans on >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Demo.loris.ca (MRI Violations module). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Christine >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The LORIS team >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> On Tue, Jul 30, 2019 at 10:47 AM Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> wrote: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I hope this is sufficient as the error >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> for the visit label disappeared. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Please see the attached file. Also >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> something i found. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> lorisadmin at hbp:/data/loris/bin/mri$ cat >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data//logs/TarLoad-17-39-xubBdv.log >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ==> Loading file from disk >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-17-39-UyQcG2/dcc0000_258024_v1_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> --> mapping DICOM parameter for >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-17-39-UyQcG2/dcc0000_258024_v1_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ==> computing md5 hash for MINC body. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> --> md5: 6b1202fd63e29de4c9be1cd9925888a5 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ==> verifying acquisition protocol >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Acquisition protocol is unknown >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> --> The minc file cannot be registered >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> since the AcquisitionProtocol is unknown >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 30 ???? 2019 ???? 4:58 ?.?., >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ?/? Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Ok I fixed the login problem by using a >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> known hash and by deleting the rows from the login_history i was able to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> login. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 30 ???? 2019 ???? 4:50 ?.?., >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ?/? Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> there was no visit label 01 in the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Visit_Windows table and i don't know how to insert it because the record >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> requires lots of attributes. Also the system for a reason asked me to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> update my password and now i don't remember it and my account got >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> suspended. Is there a way to reset it or set a simple password? I updated >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the password hash in the users table by using the hash from another LORIS >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> setup we had and i still couldn't login ( also the attribute password is >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> always NULL and the expiration date is 1999-01-01 for some reason ). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thanks >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 29 ???? 2019 ???? 5:21 ?.?., >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ?/? Cecile Madjar < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> cecile.madjar at mcin.ca> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Can you try adding the visit label >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> v01 to the Visit_Windows table? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> However, I noticed that in a previous >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> dataset, the label was V1. Does that refer to the same visit? If so, you >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> might want to harmonize the visit labels so they are all the same across >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> datasets for a given timepoint, meaning you will need to relabel scans when >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the visit label is different but referring to the same visit label (v01 = >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> V1 etc...). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helps, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> On Mon, Jul 29, 2019 at 10:15 AM >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Could you help me with the "Visit >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> label does not exist"? I had changed $subjectID{'createVisitLabel'} to 1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> as you had suggested but it appears that this problem hasn't been resolved >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> yet. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> lorisadmin at hbp:/data/loris/bin/mri$ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> cat /data/loris/data//logs/TarLoad-14-58-9Xog7H.log >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ==> Loading file from disk >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> --> mapping DICOM parameter for >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> --> using user-defined >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> filterParameters for >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Candidate Mismatch Error is Visit >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> label does not exist >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -> WARNING: This candidate was >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> invalid. Logging to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> MRICandidateErrors >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> table with reason Visit label does not exist >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 26 ???? 2019 ???? 3:02 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ?.?., ?/? Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Cecile, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The Center error was fixed. Still >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the insertion of mincs fails. Please see the output.txt file i attached. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Also is there something else i need to change at the paths configuration? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 25 ???? 2019 ???? 6:55 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ?.?., ?/? Cecile Madjar < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> cecile.madjar at mcin.ca> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> We are making progress! >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I have a feeling this error comes >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> from the fact that your psc table does not have the MRI_alias populated for >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the DCC site. Running the following query in the mysql database should fix >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> this: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> UPDATE psc SET MRI_alias="DCC", >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Alias="DCC" WHERE Name="Data Coordinating Center"; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Repeat the same with all your >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sites (make sure to change the Aliases between sites, they should all be >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> unique). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Let me know how it goes! >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> On Thu, Jul 25, 2019 at 11:43 AM >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Dear Cecile, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> You were right about your >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> guesses. I did the modifications you suggested, i still get the "no mincs >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> inserted" error, now i am getting the "No center found this candidate" >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> error ( how do i fix that? from what i see the .dcm files contains a >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 'Institution Name', is that the center? ), so i guess that's why the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> validation fails, but i changed the force variable of tarchiveLoader to 1, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> shouldn't it have inserted the mincs then? Also it is optional to have a >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> mail server, right? ( from what i see the mail error does not affect the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> $valid_study, so i assume we are okay with that ) >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you a lot, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 25 ???? 2019 ???? 5:48 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ?.?., ?/? Cecile Madjar < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> cecile.madjar at mcin.ca> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> From what I understand, I >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> believe you just need to update a few config settings from the frontend in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the Config module (under the Admin menu). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [image: Screen Shot 2019-07-25 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> at 10.31.35 AM.png] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Then go to the Paths section of >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the config module and update the "LORIS-MRI code" config setting to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri (my guess is that currently, it is set to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data) and click on the submit button. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [image: Screen Shot 2019-07-25 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> at 10.32.50 AM.png] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Then, go to Imaging Pipeline >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> section of the Configuration module and update the "Loris-MRI Data >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Directory" to /data/loris/data/ (my guess is that it is empty at the moment >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in your database which is why $data_dir is not defined when you run the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> tarchiveLoader step of the insertion pipeline). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [image: Screen Shot 2019-07-25 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> at 10.40.52 AM.png] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Finally, I took a look at your >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> environment file and it might be a good idea to update your PERL5LIB >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> variable to the following (it has been added to the code a few releases ago >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> as we realized this was needed for the libraries. Not sure which version of >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> LORIS-MRI you are using but it does not hurt to update this variable to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> what I suggest below): >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> export >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PERL5LIB=/data/loris/bin/mri/uploadNeuroDB:/data/loris/bin/mri/dicom-archive:$PERL5LIB >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helps. Sorry you are >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> experiencing so much trouble setting things up. We probably need to update >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> our WIKI. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> On Thu, Jul 25, 2019 at 9:48 AM >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The "Loris-MRI Data Directory" >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> should be in the environment file? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 25 ???? 2019 ???? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 12:59 ?.?., ?/? Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The scripts are located in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/. Somewhere I might have messed something up but i >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> remember following the instructions in the wiki.For example when i tried to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> execute the batch_uploads_imageuploader perl script the line >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> my $command = >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> "$bin_dir/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl " >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> was pointing to an invalid >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> path, for example: it was repeating a pattern and had LORIS instead of >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> loris ( i think the mistake was that in the wiki it suggested to use >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> $PROJECT for the name of the folder and i choosed 'loris' >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris/wiki/Imaging-Database >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ). See also the in image for the modification i did. Also i didn't find the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> section to config the $data_dir variable. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 24 ???? 2019 ???? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 6:05 ?.?., ?/? Cecile Madjar < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> cecile.madjar at mcin.ca> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> It looks like you have one >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Config setting not set (based on the first error message you got when >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> running it the first time). You need to set a value for "Loris-MRI Data >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Directory" in the Config module under the Imaging pipeline section (from >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> what I can see, it would be /data/loris/data/ for your setup). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The reason you got that error >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> message the second time is that the pipeline checks if the DICOM study was >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> already inserted in the tarchive table. Since you ran the study once >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> already, the study is inserted into the tarchive, hence the message. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> However, the pipeline did not complete as the MINC files were not created >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and inserted into the files/parameter_file table. In order to continue the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> insertion, you will then need to run the tarchiveLoader command suggested >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in the terminal during the second run: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -globLocation -profile prod >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive//2012/DCM_2012-12-05_ImagingUpload-17-43-ZUEFjb.tar >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -verbose >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Finally, I am a bit confused >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> by your setup. Where are the scripts located? In /data/loris/bin/mri or >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data? It feels like the Config setting "LORIS-MRI code" in the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Paths section was set to "/data/LORIS/data" but it should have been set to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the directory where the scripts are located (most probably >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helps, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> On Wed, Jul 24, 2019 at 10:55 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> AM Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Ok first i execute this >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> command: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> "lorisadmin at hbp:/data/loris/bin/mri$ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ./batch_uploads_imageuploader -profile prod < ~/Desktop/input.txt > log.txt >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> $data_dir in concatenation (.) or string at ./batch_uploads_imageuploader >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> line 143. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> $data_dir in concatenation (.) or string at ./batch_uploads_imageuploader >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> line 143. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> $_ in pattern match (m//) at ./batch_uploads_imageuploader line 147. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> base is DCC0000_258024_V01 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> path is /data/incoming/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> type is .tar.gz >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> fullpath is >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/incoming/DCC0000_258024_V01.tar.gz >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> source >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/ImagingUpload-17-43-ZUEFjb >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> targetlocation >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> $data_dir in concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 256. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> $data_dir in concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 284. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> $data_dir in concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> tarchive_validation.pl line >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 219. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> $data_dir in concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl line 270. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> $data_dir in concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 711. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Can't exec "mail": No such >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> file or directory at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 721. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> MAIL at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 722. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> MAIL at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 723. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> $data_dir in concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 724. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> MAIL at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 724. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> MAIL at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 725. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> $data_dir in concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 735. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> No Mincs inserted >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The tarchiveLoader insertion >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> script has failed. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Running now the following >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> command: /data/loris/data/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -profile prod -upload_id 3 /data/incoming/DCC0000_258024_V01.tar.gz >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -verbose" >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I inserted the VisitLabel, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> but still the Mincs are not inserted and i am getting this error >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> "lorisadmin at hbp:/data/loris/bin/mri$ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -profile prod -upload_id 3 /data/incoming/DCC0000_258024_V01.tar.gz -verbose >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> find -path >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> \/tmp\/ImagingUpload\-17\-45\-5MsWEd -name '__MACOSX' -delete >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Spool message is: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The Scan for the uploadID 3 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> has already been run with tarchiveID: 7. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> To continue with the rest of >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the insertion pipeline, please run tarchiveLoader from a terminal as >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> follows: /data/LORIS/data//uploadNeuroDB/tarchiveLoader -globLocation >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -profile prod >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive//2012/DCM_2012-12-05_ImagingUpload-17-43-ZUEFjb.tar >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -verbose" >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Which files should i delete? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I thought that deleting the files from the tarchive was enough. And i >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> executed the last proposed command to continue to rest of the insertion >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> pipeline ( check the image ). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 24 ???? 2019 ???? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 5:05 ?.?., ?/? Cecile Madjar < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> cecile.madjar at mcin.ca> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sorry I was not clear >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> before. Every visits of candidates are created in the session table with >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> one entry per CandID/VisitLabel. So if the imaging pipeline created visits >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in the session table (that are not attached to instruments) and you want to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> clean your database completely, you can delete entries in that table as >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> well. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Regarding your point 2, the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> imaging pipeline can create the visit in the session table as long as the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit label is present in the Visit_Windows table (which means the visit >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> label stored in the PatientName is a valid visit label). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> However, in your prod file, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> if the variable $subjectID{'createVisitLabel'} is set to 1 for candidates, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the visit label should be created in the Visit_Windows table I believe. Here >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> is the line of the prod file you would need to change >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> . >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> In general, we prefer >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> populating the Visit_Windows table and set the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> $subjectID{'createVisitLabel'} to 0 for candidate data to avoid insertion >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> of badly labelled MRI data that are complex to relabel. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Finally, regarding the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> candidate creation, if you execute the following steps, the pipeline should >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> be able to create candidates: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - set in the Imaging >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Pipeline section of the config module the config setting "Upload creation >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> of candidates" to Yes >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - manually transfer the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> scans to the LORIS server instead of uploading it via the imaging browser >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - run >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> batch_imaging_upload.pl as >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> you did until now. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helps! >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> On Wed, Jul 24, 2019 at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 8:47 AM Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> wrote: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> About my second question i >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> replaced the name of the patient in the .dcm files and now i am getting an >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> error that the visit label does not exist. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I thought it was supposed >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> to be automatically created. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> "Done adding archive info >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> into database >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -globLocation -profile prod >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive//DCM_2012-12-05_ImagingUpload-15-42-yUwQQV.tar >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -verbose >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> md5sum >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive/DCM_2012-12-05_ImagingUpload-15-42-yUwQQV.tar >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> candidate id 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> => No Visit labelVisit >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> label does not exist >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Set centerID = 1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Number of MINC files that >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> will be considered for inserting into the database: 1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> log dir is /logs and log >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> file is /logs/TarLoad-15-42-L6pocU.log >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> candidate id 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> => No Visit label >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Cleaning up temp files: rm >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -rf /tmp/TarLoad-15-42-J2rQms/ImagingUpload-15-42-yUwQQV*" >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 24 ???? 2019 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? 3:38 ?.?., ?/? Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 1) What are the records >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in the session table? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 2) I tried to upload a >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> non-phantom file like this >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> input_file.txt: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/incoming/DCC0000_258024_V1.tar.gz >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> N DCC0000_258024_V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Terminal: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ./batch_uploads_imageuploader >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -profile prod < ~/Desktop/input.txt > log.txt >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and i get the following >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> error in the log.txt file >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> "Running now the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> following command: /data/loris/data/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -profile prod -upload_id 7 /data/incoming/DCC0000_258024_V1.tar.gz -verbose >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> find -path >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> \/tmp\/ImagingUpload\-14\-56\-FeLCB4 -name '__MACOSX' -delete >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Spool message is: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The PatientName read from >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the DICOM header does not start with DCC0000_258024_V1 from the mri_upload >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> table >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> " >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and the spool message is >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> repeated for each .dcm file. Should i preprocess every .dcm file and change >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the PatientName to "DCC0000_258024_V1"? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 3) As far as it concerns >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the candidate profile i have to create a new one each time before i try to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> upload a file? Is there already a way to create a candidate profile and get >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the DCCID and PSCID without the user interface? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 18 ???? 2019 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? 5:00 ?.?., ?/? Cecile Madjar < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> cecile.madjar at mcin.ca> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> See answers to your >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> questions below. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> About the 1st case we >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> had a dicom with a blank studyUID, maybe someone accidentally removed it. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> That is strange. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Something must have been done to the DICOM files. I have never seen a study >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> with no StudyUID out of the scanner. Usually, you need to manually erase it >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> with some tool. However, DICOMs never cease to surprise me... >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Some other questions: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 1) What are the steps >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> to remove all of my patients and uploads?: because i want to try to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> reupload all the testing dicoms we had with a clean database. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Release 21.0 of >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> LORIS-MRI will offer a script to remove all the entries and files specific >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> to an upload. However, this release is not yet out. Hopefully in the next >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> few weeks. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> In the meantime, since >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> your case is particular and that you just want to start with a clean >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> database, the following deletes should work (hopefully I won't forget any >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> tables): >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> mri_violations_log; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> mri_protocol_violated_scans; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> MRICandidateErrors; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> parameter_file; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> files_qcstatus; # (if you played with the QC part of the imaging browser >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> for testing) >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> feedback_mri_comments; # (if you played with the QC part of the imaging >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> browser for testing) >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> tarchive_series; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> tarchive_files; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from mri_upload; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from tarchive; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from mri_scanner; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from candidate >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> where PSCID="scanner"; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I don't know if you want >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> to also delete entries in the session and candidate table too? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 2) We do not need to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> create the profile of a patient ( are the patients stored in the candidate >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> table? because i can't see the ghosts ), because will it automatically be >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> created when importing a dicom? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I am not sure I >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> understand fully this question. All candidates are stored in the candidate >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> table. The phantom scans however are attached to a scanner candidate >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> depending on where the scan happened. It is a bit of a weird concept that >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> we have to redesign eventually but never got a chance to get to it. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hopefully this answered >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> your question, otherwise, don't hesitate to let me know. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 3) What is the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> difference between uploading a dicom as phantom instead of importing as >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCCID_DCCID_VisitLabel? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> When you upload the scan >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> as PSCID_DCCID_VisitLabel, there is a check that makes sure the candidate >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> IDs and visit label are valid at the time of upload. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> When you upload a scan >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> as phantom, it expects that the DICOM field PatientName and uploaded >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> filename contains the string "phantom". We enforced this behaviour on the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> imaging uploader side in recent releases but I can't remember which one. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Probably the upcoming 21.0 release. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> All those verifications >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> might seem cumbersome but they are here to ensure that the files inserted >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> are all valid and labelled properly as it is a bit messy to have to delete >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> files that were wrongly labelled. At least, the delete script present in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> release 21.0 will make this process easier but it is still good practice to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> verify those things. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> With pleasure. Hopefully >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the answers to your questions will be helpful. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PS: loris-dev mailing >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> list: you will find the initial answer I gave Sotirios below. I forgot to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> cc the loris-dev in my earlier reply... >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 16 ???? 2019 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? 12:02 ?.?., ?/? Cecile Madjar < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> cecile.madjar at mcin.ca> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Dear Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you for reaching >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> out. Since your email was already organized in points, I will reply >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> directly below your questions below. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 1) What do we do when >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the StudyUID is blank on the header? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/minor/docs/AppendixA-Troubleshooting_guideline.md >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> There solution provided at the table 3 does not guide us how to find the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> information ( is possible ). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The StudyUID is the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> field used in our pipeline at the moment to check whether a DICOM study was >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> already inserted into LORIS with that same StudyUID since it is supposed to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> be unique for every single study. Currently, we do not support insertion of >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DICOM studies if they do not have a StudyUID associated with them. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Is there a specific >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> reason why the StudyUID is blank in the DICOM headers in your DICOM files? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Did they go through some processes before upload to LORIS? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 2) When i am about to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> upload a non-phanton case i need a 'Visit Label'. Is there already a script >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> that can create a new visit label for a specific Candidate, so i can >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> provide it as input afterwards to the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> batch_uploads_imageuploader ( See option 5.1.3 https://github.com/aces/Loris-MRI/blob/minor/docs/05-PipelineLaunchOptions.md ) >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I am not sure if the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> front-end allows for it but if you use batch_uploads_imageuploader, the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> insertion scripts could create the visit label for you. However, it does >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> need to be included in the patient name in order for the script to know >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> which label it should use. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> For example: you >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> upload V02 for MTL0123 (DCCID: 456789) but V02 was not yet created for >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> MTL0123; the insertion scripts will create a V02 visit for MTL0123 if the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PatientName field for the dataset is MTL0123_456789_V02 with Stage marked >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> as "Not Started". >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> However, *note that >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> for the script to create the visit for the candidate, you have to make sure >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> that all the visit label of your projects were inserted in the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Visit_Windows table* >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> (otherwise, the visit will never be created as they were not specified as >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> being part of the list of visit label to expect). So in the example above, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> you should have one row in Visit_Windows with Visit_label="V02" set. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 3) Section 4.3 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/minor/docs/04-Scripts.md >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> What do we do when the folder contains multiple mnc files? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> This is a case by >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> case. Most of the time, the MINC files that failed insertion into the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> imaging browser end up in the MRI violation module where you can see what >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> went wrong with the acquisitions not inserted. If you notice that the MINC >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> file should be inserted as a specific protocol, you can force the insertion >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> as explained in section 4.3. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> In your case, I have a >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> feeling that you want to be able to insert MINC files that did not go >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> through the whole pipeline insertion (DICOM archival, then dcm2mnc, then >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> protocol identification, then insertion...). In theory, you could call >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl on >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> any MINC file, provided you have at least the following information: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - path to the MINC >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> file >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - uploadID associated >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> with the MINC files or DICOM archive path from which those MINC files were >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> created from >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Then the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> script will do the subject information and protocol validation etc... >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> If all the MINC files >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> come from the same uploadID or TarchiveID, then you could run a loop in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> bash calling the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> script like this for files deriving from uploadID=1: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ls >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /path/to/mnc/folder/* | while read f; do >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -profile prod -uploadID 1 -mincPath $f; done >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helped! >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> McGill Centre for Integrative >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Neuroscience | MCIN.ca >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> | MCIN.ca >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>>>>>>>>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | >>>>>>>>>>>>>>>>>>>>>>>>>>>>> MCIN.ca >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>>>>>>>>>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>>>>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>>>>>>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | >>>>>>>>>>>>>>>>>>>>>>>>>>> MCIN.ca >>>>>>>>>>>>>>>>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>>>>>>>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>>>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>>>>>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | >>>>>>>>>>>>>>>>>>>>>>>>>> MCIN.ca >>>>>>>>>>>>>>>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>>>>>>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>>>>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | >>>>>>>>>>>>>>>>>>>>>>>>> MCIN.ca >>>>>>>>>>>>>>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>>>>>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>>>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>> Shen Wang >>>>>>>>>>>>>>> Loris Developer >>>>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>>>> McGill University >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> -- >>>>>>>>>>> Shen Wang >>>>>>>>>>> Loris Developer >>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>> McGill University >>>>>>>>>>> >>>>>>>>>>> -- >>>>>>>>>> Shen Wang >>>>>>>>>> Loris Developer >>>>>>>>>> Montreal Neurological Institute >>>>>>>>>> McGill University >>>>>>>>>> >>>>>>>>>> _______________________________________________ >>>>>>>>>> Loris-dev mailing list >>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> -- >>>>>>>>> >>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>> Montreal Neurological Institute >>>>>>>>> McGill University | Montreal | Canada >>>>>>>>> >>>>>>>> >>>>>> >>>>>> -- >>>>>> Shen Wang >>>>>> Loris Developer >>>>>> Montreal Neurological Institute >>>>>> McGill University >>>>>> >>>>>> >>>> >>>> -- >>>> Shen Wang >>>> Loris Developer >>>> Montreal Neurological Institute >>>> McGill University >>>> >>>> >> >> -- >> Shen Wang >> Loris Developer >> Montreal Neurological Institute >> McGill University >> >> _______________________________________________ > Loris-dev mailing list > Loris-dev at bic.mni.mcgill.ca > https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: ???? 2019-08-13 19.21.15.png Type: image/png Size: 508603 bytes Desc: not available URL: From wangshen.mcin at gmail.com Thu Aug 15 15:06:22 2019 From: wangshen.mcin at gmail.com (Shen Wang) Date: Thu, 15 Aug 2019 15:06:22 -0400 Subject: [Loris-dev] Upgrading to Loris 21 - new make file In-Reply-To: References: Message-ID: In my VM, I alway use sudo, if not cause an error. npm install npm WARN checkPermissions Missing write access to /var/www/Loris/node_modules npm WARN The package prop-types is included as both a dev and production dependency. npm ERR! path /var/www/Loris/node_modules npm ERR! code EACCES npm ERR! errno -13 npm ERR! syscall access npm ERR! Error: EACCES: permission denied, access '/var/www/Loris/node_modules' npm ERR! [Error: EACCES: permission denied, access '/var/www/Loris/node_modules'] { npm ERR! stack: "Error: EACCES: permission denied, access '/var/www/Loris/node_modules'", npm ERR! errno: -13, npm ERR! code: 'EACCES', npm ERR! syscall: 'access', npm ERR! path: '/var/www/Loris/node_modules' npm ERR! } npm ERR! npm ERR! The operation was rejected by your operating system. npm ERR! It is likely you do not have the permissions to access this file as the current user npm ERR! npm ERR! If you believe this might be a permissions issue, please double-check the npm ERR! permissions of the file and its containing directories, or try running npm ERR! the command again as root/Administrator (though this is not recommended). On Thu, 15 Aug 2019 at 15:03, Tom Beaudry wrote: > Any reason why you are using "sudo make" instead of just "make" ? > > On Thu, Aug 15, 2019 at 2:45 PM Sotirios Nikoloutsopoulos < > sotirisnik at gmail.com> wrote: > >> I attached the sudo make output. >> >> ???? ???, 15 ??? 2019 ???? 9:36 ?.?., ?/? Shen Wang < >> wangshen.mcin at gmail.com> ??????: >> >>> Hi, >>> You don't need to run install.sh this time. Redownload the missing file, >>> then do sudo make. >>> If it still have indent and no-def errors, then remove the lines which I >>> told you from webpack.config.js, then try do >>> sudo make again. >>> >>> >>> On Thu, 15 Aug 2019 at 14:28, Sotirios Nikoloutsopoulos < >>> sotirisnik at gmail.com> wrote: >>> >>>> Hi, >>>> >>>> should i try to redownload the files from >>>> https://github.com/aces/Loris/tree/major and execute the install.sh? I >>>> find it weird that i am missing some files. >>>> >>>> Thanks >>>> >>>> ???? ???, 15 ??? 2019 ???? 9:17 ?.?., ?/? Shen Wang < >>>> wangshen.mcin at gmail.com> ??????: >>>> >>>>> Hi Sotirios, >>>>> It seems like you are missing this file. [ .babelrc] >>>>> step 1: copy from https://github.com/aces/Loris/blob/major/.babelrc >>>>> step 2: sudo vi webpack.config.js >>>>> remove these lines >>>>> >>>>> { test: /\.js$/, >>>>> >>>>> exclude: /node_modules/, >>>>> >>>>> // use: ['babel-loader', 'eslint-loader'], >>>>> >>>>> }, >>>>> >>>>> step 3: sudo make >>>>> >>>>> >>>>> >>>>> On Wed, 14 Aug 2019 at 18:52, Sotirios Nikoloutsopoulos < >>>>> sotirisnik at gmail.com> wrote: >>>>> >>>>>> Hi Shen, >>>>>> >>>>>> That didn't work either. Also i had removed the git files because i >>>>>> was getting this error when i used make: >>>>>> >>>>>> "git describe --tags --always > VERSION >>>>>> fatal: Not a git repository (or any of the parent directories): .git >>>>>> Makefile:8: recipe for target 'VERSION' failed >>>>>> make: *** [VERSION] Error 128" >>>>>> >>>>>> Thanks >>>>>> >>>>>> ???? ???, 15 ??? 2019 ???? 1:36 ?.?., ?/? Shen Wang < >>>>>> wangshen.mcin at gmail.com> ??????: >>>>>> >>>>>>> Hi,Sotirios >>>>>>> In your special situation, there is a temporary fix. >>>>>>> step 1. sudo git stash >>>>>>> step 2. open webpack.config.js file >>>>>>> remove line 75 use: ['babel-loader', 'eslint-loader'], >>>>>>> save it. >>>>>>> step 3. sudo make >>>>>>> >>>>>>> I hope this could help you to compile the js files. >>>>>>> >>>>>>> >>>>>>> >>>>>>> On Wed, 14 Aug 2019 at 08:28, Sotirios Nikoloutsopoulos < >>>>>>> sotirisnik at gmail.com> wrote: >>>>>>> >>>>>>>> I forgot to mention that i had already moved my previous config >>>>>>>> file and re-executed the installation script. >>>>>>>> >>>>>>>> ???? ???, 14 ??? 2019 ???? 3:26 ?.?., ?/? Sotirios Nikoloutsopoulos >>>>>>>> ??????: >>>>>>>> >>>>>>>>> Hi, >>>>>>>>> >>>>>>>>> Step 1 worked and the indentation errors were fixed. About step2 i >>>>>>>>> added all of these( there are more to include in the list) these to >>>>>>>>> .eslintignore which were reported to fail at being built, but they still >>>>>>>>> appear on the errors at the make_output file. >>>>>>>>> >>>>>>>>> /jsx/DynamicDataTable.js >>>>>>>>> /jsx/StaticDataTable.js >>>>>>>>> /jsx/MultiSelectDropdown.js >>>>>>>>> /jsx/Breadcrumbs.js >>>>>>>>> /jsx/Form.js >>>>>>>>> /jsx/Markdown.js >>>>>>>>> /modules/media/jsx/mediaIndex.js >>>>>>>>> /modules/issue_tracker/jsx/issueTrackerIndex.js >>>>>>>>> /modules/issue_tracker/jsx/index.js >>>>>>>>> /modules/candidate_parameters/jsx/CandidateParameters.js >>>>>>>>> /modules/configuration/jsx/SubprojectRelations.js >>>>>>>>> /modules/conflict_resolver/jsx/conflictResolverIndex.js >>>>>>>>> /modules/conflict_resolver/jsx/resolvedConflictsIndex.js >>>>>>>>> /modules/bvl_feedback/jsx/react.behavioural_feedback_panel.js >>>>>>>>> /modules/dataquery/jsx/react.tabs.js >>>>>>>>> /modules/document_repository/jsx/docIndex.js >>>>>>>>> /modules/instrument_builder/jsx/react.instrument_builder.js >>>>>>>>> /modules/imaging_uploader/jsx/index.js >>>>>>>>> /modules/datadict/jsx/dataDictIndex.js >>>>>>>>> /modules/bvl_feedback/jsx/react.behavioural_feedback_panel.js >>>>>>>>> /modules/new_profile/jsx/NewProfileIndex.js >>>>>>>>> /modules/examiner/jsx/examinerIndex.js >>>>>>>>> /modules/configuration/jsx/SubprojectRelations.js >>>>>>>>> /modules/data_team_helper/jsx/behavioural_qc_module.js >>>>>>>>> /modules/acknowledgements/jsx/acknowledgementsIndex.js >>>>>>>>> /modules/candidate_parameters/jsx/CandidateParameters.js >>>>>>>>> /modules/imaging_browser/jsx/ImagePanel.js >>>>>>>>> >>>>>>>>> /modules/mri_violations/jsx/mri_protocol_violations_columnFormatter.js >>>>>>>>> >>>>>>>>> /modules/mri_violations/jsx/mri_protocol_check_violations_columnFormatter.js >>>>>>>>> /modules/genomic_browser/jsx/profileColumnFormatter.js >>>>>>>>> /modules/dataquery/jsx/react.tabs.js >>>>>>>>> /jsx/MultiSelectDropdown.js >>>>>>>>> /modules/mri_violations/jsx/columnFormatterUnresolved.js >>>>>>>>> /modules/dataquery/jsx/react.sidebar.js >>>>>>>>> /modules/dataquery/jsx/react.fieldselector.js >>>>>>>>> /modules/quality_control/jsx/qualityControlIndex.js >>>>>>>>> /modules/dataquery/jsx/react.paginator.js >>>>>>>>> /modules/instrument_builder/jsx/react.questions.js >>>>>>>>> /modules/dataquery/jsx/react.filterBuilder.js >>>>>>>>> /modules/conflict_resolver/jsx/conflictResolverIndex.js >>>>>>>>> /jsx/PaginationLinks.js >>>>>>>>> /modules/conflict_resolver/jsx/resolvedConflictsIndex.js >>>>>>>>> /modules/dataquery/jsx/react.app.js >>>>>>>>> /modules/candidate_list/jsx/onLoad.js >>>>>>>>> /jsx/Form.js >>>>>>>>> /modules/publication/jsx/publicationIndex.js >>>>>>>>> >>>>>>>>> /modules/server_processes_manager/jsx/server_processes_managerIndex.js >>>>>>>>> /modules/imaging_browser/jsx/imagingBrowserIndex.js >>>>>>>>> /modules/issue_tracker/jsx/issueTrackerIndex.js >>>>>>>>> /modules/survey_accounts/jsx/surveyAccountsIndex.js >>>>>>>>> /modules/data_integrity_flag/jsx/dataIntegrityFlagIndex.js >>>>>>>>> /modules/instrument_manager/jsx/instrumentManagerIndex.js >>>>>>>>> /modules/media/jsx/mediaIndex.js >>>>>>>>> /modules/user_accounts/jsx/userAccountsIndex.js >>>>>>>>> /modules/help_editor/jsx/help_editor.js >>>>>>>>> /modules/dicom_archive/jsx/dicom_archive.js >>>>>>>>> /modules/mri_violations/jsx/columnFormatter.js >>>>>>>>> /modules/brainbrowser/jsx/Brainbrowser.js >>>>>>>>> /node_modules/babel-loader/lib/index.js >>>>>>>>> /modules/document_repository/jsx/editFormIndex.js >>>>>>>>> >>>>>>>>> Thanks >>>>>>>>> >>>>>>>>> ???? ???, 14 ??? 2019 ???? 7:50 ?.?., ?/? Christine Rogers, Ms. < >>>>>>>>> christine.rogers at mcgill.ca> ??????: >>>>>>>>> >>>>>>>>>> Hi Shen and Sotirios - just a note, >>>>>>>>>> >>>>>>>>>> For the 21 release, it's best to run the install script without >>>>>>>>>> sudoing it. >>>>>>>>>> >>>>>>>>>> (Shen, I believe we discovered a minor issue with the sudo last >>>>>>>>>> week #5008) >>>>>>>>>> >>>>>>>>>> Best, >>>>>>>>>> Christine >>>>>>>>>> >>>>>>>>>> On Tue, Aug 13, 2019 at 9:22 PM Shen Wang < >>>>>>>>>> wangshen.mcin at gmail.com> wrote: >>>>>>>>>> >>>>>>>>>>> Does it work? If still doesn?t work, try to remove >>>>>>>>>>> project/config.xml file. Do sudo ./install.sh again. To reinstall Loris >>>>>>>>>>> again. >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> Shen Wang ?2019?8?13? ????9:02??? >>>>>>>>>>> >>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>> step 1: >>>>>>>>>>>> sudo ./node_modules/.bin/eslint --fix /var/www/loris >>>>>>>>>>>> step 2: >>>>>>>>>>>> put the rest error files under this line [# Ignore until >>>>>>>>>>>> ESLint is run] in the .eslintignore file. >>>>>>>>>>>> step 3: >>>>>>>>>>>> sudo make >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> On Tue, 13 Aug 2019 at 20:34, Sotirios Nikoloutsopoulos < >>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>> >>>>>>>>>>>>> I did the modifications, still there are errors. >>>>>>>>>>>>> Thanks >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> ???? ???, 14 ??? 2019 ???? 3:22 ?.?., ?/? Shen Wang < >>>>>>>>>>>>> wangshen.mcin at gmail.com> ??????: >>>>>>>>>>>>> >>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>> I saw your output file, the config issue is gone. >>>>>>>>>>>>>> you can use [sudo npm run lintfix:javascript ] to fix these >>>>>>>>>>>>>> indent issues. >>>>>>>>>>>>>> If it still has errors. >>>>>>>>>>>>>> Then try modify this file .eslintignore >>>>>>>>>>>>>> with this >>>>>>>>>>>>>> >>>>>>>>>>>>>> # Ignore until ESLint is run >>>>>>>>>>>>>> >>>>>>>>>>>>>> modules/* >>>>>>>>>>>>>> >>>>>>>>>>>>>> modules/dataquery/ >>>>>>>>>>>>>> >>>>>>>>>>>>>> node_modules/* >>>>>>>>>>>>>> >>>>>>>>>>>>>> htdocs/js/components/* >>>>>>>>>>>>>> >>>>>>>>>>>>>> jsx/* >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> # Ignore external libs >>>>>>>>>>>>>> >>>>>>>>>>>>>> htdocs/js/flot/* >>>>>>>>>>>>>> >>>>>>>>>>>>>> htdocs/js/jquery/* >>>>>>>>>>>>>> >>>>>>>>>>>>>> htdocs/js/jszip/* >>>>>>>>>>>>>> >>>>>>>>>>>>>> htdocs/js/modernizr/* >>>>>>>>>>>>>> >>>>>>>>>>>>>> htdocs/js/modules/* >>>>>>>>>>>>>> >>>>>>>>>>>>>> htdocs/js/react/* >>>>>>>>>>>>>> >>>>>>>>>>>>>> htdocs/js/shims/* >>>>>>>>>>>>>> >>>>>>>>>>>>>> htdocs/js/c3.min.js >>>>>>>>>>>>>> >>>>>>>>>>>>>> htdocs/js/d3.min.js >>>>>>>>>>>>>> >>>>>>>>>>>>>> htdocs/js/FileSaver.min.js >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> then do sudo make. >>>>>>>>>>>>>> It should work. >>>>>>>>>>>>>> Regards >>>>>>>>>>>>>> Shen >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> Sotirios Nikoloutsopoulos ?2019?8?13? >>>>>>>>>>>>>> ????7:54??? >>>>>>>>>>>>>> >>>>>>>>>>>>>>> No, it didn't work, i also tried space/tabs because most of >>>>>>>>>>>>>>> the errors where about indentation, also there are some errors about React. >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> Thanks >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> lorisadmin at hbp:/var/www/loris$ sudo >>>>>>>>>>>>>>> ./node_modules/.bin/eslint --init >>>>>>>>>>>>>>> ? How would you like to configure ESLint? Answer questions >>>>>>>>>>>>>>> about your style >>>>>>>>>>>>>>> ? Which version of ECMAScript do you use? ES2015 >>>>>>>>>>>>>>> ? Are you using ES6 modules? Yes >>>>>>>>>>>>>>> ? Where will your code run? Browser >>>>>>>>>>>>>>> ? Do you use CommonJS? Yes >>>>>>>>>>>>>>> ? Do you use JSX? Yes >>>>>>>>>>>>>>> ? Do you use React? Yes >>>>>>>>>>>>>>> ? What style of indentation do you use? Spaces >>>>>>>>>>>>>>> ? What quotes do you use for strings? Single >>>>>>>>>>>>>>> ? What line endings do you use? Unix >>>>>>>>>>>>>>> ? Do you require semicolons? Yes >>>>>>>>>>>>>>> ? What format do you want your config file to be in? JSON >>>>>>>>>>>>>>> The config that you've selected requires the following >>>>>>>>>>>>>>> dependencies: >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> eslint-plugin-react at latest >>>>>>>>>>>>>>> Successfully created .eslintrc.json file in /var/www/loris >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> lorisadmin at hbp:/var/www/loris$ sudo make > sudo_make_output >>>>>>>>>>>>>>> npm WARN The package prop-types is included as both a dev >>>>>>>>>>>>>>> and production dependency. >>>>>>>>>>>>>>> npm WARN optional SKIPPING OPTIONAL DEPENDENCY: >>>>>>>>>>>>>>> fsevents at 1.2.4 (node_modules/fsevents): >>>>>>>>>>>>>>> npm WARN notsup SKIPPING OPTIONAL DEPENDENCY: Unsupported >>>>>>>>>>>>>>> platform for fsevents at 1.2.4: wanted >>>>>>>>>>>>>>> {"os":"darwin","arch":"any"} (current: {"os":"linux","arch":"x64"}) >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> npm ERR! code ELIFECYCLE >>>>>>>>>>>>>>> npm ERR! errno 2 >>>>>>>>>>>>>>> npm ERR! loris at 1.0.0 compile: `webpack` >>>>>>>>>>>>>>> npm ERR! Exit status 2 >>>>>>>>>>>>>>> npm ERR! >>>>>>>>>>>>>>> npm ERR! Failed at the loris at 1.0.0 compile script. >>>>>>>>>>>>>>> npm ERR! This is probably not a problem with npm. There is >>>>>>>>>>>>>>> likely additional logging output above. >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> npm ERR! A complete log of this run can be found in: >>>>>>>>>>>>>>> npm ERR! >>>>>>>>>>>>>>> /home/lorisadmin/.npm/_logs/2019-08-13T23_40_58_841Z-debug.log >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> ???? ???, 14 ??? 2019 ???? 2:29 ?.?., ?/? Shen Wang < >>>>>>>>>>>>>>> wangshen.mcin at gmail.com> ??????: >>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>> When you do make command, please make sure with sudo at the >>>>>>>>>>>>>>>> beginning. [sudo make] >>>>>>>>>>>>>>>> If it still doesn't work for you. >>>>>>>>>>>>>>>> Then try the solutions below. >>>>>>>>>>>>>>>> solution 1: >>>>>>>>>>>>>>>> [image: ???? 2019-08-13 19.21.15.png] >>>>>>>>>>>>>>>> Regards >>>>>>>>>>>>>>>> Shen >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> On Tue, 13 Aug 2019 at 17:22, Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> I think that the files exists although i redownloaded the >>>>>>>>>>>>>>>>> eslintrc.json i checked others files that had similar errors. >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> lorisadmin at hbp:/var/www/loris$ ls -l >>>>>>>>>>>>>>>>> ./node_modules/eslint-loader/index.js >>>>>>>>>>>>>>>>> -rw-rw-r-- 1 lorisadmin lorisadmin 6463 ??? 26 1985 >>>>>>>>>>>>>>>>> ./node_modules/eslint-loader/index.js >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> lorisadmin at hbp:/var/www/loris$ ls -l .eslintrc.json >>>>>>>>>>>>>>>>> -rw-rw-r-- 1 lorisadmin lorisadmin 84530 ??? 14 00:04 >>>>>>>>>>>>>>>>> .eslintrc.json >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Maybe this can help >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Module build failed (from >>>>>>>>>>>>>>>>> ./node_modules/eslint-loader/index.js): >>>>>>>>>>>>>>>>> SyntaxError: Cannot read config file: >>>>>>>>>>>>>>>>> /var/www/loris/.eslintrc.json >>>>>>>>>>>>>>>>> Error: Unexpected token < in JSON at position 6 >>>>>>>>>>>>>>>>> at JSON.parse () >>>>>>>>>>>>>>>>> at loadJSONConfigFile >>>>>>>>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config/config-file.js:114:21) >>>>>>>>>>>>>>>>> at loadConfigFile >>>>>>>>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config/config-file.js:230:26) >>>>>>>>>>>>>>>>> at loadFromDisk >>>>>>>>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config/config-file.js:500:18) >>>>>>>>>>>>>>>>> at Object.load >>>>>>>>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config/config-file.js:564:20) >>>>>>>>>>>>>>>>> at Config.getLocalConfigHierarchy >>>>>>>>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config.js:227:44) >>>>>>>>>>>>>>>>> at Config.getConfigHierarchy >>>>>>>>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config.js:179:43) >>>>>>>>>>>>>>>>> at Config.getConfigVector >>>>>>>>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config.js:286:21) >>>>>>>>>>>>>>>>> at Config.getConfig >>>>>>>>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config.js:329:29) >>>>>>>>>>>>>>>>> at processText >>>>>>>>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/cli-engine.js:162:33) >>>>>>>>>>>>>>>>> at CLIEngine.executeOnText >>>>>>>>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/cli-engine.js:596:17) >>>>>>>>>>>>>>>>> at lint >>>>>>>>>>>>>>>>> (/var/www/loris/node_modules/eslint-loader/index.js:237:17) >>>>>>>>>>>>>>>>> at Object.module.exports >>>>>>>>>>>>>>>>> (/var/www/loris/node_modules/eslint-loader/index.js:232:21) >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> ERROR in ./modules/imaging_uploader/jsx/index.js >>>>>>>>>>>>>>>>> Module build failed (from >>>>>>>>>>>>>>>>> ./node_modules/eslint-loader/index.js): >>>>>>>>>>>>>>>>> SyntaxError: Cannot read config file: >>>>>>>>>>>>>>>>> /var/www/loris/.eslintrc.json >>>>>>>>>>>>>>>>> Error: Unexpected token < in JSON at position 6 >>>>>>>>>>>>>>>>> at JSON.parse () >>>>>>>>>>>>>>>>> at loadJSONConfigFile >>>>>>>>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config/config-file.js:114:21) >>>>>>>>>>>>>>>>> at loadConfigFile >>>>>>>>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config/config-file.js:230:26) >>>>>>>>>>>>>>>>> at loadFromDisk >>>>>>>>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config/config-file.js:500:18) >>>>>>>>>>>>>>>>> at Object.load >>>>>>>>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config/config-file.js:564:20) >>>>>>>>>>>>>>>>> at Config.getLocalConfigHierarchy >>>>>>>>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config.js:227:44) >>>>>>>>>>>>>>>>> at Config.getConfigHierarchy >>>>>>>>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config.js:179:43) >>>>>>>>>>>>>>>>> at Config.getConfigVector >>>>>>>>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config.js:286:21) >>>>>>>>>>>>>>>>> at Config.getConfig >>>>>>>>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config.js:329:29) >>>>>>>>>>>>>>>>> at processText >>>>>>>>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/cli-engine.js:162:33) >>>>>>>>>>>>>>>>> at CLIEngine.executeOnText >>>>>>>>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/cli-engine.js:596:17) >>>>>>>>>>>>>>>>> at lint >>>>>>>>>>>>>>>>> (/var/www/loris/node_modules/eslint-loader/index.js:237:17) >>>>>>>>>>>>>>>>> at Object.module.exports >>>>>>>>>>>>>>>>> (/var/www/loris/node_modules/eslint-loader/index.js:232:21) >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> ???? ???, 13 ??? 2019 ???? 11:52 ?.?., ?/? John Saigle < >>>>>>>>>>>>>>>>> john.saigle at mcin.ca> ??????: >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> HI Sotirios, >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> The make_output.txt file shows webpack failing because it >>>>>>>>>>>>>>>>>> can't find the ESLint config file. >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Can you confirm whether the file `.eslintrc.json` exists >>>>>>>>>>>>>>>>>> within your loris root directory (usually `/var/www/loris/`)? When I delete >>>>>>>>>>>>>>>>>> my file I get the same errors as you. >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> If you find that it's missing, you can make a local copy >>>>>>>>>>>>>>>>>> with the contents found here: >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> https://github.com/aces/Loris/blob/e26a6ad49a73fcffef0cd73bb600c4d17b200b62/.eslintrc.json >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Once you know it exists, try running `make` again. >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Let us know if that moves you forward. >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>> John >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> On Tue, Aug 13, 2019 at 2:21 PM Sotirios Nikoloutsopoulos >>>>>>>>>>>>>>>>>> wrote: >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>>>> I executed the commands for the node and now i am get >>>>>>>>>>>>>>>>>>> the followings: >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> lorisadmin at hbp:/var/www/loris$ make > ~/make_output >>>>>>>>>>>>>>>>>>> npm WARN The package prop-types is included as both a >>>>>>>>>>>>>>>>>>> dev and production dependency. >>>>>>>>>>>>>>>>>>> npm WARN optional SKIPPING OPTIONAL DEPENDENCY: >>>>>>>>>>>>>>>>>>> fsevents at 1.2.4 (node_modules/fsevents): >>>>>>>>>>>>>>>>>>> npm WARN notsup SKIPPING OPTIONAL DEPENDENCY: >>>>>>>>>>>>>>>>>>> Unsupported platform for fsevents at 1.2.4: wanted >>>>>>>>>>>>>>>>>>> {"os":"darwin","arch":"any"} (current: {"os":"linux","arch":"x64"}) >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> npm ERR! code ELIFECYCLE >>>>>>>>>>>>>>>>>>> npm ERR! errno 2 >>>>>>>>>>>>>>>>>>> npm ERR! loris at 1.0.0 compile: `webpack` >>>>>>>>>>>>>>>>>>> npm ERR! Exit status 2 >>>>>>>>>>>>>>>>>>> npm ERR! >>>>>>>>>>>>>>>>>>> npm ERR! Failed at the loris at 1.0.0 compile script. >>>>>>>>>>>>>>>>>>> npm ERR! This is probably not a problem with npm. There >>>>>>>>>>>>>>>>>>> is likely additional logging output above. >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> npm ERR! A complete log of this run can be found in: >>>>>>>>>>>>>>>>>>> npm ERR! >>>>>>>>>>>>>>>>>>> /home/lorisadmin/.npm/_logs/2019-08-13T18_12_05_378Z-debug.log >>>>>>>>>>>>>>>>>>> make: *** [javascript] Error 2 >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Thanks, >>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> ???? ???, 12 ??? 2019 ???? 10:19 ?.?., ?/? Christine >>>>>>>>>>>>>>>>>>> Rogers, Ms. ??????: >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> We've seen some users installing LORIS 21 or upgrading >>>>>>>>>>>>>>>>>>>> to 21 whose version of node doesn't work well with webpack, due to updated >>>>>>>>>>>>>>>>>>>> packages they're missing. >>>>>>>>>>>>>>>>>>>> If so, update your node : >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> curl -sL https://deb.nodesource.com/setup_8.x | sudo -E bash - >>>>>>>>>>>>>>>>>>>> sudo apt-get install -y nodejs >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Let us know how that goes -- please send us output from >>>>>>>>>>>>>>>>>>>> the same log if any issues. >>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>> Christine >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> On Thu, Aug 8, 2019 at 2:38 PM Sotirios >>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos wrote: >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> It's not a disk space issue, as you can see below i >>>>>>>>>>>>>>>>>>>>> have still 74GB available. >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> lorisadmin at hbp:/var/www/loris$ df -h >>>>>>>>>>>>>>>>>>>>> Filesystem Size Used Avail Use% Mounted on >>>>>>>>>>>>>>>>>>>>> udev 2,9G 0 2,9G 0% /dev >>>>>>>>>>>>>>>>>>>>> tmpfs 597M 8,6M 588M 2% /run >>>>>>>>>>>>>>>>>>>>> /dev/sda1 98G 19G 74G 21% / >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> Maybe we have to pass a flag to get into strict mode? >>>>>>>>>>>>>>>>>>>>> as stated "SyntaxError: Block-scoped declarations (let, const, function, >>>>>>>>>>>>>>>>>>>>> class) not yet supported outside strict mode" >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> Thanks, >>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> ???? ???, 8 ??? 2019 ???? 4:32 ?.?., ?/? Dave >>>>>>>>>>>>>>>>>>>>> MacFarlane ??????: >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> It looks like the javascript snippet shown in the >>>>>>>>>>>>>>>>>>>>>> error message when trying to compile the js is truncated. Have you run out >>>>>>>>>>>>>>>>>>>>>> of disk space? >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> On Thu, Aug 8, 2019 at 8:37 AM Sotirios >>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos wrote: >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> I runned make and also included the file it reports >>>>>>>>>>>>>>>>>>>>>>> at the end. >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> lorisadmin at hbp:/var/www/loris$ make >>>>>>>>>>>>>>>>>>>>>>> npm install >>>>>>>>>>>>>>>>>>>>>>> npm WARN optional Skipping failed optional >>>>>>>>>>>>>>>>>>>>>>> dependency /chokidar/fsevents: >>>>>>>>>>>>>>>>>>>>>>> npm WARN notsup Not compatible with your operating >>>>>>>>>>>>>>>>>>>>>>> system or architecture: fsevents at 1.2.9 >>>>>>>>>>>>>>>>>>>>>>> npm WARN optional Skipping failed optional >>>>>>>>>>>>>>>>>>>>>>> dependency /watchpack/chokidar/fsevents: >>>>>>>>>>>>>>>>>>>>>>> npm WARN notsup Not compatible with your operating >>>>>>>>>>>>>>>>>>>>>>> system or architecture: fsevents at 1.2.9 >>>>>>>>>>>>>>>>>>>>>>> npm run compile >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> > loris at 1.0.0 compile /var/www/loris >>>>>>>>>>>>>>>>>>>>>>> > webpack >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> /var/www/loris/node_modules/webpack/bin/webpack.js:86 >>>>>>>>>>>>>>>>>>>>>>> let notify = >>>>>>>>>>>>>>>>>>>>>>> ^^^ >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> SyntaxError: Block-scoped declarations (let, const, >>>>>>>>>>>>>>>>>>>>>>> function, class) not yet supported outside strict mode >>>>>>>>>>>>>>>>>>>>>>> at exports.runInThisContext (vm.js:53:16) >>>>>>>>>>>>>>>>>>>>>>> at Module._compile (module.js:374:25) >>>>>>>>>>>>>>>>>>>>>>> at Object.Module._extensions..js >>>>>>>>>>>>>>>>>>>>>>> (module.js:417:10) >>>>>>>>>>>>>>>>>>>>>>> at Module.load (module.js:344:32) >>>>>>>>>>>>>>>>>>>>>>> at Function.Module._load (module.js:301:12) >>>>>>>>>>>>>>>>>>>>>>> at Function.Module.runMain (module.js:442:10) >>>>>>>>>>>>>>>>>>>>>>> at startup (node.js:136:18) >>>>>>>>>>>>>>>>>>>>>>> at node.js:966:3 >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> npm ERR! Linux 4.15.0-55-generic >>>>>>>>>>>>>>>>>>>>>>> npm ERR! argv "/usr/bin/nodejs" "/usr/bin/npm" "run" >>>>>>>>>>>>>>>>>>>>>>> "compile" >>>>>>>>>>>>>>>>>>>>>>> npm ERR! node v4.2.6 >>>>>>>>>>>>>>>>>>>>>>> npm ERR! npm v3.5.2 >>>>>>>>>>>>>>>>>>>>>>> npm ERR! code ELIFECYCLE >>>>>>>>>>>>>>>>>>>>>>> npm ERR! loris at 1.0.0 compile: `webpack` >>>>>>>>>>>>>>>>>>>>>>> npm ERR! Exit status 1 >>>>>>>>>>>>>>>>>>>>>>> npm ERR! >>>>>>>>>>>>>>>>>>>>>>> npm ERR! Failed at the loris at 1.0.0 compile script >>>>>>>>>>>>>>>>>>>>>>> 'webpack'. >>>>>>>>>>>>>>>>>>>>>>> npm ERR! Make sure you have the latest version of >>>>>>>>>>>>>>>>>>>>>>> node.js and npm installed. >>>>>>>>>>>>>>>>>>>>>>> npm ERR! If you do, this is most likely a problem >>>>>>>>>>>>>>>>>>>>>>> with the loris package, >>>>>>>>>>>>>>>>>>>>>>> npm ERR! not with npm itself. >>>>>>>>>>>>>>>>>>>>>>> npm ERR! Tell the author that this fails on your >>>>>>>>>>>>>>>>>>>>>>> system: >>>>>>>>>>>>>>>>>>>>>>> npm ERR! webpack >>>>>>>>>>>>>>>>>>>>>>> npm ERR! You can get information on how to open an >>>>>>>>>>>>>>>>>>>>>>> issue for this project with: >>>>>>>>>>>>>>>>>>>>>>> npm ERR! npm bugs loris >>>>>>>>>>>>>>>>>>>>>>> npm ERR! Or if that isn't available, you can get >>>>>>>>>>>>>>>>>>>>>>> their info via: >>>>>>>>>>>>>>>>>>>>>>> npm ERR! npm owner ls loris >>>>>>>>>>>>>>>>>>>>>>> npm ERR! There is likely additional logging output >>>>>>>>>>>>>>>>>>>>>>> above. >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> npm ERR! Please include the following file with any >>>>>>>>>>>>>>>>>>>>>>> support request: >>>>>>>>>>>>>>>>>>>>>>> npm ERR! /var/www/loris/npm-debug.log >>>>>>>>>>>>>>>>>>>>>>> Makefile:14: recipe for target 'javascript' failed >>>>>>>>>>>>>>>>>>>>>>> make: *** [javascript] Error 1 >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> Thanks, >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> ???? ???, 7 ??? 2019 ???? 5:41 ?.?., ?/? Christine >>>>>>>>>>>>>>>>>>>>>>> Rogers, Ms. ??????: >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> Thanks, have you tried all of these steps? >>>>>>>>>>>>>>>>>>>>>>>> - clear your browser cache (and refresh a few times) >>>>>>>>>>>>>>>>>>>>>>>> - delete any files in your smarty/templates_c >>>>>>>>>>>>>>>>>>>>>>>> directory (this will clear the template cache - do Not touch >>>>>>>>>>>>>>>>>>>>>>>> smarty/templates/) >>>>>>>>>>>>>>>>>>>>>>>> - run `make` (per the 21 release notes, this >>>>>>>>>>>>>>>>>>>>>>>> replaces the composer commands used in previous releases to update your >>>>>>>>>>>>>>>>>>>>>>>> dependencies) >>>>>>>>>>>>>>>>>>>>>>>> - restart apache (doesn't hurt) >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> Let us know how it goes -- let us know what >>>>>>>>>>>>>>>>>>>>>>>> difference you see after, with your logs. A >>>>>>>>>>>>>>>>>>>>>>>> lso please send us your Config path settings (see these >>>>>>>>>>>>>>>>>>>>>>>> Troubleshooting Queries >>>>>>>>>>>>>>>>>>>>>>>> ) >>>>>>>>>>>>>>>>>>>>>>>> if you're still seeing front-end issues. >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> Thanks, >>>>>>>>>>>>>>>>>>>>>>>> Christine >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> On Wed, Aug 7, 2019 at 8:02 AM Sotirios >>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos wrote: >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> lorisadmin at hbp:/var/www/loris$ sudo cat >>>>>>>>>>>>>>>>>>>>>>>>> /var/log/apache2/error.log >>>>>>>>>>>>>>>>>>>>>>>>> [Wed Aug 07 07:35:02.422501 2019] >>>>>>>>>>>>>>>>>>>>>>>>> [mpm_prefork:notice] [pid 1267] AH00163: Apache/2.4.18 (Ubuntu) >>>>>>>>>>>>>>>>>>>>>>>>> OpenSSL/1.0.2g configured -- resuming normal operations >>>>>>>>>>>>>>>>>>>>>>>>> [Wed Aug 07 07:35:02.422514 2019] [core:notice] >>>>>>>>>>>>>>>>>>>>>>>>> [pid 1267] AH00094: Command line: '/usr/sbin/apache2' >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> And as for the access.log the content are empty >>>>>>>>>>>>>>>>>>>>>>>>> lorisadmin at hbp:/var/www/loris$ sudo ls -l >>>>>>>>>>>>>>>>>>>>>>>>> /var/log/apache2/access.log >>>>>>>>>>>>>>>>>>>>>>>>> lorisadmin at hbp:/var/www/loris$ sudo ls -l >>>>>>>>>>>>>>>>>>>>>>>>> /var/log/apache2/access.log >>>>>>>>>>>>>>>>>>>>>>>>> -rw-r----- 1 root adm 0 ???? 28 14:09 >>>>>>>>>>>>>>>>>>>>>>>>> /var/log/apache2/access.log >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> Also i noticed a loris_access.log. >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> The only non-blank pages are: >>>>>>>>>>>>>>>>>>>>>>>>> mri_violations, dataquery does not exist at all, >>>>>>>>>>>>>>>>>>>>>>>>> statistics, data_team_helper, genomic_browser, configuration and >>>>>>>>>>>>>>>>>>>>>>>>> server_processes_manager/ prints "Required configuration settings for >>>>>>>>>>>>>>>>>>>>>>>>> Server Processes Manager are missing. Cannot continue." >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> Thanks, >>>>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 6 ??? 2019 ???? 10:13 ?.?., ?/? >>>>>>>>>>>>>>>>>>>>>>>>> Christine Rogers, Ms. >>>>>>>>>>>>>>>>>>>>>>>>> ??????: >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios and LORIS community -- >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> When upgrading to brand-new release 21 -- just a >>>>>>>>>>>>>>>>>>>>>>>>>> reminder to follow the release notes and run the new >>>>>>>>>>>>>>>>>>>>>>>>>> *make* file to update your dependencies (instead >>>>>>>>>>>>>>>>>>>>>>>>>> of using *composer* commands). >>>>>>>>>>>>>>>>>>>>>>>>>> We've also updated the Wiki page >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> to clarify that the release notes for each version will tell you what to >>>>>>>>>>>>>>>>>>>>>>>>>> run. >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> If your current version is not the last release >>>>>>>>>>>>>>>>>>>>>>>>>> (20.3), it's still important to upgrade to each minor release increment >>>>>>>>>>>>>>>>>>>>>>>>>> (e.g. 20.2, 20.3) before making the leap to 21.0. >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> If you're getting blank pages, post-upgrade -- >>>>>>>>>>>>>>>>>>>>>>>>>> Try clearing your cache. >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> Got questions or feedback e.g. on the Release >>>>>>>>>>>>>>>>>>>>>>>>>> Notes? please don't hesitate to let us know. >>>>>>>>>>>>>>>>>>>>>>>>>> Thanks, >>>>>>>>>>>>>>>>>>>>>>>>>> Christine >>>>>>>>>>>>>>>>>>>>>>>>>> The LORIS team >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> On Tue, Aug 6, 2019 at 10:09 AM Christine Rogers, >>>>>>>>>>>>>>>>>>>>>>>>>> Ms. wrote: >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>> Could you also let us know -- on which pages is >>>>>>>>>>>>>>>>>>>>>>>>>>> content visible, and on which pages/modules is content not visible for you? >>>>>>>>>>>>>>>>>>>>>>>>>>> Thanks, >>>>>>>>>>>>>>>>>>>>>>>>>>> Christine >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> On Tue, Aug 6, 2019 at 9:54 AM Christine Rogers, >>>>>>>>>>>>>>>>>>>>>>>>>>> Ms. wrote: >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> Thanks Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>> That's good to know. It sounds like you've >>>>>>>>>>>>>>>>>>>>>>>>>>>> checked that your /var/www/loris/project/config.xml file get populated >>>>>>>>>>>>>>>>>>>>>>>>>>>> properly. >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> Please send us the last few errors you're >>>>>>>>>>>>>>>>>>>>>>>>>>>> seeing in your apache error log file, and your config paths and we can see >>>>>>>>>>>>>>>>>>>>>>>>>>>> what's happening with your front end -- >>>>>>>>>>>>>>>>>>>>>>>>>>>> Run these Troubleshooting Queries >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> to get your config path settings, given your front end is not displaying >>>>>>>>>>>>>>>>>>>>>>>>>>>> fully. >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> The Loris-MRI repo >>>>>>>>>>>>>>>>>>>>>>>>>>>> 21 >>>>>>>>>>>>>>>>>>>>>>>>>>>> install/upgrade would then be your next steps. >>>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>>> Christine >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> On Tue, Aug 6, 2019 at 7:53 AM Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos wrote: >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> I am using a VM. What i did was: >>>>>>>>>>>>>>>>>>>>>>>>>>>>> 1) Download the files from >>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris and replace >>>>>>>>>>>>>>>>>>>>>>>>>>>>> them to my existing /vaw/www/loris folder. >>>>>>>>>>>>>>>>>>>>>>>>>>>>> 2) Execute the composer install --no-dev and >>>>>>>>>>>>>>>>>>>>>>>>>>>>> then composer dump-autoload as mentioned >>>>>>>>>>>>>>>>>>>>>>>>>>>>> here >>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris/wiki/Updating-your-LORIS >>>>>>>>>>>>>>>>>>>>>>>>>>>>> . >>>>>>>>>>>>>>>>>>>>>>>>>>>>> 3) Execute install.sh from >>>>>>>>>>>>>>>>>>>>>>>>>>>>> /var/www/loris/tools and because LORIS >>>>>>>>>>>>>>>>>>>>>>>>>>>>> already existed i moved a .config file, then re-executed the install.sh >>>>>>>>>>>>>>>>>>>>>>>>>>>>> successfully >>>>>>>>>>>>>>>>>>>>>>>>>>>>> 4 ) As for the database, i dropped the schema >>>>>>>>>>>>>>>>>>>>>>>>>>>>> and i executed the installdb.php >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 5 ??? 2019 ???? 5:22 ?.?., ?/? >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Christine Rogers, Ms. < >>>>>>>>>>>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotorios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thanks - when you re-installed did you start >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> on a fresh root path / VM or might some of your old system setting still >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> apply? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> (And if you did any steps similar to an >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> upgrade, did you follow the Upgrade steps in the Release Notes, from both >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> repos?) >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> About the TR_range column - it was recently >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> split (MRI pr339 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ) split >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> into TR_min and _max columns. Given the code was trying to query TR_range >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> which does not exist in your mri_protocol table, double-check which version >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> of the Loris repo (tables) and the Loris-MRI repo (code) you have installed >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> to ensure they match. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Christine >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> On Mon, Aug 5, 2019 at 9:06 AM Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> wrote: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I reinstalled LORIS to 21 version and now >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the content is not visible at all at most pages. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 5 ??? 2019 ???? 3:19 ?.?., ?/? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Is it easy to upgrade to Loris 21? Also the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> following fails because the line 1985 of NeuroDB/MRIProcessingUtility.pm >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> query mri_protocol which doesn't have TR_range >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris/blob/21.0-release/SQL/0000-00-00-schema.sql#L556 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> lorisadmin at hbp:/data/loris/bin/mri$ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ./batch_uploads_imageuploader -profile prod < ~/Desktop/input.txt > log.txt >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $_ in pattern >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> match (m//) at ./batch_uploads_imageuploader line 147. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> base is DCC0000_258024_V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> path is /data/incoming/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> type is .tar.gz >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> fullpath is >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/incoming/DCC0000_258024_V1.tar.gz >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DBD::mysql::st execute failed: Unknown >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> column 'TR_range' in 'where clause' at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line 1985. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DBD::mysql::st fetchrow_array failed: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> fetch() without execute() at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line 1986. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> $count_mri_protocol in numeric gt (>) at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line 1995. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DBD::mysql::st execute failed: Unknown >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> column 'TR_range' in 'field list' at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 562. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Can't exec "mail": No such file or >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> directory at /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 721. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 722. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 723. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 724. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 725. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> No Mincs inserted >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thanks, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 3 ??? 2019 ???? 1:08 ?.?., ?/? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Christine Rogers, Ms. < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> First, just a note: we've released LORIS >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 21 this week with some major new features and cleanup -- especially if you >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> are early in your setup phase, check out the Release notes for both the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> LORIS >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and Loris-MRI >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> repos. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thanks for your screenshots -- your empty >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> mri_protocol table should be at the root of these issues : >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The mri_protocol table must be populated >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in order for your scans to be registered in LORIS -- it serves as a >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> whitelist for the insertion pipeline which filters out scans that aren't >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> identified or matched to scan types in this table. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> By default, this table is populated with >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> entries for t1, t2, fMRI and DTI (Insert >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> statements for 21 release branch are here >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ) >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Feel free to restore our default records >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and broaden their parameters to match all your scan types. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> re Defaced, native, selected -- these >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> filter the scans displayed as you move to the next page (View Session), >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> instead of viewing "all types" of scans from a given session : >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - "defaced" means that a defacing >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> script >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> has masked the subject's face in the volume (for patient privacy) >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - "native" means that no >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> pre-processing has been performed on the scan (it's raw data), >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - "selected" will show only volumes >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> that have been QC'd and "selected" as the best of their type -- used to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> display only the best quality T1 image instead of all T1s acquired in a >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> session, e.g. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> re QC Comments -- >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Once you have successfully loaded scans >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> (matched to the mri_protocol table), you'll be able to use the Imaging >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Browser's View Session subpage to enter/view QC comments on each volume, or >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> for each visit. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> These are stored directly in the database, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and linked to each scan. (Table name: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> feedback_mri_comments) >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> (Visit-level QC comments are linked to the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> session.) >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> For a walkthrough of the Imaging setup - >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> please see the Imaging Setup guide >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> An old LORIS walkthrough video >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> can >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> also walk you through some of the Imaging front-end features, starting at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 8:00 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> LORIS' imaging modules have been updated >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> many times since this video, but the functionality and workflow is similar. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Let us know how it goes once you have >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> entries in your mri_protocol table - >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Christine >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> On Fri, Aug 2, 2019 at 7:58 AM Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> wrote: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Christine, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> In the candidate_list page i can see this >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> patient >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> If i press the link under PSCID i get to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> see >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and if i press the link under Scan Done >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> it redirects me to imaging_browser >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> At the mri_violations page i also see No >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> results ( neither on resolved / not resolved ). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> At the imaging_uploader i can see the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> record that failed. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> If i click on the tarchive info i get to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> see the Protocol Name which i think is the acquisition we wanted? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Also my mri_protocol table is empty. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Furthermore i would like to ask about the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> defaced, native, selected. What exactly is native and selected? And where >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> are the qc comments stored? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Finally a walkthrough would be helpful. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thanks, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 30 ???? 2019 ???? 8:29 ?.?., >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ?/? Christine Rogers, Ms. < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Glad to hear you're making progress with >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the visit labels. To follow up on your last few emails: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> a- The Wiki's Setup Guide contains Sample >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> insert statements for the Visit Windows table >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> . >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> As Cecile mentioned, the consistency of >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit label format is important: V01, v01, V1, 01 -- whichever you select >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> to use is fine; we use V01 by default across all documentation. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> b- For Password reset, there is a script >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in the tools/ directory so that a back-end administrator can reset any >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> front-end user password, including Admin. (See info on setting up / >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> resetting User passwords in the Wiki's >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Setup Guide >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ) >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> c- The minc file not being registered -- >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> due to AcquisitionProtocol unknown. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> This means the SeriesDescription >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> (Acquisition Protocol) in you Dicom header was not matched to any scan >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> listed in the mri_protocol database table. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> (In the online Loris-MRI >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Troubleshooting Guide, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> this >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> is Table 3, 2nd-last item "no MINCs >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> inserted"). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The MRI Violations module (Readme here) >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> will show >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> you the details of this mismatch -- >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Go to the module (under the Imaging >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> menu), find your scan and click the link "Could not identify scan type" -- >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in the next subpage you can compare the scan's actual parameters against >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the mri_protocol table. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> To resolve this, adjust your >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> mri_protocol table values or perhaps ensure your DICOMs are labelled >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> consistently. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Let us know if this works for you -- we >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> can also walk you through an example of non-identified scans on >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Demo.loris.ca (MRI Violations module). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Christine >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The LORIS team >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> On Tue, Jul 30, 2019 at 10:47 AM >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I hope this is sufficient as the error >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> for the visit label disappeared. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Please see the attached file. Also >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> something i found. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> lorisadmin at hbp:/data/loris/bin/mri$ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> cat /data/loris/data//logs/TarLoad-17-39-xubBdv.log >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ==> Loading file from disk >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-17-39-UyQcG2/dcc0000_258024_v1_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> --> mapping DICOM parameter for >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-17-39-UyQcG2/dcc0000_258024_v1_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ==> computing md5 hash for MINC body. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> --> md5: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 6b1202fd63e29de4c9be1cd9925888a5 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ==> verifying acquisition protocol >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Acquisition protocol is unknown >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> --> The minc file cannot be >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> registered since the AcquisitionProtocol is unknown >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 30 ???? 2019 ???? 4:58 ?.?., >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ?/? Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Ok I fixed the login problem by using >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> a known hash and by deleting the rows from the login_history i was able to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> login. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 30 ???? 2019 ???? 4:50 ?.?., >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ?/? Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> there was no visit label 01 in the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Visit_Windows table and i don't know how to insert it because the record >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> requires lots of attributes. Also the system for a reason asked me to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> update my password and now i don't remember it and my account got >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> suspended. Is there a way to reset it or set a simple password? I updated >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the password hash in the users table by using the hash from another LORIS >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> setup we had and i still couldn't login ( also the attribute password is >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> always NULL and the expiration date is 1999-01-01 for some reason ). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thanks >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 29 ???? 2019 ???? 5:21 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ?.?., ?/? Cecile Madjar < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> cecile.madjar at mcin.ca> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Can you try adding the visit label >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> v01 to the Visit_Windows table? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> However, I noticed that in a >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> previous dataset, the label was V1. Does that refer to the same visit? If >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> so, you might want to harmonize the visit labels so they are all the same >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> across datasets for a given timepoint, meaning you will need to relabel >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> scans when the visit label is different but referring to the same visit >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> label (v01 = V1 etc...). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helps, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> On Mon, Jul 29, 2019 at 10:15 AM >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Could you help me with the "Visit >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> label does not exist"? I had changed $subjectID{'createVisitLabel'} to 1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> as you had suggested but it appears that this problem hasn't been resolved >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> yet. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> lorisadmin at hbp:/data/loris/bin/mri$ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> cat /data/loris/data//logs/TarLoad-14-58-9Xog7H.log >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ==> Loading file from disk >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> --> mapping DICOM parameter for >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> --> using user-defined >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> filterParameters for >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Candidate Mismatch Error is Visit >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> label does not exist >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -> WARNING: This candidate was >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> invalid. Logging to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> MRICandidateErrors >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> table with reason Visit label does not exist >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 26 ???? 2019 ???? 3:02 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ?.?., ?/? Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Cecile, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The Center error was fixed. Still >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the insertion of mincs fails. Please see the output.txt file i attached. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Also is there something else i need to change at the paths configuration? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 25 ???? 2019 ???? 6:55 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ?.?., ?/? Cecile Madjar < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> cecile.madjar at mcin.ca> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> We are making progress! >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I have a feeling this error comes >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> from the fact that your psc table does not have the MRI_alias populated for >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the DCC site. Running the following query in the mysql database should fix >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> this: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> UPDATE psc SET MRI_alias="DCC", >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Alias="DCC" WHERE Name="Data Coordinating Center"; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Repeat the same with all your >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sites (make sure to change the Aliases between sites, they should all be >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> unique). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Let me know how it goes! >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> On Thu, Jul 25, 2019 at 11:43 AM >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Dear Cecile, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> You were right about your >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> guesses. I did the modifications you suggested, i still get the "no mincs >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> inserted" error, now i am getting the "No center found this candidate" >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> error ( how do i fix that? from what i see the .dcm files contains a >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 'Institution Name', is that the center? ), so i guess that's why the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> validation fails, but i changed the force variable of tarchiveLoader to 1, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> shouldn't it have inserted the mincs then? Also it is optional to have a >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> mail server, right? ( from what i see the mail error does not affect the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> $valid_study, so i assume we are okay with that ) >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you a lot, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 25 ???? 2019 ???? 5:48 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ?.?., ?/? Cecile Madjar < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> cecile.madjar at mcin.ca> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> From what I understand, I >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> believe you just need to update a few config settings from the frontend in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the Config module (under the Admin menu). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [image: Screen Shot 2019-07-25 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> at 10.31.35 AM.png] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Then go to the Paths section of >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the config module and update the "LORIS-MRI code" config setting to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri (my guess is that currently, it is set to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data) and click on the submit button. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [image: Screen Shot 2019-07-25 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> at 10.32.50 AM.png] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Then, go to Imaging Pipeline >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> section of the Configuration module and update the "Loris-MRI Data >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Directory" to /data/loris/data/ (my guess is that it is empty at the moment >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in your database which is why $data_dir is not defined when you run the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> tarchiveLoader step of the insertion pipeline). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [image: Screen Shot 2019-07-25 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> at 10.40.52 AM.png] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Finally, I took a look at your >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> environment file and it might be a good idea to update your PERL5LIB >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> variable to the following (it has been added to the code a few releases ago >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> as we realized this was needed for the libraries. Not sure which version of >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> LORIS-MRI you are using but it does not hurt to update this variable to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> what I suggest below): >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> export >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PERL5LIB=/data/loris/bin/mri/uploadNeuroDB:/data/loris/bin/mri/dicom-archive:$PERL5LIB >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helps. Sorry you are >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> experiencing so much trouble setting things up. We probably need to update >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> our WIKI. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> On Thu, Jul 25, 2019 at 9:48 AM >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The "Loris-MRI Data Directory" >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> should be in the environment file? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 25 ???? 2019 ???? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 12:59 ?.?., ?/? Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The scripts are located in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/. Somewhere I might have messed something up but i >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> remember following the instructions in the wiki.For example when i tried to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> execute the batch_uploads_imageuploader perl script the line >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> my $command = >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> "$bin_dir/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl " >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> was pointing to an invalid >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> path, for example: it was repeating a pattern and had LORIS instead of >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> loris ( i think the mistake was that in the wiki it suggested to use >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> $PROJECT for the name of the folder and i choosed 'loris' >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris/wiki/Imaging-Database >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ). See also the in image for the modification i did. Also i didn't find the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> section to config the $data_dir variable. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 24 ???? 2019 ???? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 6:05 ?.?., ?/? Cecile Madjar < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> cecile.madjar at mcin.ca> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> It looks like you have one >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Config setting not set (based on the first error message you got when >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> running it the first time). You need to set a value for "Loris-MRI Data >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Directory" in the Config module under the Imaging pipeline section (from >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> what I can see, it would be /data/loris/data/ for your setup). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The reason you got that >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> error message the second time is that the pipeline checks if the DICOM >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> study was already inserted in the tarchive table. Since you ran the study >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> once already, the study is inserted into the tarchive, hence the message. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> However, the pipeline did not complete as the MINC files were not created >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and inserted into the files/parameter_file table. In order to continue the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> insertion, you will then need to run the tarchiveLoader command suggested >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in the terminal during the second run: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -globLocation -profile prod >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive//2012/DCM_2012-12-05_ImagingUpload-17-43-ZUEFjb.tar >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -verbose >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Finally, I am a bit confused >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> by your setup. Where are the scripts located? In /data/loris/bin/mri or >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data? It feels like the Config setting "LORIS-MRI code" in the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Paths section was set to "/data/LORIS/data" but it should have been set to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the directory where the scripts are located (most probably >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helps, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> On Wed, Jul 24, 2019 at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 10:55 AM Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Ok first i execute this >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> command: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> "lorisadmin at hbp:/data/loris/bin/mri$ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ./batch_uploads_imageuploader -profile prod < ~/Desktop/input.txt > log.txt >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> $data_dir in concatenation (.) or string at ./batch_uploads_imageuploader >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> line 143. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> $data_dir in concatenation (.) or string at ./batch_uploads_imageuploader >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> line 143. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> $_ in pattern match (m//) at ./batch_uploads_imageuploader line 147. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> base is DCC0000_258024_V01 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> path is /data/incoming/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> type is .tar.gz >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> fullpath is >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/incoming/DCC0000_258024_V01.tar.gz >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> source >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/ImagingUpload-17-43-ZUEFjb >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> targetlocation >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> $data_dir in concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 256. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> $data_dir in concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 284. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> $data_dir in concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> tarchive_validation.pl >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> line 219. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> $data_dir in concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl line 270. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> $data_dir in concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 711. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Can't exec "mail": No such >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> file or directory at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 721. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> filehandle MAIL at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 722. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> filehandle MAIL at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 723. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> $data_dir in concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 724. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> filehandle MAIL at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 724. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> filehandle MAIL at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 725. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> $data_dir in concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 735. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> No Mincs inserted >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The tarchiveLoader >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> insertion script has failed. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Running now the following >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> command: /data/loris/data/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -profile prod -upload_id 3 /data/incoming/DCC0000_258024_V01.tar.gz >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -verbose" >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I inserted the VisitLabel, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> but still the Mincs are not inserted and i am getting this error >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> "lorisadmin at hbp:/data/loris/bin/mri$ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -profile prod -upload_id 3 /data/incoming/DCC0000_258024_V01.tar.gz -verbose >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> find -path >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> \/tmp\/ImagingUpload\-17\-45\-5MsWEd -name '__MACOSX' -delete >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Spool message is: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The Scan for the uploadID 3 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> has already been run with tarchiveID: 7. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> To continue with the rest >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> of the insertion pipeline, please run tarchiveLoader from a terminal as >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> follows: /data/LORIS/data//uploadNeuroDB/tarchiveLoader -globLocation >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -profile prod >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive//2012/DCM_2012-12-05_ImagingUpload-17-43-ZUEFjb.tar >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -verbose" >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Which files should i >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete? I thought that deleting the files from the tarchive was enough. And >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> i executed the last proposed command to continue to rest of the insertion >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> pipeline ( check the image ). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 24 ???? 2019 ???? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 5:05 ?.?., ?/? Cecile Madjar < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> cecile.madjar at mcin.ca> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sorry I was not clear >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> before. Every visits of candidates are created in the session table with >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> one entry per CandID/VisitLabel. So if the imaging pipeline created visits >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in the session table (that are not attached to instruments) and you want to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> clean your database completely, you can delete entries in that table as >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> well. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Regarding your point 2, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the imaging pipeline can create the visit in the session table as long as >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the visit label is present in the Visit_Windows table (which means the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit label stored in the PatientName is a valid visit label). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> However, in your prod >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> file, if the variable $subjectID{'createVisitLabel'} is set to 1 for >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> candidates, the visit label should be created in the Visit_Windows table I >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> believe. Here is the line >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> of the prod file you would need to change >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> . >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> In general, we prefer >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> populating the Visit_Windows table and set the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> $subjectID{'createVisitLabel'} to 0 for candidate data to avoid insertion >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> of badly labelled MRI data that are complex to relabel. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Finally, regarding the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> candidate creation, if you execute the following steps, the pipeline should >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> be able to create candidates: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - set in the Imaging >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Pipeline section of the config module the config setting "Upload creation >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> of candidates" to Yes >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - manually transfer the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> scans to the LORIS server instead of uploading it via the imaging browser >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - run >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> batch_imaging_upload.pl >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> as you did until now. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helps! >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> On Wed, Jul 24, 2019 at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 8:47 AM Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> wrote: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> About my second question >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> i replaced the name of the patient in the .dcm files and now i am getting >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> an error that the visit label does not exist. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I thought it was supposed >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> to be automatically created. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> "Done adding archive info >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> into database >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -globLocation -profile prod >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive//DCM_2012-12-05_ImagingUpload-15-42-yUwQQV.tar >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -verbose >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> md5sum >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive/DCM_2012-12-05_ImagingUpload-15-42-yUwQQV.tar >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> candidate id 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> => No Visit labelVisit >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> label does not exist >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Set centerID = 1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Number of MINC files that >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> will be considered for inserting into the database: 1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> log dir is /logs and log >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> file is /logs/TarLoad-15-42-L6pocU.log >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> candidate id 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> => No Visit label >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Cleaning up temp files: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> rm -rf /tmp/TarLoad-15-42-J2rQms/ImagingUpload-15-42-yUwQQV*" >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 24 ???? 2019 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? 3:38 ?.?., ?/? Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 1) What are the records >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in the session table? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 2) I tried to upload a >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> non-phantom file like this >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> input_file.txt: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/incoming/DCC0000_258024_V1.tar.gz >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> N DCC0000_258024_V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Terminal: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ./batch_uploads_imageuploader >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -profile prod < ~/Desktop/input.txt > log.txt >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and i get the following >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> error in the log.txt file >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> "Running now the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> following command: /data/loris/data/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -profile prod -upload_id 7 /data/incoming/DCC0000_258024_V1.tar.gz -verbose >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> find -path >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> \/tmp\/ImagingUpload\-14\-56\-FeLCB4 -name '__MACOSX' -delete >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Spool message is: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The PatientName read >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> from the DICOM header does not start with DCC0000_258024_V1 from the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> mri_upload table >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> " >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and the spool message is >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> repeated for each .dcm file. Should i preprocess every .dcm file and change >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the PatientName to "DCC0000_258024_V1"? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 3) As far as it concerns >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the candidate profile i have to create a new one each time before i try to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> upload a file? Is there already a way to create a candidate profile and get >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the DCCID and PSCID without the user interface? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 18 ???? 2019 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? 5:00 ?.?., ?/? Cecile Madjar < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> cecile.madjar at mcin.ca> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> See answers to your >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> questions below. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> About the 1st case we >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> had a dicom with a blank studyUID, maybe someone accidentally removed it. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> That is strange. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Something must have been done to the DICOM files. I have never seen a study >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> with no StudyUID out of the scanner. Usually, you need to manually erase it >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> with some tool. However, DICOMs never cease to surprise me... >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Some other questions: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 1) What are the steps >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> to remove all of my patients and uploads?: because i want to try to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> reupload all the testing dicoms we had with a clean database. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Release 21.0 of >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> LORIS-MRI will offer a script to remove all the entries and files specific >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> to an upload. However, this release is not yet out. Hopefully in the next >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> few weeks. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> In the meantime, since >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> your case is particular and that you just want to start with a clean >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> database, the following deletes should work (hopefully I won't forget any >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> tables): >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> mri_violations_log; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> mri_protocol_violated_scans; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> MRICandidateErrors; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> parameter_file; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> files_qcstatus; # (if you played with the QC part of the imaging browser >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> for testing) >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> feedback_mri_comments; # (if you played with the QC part of the imaging >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> browser for testing) >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> tarchive_series; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> tarchive_files; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from mri_upload; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from tarchive; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from mri_scanner; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from candidate >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> where PSCID="scanner"; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I don't know if you >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> want to also delete entries in the session and candidate table too? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 2) We do not need to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> create the profile of a patient ( are the patients stored in the candidate >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> table? because i can't see the ghosts ), because will it automatically be >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> created when importing a dicom? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I am not sure I >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> understand fully this question. All candidates are stored in the candidate >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> table. The phantom scans however are attached to a scanner candidate >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> depending on where the scan happened. It is a bit of a weird concept that >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> we have to redesign eventually but never got a chance to get to it. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hopefully this answered >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> your question, otherwise, don't hesitate to let me know. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 3) What is the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> difference between uploading a dicom as phantom instead of importing as >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCCID_DCCID_VisitLabel? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> When you upload the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> scan as PSCID_DCCID_VisitLabel, there is a check that makes sure the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> candidate IDs and visit label are valid at the time of upload. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> When you upload a scan >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> as phantom, it expects that the DICOM field PatientName and uploaded >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> filename contains the string "phantom". We enforced this behaviour on the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> imaging uploader side in recent releases but I can't remember which one. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Probably the upcoming 21.0 release. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> All those verifications >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> might seem cumbersome but they are here to ensure that the files inserted >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> are all valid and labelled properly as it is a bit messy to have to delete >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> files that were wrongly labelled. At least, the delete script present in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> release 21.0 will make this process easier but it is still good practice to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> verify those things. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> With pleasure. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hopefully the answers to your questions will be helpful. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PS: loris-dev mailing >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> list: you will find the initial answer I gave Sotirios below. I forgot to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> cc the loris-dev in my earlier reply... >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 16 ???? 2019 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? 12:02 ?.?., ?/? Cecile Madjar < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> cecile.madjar at mcin.ca> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Dear Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you for >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> reaching out. Since your email was already organized in points, I will >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> reply directly below your questions below. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 1) What do we do when >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the StudyUID is blank on the header? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/minor/docs/AppendixA-Troubleshooting_guideline.md >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> There solution provided at the table 3 does not guide us how to find the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> information ( is possible ). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The StudyUID is the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> field used in our pipeline at the moment to check whether a DICOM study was >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> already inserted into LORIS with that same StudyUID since it is supposed to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> be unique for every single study. Currently, we do not support insertion of >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DICOM studies if they do not have a StudyUID associated with them. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Is there a specific >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> reason why the StudyUID is blank in the DICOM headers in your DICOM files? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Did they go through some processes before upload to LORIS? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 2) When i am about to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> upload a non-phanton case i need a 'Visit Label'. Is there already a script >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> that can create a new visit label for a specific Candidate, so i can >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> provide it as input afterwards to the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> batch_uploads_imageuploader ( See option 5.1.3 https://github.com/aces/Loris-MRI/blob/minor/docs/05-PipelineLaunchOptions.md ) >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I am not sure if the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> front-end allows for it but if you use batch_uploads_imageuploader, the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> insertion scripts could create the visit label for you. However, it does >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> need to be included in the patient name in order for the script to know >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> which label it should use. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> For example: you >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> upload V02 for MTL0123 (DCCID: 456789) but V02 was not yet created for >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> MTL0123; the insertion scripts will create a V02 visit for MTL0123 if the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PatientName field for the dataset is MTL0123_456789_V02 with Stage marked >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> as "Not Started". >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> However, *note that >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> for the script to create the visit for the candidate, you have to make sure >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> that all the visit label of your projects were inserted in the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Visit_Windows table* >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> (otherwise, the visit will never be created as they were not specified as >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> being part of the list of visit label to expect). So in the example above, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> you should have one row in Visit_Windows with Visit_label="V02" set. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 3) Section 4.3 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/minor/docs/04-Scripts.md >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> What do we do when the folder contains multiple mnc files? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> This is a case by >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> case. Most of the time, the MINC files that failed insertion into the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> imaging browser end up in the MRI violation module where you can see what >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> went wrong with the acquisitions not inserted. If you notice that the MINC >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> file should be inserted as a specific protocol, you can force the insertion >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> as explained in section 4.3. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> In your case, I have >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> a feeling that you want to be able to insert MINC files that did not go >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> through the whole pipeline insertion (DICOM archival, then dcm2mnc, then >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> protocol identification, then insertion...). In theory, you could call >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl on >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> any MINC file, provided you have at least the following information: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - path to the MINC >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> file >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - uploadID associated >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> with the MINC files or DICOM archive path from which those MINC files were >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> created from >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Then the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> script will do the subject information and protocol validation etc... >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> If all the MINC files >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> come from the same uploadID or TarchiveID, then you could run a loop in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> bash calling the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> script like this for files deriving from uploadID=1: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ls >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /path/to/mnc/folder/* | while read f; do >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -profile prod -uploadID 1 -mincPath $f; done >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helped! >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> McGill Centre for Integrative >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Neuroscience | MCIN.ca >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> | MCIN.ca >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> MCIN.ca >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>>>>>>>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | >>>>>>>>>>>>>>>>>>>>>>>>>>>> MCIN.ca >>>>>>>>>>>>>>>>>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>>>>>>>>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>>>>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>>>>>>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | >>>>>>>>>>>>>>>>>>>>>>>>>>> MCIN.ca >>>>>>>>>>>>>>>>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>>>>>>>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>>>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>>>>>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | >>>>>>>>>>>>>>>>>>>>>>>>>> MCIN.ca >>>>>>>>>>>>>>>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>>>>>>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>>>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>>>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>>>>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>>> Shen Wang >>>>>>>>>>>>>>>> Loris Developer >>>>>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>>>>> McGill University >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> -- >>>>>>>>>>>> Shen Wang >>>>>>>>>>>> Loris Developer >>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>> McGill University >>>>>>>>>>>> >>>>>>>>>>>> -- >>>>>>>>>>> Shen Wang >>>>>>>>>>> Loris Developer >>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>> McGill University >>>>>>>>>>> >>>>>>>>>>> _______________________________________________ >>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> -- >>>>>>>>>> >>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>> Montreal Neurological Institute >>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>> >>>>>>>>> >>>>>>> >>>>>>> -- >>>>>>> Shen Wang >>>>>>> Loris Developer >>>>>>> Montreal Neurological Institute >>>>>>> McGill University >>>>>>> >>>>>>> >>>>> >>>>> -- >>>>> Shen Wang >>>>> Loris Developer >>>>> Montreal Neurological Institute >>>>> McGill University >>>>> >>>>> >>> >>> -- >>> Shen Wang >>> Loris Developer >>> Montreal Neurological Institute >>> McGill University >>> >>> _______________________________________________ >> Loris-dev mailing list >> Loris-dev at bic.mni.mcgill.ca >> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >> > -- Shen Wang Loris Developer Montreal Neurological Institute McGill University -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: ???? 2019-08-13 19.21.15.png Type: image/png Size: 508603 bytes Desc: not available URL: From christine.rogers at mcgill.ca Tue Aug 20 16:01:08 2019 From: christine.rogers at mcgill.ca (Christine Rogers, Ms.) Date: Tue, 20 Aug 2019 20:01:08 +0000 Subject: [Loris-dev] LORIS installation inquiry -- regarding In-Reply-To: References: Message-ID: Hi Dr. Lee, Could you kindly clarify -- has this helped, and how can we help resolve your problem? Also, just to let you know, for the 21.0.0 release, running the install.sh script with sudo will cause errors. We are working on clarifying the messaging of the install script for the next bugfix release. Best, Christine On Tue, Aug 13, 2019 at 8:43 PM Shen Wang > wrote: Hi Yubu, I saw you error log, it is very helpful. It seems like you didn't create the config.xml in you project folder successfully. You need to run this [sudo ./install.sh ] in the tools folder. ex. [install at install-dev:/var/www/Loris/tools$ sudo ./install.sh] Then check if project/confilg.xml file exists. if it can't create the project folder and config.xml, it is definitely your ubuntu permission issue. Please do it manually in your loris folder. sudo chgrp apache project sudo chmod 770 project Then you need to do [sudo ./install.sh ] , then load the installdb.php again. Please let me know if you have any questions. Regards. Shen On Tue, 13 Aug 2019 at 20:16, ??? > wrote: Dear Shen, 1 Which version of Loris are you using? We are using Loris-21.0.0 2 Mysql version? The output of mysql -V is mysql Ver 14.14 Distrib 5.7.27, for Linux (x86_64) using EditLine wrapper 3 [sudo tail -f /var/log/apache2/loris-error.log] Please running this in the backend, then try loading the installdb.php again, with a different database name. Please send us the error message. cat loris-error.log does not show any content however loris-error.log.1 shows the following: yubu at data:/var/log/apache2$ cat loris-error.log.1 [Tue Aug 13 09:12:41.214417 2019] [php7:error] [pid 17930] [client ::1:58960] PHP Fatal error: Uncaught ConfigurationException: Config file config.xml does not exist in the defined locations. in /var/www/loris/php/libraries/NDB_Config.class.inc:139\nStack trace:\n#0 /var/www/loris/php/libraries/NDB_Config.class.inc(66): NDB_Config->configFilePath()\n#1 /var/www/loris/php/libraries/NDB_Factory.class.inc(118): NDB_Config::singleton(NULL)\n#2 /var/www/loris/php/libraries/NDB_Client.class.inc(54): NDB_Factory->config(NULL)\n#3 /var/www/loris/htdocs/index.php(27): NDB_Client->initialize()\n#4 {main}\n thrown in /var/www/loris/php/libraries/NDB_Config.class.inc on line 139, referer: http://localhost/installdb.php [Tue Aug 13 09:14:53.843582 2019] [php7:notice] [pid 17932] [client ::1:58992] SQLSTATE[HY000] [1698] Access denied for user 'root'@'localhost', referer: http://localhost/installdb.php [Tue Aug 13 09:14:53.843708 2019] [php7:error] [pid 17932] [client ::1:58992] PHP Fatal error: Uncaught Error: Call to a member function exec() on null in /var/www/loris/php/installer/Installer.class.inc:374\nStack trace:\n#0 /var/www/loris/php/installer/Installer.class.inc(235): LORIS\\Installer\\Installer->_sourceSchemaFile(Object(LORIS\\Installer\\Database), '00-schema.sql')\n#1 /var/www/loris/htdocs/installdb.php(109): LORIS\\Installer\\Installer->sourceSchema(Array)\n#2 {main}\n thrown in /var/www/loris/php/installer/Installer.class.inc on line 374, referer: http://localhost/installdb.php Further, we accidentally deleted the loris-error.log and loris-error.log.1 files. Is there a way to generate them again? Thanks for the prompt reply Yours Sincerely, ====================================================== Yubu Lee, Ph.D. Research Professor, Center for Neuroscience Imaging Research, Institute for Basic Science #86332, N Center, SungKyunKwan University 2066, Seobu-Ro, Jangan-gu, Suwon, Gyeonggi-do, 16419, Korea E-mail: basilia1123 at gmail.com Tel: +82-31-299-4411 Fax: +82-31-299-4506 ====================================================== 2019? 8? 13? (?) ?? 10:21, Shen Wang >?? ??: Hi Yubu, We need more information to debug this issue. 1 Which version of Loris are you using? 2 Mysql version? 3 [sudo tail -f /var/log/apache2/loris-error.log] Please running this in the backend, then try loading the installdb.php again, with a different database name. Please send us the error message. Your Sincerely, Shen On Mon, 12 Aug 2019 at 22:27, ??? > wrote: Dear Sir/Madam, We are currently trying to install LORIS on Ubuntu 18.04 platform following the steps from https://github.com/aces/Loris/wiki/Installing-Loris-in-Depth 1. Following the above link, we installed the prerequisites mentioned in https://github.com/aces/Loris/wiki/Installing-Loris-in-Depth#getting-prerequisites, which are all verified to be installed normally. 2. We ensured that mySQL credentials are set up properly (as pasted below) mysql> select host, user, authentication_string from user -> ; +-----------+------------------+-------------------------------------------+ | host | user | authentication_string | +-----------+------------------+-------------------------------------------+ | localhost | root | | | localhost | mysql.session | *THISISNOTAVALIDPASSWORDTHATCANBEUSEDHERE | | localhost | mysql.sys | *THISISNOTAVALIDPASSWORDTHATCANBEUSEDHERE | | localhost | debian-sys-maint | *C9BF7C6E59BFF0FA879E6650D174264C9EE87F25 | +-----------+------------------+-------------------------------------------+ 4 rows in set (0.00 sec) mysql> update user set authentication_string=password('yubu') where user='root'; Query OK, 1 row affected, 1 warning (0.00 sec) Rows matched: 1 Changed: 1 Warnings: 1 mysql> flush privileges; Query OK, 0 rows affected (0.01 sec) mysql> select host, user, authentication_string from user -> ; +-----------+------------------+-------------------------------------------+ | host | user | authentication_string | +-----------+------------------+-------------------------------------------+ | localhost | root | *E311E16EECE7E8900098CFEB4103D5266A343F5F | | localhost | mysql.session | *THISISNOTAVALIDPASSWORDTHATCANBEUSEDHERE | | localhost | mysql.sys | *THISISNOTAVALIDPASSWORDTHATCANBEUSEDHERE | | localhost | debian-sys-maint | *C9BF7C6E59BFF0FA879E6650D174264C9EE87F25 | +-----------+------------------+-------------------------------------------+ 4 rows in set (0.00 sec) 3. We then opened http://localhost/installdb.php and have gotten the login page for LORIS installation and typed the credentials as follows: [Screenshot from 2019-08-13 09-14-51.png] 4. Once we submitted the page we obtained error as follows [Screenshot from 2019-08-13 09-14-56.png] We really do not know how to proceed further from this point onward. Kindly let us know how to proceed further in order to get the LORIS installed. Thank you. Your Sincerely, ====================================================== Yubu Lee, Ph.D. Research Professor, Center for Neuroscience Imaging Research, Institute for Basic Science #86332, N Center, SungKyunKwan University 2066, Seobu-Ro, Jangan-gu, Suwon, Gyeonggi-do, 16419, Korea E-mail: basilia1123 at gmail.com Tel: +82-31-299-4411 Fax: +82-31-299-4506 ====================================================== _______________________________________________ Loris-dev mailing list Loris-dev at bic.mni.mcgill.ca https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev -- Shen Wang Loris Developer Montreal Neurological Institute McGill University -- Shen Wang Loris Developer Montreal Neurological Institute McGill University _______________________________________________ Loris-dev mailing list Loris-dev at bic.mni.mcgill.ca https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev -- christine.rogers at mcgill.ca McGill Centre for Integrative Neuroscience | MCIN.ca Montreal Neurological Institute McGill University | Montreal | Canada -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Screenshot from 2019-08-13 09-14-51.png Type: image/png Size: 283124 bytes Desc: Screenshot from 2019-08-13 09-14-51.png URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Screenshot from 2019-08-13 09-14-56.png Type: image/png Size: 124916 bytes Desc: Screenshot from 2019-08-13 09-14-56.png URL: From sotirisnik at gmail.com Tue Aug 27 14:04:05 2019 From: sotirisnik at gmail.com (Sotirios Nikoloutsopoulos) Date: Tue, 27 Aug 2019 21:04:05 +0300 Subject: [Loris-dev] Import mri - scripts In-Reply-To: References: <65ad2b70c3084ffdb1e4a9dcdad948cd@YTOPR0101MB1803.CANPRD01.PROD.OUTLOOK.COM> Message-ID: Hi, i still haven't resolved the previous issue. Also i tried to install Loris to a new virtual machine and when i execute install.sh i get the following error lorisadmin at loris-VirtualBox:/var/www/loris/tools$ ./install.sh LORIS Installation Script starting at 2019-08-27T21:00:42 The log for this session will be stored in file /var/www/loris/tools/logs/install-2019-08-27T21:00:42.log --------------------------------------------------------------------- LORIS Installation Script --------------------------------------------------------------------- PHP appears to be installed. PHP Composer appears to be installed. This install script will ask you to provide inputs for different steps. Please ensure you have the following information ready (if applicable): 1) Your project directory name. (Will be used to modify the paths for Imaging data in the generated config.xml file for LORIS, and may also be used to automatically create/install apache config files.) If unsure, a default like "LORIS" should be acceptable. Please also consult the Loris WIKI on GitHub for more information on these Install Script input parameters. Ready to continue? [yn] y ./install.sh: line 132: projectname: unbound variable Thanks ???? ???, 6 ??? 2019 ???? 5:09 ?.?., ?/? Christine Rogers, Ms. < christine.rogers at mcgill.ca> ??????: > Hi Sotirios, > Could you also let us know -- on which pages is content visible, and on > which pages/modules is content not visible for you? > Thanks, > Christine > > On Tue, Aug 6, 2019 at 9:54 AM Christine Rogers, Ms. < > christine.rogers at mcgill.ca> wrote: > >> Thanks Sotirios, >> That's good to know. It sounds like you've checked that your >> /var/www/loris/project/config.xml file get populated properly. >> >> Please send us the last few errors you're seeing in your apache error log >> file, and your config paths and we can see what's happening with your front >> end -- >> Run these Troubleshooting Queries >> >> to get your config path settings, given your front end is not displaying >> fully. >> >> The Loris-MRI repo >> 21 >> install/upgrade would then be your next steps. >> Best, >> Christine >> >> On Tue, Aug 6, 2019 at 7:53 AM Sotirios Nikoloutsopoulos < >> sotirisnik at gmail.com> wrote: >> >>> I am using a VM. What i did was: >>> 1) Download the files from https://github.com/aces/Loris and replace >>> them to my existing /vaw/www/loris folder. >>> 2) Execute the composer install --no-dev and then composer dump-autoload >>> as mentioned here https://github.com/aces/Loris/wiki/Updating-your-LORIS >>> . >>> 3) Execute install.sh from /var/www/loris/tools and because LORIS >>> already existed i moved a .config file, then re-executed the install.sh >>> successfully >>> 4 ) As for the database, i dropped the schema and i executed the >>> installdb.php >>> >>> ???? ???, 5 ??? 2019 ???? 5:22 ?.?., ?/? Christine Rogers, Ms. < >>> christine.rogers at mcgill.ca> ??????: >>> >>>> Hi Sotorios, >>>> >>>> Thanks - when you re-installed did you start on a fresh root path / VM >>>> or might some of your old system setting still apply? >>>> (And if you did any steps similar to an upgrade, did you follow the >>>> Upgrade steps in the Release Notes, from both repos?) >>>> >>>> About the TR_range column - it was recently split (MRI pr339 >>>> ) split into TR_min and >>>> _max columns. Given the code was trying to query TR_range which does not >>>> exist in your mri_protocol table, double-check which version of the Loris >>>> repo (tables) and the Loris-MRI repo (code) you have installed to ensure >>>> they match. >>>> >>>> Christine >>>> >>>> >>>> On Mon, Aug 5, 2019 at 9:06 AM Sotirios Nikoloutsopoulos < >>>> sotirisnik at gmail.com> wrote: >>>> >>>>> I reinstalled LORIS to 21 version and now the content is not visible >>>>> at all at most pages. >>>>> >>>>> [image: image.png] >>>>> >>>>> ???? ???, 5 ??? 2019 ???? 3:19 ?.?., ?/? Sotirios Nikoloutsopoulos < >>>>> sotirisnik at gmail.com> ??????: >>>>> >>>>>> Hi, >>>>>> >>>>>> Is it easy to upgrade to Loris 21? Also the following fails because >>>>>> the line 1985 of NeuroDB/MRIProcessingUtility.pm query mri_protocol which >>>>>> doesn't have TR_range >>>>>> https://github.com/aces/Loris/blob/21.0-release/SQL/0000-00-00-schema.sql#L556 >>>>>> >>>>>> [image: image.png] >>>>>> >>>>>> lorisadmin at hbp:/data/loris/bin/mri$ ./batch_uploads_imageuploader >>>>>> -profile prod < ~/Desktop/input.txt > log.txt >>>>>> Use of uninitialized value $_ in pattern match (m//) at >>>>>> ./batch_uploads_imageuploader line 147. >>>>>> base is DCC0000_258024_V1 >>>>>> path is /data/incoming/ >>>>>> type is .tar.gz >>>>>> fullpath is /data/incoming/DCC0000_258024_V1.tar.gz >>>>>> DBD::mysql::st execute failed: Unknown column 'TR_range' in 'where >>>>>> clause' at >>>>>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line 1985. >>>>>> DBD::mysql::st fetchrow_array failed: fetch() without execute() at >>>>>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line 1986. >>>>>> Use of uninitialized value $count_mri_protocol in numeric gt (>) at >>>>>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line 1995. >>>>>> DBD::mysql::st execute failed: Unknown column 'TR_range' in 'field >>>>>> list' at /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 562. >>>>>> Can't exec "mail": No such file or directory at >>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 721. >>>>>> print() on closed filehandle MAIL at >>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 722. >>>>>> print() on closed filehandle MAIL at >>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 723. >>>>>> print() on closed filehandle MAIL at >>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 724. >>>>>> print() on closed filehandle MAIL at >>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 725. >>>>>> >>>>>> No Mincs inserted >>>>>> >>>>>> Thanks, >>>>>> >>>>>> Sotirios >>>>>> >>>>>> ???? ???, 3 ??? 2019 ???? 1:08 ?.?., ?/? Christine Rogers, Ms. < >>>>>> christine.rogers at mcgill.ca> ??????: >>>>>> >>>>>>> Hi Sotirios, >>>>>>> >>>>>>> First, just a note: we've released LORIS 21 this week with some >>>>>>> major new features and cleanup -- especially if you are early in your setup >>>>>>> phase, check out the Release notes for both the LORIS >>>>>>> and Loris-MRI >>>>>>> repos. >>>>>>> >>>>>>> Thanks for your screenshots -- your empty mri_protocol table should >>>>>>> be at the root of these issues : >>>>>>> >>>>>>> The mri_protocol table must be populated >>>>>>> >>>>>>> in order for your scans to be registered in LORIS -- it serves as a >>>>>>> whitelist for the insertion pipeline which filters out scans that aren't >>>>>>> identified or matched to scan types in this table. >>>>>>> >>>>>>> By default, this table is populated with entries for t1, t2, fMRI >>>>>>> and DTI (Insert statements for 21 release branch are here >>>>>>> >>>>>>> ) >>>>>>> Feel free to restore our default records and broaden their >>>>>>> parameters to match all your scan types. >>>>>>> >>>>>>> re Defaced, native, selected -- these filter the scans displayed as >>>>>>> you move to the next page (View Session), instead of viewing "all types" of >>>>>>> scans from a given session : >>>>>>> >>>>>>> - "defaced" means that a defacing script >>>>>>> >>>>>>> has masked the subject's face in the volume (for patient privacy) >>>>>>> - "native" means that no pre-processing has been performed on >>>>>>> the scan (it's raw data), >>>>>>> - "selected" will show only volumes that have been QC'd and >>>>>>> "selected" as the best of their type -- used to display only the best >>>>>>> quality T1 image instead of all T1s acquired in a session, e.g. >>>>>>> >>>>>>> re QC Comments -- >>>>>>> Once you have successfully loaded scans (matched to the mri_protocol >>>>>>> table), you'll be able to use the Imaging Browser's View Session subpage to >>>>>>> enter/view QC comments on each volume, or for each visit. >>>>>>> These are stored directly in the database, and linked to each scan. >>>>>>> (Table name: feedback_mri_comments) >>>>>>> (Visit-level QC comments are linked to the session.) >>>>>>> >>>>>>> For a walkthrough of the Imaging setup - please see the Imaging >>>>>>> Setup guide >>>>>>> >>>>>>> - >>>>>>> >>>>>>> An old LORIS walkthrough video >>>>>>> can also walk you >>>>>>> through some of the Imaging front-end features, starting at 8:00 >>>>>>> LORIS' imaging modules have been updated many times since this >>>>>>> video, but the functionality and workflow is similar. >>>>>>> >>>>>>> Let us know how it goes once you have entries in your mri_protocol >>>>>>> table - >>>>>>> Best, >>>>>>> Christine >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> On Fri, Aug 2, 2019 at 7:58 AM Sotirios Nikoloutsopoulos < >>>>>>> sotirisnik at gmail.com> wrote: >>>>>>> >>>>>>>> Hi Christine, >>>>>>>> >>>>>>>> In the candidate_list page i can see this patient >>>>>>>> >>>>>>>> [image: image.png] >>>>>>>> >>>>>>>> If i press the link under PSCID i get to see >>>>>>>> [image: image.png] >>>>>>>> >>>>>>>> and if i press the link under Scan Done it redirects me to >>>>>>>> imaging_browser >>>>>>>> >>>>>>>> [image: image.png] >>>>>>>> >>>>>>>> At the mri_violations page i also see No results ( neither on >>>>>>>> resolved / not resolved ). >>>>>>>> >>>>>>>> At the imaging_uploader i can see the record that failed. >>>>>>>> >>>>>>>> [image: image.png] >>>>>>>> >>>>>>>> If i click on the tarchive info i get to see the Protocol Name >>>>>>>> which i think is the acquisition we wanted? >>>>>>>> [image: image.png] >>>>>>>> >>>>>>>> Also my mri_protocol table is empty. >>>>>>>> >>>>>>>> Furthermore i would like to ask about the defaced, native, >>>>>>>> selected. What exactly is native and selected? And where are the qc >>>>>>>> comments stored? >>>>>>>> >>>>>>>> [image: image.png] >>>>>>>> >>>>>>>> Finally a walkthrough would be helpful. >>>>>>>> >>>>>>>> Thanks, >>>>>>>> >>>>>>>> Sotirios >>>>>>>> >>>>>>>> ???? ???, 30 ???? 2019 ???? 8:29 ?.?., ?/? Christine Rogers, Ms. < >>>>>>>> christine.rogers at mcgill.ca> ??????: >>>>>>>> >>>>>>>>> Hi Sotirios, >>>>>>>>> Glad to hear you're making progress with the visit labels. To >>>>>>>>> follow up on your last few emails: >>>>>>>>> >>>>>>>>> a- The Wiki's Setup Guide contains Sample insert statements for >>>>>>>>> the Visit Windows table >>>>>>>>> >>>>>>>>> . >>>>>>>>> >>>>>>>>> As Cecile mentioned, the consistency of visit label format is >>>>>>>>> important: V01, v01, V1, 01 -- whichever you select to use is fine; we use >>>>>>>>> V01 by default across all documentation. >>>>>>>>> >>>>>>>>> b- For Password reset, there is a script in the tools/ directory >>>>>>>>> so that a back-end administrator can reset any front-end user password, >>>>>>>>> including Admin. (See info on setting up / resetting User passwords in the Wiki's >>>>>>>>> Setup Guide >>>>>>>>> >>>>>>>>> ) >>>>>>>>> >>>>>>>>> c- The minc file not being registered -- due to >>>>>>>>> AcquisitionProtocol unknown. >>>>>>>>> This means the SeriesDescription (Acquisition Protocol) in you >>>>>>>>> Dicom header was not matched to any scan listed in the mri_protocol >>>>>>>>> database table. >>>>>>>>> (In the online Loris-MRI Troubleshooting Guide, >>>>>>>>> this >>>>>>>>> is Table 3, 2nd-last item "no MINCs inserted"). >>>>>>>>> >>>>>>>>> The MRI Violations module (Readme here) >>>>>>>>> will show >>>>>>>>> you the details of this mismatch -- >>>>>>>>> Go to the module (under the Imaging menu), find your scan and >>>>>>>>> click the link "Could not identify scan type" -- in the next subpage you >>>>>>>>> can compare the scan's actual parameters against the mri_protocol table. >>>>>>>>> >>>>>>>>> To resolve this, adjust your mri_protocol table values or perhaps >>>>>>>>> ensure your DICOMs are labelled consistently. >>>>>>>>> >>>>>>>>> Let us know if this works for you -- we can also walk you through >>>>>>>>> an example of non-identified scans on Demo.loris.ca (MRI >>>>>>>>> Violations module). >>>>>>>>> >>>>>>>>> Best, >>>>>>>>> Christine >>>>>>>>> >>>>>>>>> The LORIS team >>>>>>>>> >>>>>>>>> >>>>>>>>> On Tue, Jul 30, 2019 at 10:47 AM Sotirios Nikoloutsopoulos < >>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>> >>>>>>>>>> I hope this is sufficient as the error for the visit label >>>>>>>>>> disappeared. >>>>>>>>>> [image: image.png] >>>>>>>>>> >>>>>>>>>> Please see the attached file. Also something i found. >>>>>>>>>> >>>>>>>>>> lorisadmin at hbp:/data/loris/bin/mri$ cat >>>>>>>>>> /data/loris/data//logs/TarLoad-17-39-xubBdv.log >>>>>>>>>> >>>>>>>>>> ==> Loading file from disk >>>>>>>>>> /tmp/TarLoad-17-39-UyQcG2/dcc0000_258024_v1_20121205_102108_501e1_mri.mnc >>>>>>>>>> >>>>>>>>>> --> mapping DICOM parameter for >>>>>>>>>> /tmp/TarLoad-17-39-UyQcG2/dcc0000_258024_v1_20121205_102108_501e1_mri.mnc >>>>>>>>>> >>>>>>>>>> ==> computing md5 hash for MINC body. >>>>>>>>>> >>>>>>>>>> --> md5: 6b1202fd63e29de4c9be1cd9925888a5 >>>>>>>>>> >>>>>>>>>> ==> verifying acquisition protocol >>>>>>>>>> >>>>>>>>>> Acquisition protocol is unknown >>>>>>>>>> >>>>>>>>>> --> The minc file cannot be registered since the >>>>>>>>>> AcquisitionProtocol is unknown >>>>>>>>>> >>>>>>>>>> ???? ???, 30 ???? 2019 ???? 4:58 ?.?., ?/? Sotirios >>>>>>>>>> Nikoloutsopoulos ??????: >>>>>>>>>> >>>>>>>>>>> Ok I fixed the login problem by using a known hash and by >>>>>>>>>>> deleting the rows from the login_history i was able to login. >>>>>>>>>>> >>>>>>>>>>> ???? ???, 30 ???? 2019 ???? 4:50 ?.?., ?/? Sotirios >>>>>>>>>>> Nikoloutsopoulos ??????: >>>>>>>>>>> >>>>>>>>>>>> Hi, >>>>>>>>>>>> >>>>>>>>>>>> there was no visit label 01 in the Visit_Windows table and i >>>>>>>>>>>> don't know how to insert it because the record requires lots of attributes. >>>>>>>>>>>> Also the system for a reason asked me to update my password and now i don't >>>>>>>>>>>> remember it and my account got suspended. Is there a way to reset it or set >>>>>>>>>>>> a simple password? I updated the password hash in the users table by using >>>>>>>>>>>> the hash from another LORIS setup we had and i still couldn't login ( also >>>>>>>>>>>> the attribute password is always NULL and the expiration date is 1999-01-01 >>>>>>>>>>>> for some reason ). >>>>>>>>>>>> >>>>>>>>>>>> Thanks >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> ???? ???, 29 ???? 2019 ???? 5:21 ?.?., ?/? Cecile Madjar < >>>>>>>>>>>> cecile.madjar at mcin.ca> ??????: >>>>>>>>>>>> >>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>> >>>>>>>>>>>>> Can you try adding the visit label v01 to the Visit_Windows >>>>>>>>>>>>> table? >>>>>>>>>>>>> >>>>>>>>>>>>> However, I noticed that in a previous dataset, the label was >>>>>>>>>>>>> V1. Does that refer to the same visit? If so, you might want to harmonize >>>>>>>>>>>>> the visit labels so they are all the same across datasets for a given >>>>>>>>>>>>> timepoint, meaning you will need to relabel scans when the visit label is >>>>>>>>>>>>> different but referring to the same visit label (v01 = V1 etc...). >>>>>>>>>>>>> >>>>>>>>>>>>> Hope this helps, >>>>>>>>>>>>> >>>>>>>>>>>>> C?cile >>>>>>>>>>>>> >>>>>>>>>>>>> On Mon, Jul 29, 2019 at 10:15 AM Sotirios Nikoloutsopoulos < >>>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>> >>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>> >>>>>>>>>>>>>> Could you help me with the "Visit label does not exist"? I >>>>>>>>>>>>>> had changed $subjectID{'createVisitLabel'} to 1 as you had suggested but >>>>>>>>>>>>>> it appears that this problem hasn't been resolved yet. >>>>>>>>>>>>>> >>>>>>>>>>>>>> lorisadmin at hbp:/data/loris/bin/mri$ cat >>>>>>>>>>>>>> /data/loris/data//logs/TarLoad-14-58-9Xog7H.log >>>>>>>>>>>>>> >>>>>>>>>>>>>> ==> Loading file from disk >>>>>>>>>>>>>> /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>> >>>>>>>>>>>>>> --> mapping DICOM parameter for >>>>>>>>>>>>>> /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>> >>>>>>>>>>>>>> --> using user-defined filterParameters for >>>>>>>>>>>>>> /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>> >>>>>>>>>>>>>> Candidate Mismatch Error is Visit label does not exist >>>>>>>>>>>>>> -> WARNING: This candidate was invalid. Logging to >>>>>>>>>>>>>> MRICandidateErrors table with reason Visit >>>>>>>>>>>>>> label does not exist >>>>>>>>>>>>>> >>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>> >>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>> >>>>>>>>>>>>>> ???? ???, 26 ???? 2019 ???? 3:02 ?.?., ?/? Sotirios >>>>>>>>>>>>>> Nikoloutsopoulos ??????: >>>>>>>>>>>>>> >>>>>>>>>>>>>>> Hi Cecile, >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> The Center error was fixed. Still the insertion of mincs >>>>>>>>>>>>>>> fails. Please see the output.txt file i attached. Also is there something >>>>>>>>>>>>>>> else i need to change at the paths configuration? >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> ???? ???, 25 ???? 2019 ???? 6:55 ?.?., ?/? Cecile Madjar < >>>>>>>>>>>>>>> cecile.madjar at mcin.ca> ??????: >>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> We are making progress! >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> I have a feeling this error comes from the fact that your >>>>>>>>>>>>>>>> psc table does not have the MRI_alias populated for the DCC site. Running >>>>>>>>>>>>>>>> the following query in the mysql database should fix this: >>>>>>>>>>>>>>>> UPDATE psc SET MRI_alias="DCC", Alias="DCC" WHERE >>>>>>>>>>>>>>>> Name="Data Coordinating Center"; >>>>>>>>>>>>>>>> Repeat the same with all your sites (make sure to change >>>>>>>>>>>>>>>> the Aliases between sites, they should all be unique). >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Let me know how it goes! >>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> On Thu, Jul 25, 2019 at 11:43 AM Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Dear Cecile, >>>>>>>>>>>>>>>>> You were right about your guesses. I did the modifications >>>>>>>>>>>>>>>>> you suggested, i still get the "no mincs inserted" error, now i am getting >>>>>>>>>>>>>>>>> the "No center found this candidate" error ( how do i fix that? from what i >>>>>>>>>>>>>>>>> see the .dcm files contains a 'Institution Name', is that the center? ), so >>>>>>>>>>>>>>>>> i guess that's why the validation fails, but i changed the force variable >>>>>>>>>>>>>>>>> of tarchiveLoader to 1, shouldn't it have inserted the mincs then? Also it >>>>>>>>>>>>>>>>> is optional to have a mail server, right? ( from what i see the mail error >>>>>>>>>>>>>>>>> does not affect the $valid_study, so i assume we are okay with that ) >>>>>>>>>>>>>>>>> Thank you a lot, >>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> ???? ???, 25 ???? 2019 ???? 5:48 ?.?., ?/? Cecile Madjar < >>>>>>>>>>>>>>>>> cecile.madjar at mcin.ca> ??????: >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> From what I understand, I believe you just need to update >>>>>>>>>>>>>>>>>> a few config settings from the frontend in the Config module (under the >>>>>>>>>>>>>>>>>> Admin menu). >>>>>>>>>>>>>>>>>> [image: Screen Shot 2019-07-25 at 10.31.35 AM.png] >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Then go to the Paths section of the config module and >>>>>>>>>>>>>>>>>> update the "LORIS-MRI code" config setting to /data/loris/bin/mri (my guess >>>>>>>>>>>>>>>>>> is that currently, it is set to /data/LORIS/data) and click on the submit >>>>>>>>>>>>>>>>>> button. >>>>>>>>>>>>>>>>>> [image: Screen Shot 2019-07-25 at 10.32.50 AM.png] >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Then, go to Imaging Pipeline section of the Configuration >>>>>>>>>>>>>>>>>> module and update the "Loris-MRI Data Directory" to /data/loris/data/ (my >>>>>>>>>>>>>>>>>> guess is that it is empty at the moment in your database which is why >>>>>>>>>>>>>>>>>> $data_dir is not defined when you run the tarchiveLoader step of the >>>>>>>>>>>>>>>>>> insertion pipeline). >>>>>>>>>>>>>>>>>> [image: Screen Shot 2019-07-25 at 10.40.52 AM.png] >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Finally, I took a look at your environment file and it >>>>>>>>>>>>>>>>>> might be a good idea to update your PERL5LIB variable to the following (it >>>>>>>>>>>>>>>>>> has been added to the code a few releases ago as we realized this was >>>>>>>>>>>>>>>>>> needed for the libraries. Not sure which version of LORIS-MRI you are using >>>>>>>>>>>>>>>>>> but it does not hurt to update this variable to what I suggest below): >>>>>>>>>>>>>>>>>> export >>>>>>>>>>>>>>>>>> PERL5LIB=/data/loris/bin/mri/uploadNeuroDB:/data/loris/bin/mri/dicom-archive:$PERL5LIB >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Hope this helps. Sorry you are experiencing so much >>>>>>>>>>>>>>>>>> trouble setting things up. We probably need to update our WIKI. >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> On Thu, Jul 25, 2019 at 9:48 AM Sotirios Nikoloutsopoulos >>>>>>>>>>>>>>>>>> wrote: >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> The "Loris-MRI Data Directory" should be in the >>>>>>>>>>>>>>>>>>> environment file? >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> ???? ???, 25 ???? 2019 ???? 12:59 ?.?., ?/? Sotirios >>>>>>>>>>>>>>>>>>> Nikoloutsopoulos ??????: >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> The scripts are located in /data/loris/bin/mri/. >>>>>>>>>>>>>>>>>>>> Somewhere I might have messed something up but i remember following the >>>>>>>>>>>>>>>>>>>> instructions in the wiki.For example when i tried to execute the >>>>>>>>>>>>>>>>>>>> batch_uploads_imageuploader perl script the line >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> my $command = "$bin_dir/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl " >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> was pointing to an invalid path, for example: it was >>>>>>>>>>>>>>>>>>>> repeating a pattern and had LORIS instead of loris ( i think the mistake >>>>>>>>>>>>>>>>>>>> was that in the wiki it suggested to use $PROJECT for the name of the >>>>>>>>>>>>>>>>>>>> folder and i choosed 'loris' >>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris/wiki/Imaging-Database ). >>>>>>>>>>>>>>>>>>>> See also the in image for the modification i did. Also i didn't find the >>>>>>>>>>>>>>>>>>>> section to config the $data_dir variable. >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> ???? ???, 24 ???? 2019 ???? 6:05 ?.?., ?/? Cecile >>>>>>>>>>>>>>>>>>>> Madjar ??????: >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> It looks like you have one Config setting not set >>>>>>>>>>>>>>>>>>>>> (based on the first error message you got when running it the first time). >>>>>>>>>>>>>>>>>>>>> You need to set a value for "Loris-MRI Data Directory" in the Config module >>>>>>>>>>>>>>>>>>>>> under the Imaging pipeline section (from what I can see, it would be >>>>>>>>>>>>>>>>>>>>> /data/loris/data/ for your setup). >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> The reason you got that error message the second time >>>>>>>>>>>>>>>>>>>>> is that the pipeline checks if the DICOM study was already inserted in the >>>>>>>>>>>>>>>>>>>>> tarchive table. Since you ran the study once already, the study is inserted >>>>>>>>>>>>>>>>>>>>> into the tarchive, hence the message. However, the pipeline did not >>>>>>>>>>>>>>>>>>>>> complete as the MINC files were not created and inserted into the >>>>>>>>>>>>>>>>>>>>> files/parameter_file table. In order to continue the insertion, you will >>>>>>>>>>>>>>>>>>>>> then need to run the tarchiveLoader command suggested in the terminal >>>>>>>>>>>>>>>>>>>>> during the second run: >>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader >>>>>>>>>>>>>>>>>>>>> -globLocation -profile prod >>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive//2012/DCM_2012-12-05_ImagingUpload-17-43-ZUEFjb.tar >>>>>>>>>>>>>>>>>>>>> -verbose >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> Finally, I am a bit confused by your setup. Where are >>>>>>>>>>>>>>>>>>>>> the scripts located? In /data/loris/bin/mri or /data/loris/data? It feels >>>>>>>>>>>>>>>>>>>>> like the Config setting "LORIS-MRI code" in the Paths section was set to >>>>>>>>>>>>>>>>>>>>> "/data/LORIS/data" but it should have been set to the directory where the >>>>>>>>>>>>>>>>>>>>> scripts are located (most probably /data/loris/bin/mri). >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> Hope this helps, >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> On Wed, Jul 24, 2019 at 10:55 AM Sotirios >>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos wrote: >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> Ok first i execute this command: >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> "lorisadmin at hbp:/data/loris/bin/mri$ >>>>>>>>>>>>>>>>>>>>>> ./batch_uploads_imageuploader -profile prod < ~/Desktop/input.txt > log.txt >>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in concatenation >>>>>>>>>>>>>>>>>>>>>> (.) or string at ./batch_uploads_imageuploader line 143. >>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in concatenation >>>>>>>>>>>>>>>>>>>>>> (.) or string at ./batch_uploads_imageuploader line 143. >>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $_ in pattern match (m//) >>>>>>>>>>>>>>>>>>>>>> at ./batch_uploads_imageuploader line 147. >>>>>>>>>>>>>>>>>>>>>> base is DCC0000_258024_V01 >>>>>>>>>>>>>>>>>>>>>> path is /data/incoming/ >>>>>>>>>>>>>>>>>>>>>> type is .tar.gz >>>>>>>>>>>>>>>>>>>>>> fullpath is /data/incoming/DCC0000_258024_V01.tar.gz >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> source /tmp/ImagingUpload-17-43-ZUEFjb >>>>>>>>>>>>>>>>>>>>>> targetlocation /data/loris/data/tarchive >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in concatenation >>>>>>>>>>>>>>>>>>>>>> (.) or string at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 256. >>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in concatenation >>>>>>>>>>>>>>>>>>>>>> (.) or string at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 284. >>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in concatenation >>>>>>>>>>>>>>>>>>>>>> (.) or string at /data/loris/bin/mri/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>> tarchive_validation.pl line 219. >>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in concatenation >>>>>>>>>>>>>>>>>>>>>> (.) or string at /data/loris/bin/mri/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl line 270. >>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in concatenation >>>>>>>>>>>>>>>>>>>>>> (.) or string at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 711. >>>>>>>>>>>>>>>>>>>>>> Can't exec "mail": No such file or directory at >>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 721. >>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 722. >>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 723. >>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in concatenation >>>>>>>>>>>>>>>>>>>>>> (.) or string at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 724. >>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 724. >>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 725. >>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in concatenation >>>>>>>>>>>>>>>>>>>>>> (.) or string at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 735. >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> No Mincs inserted >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> The tarchiveLoader insertion script has failed. >>>>>>>>>>>>>>>>>>>>>> Running now the following command: >>>>>>>>>>>>>>>>>>>>>> /data/loris/data/uploadNeuroDB/imaging_upload_file.pl >>>>>>>>>>>>>>>>>>>>>> -profile prod -upload_id 3 /data/incoming/DCC0000_258024_V01.tar.gz >>>>>>>>>>>>>>>>>>>>>> -verbose" >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> I inserted the VisitLabel, but still the Mincs are >>>>>>>>>>>>>>>>>>>>>> not inserted and i am getting this error >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> "lorisadmin at hbp:/data/loris/bin/mri$ >>>>>>>>>>>>>>>>>>>>>> /data/loris/data/uploadNeuroDB/imaging_upload_file.pl >>>>>>>>>>>>>>>>>>>>>> -profile prod -upload_id 3 /data/incoming/DCC0000_258024_V01.tar.gz -verbose >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> find -path \/tmp\/ImagingUpload\-17\-45\-5MsWEd >>>>>>>>>>>>>>>>>>>>>> -name '__MACOSX' -delete >>>>>>>>>>>>>>>>>>>>>> Spool message is: >>>>>>>>>>>>>>>>>>>>>> The Scan for the uploadID 3 has already been run with >>>>>>>>>>>>>>>>>>>>>> tarchiveID: 7. >>>>>>>>>>>>>>>>>>>>>> To continue with the rest of the insertion pipeline, >>>>>>>>>>>>>>>>>>>>>> please run tarchiveLoader from a terminal as follows: >>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader -globLocation -profile prod >>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive//2012/DCM_2012-12-05_ImagingUpload-17-43-ZUEFjb.tar >>>>>>>>>>>>>>>>>>>>>> -verbose" >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> Which files should i delete? I thought that deleting >>>>>>>>>>>>>>>>>>>>>> the files from the tarchive was enough. And i executed the last proposed >>>>>>>>>>>>>>>>>>>>>> command to continue to rest of the insertion pipeline ( check the image ). >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> Thank you >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> ???? ???, 24 ???? 2019 ???? 5:05 ?.?., ?/? Cecile >>>>>>>>>>>>>>>>>>>>>> Madjar ??????: >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> Sorry I was not clear before. Every visits of >>>>>>>>>>>>>>>>>>>>>>> candidates are created in the session table with one entry per >>>>>>>>>>>>>>>>>>>>>>> CandID/VisitLabel. So if the imaging pipeline created visits in the session >>>>>>>>>>>>>>>>>>>>>>> table (that are not attached to instruments) and you want to clean your >>>>>>>>>>>>>>>>>>>>>>> database completely, you can delete entries in that table as well. >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> Regarding your point 2, the imaging pipeline can >>>>>>>>>>>>>>>>>>>>>>> create the visit in the session table as long as the visit label is present >>>>>>>>>>>>>>>>>>>>>>> in the Visit_Windows table (which means the visit label stored in the >>>>>>>>>>>>>>>>>>>>>>> PatientName is a valid visit label). >>>>>>>>>>>>>>>>>>>>>>> However, in your prod file, if the >>>>>>>>>>>>>>>>>>>>>>> variable $subjectID{'createVisitLabel'} is set to 1 for candidates, the >>>>>>>>>>>>>>>>>>>>>>> visit label should be created in the Visit_Windows table I believe. Here >>>>>>>>>>>>>>>>>>>>>>> is the line of the prod file you would need to change >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> . >>>>>>>>>>>>>>>>>>>>>>> In general, we prefer populating the Visit_Windows >>>>>>>>>>>>>>>>>>>>>>> table and set the $subjectID{'createVisitLabel'} to 0 for candidate data to >>>>>>>>>>>>>>>>>>>>>>> avoid insertion of badly labelled MRI data that are complex to relabel. >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> Finally, regarding the candidate creation, if you >>>>>>>>>>>>>>>>>>>>>>> execute the following steps, the pipeline should be able to create >>>>>>>>>>>>>>>>>>>>>>> candidates: >>>>>>>>>>>>>>>>>>>>>>> - set in the Imaging Pipeline section of the config >>>>>>>>>>>>>>>>>>>>>>> module the config setting "Upload creation of candidates" to Yes >>>>>>>>>>>>>>>>>>>>>>> - manually transfer the scans to the LORIS server >>>>>>>>>>>>>>>>>>>>>>> instead of uploading it via the imaging browser >>>>>>>>>>>>>>>>>>>>>>> - run batch_imaging_upload.pl as you did until now. >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> Hope this helps! >>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> On Wed, Jul 24, 2019 at 8:47 AM Sotirios >>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos wrote: >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> About my second question i replaced the name of the >>>>>>>>>>>>>>>>>>>>>>>> patient in the .dcm files and now i am getting an error that the visit >>>>>>>>>>>>>>>>>>>>>>>> label does not exist. >>>>>>>>>>>>>>>>>>>>>>>> I thought it was supposed to be automatically >>>>>>>>>>>>>>>>>>>>>>>> created. >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> "Done adding archive info into database >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader >>>>>>>>>>>>>>>>>>>>>>>> -globLocation -profile prod >>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive//DCM_2012-12-05_ImagingUpload-15-42-yUwQQV.tar >>>>>>>>>>>>>>>>>>>>>>>> -verbose >>>>>>>>>>>>>>>>>>>>>>>> md5sum >>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive/DCM_2012-12-05_ImagingUpload-15-42-yUwQQV.tar >>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>> candidate id 258024 >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> => No Visit labelVisit label does not exist >>>>>>>>>>>>>>>>>>>>>>>> Set centerID = 1 >>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> Number of MINC files that will be considered for >>>>>>>>>>>>>>>>>>>>>>>> inserting into the database: 1 >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> log dir is /logs and log file is >>>>>>>>>>>>>>>>>>>>>>>> /logs/TarLoad-15-42-L6pocU.log >>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>> candidate id 258024 >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> => No Visit label >>>>>>>>>>>>>>>>>>>>>>>> Cleaning up temp files: rm -rf >>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-15-42-J2rQms/ImagingUpload-15-42-yUwQQV*" >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 24 ???? 2019 ???? 3:38 ?.?., ?/? Sotirios >>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos ??????: >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> 1) What are the records in the session table? >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> 2) I tried to upload a non-phantom file like this >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> input_file.txt: >>>>>>>>>>>>>>>>>>>>>>>>> /data/incoming/DCC0000_258024_V1.tar.gz N >>>>>>>>>>>>>>>>>>>>>>>>> DCC0000_258024_V1 >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> Terminal: >>>>>>>>>>>>>>>>>>>>>>>>> ./batch_uploads_imageuploader -profile prod < >>>>>>>>>>>>>>>>>>>>>>>>> ~/Desktop/input.txt > log.txt >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> and i get the following error in the log.txt file >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> "Running now the following command: >>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl -profile prod -upload_id 7 >>>>>>>>>>>>>>>>>>>>>>>>> /data/incoming/DCC0000_258024_V1.tar.gz -verbose >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> find -path \/tmp\/ImagingUpload\-14\-56\-FeLCB4 >>>>>>>>>>>>>>>>>>>>>>>>> -name '__MACOSX' -delete >>>>>>>>>>>>>>>>>>>>>>>>> Spool message is: >>>>>>>>>>>>>>>>>>>>>>>>> The PatientName read from the DICOM header does >>>>>>>>>>>>>>>>>>>>>>>>> not start with DCC0000_258024_V1 from the mri_upload table >>>>>>>>>>>>>>>>>>>>>>>>> " >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> and the spool message is repeated for each .dcm >>>>>>>>>>>>>>>>>>>>>>>>> file. Should i preprocess every .dcm file and change the PatientName to >>>>>>>>>>>>>>>>>>>>>>>>> "DCC0000_258024_V1"? >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> 3) As far as it concerns the candidate profile i >>>>>>>>>>>>>>>>>>>>>>>>> have to create a new one each time before i try to upload a file? Is there >>>>>>>>>>>>>>>>>>>>>>>>> already a way to create a candidate profile and get the DCCID and PSCID >>>>>>>>>>>>>>>>>>>>>>>>> without the user interface? >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 18 ???? 2019 ???? 5:00 ?.?., ?/? Cecile >>>>>>>>>>>>>>>>>>>>>>>>> Madjar ??????: >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> See answers to your questions below. >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> About the 1st case we had a dicom with a blank >>>>>>>>>>>>>>>>>>>>>>>>>>> studyUID, maybe someone accidentally removed it. >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> That is strange. Something must have been done to >>>>>>>>>>>>>>>>>>>>>>>>>> the DICOM files. I have never seen a study with no StudyUID out of the >>>>>>>>>>>>>>>>>>>>>>>>>> scanner. Usually, you need to manually erase it with some tool. However, >>>>>>>>>>>>>>>>>>>>>>>>>> DICOMs never cease to surprise me... >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> Some other questions: >>>>>>>>>>>>>>>>>>>>>>>>>>> 1) What are the steps to remove all of my >>>>>>>>>>>>>>>>>>>>>>>>>>> patients and uploads?: because i want to try to reupload all the testing >>>>>>>>>>>>>>>>>>>>>>>>>>> dicoms we had with a clean database. >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> Release 21.0 of LORIS-MRI will offer a script to >>>>>>>>>>>>>>>>>>>>>>>>>> remove all the entries and files specific to an upload. However, this >>>>>>>>>>>>>>>>>>>>>>>>>> release is not yet out. Hopefully in the next few weeks. >>>>>>>>>>>>>>>>>>>>>>>>>> In the meantime, since your case is particular >>>>>>>>>>>>>>>>>>>>>>>>>> and that you just want to start with a clean database, the following >>>>>>>>>>>>>>>>>>>>>>>>>> deletes should work (hopefully I won't forget any tables): >>>>>>>>>>>>>>>>>>>>>>>>>> delete from mri_violations_log; >>>>>>>>>>>>>>>>>>>>>>>>>> delete from mri_protocol_violated_scans; >>>>>>>>>>>>>>>>>>>>>>>>>> delete from MRICandidateErrors; >>>>>>>>>>>>>>>>>>>>>>>>>> delete from parameter_file; >>>>>>>>>>>>>>>>>>>>>>>>>> delete from files_qcstatus; # (if you played with >>>>>>>>>>>>>>>>>>>>>>>>>> the QC part of the imaging browser for testing) >>>>>>>>>>>>>>>>>>>>>>>>>> delete from feedback_mri_comments; # (if you >>>>>>>>>>>>>>>>>>>>>>>>>> played with the QC part of the imaging browser for testing) >>>>>>>>>>>>>>>>>>>>>>>>>> delete from tarchive_series; >>>>>>>>>>>>>>>>>>>>>>>>>> delete from tarchive_files; >>>>>>>>>>>>>>>>>>>>>>>>>> delete from mri_upload; >>>>>>>>>>>>>>>>>>>>>>>>>> delete from tarchive; >>>>>>>>>>>>>>>>>>>>>>>>>> delete from mri_scanner; >>>>>>>>>>>>>>>>>>>>>>>>>> delete from candidate where PSCID="scanner"; >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> I don't know if you want to also delete entries >>>>>>>>>>>>>>>>>>>>>>>>>> in the session and candidate table too? >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> 2) We do not need to create the profile of a >>>>>>>>>>>>>>>>>>>>>>>>>>> patient ( are the patients stored in the candidate table? because i can't >>>>>>>>>>>>>>>>>>>>>>>>>>> see the ghosts ), because will it automatically be created when importing a >>>>>>>>>>>>>>>>>>>>>>>>>>> dicom? >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> I am not sure I understand fully this question. >>>>>>>>>>>>>>>>>>>>>>>>>> All candidates are stored in the candidate table. The phantom scans however >>>>>>>>>>>>>>>>>>>>>>>>>> are attached to a scanner candidate depending on where the scan happened. >>>>>>>>>>>>>>>>>>>>>>>>>> It is a bit of a weird concept that we have to redesign eventually but >>>>>>>>>>>>>>>>>>>>>>>>>> never got a chance to get to it. >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> Hopefully this answered your question, otherwise, >>>>>>>>>>>>>>>>>>>>>>>>>> don't hesitate to let me know. >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> 3) What is the difference between uploading a >>>>>>>>>>>>>>>>>>>>>>>>>>> dicom as phantom instead of importing as PSCCID_DCCID_VisitLabel? >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> When you upload the scan as >>>>>>>>>>>>>>>>>>>>>>>>>> PSCID_DCCID_VisitLabel, there is a check that makes sure the candidate IDs >>>>>>>>>>>>>>>>>>>>>>>>>> and visit label are valid at the time of upload. >>>>>>>>>>>>>>>>>>>>>>>>>> When you upload a scan as phantom, it expects >>>>>>>>>>>>>>>>>>>>>>>>>> that the DICOM field PatientName and uploaded filename contains the string >>>>>>>>>>>>>>>>>>>>>>>>>> "phantom". We enforced this behaviour on the imaging uploader side in >>>>>>>>>>>>>>>>>>>>>>>>>> recent releases but I can't remember which one. Probably the upcoming 21.0 >>>>>>>>>>>>>>>>>>>>>>>>>> release. >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> All those verifications might seem cumbersome but >>>>>>>>>>>>>>>>>>>>>>>>>> they are here to ensure that the files inserted are all valid and labelled >>>>>>>>>>>>>>>>>>>>>>>>>> properly as it is a bit messy to have to delete files that were wrongly >>>>>>>>>>>>>>>>>>>>>>>>>> labelled. At least, the delete script present in release 21.0 will make >>>>>>>>>>>>>>>>>>>>>>>>>> this process easier but it is still good practice to verify those things. >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> With pleasure. Hopefully the answers to your >>>>>>>>>>>>>>>>>>>>>>>>>> questions will be helpful. >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> PS: loris-dev mailing list: you will find the >>>>>>>>>>>>>>>>>>>>>>>>>> initial answer I gave Sotirios below. I forgot to cc the loris-dev in my >>>>>>>>>>>>>>>>>>>>>>>>>> earlier reply... >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 16 ???? 2019 ???? 12:02 ?.?., ?/? >>>>>>>>>>>>>>>>>>>>>>>>>>> Cecile Madjar ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> Dear Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you for reaching out. Since your email >>>>>>>>>>>>>>>>>>>>>>>>>>>> was already organized in points, I will reply directly below your questions >>>>>>>>>>>>>>>>>>>>>>>>>>>> below. >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> 1) What do we do when the StudyUID is blank on >>>>>>>>>>>>>>>>>>>>>>>>>>>>> the header? >>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/minor/docs/AppendixA-Troubleshooting_guideline.md >>>>>>>>>>>>>>>>>>>>>>>>>>>>> There solution provided at the table 3 does not guide us how to find the >>>>>>>>>>>>>>>>>>>>>>>>>>>>> information ( is possible ). >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> The StudyUID is the field used in our pipeline >>>>>>>>>>>>>>>>>>>>>>>>>>>> at the moment to check whether a DICOM study was already inserted into >>>>>>>>>>>>>>>>>>>>>>>>>>>> LORIS with that same StudyUID since it is supposed to be unique for every >>>>>>>>>>>>>>>>>>>>>>>>>>>> single study. Currently, we do not support insertion of DICOM studies if >>>>>>>>>>>>>>>>>>>>>>>>>>>> they do not have a StudyUID associated with them. >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> Is there a specific reason why the StudyUID is >>>>>>>>>>>>>>>>>>>>>>>>>>>> blank in the DICOM headers in your DICOM files? Did they go through some >>>>>>>>>>>>>>>>>>>>>>>>>>>> processes before upload to LORIS? >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> 2) When i am about to upload a non-phanton case >>>>>>>>>>>>>>>>>>>>>>>>>>>>> i need a 'Visit Label'. Is there already a script that can create a new >>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit label for a specific Candidate, so i can provide it as input >>>>>>>>>>>>>>>>>>>>>>>>>>>>> afterwards to the >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> batch_uploads_imageuploader ( See option 5.1.3 https://github.com/aces/Loris-MRI/blob/minor/docs/05-PipelineLaunchOptions.md ) >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> I am not sure if the front-end allows for it >>>>>>>>>>>>>>>>>>>>>>>>>>>> but if you use batch_uploads_imageuploader, the insertion scripts could >>>>>>>>>>>>>>>>>>>>>>>>>>>> create the visit label for you. However, it does need to be included in the >>>>>>>>>>>>>>>>>>>>>>>>>>>> patient name in order for the script to know which label it should use. >>>>>>>>>>>>>>>>>>>>>>>>>>>> For example: you upload V02 for MTL0123 (DCCID: >>>>>>>>>>>>>>>>>>>>>>>>>>>> 456789) but V02 was not yet created for MTL0123; the insertion scripts >>>>>>>>>>>>>>>>>>>>>>>>>>>> will create a V02 visit for MTL0123 if the PatientName field for the >>>>>>>>>>>>>>>>>>>>>>>>>>>> dataset is MTL0123_456789_V02 with Stage marked as "Not Started". >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> However, *note that for the script to create >>>>>>>>>>>>>>>>>>>>>>>>>>>> the visit for the candidate, you have to make sure that all the visit label >>>>>>>>>>>>>>>>>>>>>>>>>>>> of your projects were inserted in the Visit_Windows table* >>>>>>>>>>>>>>>>>>>>>>>>>>>> (otherwise, the visit will never be created as they were not specified as >>>>>>>>>>>>>>>>>>>>>>>>>>>> being part of the list of visit label to expect). So in the example above, >>>>>>>>>>>>>>>>>>>>>>>>>>>> you should have one row in Visit_Windows with Visit_label="V02" set. >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> 3) Section 4.3 >>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/minor/docs/04-Scripts.md >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> What do we do when the folder contains multiple mnc files? >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> This is a case by case. Most of the time, the >>>>>>>>>>>>>>>>>>>>>>>>>>>> MINC files that failed insertion into the imaging browser end up in the MRI >>>>>>>>>>>>>>>>>>>>>>>>>>>> violation module where you can see what went wrong with the acquisitions >>>>>>>>>>>>>>>>>>>>>>>>>>>> not inserted. If you notice that the MINC file should be inserted as a >>>>>>>>>>>>>>>>>>>>>>>>>>>> specific protocol, you can force the insertion as explained in section 4.3. >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> In your case, I have a feeling that you want to >>>>>>>>>>>>>>>>>>>>>>>>>>>> be able to insert MINC files that did not go through the whole pipeline >>>>>>>>>>>>>>>>>>>>>>>>>>>> insertion (DICOM archival, then dcm2mnc, then protocol identification, then >>>>>>>>>>>>>>>>>>>>>>>>>>>> insertion...). In theory, you could call >>>>>>>>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl on any MINC file, provided >>>>>>>>>>>>>>>>>>>>>>>>>>>> you have at least the following information: >>>>>>>>>>>>>>>>>>>>>>>>>>>> - path to the MINC file >>>>>>>>>>>>>>>>>>>>>>>>>>>> - uploadID associated with the MINC files or >>>>>>>>>>>>>>>>>>>>>>>>>>>> DICOM archive path from which those MINC files were created from >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> Then the minc_insertion.pl script will do the >>>>>>>>>>>>>>>>>>>>>>>>>>>> subject information and protocol validation etc... >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> If all the MINC files come from the same >>>>>>>>>>>>>>>>>>>>>>>>>>>> uploadID or TarchiveID, then you could run a loop in bash calling the >>>>>>>>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl script like this for files >>>>>>>>>>>>>>>>>>>>>>>>>>>> deriving from uploadID=1: >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> ls /path/to/mnc/folder/* | while read f; do >>>>>>>>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl -profile prod -uploadID 1 >>>>>>>>>>>>>>>>>>>>>>>>>>>> -mincPath $f; done >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helped! >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>> Loris-dev mailing list >>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> -- >>>>>>>>> >>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>> Montreal Neurological Institute >>>>>>>>> McGill University | Montreal | Canada >>>>>>>>> >>>>>>>> >>>>>>> >>>>>>> -- >>>>>>> >>>>>>> christine.rogers at mcgill.ca >>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>> Montreal Neurological Institute >>>>>>> McGill University | Montreal | Canada >>>>>>> >>>>>> _______________________________________________ >>>>> Loris-dev mailing list >>>>> Loris-dev at bic.mni.mcgill.ca >>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>> >>>> >>>> >>>> -- >>>> >>>> christine.rogers at mcgill.ca >>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>> Montreal Neurological Institute >>>> McGill University | Montreal | Canada >>>> >>> _______________________________________________ >>> Loris-dev mailing list >>> Loris-dev at bic.mni.mcgill.ca >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>> >> >> >> -- >> >> christine.rogers at mcgill.ca >> McGill Centre for Integrative Neuroscience | MCIN.ca >> Montreal Neurological Institute >> McGill University | Montreal | Canada >> _______________________________________________ >> Loris-dev mailing list >> Loris-dev at bic.mni.mcgill.ca >> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >> > > > -- > > christine.rogers at mcgill.ca > McGill Centre for Integrative Neuroscience | MCIN.ca > Montreal Neurological Institute > McGill University | Montreal | Canada > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 78176 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 20518 bytes Desc: not available URL: From wangshen.mcin at gmail.com Tue Aug 27 14:28:09 2019 From: wangshen.mcin at gmail.com (Shen Wang) Date: Tue, 27 Aug 2019 14:28:09 -0400 Subject: [Loris-dev] Import mri - scripts In-Reply-To: References: <65ad2b70c3084ffdb1e4a9dcdad948cd@YTOPR0101MB1803.CANPRD01.PROD.OUTLOOK.COM> Message-ID: Hi, Please remove "set -euo pipefail" line 10 in the install.sh file. Then try again. On Tue, 27 Aug 2019 at 14:05, Sotirios Nikoloutsopoulos < sotirisnik at gmail.com> wrote: > Hi, > > i still haven't resolved the previous issue. Also i tried to install Loris > to a new virtual machine and when i execute install.sh i get the following > error > > lorisadmin at loris-VirtualBox:/var/www/loris/tools$ ./install.sh > LORIS Installation Script starting at 2019-08-27T21:00:42 > The log for this session will be stored in file > /var/www/loris/tools/logs/install-2019-08-27T21:00:42.log > --------------------------------------------------------------------- > LORIS Installation Script > --------------------------------------------------------------------- > > PHP appears to be installed. > > PHP Composer appears to be installed. > > This install script will ask you to provide inputs for different steps. > Please ensure you have the following information ready (if applicable): > > 1) Your project directory name. > (Will be used to modify the paths for Imaging data in the generated > config.xml file for LORIS, and may also be used to automatically > create/install apache config files.) If unsure, a default like "LORIS" > should be acceptable. > > Please also consult the Loris WIKI on GitHub for more information on these > Install Script input parameters. > > Ready to continue? [yn] y > > ./install.sh: line 132: projectname: unbound variable > > Thanks > > ???? ???, 6 ??? 2019 ???? 5:09 ?.?., ?/? Christine Rogers, Ms. < > christine.rogers at mcgill.ca> ??????: > >> Hi Sotirios, >> Could you also let us know -- on which pages is content visible, and on >> which pages/modules is content not visible for you? >> Thanks, >> Christine >> >> On Tue, Aug 6, 2019 at 9:54 AM Christine Rogers, Ms. < >> christine.rogers at mcgill.ca> wrote: >> >>> Thanks Sotirios, >>> That's good to know. It sounds like you've checked that your >>> /var/www/loris/project/config.xml file get populated properly. >>> >>> Please send us the last few errors you're seeing in your apache error >>> log file, and your config paths and we can see what's happening with your >>> front end -- >>> Run these Troubleshooting Queries >>> >>> to get your config path settings, given your front end is not displaying >>> fully. >>> >>> The Loris-MRI repo >>> 21 >>> install/upgrade would then be your next steps. >>> Best, >>> Christine >>> >>> On Tue, Aug 6, 2019 at 7:53 AM Sotirios Nikoloutsopoulos < >>> sotirisnik at gmail.com> wrote: >>> >>>> I am using a VM. What i did was: >>>> 1) Download the files from https://github.com/aces/Loris and replace >>>> them to my existing /vaw/www/loris folder. >>>> 2) Execute the composer install --no-dev and then composer >>>> dump-autoload as mentioned here >>>> https://github.com/aces/Loris/wiki/Updating-your-LORIS. >>>> 3) Execute install.sh from /var/www/loris/tools and because LORIS >>>> already existed i moved a .config file, then re-executed the install.sh >>>> successfully >>>> 4 ) As for the database, i dropped the schema and i executed the >>>> installdb.php >>>> >>>> ???? ???, 5 ??? 2019 ???? 5:22 ?.?., ?/? Christine Rogers, Ms. < >>>> christine.rogers at mcgill.ca> ??????: >>>> >>>>> Hi Sotorios, >>>>> >>>>> Thanks - when you re-installed did you start on a fresh root path / VM >>>>> or might some of your old system setting still apply? >>>>> (And if you did any steps similar to an upgrade, did you follow the >>>>> Upgrade steps in the Release Notes, from both repos?) >>>>> >>>>> About the TR_range column - it was recently split (MRI pr339 >>>>> ) split into TR_min and >>>>> _max columns. Given the code was trying to query TR_range which does not >>>>> exist in your mri_protocol table, double-check which version of the Loris >>>>> repo (tables) and the Loris-MRI repo (code) you have installed to ensure >>>>> they match. >>>>> >>>>> Christine >>>>> >>>>> >>>>> On Mon, Aug 5, 2019 at 9:06 AM Sotirios Nikoloutsopoulos < >>>>> sotirisnik at gmail.com> wrote: >>>>> >>>>>> I reinstalled LORIS to 21 version and now the content is not visible >>>>>> at all at most pages. >>>>>> >>>>>> [image: image.png] >>>>>> >>>>>> ???? ???, 5 ??? 2019 ???? 3:19 ?.?., ?/? Sotirios Nikoloutsopoulos < >>>>>> sotirisnik at gmail.com> ??????: >>>>>> >>>>>>> Hi, >>>>>>> >>>>>>> Is it easy to upgrade to Loris 21? Also the following fails because >>>>>>> the line 1985 of NeuroDB/MRIProcessingUtility.pm query mri_protocol which >>>>>>> doesn't have TR_range >>>>>>> https://github.com/aces/Loris/blob/21.0-release/SQL/0000-00-00-schema.sql#L556 >>>>>>> >>>>>>> [image: image.png] >>>>>>> >>>>>>> lorisadmin at hbp:/data/loris/bin/mri$ ./batch_uploads_imageuploader >>>>>>> -profile prod < ~/Desktop/input.txt > log.txt >>>>>>> Use of uninitialized value $_ in pattern match (m//) at >>>>>>> ./batch_uploads_imageuploader line 147. >>>>>>> base is DCC0000_258024_V1 >>>>>>> path is /data/incoming/ >>>>>>> type is .tar.gz >>>>>>> fullpath is /data/incoming/DCC0000_258024_V1.tar.gz >>>>>>> DBD::mysql::st execute failed: Unknown column 'TR_range' in 'where >>>>>>> clause' at >>>>>>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line 1985. >>>>>>> DBD::mysql::st fetchrow_array failed: fetch() without execute() at >>>>>>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line 1986. >>>>>>> Use of uninitialized value $count_mri_protocol in numeric gt (>) at >>>>>>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line 1995. >>>>>>> DBD::mysql::st execute failed: Unknown column 'TR_range' in 'field >>>>>>> list' at /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 562. >>>>>>> Can't exec "mail": No such file or directory at >>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 721. >>>>>>> print() on closed filehandle MAIL at >>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 722. >>>>>>> print() on closed filehandle MAIL at >>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 723. >>>>>>> print() on closed filehandle MAIL at >>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 724. >>>>>>> print() on closed filehandle MAIL at >>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 725. >>>>>>> >>>>>>> No Mincs inserted >>>>>>> >>>>>>> Thanks, >>>>>>> >>>>>>> Sotirios >>>>>>> >>>>>>> ???? ???, 3 ??? 2019 ???? 1:08 ?.?., ?/? Christine Rogers, Ms. < >>>>>>> christine.rogers at mcgill.ca> ??????: >>>>>>> >>>>>>>> Hi Sotirios, >>>>>>>> >>>>>>>> First, just a note: we've released LORIS 21 this week with some >>>>>>>> major new features and cleanup -- especially if you are early in your setup >>>>>>>> phase, check out the Release notes for both the LORIS >>>>>>>> and Loris-MRI >>>>>>>> repos. >>>>>>>> >>>>>>>> Thanks for your screenshots -- your empty mri_protocol table should >>>>>>>> be at the root of these issues : >>>>>>>> >>>>>>>> The mri_protocol table must be populated >>>>>>>> >>>>>>>> in order for your scans to be registered in LORIS -- it serves as a >>>>>>>> whitelist for the insertion pipeline which filters out scans that aren't >>>>>>>> identified or matched to scan types in this table. >>>>>>>> >>>>>>>> By default, this table is populated with entries for t1, t2, fMRI >>>>>>>> and DTI (Insert statements for 21 release branch are here >>>>>>>> >>>>>>>> ) >>>>>>>> Feel free to restore our default records and broaden their >>>>>>>> parameters to match all your scan types. >>>>>>>> >>>>>>>> re Defaced, native, selected -- these filter the scans displayed as >>>>>>>> you move to the next page (View Session), instead of viewing "all types" of >>>>>>>> scans from a given session : >>>>>>>> >>>>>>>> - "defaced" means that a defacing script >>>>>>>> >>>>>>>> has masked the subject's face in the volume (for patient privacy) >>>>>>>> - "native" means that no pre-processing has been performed on >>>>>>>> the scan (it's raw data), >>>>>>>> - "selected" will show only volumes that have been QC'd and >>>>>>>> "selected" as the best of their type -- used to display only the best >>>>>>>> quality T1 image instead of all T1s acquired in a session, e.g. >>>>>>>> >>>>>>>> re QC Comments -- >>>>>>>> Once you have successfully loaded scans (matched to the >>>>>>>> mri_protocol table), you'll be able to use the Imaging Browser's View >>>>>>>> Session subpage to enter/view QC comments on each volume, or for each >>>>>>>> visit. >>>>>>>> These are stored directly in the database, and linked to each >>>>>>>> scan. (Table name: feedback_mri_comments) >>>>>>>> (Visit-level QC comments are linked to the session.) >>>>>>>> >>>>>>>> For a walkthrough of the Imaging setup - please see the Imaging >>>>>>>> Setup guide >>>>>>>> >>>>>>>> - >>>>>>>> >>>>>>>> An old LORIS walkthrough video >>>>>>>> can also walk you >>>>>>>> through some of the Imaging front-end features, starting at 8:00 >>>>>>>> LORIS' imaging modules have been updated many times since this >>>>>>>> video, but the functionality and workflow is similar. >>>>>>>> >>>>>>>> Let us know how it goes once you have entries in your mri_protocol >>>>>>>> table - >>>>>>>> Best, >>>>>>>> Christine >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> On Fri, Aug 2, 2019 at 7:58 AM Sotirios Nikoloutsopoulos < >>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>> >>>>>>>>> Hi Christine, >>>>>>>>> >>>>>>>>> In the candidate_list page i can see this patient >>>>>>>>> >>>>>>>>> [image: image.png] >>>>>>>>> >>>>>>>>> If i press the link under PSCID i get to see >>>>>>>>> [image: image.png] >>>>>>>>> >>>>>>>>> and if i press the link under Scan Done it redirects me to >>>>>>>>> imaging_browser >>>>>>>>> >>>>>>>>> [image: image.png] >>>>>>>>> >>>>>>>>> At the mri_violations page i also see No results ( neither on >>>>>>>>> resolved / not resolved ). >>>>>>>>> >>>>>>>>> At the imaging_uploader i can see the record that failed. >>>>>>>>> >>>>>>>>> [image: image.png] >>>>>>>>> >>>>>>>>> If i click on the tarchive info i get to see the Protocol Name >>>>>>>>> which i think is the acquisition we wanted? >>>>>>>>> [image: image.png] >>>>>>>>> >>>>>>>>> Also my mri_protocol table is empty. >>>>>>>>> >>>>>>>>> Furthermore i would like to ask about the defaced, native, >>>>>>>>> selected. What exactly is native and selected? And where are the qc >>>>>>>>> comments stored? >>>>>>>>> >>>>>>>>> [image: image.png] >>>>>>>>> >>>>>>>>> Finally a walkthrough would be helpful. >>>>>>>>> >>>>>>>>> Thanks, >>>>>>>>> >>>>>>>>> Sotirios >>>>>>>>> >>>>>>>>> ???? ???, 30 ???? 2019 ???? 8:29 ?.?., ?/? Christine Rogers, Ms. < >>>>>>>>> christine.rogers at mcgill.ca> ??????: >>>>>>>>> >>>>>>>>>> Hi Sotirios, >>>>>>>>>> Glad to hear you're making progress with the visit labels. To >>>>>>>>>> follow up on your last few emails: >>>>>>>>>> >>>>>>>>>> a- The Wiki's Setup Guide contains Sample insert statements for >>>>>>>>>> the Visit Windows table >>>>>>>>>> >>>>>>>>>> . >>>>>>>>>> >>>>>>>>>> As Cecile mentioned, the consistency of visit label format is >>>>>>>>>> important: V01, v01, V1, 01 -- whichever you select to use is fine; we use >>>>>>>>>> V01 by default across all documentation. >>>>>>>>>> >>>>>>>>>> b- For Password reset, there is a script in the tools/ directory >>>>>>>>>> so that a back-end administrator can reset any front-end user password, >>>>>>>>>> including Admin. (See info on setting up / resetting User passwords in the Wiki's >>>>>>>>>> Setup Guide >>>>>>>>>> >>>>>>>>>> ) >>>>>>>>>> >>>>>>>>>> c- The minc file not being registered -- due to >>>>>>>>>> AcquisitionProtocol unknown. >>>>>>>>>> This means the SeriesDescription (Acquisition Protocol) in you >>>>>>>>>> Dicom header was not matched to any scan listed in the mri_protocol >>>>>>>>>> database table. >>>>>>>>>> (In the online Loris-MRI Troubleshooting Guide, >>>>>>>>>> this >>>>>>>>>> is Table 3, 2nd-last item "no MINCs inserted"). >>>>>>>>>> >>>>>>>>>> The MRI Violations module (Readme here) >>>>>>>>>> will show >>>>>>>>>> you the details of this mismatch -- >>>>>>>>>> Go to the module (under the Imaging menu), find your scan and >>>>>>>>>> click the link "Could not identify scan type" -- in the next subpage you >>>>>>>>>> can compare the scan's actual parameters against the mri_protocol table. >>>>>>>>>> >>>>>>>>>> To resolve this, adjust your mri_protocol table values or perhaps >>>>>>>>>> ensure your DICOMs are labelled consistently. >>>>>>>>>> >>>>>>>>>> Let us know if this works for you -- we can also walk you through >>>>>>>>>> an example of non-identified scans on Demo.loris.ca (MRI >>>>>>>>>> Violations module). >>>>>>>>>> >>>>>>>>>> Best, >>>>>>>>>> Christine >>>>>>>>>> >>>>>>>>>> The LORIS team >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> On Tue, Jul 30, 2019 at 10:47 AM Sotirios Nikoloutsopoulos < >>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>> >>>>>>>>>>> I hope this is sufficient as the error for the visit label >>>>>>>>>>> disappeared. >>>>>>>>>>> [image: image.png] >>>>>>>>>>> >>>>>>>>>>> Please see the attached file. Also something i found. >>>>>>>>>>> >>>>>>>>>>> lorisadmin at hbp:/data/loris/bin/mri$ cat >>>>>>>>>>> /data/loris/data//logs/TarLoad-17-39-xubBdv.log >>>>>>>>>>> >>>>>>>>>>> ==> Loading file from disk >>>>>>>>>>> /tmp/TarLoad-17-39-UyQcG2/dcc0000_258024_v1_20121205_102108_501e1_mri.mnc >>>>>>>>>>> >>>>>>>>>>> --> mapping DICOM parameter for >>>>>>>>>>> /tmp/TarLoad-17-39-UyQcG2/dcc0000_258024_v1_20121205_102108_501e1_mri.mnc >>>>>>>>>>> >>>>>>>>>>> ==> computing md5 hash for MINC body. >>>>>>>>>>> >>>>>>>>>>> --> md5: 6b1202fd63e29de4c9be1cd9925888a5 >>>>>>>>>>> >>>>>>>>>>> ==> verifying acquisition protocol >>>>>>>>>>> >>>>>>>>>>> Acquisition protocol is unknown >>>>>>>>>>> >>>>>>>>>>> --> The minc file cannot be registered since the >>>>>>>>>>> AcquisitionProtocol is unknown >>>>>>>>>>> >>>>>>>>>>> ???? ???, 30 ???? 2019 ???? 4:58 ?.?., ?/? Sotirios >>>>>>>>>>> Nikoloutsopoulos ??????: >>>>>>>>>>> >>>>>>>>>>>> Ok I fixed the login problem by using a known hash and by >>>>>>>>>>>> deleting the rows from the login_history i was able to login. >>>>>>>>>>>> >>>>>>>>>>>> ???? ???, 30 ???? 2019 ???? 4:50 ?.?., ?/? Sotirios >>>>>>>>>>>> Nikoloutsopoulos ??????: >>>>>>>>>>>> >>>>>>>>>>>>> Hi, >>>>>>>>>>>>> >>>>>>>>>>>>> there was no visit label 01 in the Visit_Windows table and i >>>>>>>>>>>>> don't know how to insert it because the record requires lots of attributes. >>>>>>>>>>>>> Also the system for a reason asked me to update my password and now i don't >>>>>>>>>>>>> remember it and my account got suspended. Is there a way to reset it or set >>>>>>>>>>>>> a simple password? I updated the password hash in the users table by using >>>>>>>>>>>>> the hash from another LORIS setup we had and i still couldn't login ( also >>>>>>>>>>>>> the attribute password is always NULL and the expiration date is 1999-01-01 >>>>>>>>>>>>> for some reason ). >>>>>>>>>>>>> >>>>>>>>>>>>> Thanks >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> ???? ???, 29 ???? 2019 ???? 5:21 ?.?., ?/? Cecile Madjar < >>>>>>>>>>>>> cecile.madjar at mcin.ca> ??????: >>>>>>>>>>>>> >>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>> >>>>>>>>>>>>>> Can you try adding the visit label v01 to the Visit_Windows >>>>>>>>>>>>>> table? >>>>>>>>>>>>>> >>>>>>>>>>>>>> However, I noticed that in a previous dataset, the label was >>>>>>>>>>>>>> V1. Does that refer to the same visit? If so, you might want to harmonize >>>>>>>>>>>>>> the visit labels so they are all the same across datasets for a given >>>>>>>>>>>>>> timepoint, meaning you will need to relabel scans when the visit label is >>>>>>>>>>>>>> different but referring to the same visit label (v01 = V1 etc...). >>>>>>>>>>>>>> >>>>>>>>>>>>>> Hope this helps, >>>>>>>>>>>>>> >>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>> >>>>>>>>>>>>>> On Mon, Jul 29, 2019 at 10:15 AM Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>> >>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> Could you help me with the "Visit label does not exist"? I >>>>>>>>>>>>>>> had changed $subjectID{'createVisitLabel'} to 1 as you had suggested but >>>>>>>>>>>>>>> it appears that this problem hasn't been resolved yet. >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> lorisadmin at hbp:/data/loris/bin/mri$ cat >>>>>>>>>>>>>>> /data/loris/data//logs/TarLoad-14-58-9Xog7H.log >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> ==> Loading file from disk >>>>>>>>>>>>>>> /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> --> mapping DICOM parameter for >>>>>>>>>>>>>>> /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> --> using user-defined filterParameters for >>>>>>>>>>>>>>> /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> Candidate Mismatch Error is Visit label does not exist >>>>>>>>>>>>>>> -> WARNING: This candidate was invalid. Logging to >>>>>>>>>>>>>>> MRICandidateErrors table with reason Visit >>>>>>>>>>>>>>> label does not exist >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> ???? ???, 26 ???? 2019 ???? 3:02 ?.?., ?/? Sotirios >>>>>>>>>>>>>>> Nikoloutsopoulos ??????: >>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Hi Cecile, >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> The Center error was fixed. Still the insertion of mincs >>>>>>>>>>>>>>>> fails. Please see the output.txt file i attached. Also is there something >>>>>>>>>>>>>>>> else i need to change at the paths configuration? >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> ???? ???, 25 ???? 2019 ???? 6:55 ?.?., ?/? Cecile Madjar < >>>>>>>>>>>>>>>> cecile.madjar at mcin.ca> ??????: >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> We are making progress! >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> I have a feeling this error comes from the fact that your >>>>>>>>>>>>>>>>> psc table does not have the MRI_alias populated for the DCC site. Running >>>>>>>>>>>>>>>>> the following query in the mysql database should fix this: >>>>>>>>>>>>>>>>> UPDATE psc SET MRI_alias="DCC", Alias="DCC" WHERE >>>>>>>>>>>>>>>>> Name="Data Coordinating Center"; >>>>>>>>>>>>>>>>> Repeat the same with all your sites (make sure to change >>>>>>>>>>>>>>>>> the Aliases between sites, they should all be unique). >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Let me know how it goes! >>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> On Thu, Jul 25, 2019 at 11:43 AM Sotirios Nikoloutsopoulos >>>>>>>>>>>>>>>>> wrote: >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Dear Cecile, >>>>>>>>>>>>>>>>>> You were right about your guesses. I did the >>>>>>>>>>>>>>>>>> modifications you suggested, i still get the "no mincs inserted" error, now >>>>>>>>>>>>>>>>>> i am getting the "No center found this candidate" error ( how do i fix >>>>>>>>>>>>>>>>>> that? from what i see the .dcm files contains a 'Institution Name', is that >>>>>>>>>>>>>>>>>> the center? ), so i guess that's why the validation fails, but i changed >>>>>>>>>>>>>>>>>> the force variable of tarchiveLoader to 1, shouldn't it have inserted the >>>>>>>>>>>>>>>>>> mincs then? Also it is optional to have a mail server, right? ( from what i >>>>>>>>>>>>>>>>>> see the mail error does not affect the $valid_study, so i assume we are >>>>>>>>>>>>>>>>>> okay with that ) >>>>>>>>>>>>>>>>>> Thank you a lot, >>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> ???? ???, 25 ???? 2019 ???? 5:48 ?.?., ?/? Cecile Madjar < >>>>>>>>>>>>>>>>>> cecile.madjar at mcin.ca> ??????: >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> From what I understand, I believe you just need to >>>>>>>>>>>>>>>>>>> update a few config settings from the frontend in the Config module (under >>>>>>>>>>>>>>>>>>> the Admin menu). >>>>>>>>>>>>>>>>>>> [image: Screen Shot 2019-07-25 at 10.31.35 AM.png] >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Then go to the Paths section of the config module and >>>>>>>>>>>>>>>>>>> update the "LORIS-MRI code" config setting to /data/loris/bin/mri (my guess >>>>>>>>>>>>>>>>>>> is that currently, it is set to /data/LORIS/data) and click on the submit >>>>>>>>>>>>>>>>>>> button. >>>>>>>>>>>>>>>>>>> [image: Screen Shot 2019-07-25 at 10.32.50 AM.png] >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Then, go to Imaging Pipeline section of the >>>>>>>>>>>>>>>>>>> Configuration module and update the "Loris-MRI Data Directory" to >>>>>>>>>>>>>>>>>>> /data/loris/data/ (my guess is that it is empty at the moment in your >>>>>>>>>>>>>>>>>>> database which is why $data_dir is not defined when you run the >>>>>>>>>>>>>>>>>>> tarchiveLoader step of the insertion pipeline). >>>>>>>>>>>>>>>>>>> [image: Screen Shot 2019-07-25 at 10.40.52 AM.png] >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Finally, I took a look at your environment file and it >>>>>>>>>>>>>>>>>>> might be a good idea to update your PERL5LIB variable to the following (it >>>>>>>>>>>>>>>>>>> has been added to the code a few releases ago as we realized this was >>>>>>>>>>>>>>>>>>> needed for the libraries. Not sure which version of LORIS-MRI you are using >>>>>>>>>>>>>>>>>>> but it does not hurt to update this variable to what I suggest below): >>>>>>>>>>>>>>>>>>> export >>>>>>>>>>>>>>>>>>> PERL5LIB=/data/loris/bin/mri/uploadNeuroDB:/data/loris/bin/mri/dicom-archive:$PERL5LIB >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Hope this helps. Sorry you are experiencing so much >>>>>>>>>>>>>>>>>>> trouble setting things up. We probably need to update our WIKI. >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> On Thu, Jul 25, 2019 at 9:48 AM Sotirios >>>>>>>>>>>>>>>>>>> Nikoloutsopoulos wrote: >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> The "Loris-MRI Data Directory" should be in the >>>>>>>>>>>>>>>>>>>> environment file? >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> ???? ???, 25 ???? 2019 ???? 12:59 ?.?., ?/? Sotirios >>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos ??????: >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> The scripts are located in /data/loris/bin/mri/. >>>>>>>>>>>>>>>>>>>>> Somewhere I might have messed something up but i remember following the >>>>>>>>>>>>>>>>>>>>> instructions in the wiki.For example when i tried to execute the >>>>>>>>>>>>>>>>>>>>> batch_uploads_imageuploader perl script the line >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> my $command = "$bin_dir/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl " >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> was pointing to an invalid path, for example: it was >>>>>>>>>>>>>>>>>>>>> repeating a pattern and had LORIS instead of loris ( i think the mistake >>>>>>>>>>>>>>>>>>>>> was that in the wiki it suggested to use $PROJECT for the name of the >>>>>>>>>>>>>>>>>>>>> folder and i choosed 'loris' >>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris/wiki/Imaging-Database >>>>>>>>>>>>>>>>>>>>> ). See also the in image for the modification i did. Also i didn't find the >>>>>>>>>>>>>>>>>>>>> section to config the $data_dir variable. >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> ???? ???, 24 ???? 2019 ???? 6:05 ?.?., ?/? Cecile >>>>>>>>>>>>>>>>>>>>> Madjar ??????: >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> It looks like you have one Config setting not set >>>>>>>>>>>>>>>>>>>>>> (based on the first error message you got when running it the first time). >>>>>>>>>>>>>>>>>>>>>> You need to set a value for "Loris-MRI Data Directory" in the Config module >>>>>>>>>>>>>>>>>>>>>> under the Imaging pipeline section (from what I can see, it would be >>>>>>>>>>>>>>>>>>>>>> /data/loris/data/ for your setup). >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> The reason you got that error message the second time >>>>>>>>>>>>>>>>>>>>>> is that the pipeline checks if the DICOM study was already inserted in the >>>>>>>>>>>>>>>>>>>>>> tarchive table. Since you ran the study once already, the study is inserted >>>>>>>>>>>>>>>>>>>>>> into the tarchive, hence the message. However, the pipeline did not >>>>>>>>>>>>>>>>>>>>>> complete as the MINC files were not created and inserted into the >>>>>>>>>>>>>>>>>>>>>> files/parameter_file table. In order to continue the insertion, you will >>>>>>>>>>>>>>>>>>>>>> then need to run the tarchiveLoader command suggested in the terminal >>>>>>>>>>>>>>>>>>>>>> during the second run: >>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader >>>>>>>>>>>>>>>>>>>>>> -globLocation -profile prod >>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive//2012/DCM_2012-12-05_ImagingUpload-17-43-ZUEFjb.tar >>>>>>>>>>>>>>>>>>>>>> -verbose >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> Finally, I am a bit confused by your setup. Where are >>>>>>>>>>>>>>>>>>>>>> the scripts located? In /data/loris/bin/mri or /data/loris/data? It feels >>>>>>>>>>>>>>>>>>>>>> like the Config setting "LORIS-MRI code" in the Paths section was set to >>>>>>>>>>>>>>>>>>>>>> "/data/LORIS/data" but it should have been set to the directory where the >>>>>>>>>>>>>>>>>>>>>> scripts are located (most probably /data/loris/bin/mri). >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> Hope this helps, >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> On Wed, Jul 24, 2019 at 10:55 AM Sotirios >>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos wrote: >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> Ok first i execute this command: >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> "lorisadmin at hbp:/data/loris/bin/mri$ >>>>>>>>>>>>>>>>>>>>>>> ./batch_uploads_imageuploader -profile prod < ~/Desktop/input.txt > log.txt >>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at ./batch_uploads_imageuploader line 143. >>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at ./batch_uploads_imageuploader line 143. >>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $_ in pattern match (m//) >>>>>>>>>>>>>>>>>>>>>>> at ./batch_uploads_imageuploader line 147. >>>>>>>>>>>>>>>>>>>>>>> base is DCC0000_258024_V01 >>>>>>>>>>>>>>>>>>>>>>> path is /data/incoming/ >>>>>>>>>>>>>>>>>>>>>>> type is .tar.gz >>>>>>>>>>>>>>>>>>>>>>> fullpath is /data/incoming/DCC0000_258024_V01.tar.gz >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> source /tmp/ImagingUpload-17-43-ZUEFjb >>>>>>>>>>>>>>>>>>>>>>> targetlocation /data/loris/data/tarchive >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 256. >>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 284. >>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at /data/loris/bin/mri/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>> tarchive_validation.pl line 219. >>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at /data/loris/bin/mri/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl line 270. >>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 711. >>>>>>>>>>>>>>>>>>>>>>> Can't exec "mail": No such file or directory at >>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 721. >>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 722. >>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 723. >>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 724. >>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 724. >>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 725. >>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 735. >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> No Mincs inserted >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> The tarchiveLoader insertion script has failed. >>>>>>>>>>>>>>>>>>>>>>> Running now the following command: >>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl -profile prod -upload_id 3 >>>>>>>>>>>>>>>>>>>>>>> /data/incoming/DCC0000_258024_V01.tar.gz -verbose" >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> I inserted the VisitLabel, but still the Mincs are >>>>>>>>>>>>>>>>>>>>>>> not inserted and i am getting this error >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> "lorisadmin at hbp:/data/loris/bin/mri$ >>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl -profile prod -upload_id 3 >>>>>>>>>>>>>>>>>>>>>>> /data/incoming/DCC0000_258024_V01.tar.gz -verbose >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> find -path \/tmp\/ImagingUpload\-17\-45\-5MsWEd >>>>>>>>>>>>>>>>>>>>>>> -name '__MACOSX' -delete >>>>>>>>>>>>>>>>>>>>>>> Spool message is: >>>>>>>>>>>>>>>>>>>>>>> The Scan for the uploadID 3 has already been run >>>>>>>>>>>>>>>>>>>>>>> with tarchiveID: 7. >>>>>>>>>>>>>>>>>>>>>>> To continue with the rest of the insertion pipeline, >>>>>>>>>>>>>>>>>>>>>>> please run tarchiveLoader from a terminal as follows: >>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader -globLocation -profile prod >>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive//2012/DCM_2012-12-05_ImagingUpload-17-43-ZUEFjb.tar >>>>>>>>>>>>>>>>>>>>>>> -verbose" >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> Which files should i delete? I thought that deleting >>>>>>>>>>>>>>>>>>>>>>> the files from the tarchive was enough. And i executed the last proposed >>>>>>>>>>>>>>>>>>>>>>> command to continue to rest of the insertion pipeline ( check the image ). >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> Thank you >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> ???? ???, 24 ???? 2019 ???? 5:05 ?.?., ?/? Cecile >>>>>>>>>>>>>>>>>>>>>>> Madjar ??????: >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> Sorry I was not clear before. Every visits of >>>>>>>>>>>>>>>>>>>>>>>> candidates are created in the session table with one entry per >>>>>>>>>>>>>>>>>>>>>>>> CandID/VisitLabel. So if the imaging pipeline created visits in the session >>>>>>>>>>>>>>>>>>>>>>>> table (that are not attached to instruments) and you want to clean your >>>>>>>>>>>>>>>>>>>>>>>> database completely, you can delete entries in that table as well. >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> Regarding your point 2, the imaging pipeline can >>>>>>>>>>>>>>>>>>>>>>>> create the visit in the session table as long as the visit label is present >>>>>>>>>>>>>>>>>>>>>>>> in the Visit_Windows table (which means the visit label stored in the >>>>>>>>>>>>>>>>>>>>>>>> PatientName is a valid visit label). >>>>>>>>>>>>>>>>>>>>>>>> However, in your prod file, if the >>>>>>>>>>>>>>>>>>>>>>>> variable $subjectID{'createVisitLabel'} is set to 1 for candidates, the >>>>>>>>>>>>>>>>>>>>>>>> visit label should be created in the Visit_Windows table I believe. Here >>>>>>>>>>>>>>>>>>>>>>>> is the line of the prod file you would need to change >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> . >>>>>>>>>>>>>>>>>>>>>>>> In general, we prefer populating the Visit_Windows >>>>>>>>>>>>>>>>>>>>>>>> table and set the $subjectID{'createVisitLabel'} to 0 for candidate data to >>>>>>>>>>>>>>>>>>>>>>>> avoid insertion of badly labelled MRI data that are complex to relabel. >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> Finally, regarding the candidate creation, if you >>>>>>>>>>>>>>>>>>>>>>>> execute the following steps, the pipeline should be able to create >>>>>>>>>>>>>>>>>>>>>>>> candidates: >>>>>>>>>>>>>>>>>>>>>>>> - set in the Imaging Pipeline section of the config >>>>>>>>>>>>>>>>>>>>>>>> module the config setting "Upload creation of candidates" to Yes >>>>>>>>>>>>>>>>>>>>>>>> - manually transfer the scans to the LORIS server >>>>>>>>>>>>>>>>>>>>>>>> instead of uploading it via the imaging browser >>>>>>>>>>>>>>>>>>>>>>>> - run batch_imaging_upload.pl as you did until now. >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> Hope this helps! >>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> On Wed, Jul 24, 2019 at 8:47 AM Sotirios >>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos wrote: >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> About my second question i replaced the name of >>>>>>>>>>>>>>>>>>>>>>>>> the patient in the .dcm files and now i am getting an error that the visit >>>>>>>>>>>>>>>>>>>>>>>>> label does not exist. >>>>>>>>>>>>>>>>>>>>>>>>> I thought it was supposed to be automatically >>>>>>>>>>>>>>>>>>>>>>>>> created. >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> "Done adding archive info into database >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader >>>>>>>>>>>>>>>>>>>>>>>>> -globLocation -profile prod >>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive//DCM_2012-12-05_ImagingUpload-15-42-yUwQQV.tar >>>>>>>>>>>>>>>>>>>>>>>>> -verbose >>>>>>>>>>>>>>>>>>>>>>>>> md5sum >>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive/DCM_2012-12-05_ImagingUpload-15-42-yUwQQV.tar >>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>> candidate id 258024 >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> => No Visit labelVisit label does not exist >>>>>>>>>>>>>>>>>>>>>>>>> Set centerID = 1 >>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> Number of MINC files that will be considered for >>>>>>>>>>>>>>>>>>>>>>>>> inserting into the database: 1 >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> log dir is /logs and log file is >>>>>>>>>>>>>>>>>>>>>>>>> /logs/TarLoad-15-42-L6pocU.log >>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>> candidate id 258024 >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> => No Visit label >>>>>>>>>>>>>>>>>>>>>>>>> Cleaning up temp files: rm -rf >>>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-15-42-J2rQms/ImagingUpload-15-42-yUwQQV*" >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 24 ???? 2019 ???? 3:38 ?.?., ?/? >>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos >>>>>>>>>>>>>>>>>>>>>>>>> ??????: >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> 1) What are the records in the session table? >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> 2) I tried to upload a non-phantom file like this >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> input_file.txt: >>>>>>>>>>>>>>>>>>>>>>>>>> /data/incoming/DCC0000_258024_V1.tar.gz N >>>>>>>>>>>>>>>>>>>>>>>>>> DCC0000_258024_V1 >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> Terminal: >>>>>>>>>>>>>>>>>>>>>>>>>> ./batch_uploads_imageuploader -profile prod < >>>>>>>>>>>>>>>>>>>>>>>>>> ~/Desktop/input.txt > log.txt >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> and i get the following error in the log.txt file >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> "Running now the following command: >>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl -profile prod -upload_id >>>>>>>>>>>>>>>>>>>>>>>>>> 7 /data/incoming/DCC0000_258024_V1.tar.gz -verbose >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> find -path \/tmp\/ImagingUpload\-14\-56\-FeLCB4 >>>>>>>>>>>>>>>>>>>>>>>>>> -name '__MACOSX' -delete >>>>>>>>>>>>>>>>>>>>>>>>>> Spool message is: >>>>>>>>>>>>>>>>>>>>>>>>>> The PatientName read from the DICOM header does >>>>>>>>>>>>>>>>>>>>>>>>>> not start with DCC0000_258024_V1 from the mri_upload table >>>>>>>>>>>>>>>>>>>>>>>>>> " >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> and the spool message is repeated for each .dcm >>>>>>>>>>>>>>>>>>>>>>>>>> file. Should i preprocess every .dcm file and change the PatientName to >>>>>>>>>>>>>>>>>>>>>>>>>> "DCC0000_258024_V1"? >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> 3) As far as it concerns the candidate profile i >>>>>>>>>>>>>>>>>>>>>>>>>> have to create a new one each time before i try to upload a file? Is there >>>>>>>>>>>>>>>>>>>>>>>>>> already a way to create a candidate profile and get the DCCID and PSCID >>>>>>>>>>>>>>>>>>>>>>>>>> without the user interface? >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 18 ???? 2019 ???? 5:00 ?.?., ?/? Cecile >>>>>>>>>>>>>>>>>>>>>>>>>> Madjar ??????: >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> See answers to your questions below. >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> About the 1st case we had a dicom with a blank >>>>>>>>>>>>>>>>>>>>>>>>>>>> studyUID, maybe someone accidentally removed it. >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> That is strange. Something must have been done >>>>>>>>>>>>>>>>>>>>>>>>>>> to the DICOM files. I have never seen a study with no StudyUID out of the >>>>>>>>>>>>>>>>>>>>>>>>>>> scanner. Usually, you need to manually erase it with some tool. However, >>>>>>>>>>>>>>>>>>>>>>>>>>> DICOMs never cease to surprise me... >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> Some other questions: >>>>>>>>>>>>>>>>>>>>>>>>>>>> 1) What are the steps to remove all of my >>>>>>>>>>>>>>>>>>>>>>>>>>>> patients and uploads?: because i want to try to reupload all the testing >>>>>>>>>>>>>>>>>>>>>>>>>>>> dicoms we had with a clean database. >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> Release 21.0 of LORIS-MRI will offer a script to >>>>>>>>>>>>>>>>>>>>>>>>>>> remove all the entries and files specific to an upload. However, this >>>>>>>>>>>>>>>>>>>>>>>>>>> release is not yet out. Hopefully in the next few weeks. >>>>>>>>>>>>>>>>>>>>>>>>>>> In the meantime, since your case is particular >>>>>>>>>>>>>>>>>>>>>>>>>>> and that you just want to start with a clean database, the following >>>>>>>>>>>>>>>>>>>>>>>>>>> deletes should work (hopefully I won't forget any tables): >>>>>>>>>>>>>>>>>>>>>>>>>>> delete from mri_violations_log; >>>>>>>>>>>>>>>>>>>>>>>>>>> delete from mri_protocol_violated_scans; >>>>>>>>>>>>>>>>>>>>>>>>>>> delete from MRICandidateErrors; >>>>>>>>>>>>>>>>>>>>>>>>>>> delete from parameter_file; >>>>>>>>>>>>>>>>>>>>>>>>>>> delete from files_qcstatus; # (if you played >>>>>>>>>>>>>>>>>>>>>>>>>>> with the QC part of the imaging browser for testing) >>>>>>>>>>>>>>>>>>>>>>>>>>> delete from feedback_mri_comments; # (if you >>>>>>>>>>>>>>>>>>>>>>>>>>> played with the QC part of the imaging browser for testing) >>>>>>>>>>>>>>>>>>>>>>>>>>> delete from tarchive_series; >>>>>>>>>>>>>>>>>>>>>>>>>>> delete from tarchive_files; >>>>>>>>>>>>>>>>>>>>>>>>>>> delete from mri_upload; >>>>>>>>>>>>>>>>>>>>>>>>>>> delete from tarchive; >>>>>>>>>>>>>>>>>>>>>>>>>>> delete from mri_scanner; >>>>>>>>>>>>>>>>>>>>>>>>>>> delete from candidate where PSCID="scanner"; >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> I don't know if you want to also delete entries >>>>>>>>>>>>>>>>>>>>>>>>>>> in the session and candidate table too? >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> 2) We do not need to create the profile of a >>>>>>>>>>>>>>>>>>>>>>>>>>>> patient ( are the patients stored in the candidate table? because i can't >>>>>>>>>>>>>>>>>>>>>>>>>>>> see the ghosts ), because will it automatically be created when importing a >>>>>>>>>>>>>>>>>>>>>>>>>>>> dicom? >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> I am not sure I understand fully this question. >>>>>>>>>>>>>>>>>>>>>>>>>>> All candidates are stored in the candidate table. The phantom scans however >>>>>>>>>>>>>>>>>>>>>>>>>>> are attached to a scanner candidate depending on where the scan happened. >>>>>>>>>>>>>>>>>>>>>>>>>>> It is a bit of a weird concept that we have to redesign eventually but >>>>>>>>>>>>>>>>>>>>>>>>>>> never got a chance to get to it. >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> Hopefully this answered your question, >>>>>>>>>>>>>>>>>>>>>>>>>>> otherwise, don't hesitate to let me know. >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> 3) What is the difference between uploading a >>>>>>>>>>>>>>>>>>>>>>>>>>>> dicom as phantom instead of importing as PSCCID_DCCID_VisitLabel? >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> When you upload the scan as >>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID_DCCID_VisitLabel, there is a check that makes sure the candidate IDs >>>>>>>>>>>>>>>>>>>>>>>>>>> and visit label are valid at the time of upload. >>>>>>>>>>>>>>>>>>>>>>>>>>> When you upload a scan as phantom, it expects >>>>>>>>>>>>>>>>>>>>>>>>>>> that the DICOM field PatientName and uploaded filename contains the string >>>>>>>>>>>>>>>>>>>>>>>>>>> "phantom". We enforced this behaviour on the imaging uploader side in >>>>>>>>>>>>>>>>>>>>>>>>>>> recent releases but I can't remember which one. Probably the upcoming 21.0 >>>>>>>>>>>>>>>>>>>>>>>>>>> release. >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> All those verifications might seem cumbersome >>>>>>>>>>>>>>>>>>>>>>>>>>> but they are here to ensure that the files inserted are all valid and >>>>>>>>>>>>>>>>>>>>>>>>>>> labelled properly as it is a bit messy to have to delete files that were >>>>>>>>>>>>>>>>>>>>>>>>>>> wrongly labelled. At least, the delete script present in release 21.0 will >>>>>>>>>>>>>>>>>>>>>>>>>>> make this process easier but it is still good practice to verify those >>>>>>>>>>>>>>>>>>>>>>>>>>> things. >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> With pleasure. Hopefully the answers to your >>>>>>>>>>>>>>>>>>>>>>>>>>> questions will be helpful. >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> PS: loris-dev mailing list: you will find the >>>>>>>>>>>>>>>>>>>>>>>>>>> initial answer I gave Sotirios below. I forgot to cc the loris-dev in my >>>>>>>>>>>>>>>>>>>>>>>>>>> earlier reply... >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 16 ???? 2019 ???? 12:02 ?.?., ?/? >>>>>>>>>>>>>>>>>>>>>>>>>>>> Cecile Madjar ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Dear Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you for reaching out. Since your email >>>>>>>>>>>>>>>>>>>>>>>>>>>>> was already organized in points, I will reply directly below your questions >>>>>>>>>>>>>>>>>>>>>>>>>>>>> below. >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> 1) What do we do when the StudyUID is blank on >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the header? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/minor/docs/AppendixA-Troubleshooting_guideline.md >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> There solution provided at the table 3 does not guide us how to find the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> information ( is possible ). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> The StudyUID is the field used in our pipeline >>>>>>>>>>>>>>>>>>>>>>>>>>>>> at the moment to check whether a DICOM study was already inserted into >>>>>>>>>>>>>>>>>>>>>>>>>>>>> LORIS with that same StudyUID since it is supposed to be unique for every >>>>>>>>>>>>>>>>>>>>>>>>>>>>> single study. Currently, we do not support insertion of DICOM studies if >>>>>>>>>>>>>>>>>>>>>>>>>>>>> they do not have a StudyUID associated with them. >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Is there a specific reason why the StudyUID is >>>>>>>>>>>>>>>>>>>>>>>>>>>>> blank in the DICOM headers in your DICOM files? Did they go through some >>>>>>>>>>>>>>>>>>>>>>>>>>>>> processes before upload to LORIS? >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> 2) When i am about to upload a non-phanton >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> case i need a 'Visit Label'. Is there already a script that can create a >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> new visit label for a specific Candidate, so i can provide it as input >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> afterwards to the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> batch_uploads_imageuploader ( See option 5.1.3 https://github.com/aces/Loris-MRI/blob/minor/docs/05-PipelineLaunchOptions.md ) >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> I am not sure if the front-end allows for it >>>>>>>>>>>>>>>>>>>>>>>>>>>>> but if you use batch_uploads_imageuploader, the insertion scripts could >>>>>>>>>>>>>>>>>>>>>>>>>>>>> create the visit label for you. However, it does need to be included in the >>>>>>>>>>>>>>>>>>>>>>>>>>>>> patient name in order for the script to know which label it should use. >>>>>>>>>>>>>>>>>>>>>>>>>>>>> For example: you upload V02 for MTL0123 >>>>>>>>>>>>>>>>>>>>>>>>>>>>> (DCCID: 456789) but V02 was not yet created for MTL0123; the insertion >>>>>>>>>>>>>>>>>>>>>>>>>>>>> scripts will create a V02 visit for MTL0123 if the PatientName field for >>>>>>>>>>>>>>>>>>>>>>>>>>>>> the dataset is MTL0123_456789_V02 with Stage marked as "Not Started". >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> However, *note that for the script to create >>>>>>>>>>>>>>>>>>>>>>>>>>>>> the visit for the candidate, you have to make sure that all the visit label >>>>>>>>>>>>>>>>>>>>>>>>>>>>> of your projects were inserted in the Visit_Windows table* >>>>>>>>>>>>>>>>>>>>>>>>>>>>> (otherwise, the visit will never be created as they were not specified as >>>>>>>>>>>>>>>>>>>>>>>>>>>>> being part of the list of visit label to expect). So in the example above, >>>>>>>>>>>>>>>>>>>>>>>>>>>>> you should have one row in Visit_Windows with Visit_label="V02" set. >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 3) Section 4.3 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/minor/docs/04-Scripts.md >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> What do we do when the folder contains multiple mnc files? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> This is a case by case. Most of the time, the >>>>>>>>>>>>>>>>>>>>>>>>>>>>> MINC files that failed insertion into the imaging browser end up in the MRI >>>>>>>>>>>>>>>>>>>>>>>>>>>>> violation module where you can see what went wrong with the acquisitions >>>>>>>>>>>>>>>>>>>>>>>>>>>>> not inserted. If you notice that the MINC file should be inserted as a >>>>>>>>>>>>>>>>>>>>>>>>>>>>> specific protocol, you can force the insertion as explained in section 4.3. >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> In your case, I have a feeling that you want >>>>>>>>>>>>>>>>>>>>>>>>>>>>> to be able to insert MINC files that did not go through the whole pipeline >>>>>>>>>>>>>>>>>>>>>>>>>>>>> insertion (DICOM archival, then dcm2mnc, then protocol identification, then >>>>>>>>>>>>>>>>>>>>>>>>>>>>> insertion...). In theory, you could call >>>>>>>>>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl on any MINC file, provided >>>>>>>>>>>>>>>>>>>>>>>>>>>>> you have at least the following information: >>>>>>>>>>>>>>>>>>>>>>>>>>>>> - path to the MINC file >>>>>>>>>>>>>>>>>>>>>>>>>>>>> - uploadID associated with the MINC files or >>>>>>>>>>>>>>>>>>>>>>>>>>>>> DICOM archive path from which those MINC files were created from >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Then the minc_insertion.pl script will do the >>>>>>>>>>>>>>>>>>>>>>>>>>>>> subject information and protocol validation etc... >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> If all the MINC files come from the same >>>>>>>>>>>>>>>>>>>>>>>>>>>>> uploadID or TarchiveID, then you could run a loop in bash calling the >>>>>>>>>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl script like this for files >>>>>>>>>>>>>>>>>>>>>>>>>>>>> deriving from uploadID=1: >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> ls /path/to/mnc/folder/* | while read f; do >>>>>>>>>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl -profile prod -uploadID 1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>> -mincPath $f; done >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helped! >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> -- >>>>>>>>>> >>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>> Montreal Neurological Institute >>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>> >>>>>>>>> >>>>>>>> >>>>>>>> -- >>>>>>>> >>>>>>>> christine.rogers at mcgill.ca >>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>> Montreal Neurological Institute >>>>>>>> McGill University | Montreal | Canada >>>>>>>> >>>>>>> _______________________________________________ >>>>>> Loris-dev mailing list >>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>> >>>>> >>>>> >>>>> -- >>>>> >>>>> christine.rogers at mcgill.ca >>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>> Montreal Neurological Institute >>>>> McGill University | Montreal | Canada >>>>> >>>> _______________________________________________ >>>> Loris-dev mailing list >>>> Loris-dev at bic.mni.mcgill.ca >>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>> >>> >>> >>> -- >>> >>> christine.rogers at mcgill.ca >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>> Montreal Neurological Institute >>> McGill University | Montreal | Canada >>> _______________________________________________ >>> Loris-dev mailing list >>> Loris-dev at bic.mni.mcgill.ca >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>> >> >> >> -- >> >> christine.rogers at mcgill.ca >> McGill Centre for Integrative Neuroscience | MCIN.ca >> Montreal Neurological Institute >> McGill University | Montreal | Canada >> > _______________________________________________ > Loris-dev mailing list > Loris-dev at bic.mni.mcgill.ca > https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > -- Shen Wang Loris Developer Montreal Neurological Institute McGill University -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 78176 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 20518 bytes Desc: not available URL: From wangshen.mcin at gmail.com Tue Aug 27 14:42:08 2019 From: wangshen.mcin at gmail.com (Shen Wang) Date: Tue, 27 Aug 2019 14:42:08 -0400 Subject: [Loris-dev] Import mri - scripts In-Reply-To: References: <65ad2b70c3084ffdb1e4a9dcdad948cd@YTOPR0101MB1803.CANPRD01.PROD.OUTLOOK.COM> Message-ID: Hi, This is a bug for install.sh file, we will fix it later. Thank for letting me know your Loris install situation. regards Shen On Tue, 27 Aug 2019 at 14:28, Shen Wang wrote: > Hi, > Please remove "set -euo pipefail" line 10 in the install.sh file. > Then try again. > > > > On Tue, 27 Aug 2019 at 14:05, Sotirios Nikoloutsopoulos < > sotirisnik at gmail.com> wrote: > >> Hi, >> >> i still haven't resolved the previous issue. Also i tried to install >> Loris to a new virtual machine and when i execute install.sh i get the >> following error >> >> lorisadmin at loris-VirtualBox:/var/www/loris/tools$ ./install.sh >> LORIS Installation Script starting at 2019-08-27T21:00:42 >> The log for this session will be stored in file >> /var/www/loris/tools/logs/install-2019-08-27T21:00:42.log >> --------------------------------------------------------------------- >> LORIS Installation Script >> --------------------------------------------------------------------- >> >> PHP appears to be installed. >> >> PHP Composer appears to be installed. >> >> This install script will ask you to provide inputs for different steps. >> Please ensure you have the following information ready (if applicable): >> >> 1) Your project directory name. >> (Will be used to modify the paths for Imaging data in the generated >> config.xml file for LORIS, and may also be used to automatically >> create/install apache config files.) If unsure, a default like >> "LORIS" >> should be acceptable. >> >> Please also consult the Loris WIKI on GitHub for more information on these >> Install Script input parameters. >> >> Ready to continue? [yn] y >> >> ./install.sh: line 132: projectname: unbound variable >> >> Thanks >> >> ???? ???, 6 ??? 2019 ???? 5:09 ?.?., ?/? Christine Rogers, Ms. < >> christine.rogers at mcgill.ca> ??????: >> >>> Hi Sotirios, >>> Could you also let us know -- on which pages is content visible, and on >>> which pages/modules is content not visible for you? >>> Thanks, >>> Christine >>> >>> On Tue, Aug 6, 2019 at 9:54 AM Christine Rogers, Ms. < >>> christine.rogers at mcgill.ca> wrote: >>> >>>> Thanks Sotirios, >>>> That's good to know. It sounds like you've checked that your >>>> /var/www/loris/project/config.xml file get populated properly. >>>> >>>> Please send us the last few errors you're seeing in your apache error >>>> log file, and your config paths and we can see what's happening with your >>>> front end -- >>>> Run these Troubleshooting Queries >>>> >>>> to get your config path settings, given your front end is not displaying >>>> fully. >>>> >>>> The Loris-MRI repo >>>> 21 >>>> install/upgrade would then be your next steps. >>>> Best, >>>> Christine >>>> >>>> On Tue, Aug 6, 2019 at 7:53 AM Sotirios Nikoloutsopoulos < >>>> sotirisnik at gmail.com> wrote: >>>> >>>>> I am using a VM. What i did was: >>>>> 1) Download the files from https://github.com/aces/Loris and replace >>>>> them to my existing /vaw/www/loris folder. >>>>> 2) Execute the composer install --no-dev and then composer >>>>> dump-autoload as mentioned here >>>>> https://github.com/aces/Loris/wiki/Updating-your-LORIS. >>>>> 3) Execute install.sh from /var/www/loris/tools and because LORIS >>>>> already existed i moved a .config file, then re-executed the install.sh >>>>> successfully >>>>> 4 ) As for the database, i dropped the schema and i executed the >>>>> installdb.php >>>>> >>>>> ???? ???, 5 ??? 2019 ???? 5:22 ?.?., ?/? Christine Rogers, Ms. < >>>>> christine.rogers at mcgill.ca> ??????: >>>>> >>>>>> Hi Sotorios, >>>>>> >>>>>> Thanks - when you re-installed did you start on a fresh root path / >>>>>> VM or might some of your old system setting still apply? >>>>>> (And if you did any steps similar to an upgrade, did you follow the >>>>>> Upgrade steps in the Release Notes, from both repos?) >>>>>> >>>>>> About the TR_range column - it was recently split (MRI pr339 >>>>>> ) split into TR_min and >>>>>> _max columns. Given the code was trying to query TR_range which does not >>>>>> exist in your mri_protocol table, double-check which version of the Loris >>>>>> repo (tables) and the Loris-MRI repo (code) you have installed to ensure >>>>>> they match. >>>>>> >>>>>> Christine >>>>>> >>>>>> >>>>>> On Mon, Aug 5, 2019 at 9:06 AM Sotirios Nikoloutsopoulos < >>>>>> sotirisnik at gmail.com> wrote: >>>>>> >>>>>>> I reinstalled LORIS to 21 version and now the content is not visible >>>>>>> at all at most pages. >>>>>>> >>>>>>> [image: image.png] >>>>>>> >>>>>>> ???? ???, 5 ??? 2019 ???? 3:19 ?.?., ?/? Sotirios Nikoloutsopoulos < >>>>>>> sotirisnik at gmail.com> ??????: >>>>>>> >>>>>>>> Hi, >>>>>>>> >>>>>>>> Is it easy to upgrade to Loris 21? Also the following fails because >>>>>>>> the line 1985 of NeuroDB/MRIProcessingUtility.pm query mri_protocol which >>>>>>>> doesn't have TR_range >>>>>>>> https://github.com/aces/Loris/blob/21.0-release/SQL/0000-00-00-schema.sql#L556 >>>>>>>> >>>>>>>> [image: image.png] >>>>>>>> >>>>>>>> lorisadmin at hbp:/data/loris/bin/mri$ ./batch_uploads_imageuploader >>>>>>>> -profile prod < ~/Desktop/input.txt > log.txt >>>>>>>> Use of uninitialized value $_ in pattern match (m//) at >>>>>>>> ./batch_uploads_imageuploader line 147. >>>>>>>> base is DCC0000_258024_V1 >>>>>>>> path is /data/incoming/ >>>>>>>> type is .tar.gz >>>>>>>> fullpath is /data/incoming/DCC0000_258024_V1.tar.gz >>>>>>>> DBD::mysql::st execute failed: Unknown column 'TR_range' in 'where >>>>>>>> clause' at >>>>>>>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line 1985. >>>>>>>> DBD::mysql::st fetchrow_array failed: fetch() without execute() at >>>>>>>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line 1986. >>>>>>>> Use of uninitialized value $count_mri_protocol in numeric gt (>) at >>>>>>>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line 1995. >>>>>>>> DBD::mysql::st execute failed: Unknown column 'TR_range' in 'field >>>>>>>> list' at /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 562. >>>>>>>> Can't exec "mail": No such file or directory at >>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 721. >>>>>>>> print() on closed filehandle MAIL at >>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 722. >>>>>>>> print() on closed filehandle MAIL at >>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 723. >>>>>>>> print() on closed filehandle MAIL at >>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 724. >>>>>>>> print() on closed filehandle MAIL at >>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 725. >>>>>>>> >>>>>>>> No Mincs inserted >>>>>>>> >>>>>>>> Thanks, >>>>>>>> >>>>>>>> Sotirios >>>>>>>> >>>>>>>> ???? ???, 3 ??? 2019 ???? 1:08 ?.?., ?/? Christine Rogers, Ms. < >>>>>>>> christine.rogers at mcgill.ca> ??????: >>>>>>>> >>>>>>>>> Hi Sotirios, >>>>>>>>> >>>>>>>>> First, just a note: we've released LORIS 21 this week with some >>>>>>>>> major new features and cleanup -- especially if you are early in your setup >>>>>>>>> phase, check out the Release notes for both the LORIS >>>>>>>>> and Loris-MRI >>>>>>>>> repos. >>>>>>>>> >>>>>>>>> Thanks for your screenshots -- your empty mri_protocol table >>>>>>>>> should be at the root of these issues : >>>>>>>>> >>>>>>>>> The mri_protocol table must be populated >>>>>>>>> >>>>>>>>> in order for your scans to be registered in LORIS -- it serves as a >>>>>>>>> whitelist for the insertion pipeline which filters out scans that aren't >>>>>>>>> identified or matched to scan types in this table. >>>>>>>>> >>>>>>>>> By default, this table is populated with entries for t1, t2, fMRI >>>>>>>>> and DTI (Insert statements for 21 release branch are here >>>>>>>>> >>>>>>>>> ) >>>>>>>>> Feel free to restore our default records and broaden their >>>>>>>>> parameters to match all your scan types. >>>>>>>>> >>>>>>>>> re Defaced, native, selected -- these filter the scans displayed >>>>>>>>> as you move to the next page (View Session), instead of viewing "all types" >>>>>>>>> of scans from a given session : >>>>>>>>> >>>>>>>>> - "defaced" means that a defacing script >>>>>>>>> >>>>>>>>> has masked the subject's face in the volume (for patient privacy) >>>>>>>>> - "native" means that no pre-processing has been performed on >>>>>>>>> the scan (it's raw data), >>>>>>>>> - "selected" will show only volumes that have been QC'd and >>>>>>>>> "selected" as the best of their type -- used to display only the best >>>>>>>>> quality T1 image instead of all T1s acquired in a session, e.g. >>>>>>>>> >>>>>>>>> re QC Comments -- >>>>>>>>> Once you have successfully loaded scans (matched to the >>>>>>>>> mri_protocol table), you'll be able to use the Imaging Browser's View >>>>>>>>> Session subpage to enter/view QC comments on each volume, or for each >>>>>>>>> visit. >>>>>>>>> These are stored directly in the database, and linked to each >>>>>>>>> scan. (Table name: feedback_mri_comments) >>>>>>>>> (Visit-level QC comments are linked to the session.) >>>>>>>>> >>>>>>>>> For a walkthrough of the Imaging setup - please see the Imaging >>>>>>>>> Setup guide >>>>>>>>> >>>>>>>>> - >>>>>>>>> >>>>>>>>> An old LORIS walkthrough video >>>>>>>>> can also walk you >>>>>>>>> through some of the Imaging front-end features, starting at 8:00 >>>>>>>>> LORIS' imaging modules have been updated many times since this >>>>>>>>> video, but the functionality and workflow is similar. >>>>>>>>> >>>>>>>>> Let us know how it goes once you have entries in your mri_protocol >>>>>>>>> table - >>>>>>>>> Best, >>>>>>>>> Christine >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> On Fri, Aug 2, 2019 at 7:58 AM Sotirios Nikoloutsopoulos < >>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>> >>>>>>>>>> Hi Christine, >>>>>>>>>> >>>>>>>>>> In the candidate_list page i can see this patient >>>>>>>>>> >>>>>>>>>> [image: image.png] >>>>>>>>>> >>>>>>>>>> If i press the link under PSCID i get to see >>>>>>>>>> [image: image.png] >>>>>>>>>> >>>>>>>>>> and if i press the link under Scan Done it redirects me to >>>>>>>>>> imaging_browser >>>>>>>>>> >>>>>>>>>> [image: image.png] >>>>>>>>>> >>>>>>>>>> At the mri_violations page i also see No results ( neither on >>>>>>>>>> resolved / not resolved ). >>>>>>>>>> >>>>>>>>>> At the imaging_uploader i can see the record that failed. >>>>>>>>>> >>>>>>>>>> [image: image.png] >>>>>>>>>> >>>>>>>>>> If i click on the tarchive info i get to see the Protocol Name >>>>>>>>>> which i think is the acquisition we wanted? >>>>>>>>>> [image: image.png] >>>>>>>>>> >>>>>>>>>> Also my mri_protocol table is empty. >>>>>>>>>> >>>>>>>>>> Furthermore i would like to ask about the defaced, native, >>>>>>>>>> selected. What exactly is native and selected? And where are the qc >>>>>>>>>> comments stored? >>>>>>>>>> >>>>>>>>>> [image: image.png] >>>>>>>>>> >>>>>>>>>> Finally a walkthrough would be helpful. >>>>>>>>>> >>>>>>>>>> Thanks, >>>>>>>>>> >>>>>>>>>> Sotirios >>>>>>>>>> >>>>>>>>>> ???? ???, 30 ???? 2019 ???? 8:29 ?.?., ?/? Christine Rogers, Ms. < >>>>>>>>>> christine.rogers at mcgill.ca> ??????: >>>>>>>>>> >>>>>>>>>>> Hi Sotirios, >>>>>>>>>>> Glad to hear you're making progress with the visit labels. To >>>>>>>>>>> follow up on your last few emails: >>>>>>>>>>> >>>>>>>>>>> a- The Wiki's Setup Guide contains Sample insert statements for >>>>>>>>>>> the Visit Windows table >>>>>>>>>>> >>>>>>>>>>> . >>>>>>>>>>> >>>>>>>>>>> As Cecile mentioned, the consistency of visit label format is >>>>>>>>>>> important: V01, v01, V1, 01 -- whichever you select to use is fine; we use >>>>>>>>>>> V01 by default across all documentation. >>>>>>>>>>> >>>>>>>>>>> b- For Password reset, there is a script in the tools/ directory >>>>>>>>>>> so that a back-end administrator can reset any front-end user password, >>>>>>>>>>> including Admin. (See info on setting up / resetting User passwords in the Wiki's >>>>>>>>>>> Setup Guide >>>>>>>>>>> >>>>>>>>>>> ) >>>>>>>>>>> >>>>>>>>>>> c- The minc file not being registered -- due to >>>>>>>>>>> AcquisitionProtocol unknown. >>>>>>>>>>> This means the SeriesDescription (Acquisition Protocol) in you >>>>>>>>>>> Dicom header was not matched to any scan listed in the mri_protocol >>>>>>>>>>> database table. >>>>>>>>>>> (In the online Loris-MRI Troubleshooting Guide, >>>>>>>>>>> this >>>>>>>>>>> is Table 3, 2nd-last item "no MINCs inserted"). >>>>>>>>>>> >>>>>>>>>>> The MRI Violations module (Readme here) >>>>>>>>>>> will show >>>>>>>>>>> you the details of this mismatch -- >>>>>>>>>>> Go to the module (under the Imaging menu), find your scan and >>>>>>>>>>> click the link "Could not identify scan type" -- in the next subpage you >>>>>>>>>>> can compare the scan's actual parameters against the mri_protocol table. >>>>>>>>>>> >>>>>>>>>>> To resolve this, adjust your mri_protocol table values or >>>>>>>>>>> perhaps ensure your DICOMs are labelled consistently. >>>>>>>>>>> >>>>>>>>>>> Let us know if this works for you -- we can also walk you >>>>>>>>>>> through an example of non-identified scans on Demo.loris.ca >>>>>>>>>>> (MRI Violations module). >>>>>>>>>>> >>>>>>>>>>> Best, >>>>>>>>>>> Christine >>>>>>>>>>> >>>>>>>>>>> The LORIS team >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> On Tue, Jul 30, 2019 at 10:47 AM Sotirios Nikoloutsopoulos < >>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>> >>>>>>>>>>>> I hope this is sufficient as the error for the visit label >>>>>>>>>>>> disappeared. >>>>>>>>>>>> [image: image.png] >>>>>>>>>>>> >>>>>>>>>>>> Please see the attached file. Also something i found. >>>>>>>>>>>> >>>>>>>>>>>> lorisadmin at hbp:/data/loris/bin/mri$ cat >>>>>>>>>>>> /data/loris/data//logs/TarLoad-17-39-xubBdv.log >>>>>>>>>>>> >>>>>>>>>>>> ==> Loading file from disk >>>>>>>>>>>> /tmp/TarLoad-17-39-UyQcG2/dcc0000_258024_v1_20121205_102108_501e1_mri.mnc >>>>>>>>>>>> >>>>>>>>>>>> --> mapping DICOM parameter for >>>>>>>>>>>> /tmp/TarLoad-17-39-UyQcG2/dcc0000_258024_v1_20121205_102108_501e1_mri.mnc >>>>>>>>>>>> >>>>>>>>>>>> ==> computing md5 hash for MINC body. >>>>>>>>>>>> >>>>>>>>>>>> --> md5: 6b1202fd63e29de4c9be1cd9925888a5 >>>>>>>>>>>> >>>>>>>>>>>> ==> verifying acquisition protocol >>>>>>>>>>>> >>>>>>>>>>>> Acquisition protocol is unknown >>>>>>>>>>>> >>>>>>>>>>>> --> The minc file cannot be registered since the >>>>>>>>>>>> AcquisitionProtocol is unknown >>>>>>>>>>>> >>>>>>>>>>>> ???? ???, 30 ???? 2019 ???? 4:58 ?.?., ?/? Sotirios >>>>>>>>>>>> Nikoloutsopoulos ??????: >>>>>>>>>>>> >>>>>>>>>>>>> Ok I fixed the login problem by using a known hash and by >>>>>>>>>>>>> deleting the rows from the login_history i was able to login. >>>>>>>>>>>>> >>>>>>>>>>>>> ???? ???, 30 ???? 2019 ???? 4:50 ?.?., ?/? Sotirios >>>>>>>>>>>>> Nikoloutsopoulos ??????: >>>>>>>>>>>>> >>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>> >>>>>>>>>>>>>> there was no visit label 01 in the Visit_Windows table and i >>>>>>>>>>>>>> don't know how to insert it because the record requires lots of attributes. >>>>>>>>>>>>>> Also the system for a reason asked me to update my password and now i don't >>>>>>>>>>>>>> remember it and my account got suspended. Is there a way to reset it or set >>>>>>>>>>>>>> a simple password? I updated the password hash in the users table by using >>>>>>>>>>>>>> the hash from another LORIS setup we had and i still couldn't login ( also >>>>>>>>>>>>>> the attribute password is always NULL and the expiration date is 1999-01-01 >>>>>>>>>>>>>> for some reason ). >>>>>>>>>>>>>> >>>>>>>>>>>>>> Thanks >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> ???? ???, 29 ???? 2019 ???? 5:21 ?.?., ?/? Cecile Madjar < >>>>>>>>>>>>>> cecile.madjar at mcin.ca> ??????: >>>>>>>>>>>>>> >>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> Can you try adding the visit label v01 to the Visit_Windows >>>>>>>>>>>>>>> table? >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> However, I noticed that in a previous dataset, the label was >>>>>>>>>>>>>>> V1. Does that refer to the same visit? If so, you might want to harmonize >>>>>>>>>>>>>>> the visit labels so they are all the same across datasets for a given >>>>>>>>>>>>>>> timepoint, meaning you will need to relabel scans when the visit label is >>>>>>>>>>>>>>> different but referring to the same visit label (v01 = V1 etc...). >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> Hope this helps, >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> On Mon, Jul 29, 2019 at 10:15 AM Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Could you help me with the "Visit label does not exist"? I >>>>>>>>>>>>>>>> had changed $subjectID{'createVisitLabel'} to 1 as you had suggested but >>>>>>>>>>>>>>>> it appears that this problem hasn't been resolved yet. >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> lorisadmin at hbp:/data/loris/bin/mri$ cat >>>>>>>>>>>>>>>> /data/loris/data//logs/TarLoad-14-58-9Xog7H.log >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> ==> Loading file from disk >>>>>>>>>>>>>>>> /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> --> mapping DICOM parameter for >>>>>>>>>>>>>>>> /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> --> using user-defined filterParameters for >>>>>>>>>>>>>>>> /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Candidate Mismatch Error is Visit label does not exist >>>>>>>>>>>>>>>> -> WARNING: This candidate was invalid. Logging to >>>>>>>>>>>>>>>> MRICandidateErrors table with reason Visit >>>>>>>>>>>>>>>> label does not exist >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> ???? ???, 26 ???? 2019 ???? 3:02 ?.?., ?/? Sotirios >>>>>>>>>>>>>>>> Nikoloutsopoulos ??????: >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Hi Cecile, >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> The Center error was fixed. Still the insertion of mincs >>>>>>>>>>>>>>>>> fails. Please see the output.txt file i attached. Also is there something >>>>>>>>>>>>>>>>> else i need to change at the paths configuration? >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> ???? ???, 25 ???? 2019 ???? 6:55 ?.?., ?/? Cecile Madjar < >>>>>>>>>>>>>>>>> cecile.madjar at mcin.ca> ??????: >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> We are making progress! >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> I have a feeling this error comes from the fact that your >>>>>>>>>>>>>>>>>> psc table does not have the MRI_alias populated for the DCC site. Running >>>>>>>>>>>>>>>>>> the following query in the mysql database should fix this: >>>>>>>>>>>>>>>>>> UPDATE psc SET MRI_alias="DCC", Alias="DCC" WHERE >>>>>>>>>>>>>>>>>> Name="Data Coordinating Center"; >>>>>>>>>>>>>>>>>> Repeat the same with all your sites (make sure to change >>>>>>>>>>>>>>>>>> the Aliases between sites, they should all be unique). >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Let me know how it goes! >>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> On Thu, Jul 25, 2019 at 11:43 AM Sotirios >>>>>>>>>>>>>>>>>> Nikoloutsopoulos wrote: >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Dear Cecile, >>>>>>>>>>>>>>>>>>> You were right about your guesses. I did the >>>>>>>>>>>>>>>>>>> modifications you suggested, i still get the "no mincs inserted" error, now >>>>>>>>>>>>>>>>>>> i am getting the "No center found this candidate" error ( how do i fix >>>>>>>>>>>>>>>>>>> that? from what i see the .dcm files contains a 'Institution Name', is that >>>>>>>>>>>>>>>>>>> the center? ), so i guess that's why the validation fails, but i changed >>>>>>>>>>>>>>>>>>> the force variable of tarchiveLoader to 1, shouldn't it have inserted the >>>>>>>>>>>>>>>>>>> mincs then? Also it is optional to have a mail server, right? ( from what i >>>>>>>>>>>>>>>>>>> see the mail error does not affect the $valid_study, so i assume we are >>>>>>>>>>>>>>>>>>> okay with that ) >>>>>>>>>>>>>>>>>>> Thank you a lot, >>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> ???? ???, 25 ???? 2019 ???? 5:48 ?.?., ?/? Cecile Madjar >>>>>>>>>>>>>>>>>>> ??????: >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> From what I understand, I believe you just need to >>>>>>>>>>>>>>>>>>>> update a few config settings from the frontend in the Config module (under >>>>>>>>>>>>>>>>>>>> the Admin menu). >>>>>>>>>>>>>>>>>>>> [image: Screen Shot 2019-07-25 at 10.31.35 AM.png] >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Then go to the Paths section of the config module and >>>>>>>>>>>>>>>>>>>> update the "LORIS-MRI code" config setting to /data/loris/bin/mri (my guess >>>>>>>>>>>>>>>>>>>> is that currently, it is set to /data/LORIS/data) and click on the submit >>>>>>>>>>>>>>>>>>>> button. >>>>>>>>>>>>>>>>>>>> [image: Screen Shot 2019-07-25 at 10.32.50 AM.png] >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Then, go to Imaging Pipeline section of the >>>>>>>>>>>>>>>>>>>> Configuration module and update the "Loris-MRI Data Directory" to >>>>>>>>>>>>>>>>>>>> /data/loris/data/ (my guess is that it is empty at the moment in your >>>>>>>>>>>>>>>>>>>> database which is why $data_dir is not defined when you run the >>>>>>>>>>>>>>>>>>>> tarchiveLoader step of the insertion pipeline). >>>>>>>>>>>>>>>>>>>> [image: Screen Shot 2019-07-25 at 10.40.52 AM.png] >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Finally, I took a look at your environment file and it >>>>>>>>>>>>>>>>>>>> might be a good idea to update your PERL5LIB variable to the following (it >>>>>>>>>>>>>>>>>>>> has been added to the code a few releases ago as we realized this was >>>>>>>>>>>>>>>>>>>> needed for the libraries. Not sure which version of LORIS-MRI you are using >>>>>>>>>>>>>>>>>>>> but it does not hurt to update this variable to what I suggest below): >>>>>>>>>>>>>>>>>>>> export >>>>>>>>>>>>>>>>>>>> PERL5LIB=/data/loris/bin/mri/uploadNeuroDB:/data/loris/bin/mri/dicom-archive:$PERL5LIB >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Hope this helps. Sorry you are experiencing so much >>>>>>>>>>>>>>>>>>>> trouble setting things up. We probably need to update our WIKI. >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> On Thu, Jul 25, 2019 at 9:48 AM Sotirios >>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos wrote: >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> The "Loris-MRI Data Directory" should be in the >>>>>>>>>>>>>>>>>>>>> environment file? >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> ???? ???, 25 ???? 2019 ???? 12:59 ?.?., ?/? Sotirios >>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos ??????: >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> The scripts are located in /data/loris/bin/mri/. >>>>>>>>>>>>>>>>>>>>>> Somewhere I might have messed something up but i remember following the >>>>>>>>>>>>>>>>>>>>>> instructions in the wiki.For example when i tried to execute the >>>>>>>>>>>>>>>>>>>>>> batch_uploads_imageuploader perl script the line >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> my $command = "$bin_dir/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl " >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> was pointing to an invalid path, for example: it was >>>>>>>>>>>>>>>>>>>>>> repeating a pattern and had LORIS instead of loris ( i think the mistake >>>>>>>>>>>>>>>>>>>>>> was that in the wiki it suggested to use $PROJECT for the name of the >>>>>>>>>>>>>>>>>>>>>> folder and i choosed 'loris' >>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris/wiki/Imaging-Database >>>>>>>>>>>>>>>>>>>>>> ). See also the in image for the modification i did. Also i didn't find the >>>>>>>>>>>>>>>>>>>>>> section to config the $data_dir variable. >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> ???? ???, 24 ???? 2019 ???? 6:05 ?.?., ?/? Cecile >>>>>>>>>>>>>>>>>>>>>> Madjar ??????: >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> It looks like you have one Config setting not set >>>>>>>>>>>>>>>>>>>>>>> (based on the first error message you got when running it the first time). >>>>>>>>>>>>>>>>>>>>>>> You need to set a value for "Loris-MRI Data Directory" in the Config module >>>>>>>>>>>>>>>>>>>>>>> under the Imaging pipeline section (from what I can see, it would be >>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/ for your setup). >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> The reason you got that error message the second >>>>>>>>>>>>>>>>>>>>>>> time is that the pipeline checks if the DICOM study was already inserted in >>>>>>>>>>>>>>>>>>>>>>> the tarchive table. Since you ran the study once already, the study is >>>>>>>>>>>>>>>>>>>>>>> inserted into the tarchive, hence the message. However, the pipeline did >>>>>>>>>>>>>>>>>>>>>>> not complete as the MINC files were not created and inserted into the >>>>>>>>>>>>>>>>>>>>>>> files/parameter_file table. In order to continue the insertion, you will >>>>>>>>>>>>>>>>>>>>>>> then need to run the tarchiveLoader command suggested in the terminal >>>>>>>>>>>>>>>>>>>>>>> during the second run: >>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader >>>>>>>>>>>>>>>>>>>>>>> -globLocation -profile prod >>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive//2012/DCM_2012-12-05_ImagingUpload-17-43-ZUEFjb.tar >>>>>>>>>>>>>>>>>>>>>>> -verbose >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> Finally, I am a bit confused by your setup. Where >>>>>>>>>>>>>>>>>>>>>>> are the scripts located? In /data/loris/bin/mri or /data/loris/data? It >>>>>>>>>>>>>>>>>>>>>>> feels like the Config setting "LORIS-MRI code" in the Paths section was set >>>>>>>>>>>>>>>>>>>>>>> to "/data/LORIS/data" but it should have been set to the directory where >>>>>>>>>>>>>>>>>>>>>>> the scripts are located (most probably /data/loris/bin/mri). >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> Hope this helps, >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> On Wed, Jul 24, 2019 at 10:55 AM Sotirios >>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos wrote: >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> Ok first i execute this command: >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> "lorisadmin at hbp:/data/loris/bin/mri$ >>>>>>>>>>>>>>>>>>>>>>>> ./batch_uploads_imageuploader -profile prod < ~/Desktop/input.txt > log.txt >>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at ./batch_uploads_imageuploader line 143. >>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at ./batch_uploads_imageuploader line 143. >>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $_ in pattern match >>>>>>>>>>>>>>>>>>>>>>>> (m//) at ./batch_uploads_imageuploader line 147. >>>>>>>>>>>>>>>>>>>>>>>> base is DCC0000_258024_V01 >>>>>>>>>>>>>>>>>>>>>>>> path is /data/incoming/ >>>>>>>>>>>>>>>>>>>>>>>> type is .tar.gz >>>>>>>>>>>>>>>>>>>>>>>> fullpath is >>>>>>>>>>>>>>>>>>>>>>>> /data/incoming/DCC0000_258024_V01.tar.gz >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> source /tmp/ImagingUpload-17-43-ZUEFjb >>>>>>>>>>>>>>>>>>>>>>>> targetlocation /data/loris/data/tarchive >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 256. >>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 284. >>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at /data/loris/bin/mri/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>> tarchive_validation.pl line 219. >>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at /data/loris/bin/mri/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl line 270. >>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 711. >>>>>>>>>>>>>>>>>>>>>>>> Can't exec "mail": No such file or directory at >>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 721. >>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 722. >>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 723. >>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 724. >>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 724. >>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 725. >>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 735. >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> No Mincs inserted >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> The tarchiveLoader insertion script has failed. >>>>>>>>>>>>>>>>>>>>>>>> Running now the following command: >>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl -profile prod -upload_id 3 >>>>>>>>>>>>>>>>>>>>>>>> /data/incoming/DCC0000_258024_V01.tar.gz -verbose" >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> I inserted the VisitLabel, but still the Mincs are >>>>>>>>>>>>>>>>>>>>>>>> not inserted and i am getting this error >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> "lorisadmin at hbp:/data/loris/bin/mri$ >>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl -profile prod -upload_id 3 >>>>>>>>>>>>>>>>>>>>>>>> /data/incoming/DCC0000_258024_V01.tar.gz -verbose >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> find -path \/tmp\/ImagingUpload\-17\-45\-5MsWEd >>>>>>>>>>>>>>>>>>>>>>>> -name '__MACOSX' -delete >>>>>>>>>>>>>>>>>>>>>>>> Spool message is: >>>>>>>>>>>>>>>>>>>>>>>> The Scan for the uploadID 3 has already been run >>>>>>>>>>>>>>>>>>>>>>>> with tarchiveID: 7. >>>>>>>>>>>>>>>>>>>>>>>> To continue with the rest of the insertion >>>>>>>>>>>>>>>>>>>>>>>> pipeline, please run tarchiveLoader from a terminal as follows: >>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader -globLocation -profile prod >>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive//2012/DCM_2012-12-05_ImagingUpload-17-43-ZUEFjb.tar >>>>>>>>>>>>>>>>>>>>>>>> -verbose" >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> Which files should i delete? I thought that >>>>>>>>>>>>>>>>>>>>>>>> deleting the files from the tarchive was enough. And i executed the last >>>>>>>>>>>>>>>>>>>>>>>> proposed command to continue to rest of the insertion pipeline ( check the >>>>>>>>>>>>>>>>>>>>>>>> image ). >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> Thank you >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 24 ???? 2019 ???? 5:05 ?.?., ?/? Cecile >>>>>>>>>>>>>>>>>>>>>>>> Madjar ??????: >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> Sorry I was not clear before. Every visits of >>>>>>>>>>>>>>>>>>>>>>>>> candidates are created in the session table with one entry per >>>>>>>>>>>>>>>>>>>>>>>>> CandID/VisitLabel. So if the imaging pipeline created visits in the session >>>>>>>>>>>>>>>>>>>>>>>>> table (that are not attached to instruments) and you want to clean your >>>>>>>>>>>>>>>>>>>>>>>>> database completely, you can delete entries in that table as well. >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> Regarding your point 2, the imaging pipeline can >>>>>>>>>>>>>>>>>>>>>>>>> create the visit in the session table as long as the visit label is present >>>>>>>>>>>>>>>>>>>>>>>>> in the Visit_Windows table (which means the visit label stored in the >>>>>>>>>>>>>>>>>>>>>>>>> PatientName is a valid visit label). >>>>>>>>>>>>>>>>>>>>>>>>> However, in your prod file, if the >>>>>>>>>>>>>>>>>>>>>>>>> variable $subjectID{'createVisitLabel'} is set to 1 for candidates, the >>>>>>>>>>>>>>>>>>>>>>>>> visit label should be created in the Visit_Windows table I believe. Here >>>>>>>>>>>>>>>>>>>>>>>>> is the line of the prod file you would need to change >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> . >>>>>>>>>>>>>>>>>>>>>>>>> In general, we prefer populating the Visit_Windows >>>>>>>>>>>>>>>>>>>>>>>>> table and set the $subjectID{'createVisitLabel'} to 0 for candidate data to >>>>>>>>>>>>>>>>>>>>>>>>> avoid insertion of badly labelled MRI data that are complex to relabel. >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> Finally, regarding the candidate creation, if you >>>>>>>>>>>>>>>>>>>>>>>>> execute the following steps, the pipeline should be able to create >>>>>>>>>>>>>>>>>>>>>>>>> candidates: >>>>>>>>>>>>>>>>>>>>>>>>> - set in the Imaging Pipeline section of the >>>>>>>>>>>>>>>>>>>>>>>>> config module the config setting "Upload creation of candidates" to Yes >>>>>>>>>>>>>>>>>>>>>>>>> - manually transfer the scans to the LORIS server >>>>>>>>>>>>>>>>>>>>>>>>> instead of uploading it via the imaging browser >>>>>>>>>>>>>>>>>>>>>>>>> - run batch_imaging_upload.pl as you did until >>>>>>>>>>>>>>>>>>>>>>>>> now. >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> Hope this helps! >>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> On Wed, Jul 24, 2019 at 8:47 AM Sotirios >>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos wrote: >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> About my second question i replaced the name of >>>>>>>>>>>>>>>>>>>>>>>>>> the patient in the .dcm files and now i am getting an error that the visit >>>>>>>>>>>>>>>>>>>>>>>>>> label does not exist. >>>>>>>>>>>>>>>>>>>>>>>>>> I thought it was supposed to be automatically >>>>>>>>>>>>>>>>>>>>>>>>>> created. >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> "Done adding archive info into database >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader >>>>>>>>>>>>>>>>>>>>>>>>>> -globLocation -profile prod >>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive//DCM_2012-12-05_ImagingUpload-15-42-yUwQQV.tar >>>>>>>>>>>>>>>>>>>>>>>>>> -verbose >>>>>>>>>>>>>>>>>>>>>>>>>> md5sum >>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive/DCM_2012-12-05_ImagingUpload-15-42-yUwQQV.tar >>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>> candidate id 258024 >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> => No Visit labelVisit label does not exist >>>>>>>>>>>>>>>>>>>>>>>>>> Set centerID = 1 >>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> Number of MINC files that will be considered for >>>>>>>>>>>>>>>>>>>>>>>>>> inserting into the database: 1 >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> log dir is /logs and log file is >>>>>>>>>>>>>>>>>>>>>>>>>> /logs/TarLoad-15-42-L6pocU.log >>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>> candidate id 258024 >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> => No Visit label >>>>>>>>>>>>>>>>>>>>>>>>>> Cleaning up temp files: rm -rf >>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-15-42-J2rQms/ImagingUpload-15-42-yUwQQV*" >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 24 ???? 2019 ???? 3:38 ?.?., ?/? >>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos >>>>>>>>>>>>>>>>>>>>>>>>>> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> 1) What are the records in the session table? >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> 2) I tried to upload a non-phantom file like this >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> input_file.txt: >>>>>>>>>>>>>>>>>>>>>>>>>>> /data/incoming/DCC0000_258024_V1.tar.gz N >>>>>>>>>>>>>>>>>>>>>>>>>>> DCC0000_258024_V1 >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> Terminal: >>>>>>>>>>>>>>>>>>>>>>>>>>> ./batch_uploads_imageuploader -profile prod < >>>>>>>>>>>>>>>>>>>>>>>>>>> ~/Desktop/input.txt > log.txt >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> and i get the following error in the log.txt file >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> "Running now the following command: >>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl -profile prod -upload_id >>>>>>>>>>>>>>>>>>>>>>>>>>> 7 /data/incoming/DCC0000_258024_V1.tar.gz -verbose >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> find -path \/tmp\/ImagingUpload\-14\-56\-FeLCB4 >>>>>>>>>>>>>>>>>>>>>>>>>>> -name '__MACOSX' -delete >>>>>>>>>>>>>>>>>>>>>>>>>>> Spool message is: >>>>>>>>>>>>>>>>>>>>>>>>>>> The PatientName read from the DICOM header does >>>>>>>>>>>>>>>>>>>>>>>>>>> not start with DCC0000_258024_V1 from the mri_upload table >>>>>>>>>>>>>>>>>>>>>>>>>>> " >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> and the spool message is repeated for each .dcm >>>>>>>>>>>>>>>>>>>>>>>>>>> file. Should i preprocess every .dcm file and change the PatientName to >>>>>>>>>>>>>>>>>>>>>>>>>>> "DCC0000_258024_V1"? >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> 3) As far as it concerns the candidate profile i >>>>>>>>>>>>>>>>>>>>>>>>>>> have to create a new one each time before i try to upload a file? Is there >>>>>>>>>>>>>>>>>>>>>>>>>>> already a way to create a candidate profile and get the DCCID and PSCID >>>>>>>>>>>>>>>>>>>>>>>>>>> without the user interface? >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 18 ???? 2019 ???? 5:00 ?.?., ?/? >>>>>>>>>>>>>>>>>>>>>>>>>>> Cecile Madjar ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> See answers to your questions below. >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> About the 1st case we had a dicom with a blank >>>>>>>>>>>>>>>>>>>>>>>>>>>>> studyUID, maybe someone accidentally removed it. >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> That is strange. Something must have been done >>>>>>>>>>>>>>>>>>>>>>>>>>>> to the DICOM files. I have never seen a study with no StudyUID out of the >>>>>>>>>>>>>>>>>>>>>>>>>>>> scanner. Usually, you need to manually erase it with some tool. However, >>>>>>>>>>>>>>>>>>>>>>>>>>>> DICOMs never cease to surprise me... >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Some other questions: >>>>>>>>>>>>>>>>>>>>>>>>>>>>> 1) What are the steps to remove all of my >>>>>>>>>>>>>>>>>>>>>>>>>>>>> patients and uploads?: because i want to try to reupload all the testing >>>>>>>>>>>>>>>>>>>>>>>>>>>>> dicoms we had with a clean database. >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> Release 21.0 of LORIS-MRI will offer a script >>>>>>>>>>>>>>>>>>>>>>>>>>>> to remove all the entries and files specific to an upload. However, this >>>>>>>>>>>>>>>>>>>>>>>>>>>> release is not yet out. Hopefully in the next few weeks. >>>>>>>>>>>>>>>>>>>>>>>>>>>> In the meantime, since your case is particular >>>>>>>>>>>>>>>>>>>>>>>>>>>> and that you just want to start with a clean database, the following >>>>>>>>>>>>>>>>>>>>>>>>>>>> deletes should work (hopefully I won't forget any tables): >>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from mri_violations_log; >>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from mri_protocol_violated_scans; >>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from MRICandidateErrors; >>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from parameter_file; >>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from files_qcstatus; # (if you played >>>>>>>>>>>>>>>>>>>>>>>>>>>> with the QC part of the imaging browser for testing) >>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from feedback_mri_comments; # (if you >>>>>>>>>>>>>>>>>>>>>>>>>>>> played with the QC part of the imaging browser for testing) >>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from tarchive_series; >>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from tarchive_files; >>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from mri_upload; >>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from tarchive; >>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from mri_scanner; >>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from candidate where PSCID="scanner"; >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> I don't know if you want to also delete entries >>>>>>>>>>>>>>>>>>>>>>>>>>>> in the session and candidate table too? >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> 2) We do not need to create the profile of a >>>>>>>>>>>>>>>>>>>>>>>>>>>>> patient ( are the patients stored in the candidate table? because i can't >>>>>>>>>>>>>>>>>>>>>>>>>>>>> see the ghosts ), because will it automatically be created when importing a >>>>>>>>>>>>>>>>>>>>>>>>>>>>> dicom? >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> I am not sure I understand fully this question. >>>>>>>>>>>>>>>>>>>>>>>>>>>> All candidates are stored in the candidate table. The phantom scans however >>>>>>>>>>>>>>>>>>>>>>>>>>>> are attached to a scanner candidate depending on where the scan happened. >>>>>>>>>>>>>>>>>>>>>>>>>>>> It is a bit of a weird concept that we have to redesign eventually but >>>>>>>>>>>>>>>>>>>>>>>>>>>> never got a chance to get to it. >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> Hopefully this answered your question, >>>>>>>>>>>>>>>>>>>>>>>>>>>> otherwise, don't hesitate to let me know. >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> 3) What is the difference between uploading a >>>>>>>>>>>>>>>>>>>>>>>>>>>>> dicom as phantom instead of importing as PSCCID_DCCID_VisitLabel? >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> When you upload the scan as >>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID_DCCID_VisitLabel, there is a check that makes sure the candidate IDs >>>>>>>>>>>>>>>>>>>>>>>>>>>> and visit label are valid at the time of upload. >>>>>>>>>>>>>>>>>>>>>>>>>>>> When you upload a scan as phantom, it expects >>>>>>>>>>>>>>>>>>>>>>>>>>>> that the DICOM field PatientName and uploaded filename contains the string >>>>>>>>>>>>>>>>>>>>>>>>>>>> "phantom". We enforced this behaviour on the imaging uploader side in >>>>>>>>>>>>>>>>>>>>>>>>>>>> recent releases but I can't remember which one. Probably the upcoming 21.0 >>>>>>>>>>>>>>>>>>>>>>>>>>>> release. >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> All those verifications might seem cumbersome >>>>>>>>>>>>>>>>>>>>>>>>>>>> but they are here to ensure that the files inserted are all valid and >>>>>>>>>>>>>>>>>>>>>>>>>>>> labelled properly as it is a bit messy to have to delete files that were >>>>>>>>>>>>>>>>>>>>>>>>>>>> wrongly labelled. At least, the delete script present in release 21.0 will >>>>>>>>>>>>>>>>>>>>>>>>>>>> make this process easier but it is still good practice to verify those >>>>>>>>>>>>>>>>>>>>>>>>>>>> things. >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> With pleasure. Hopefully the answers to your >>>>>>>>>>>>>>>>>>>>>>>>>>>> questions will be helpful. >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> PS: loris-dev mailing list: you will find the >>>>>>>>>>>>>>>>>>>>>>>>>>>> initial answer I gave Sotirios below. I forgot to cc the loris-dev in my >>>>>>>>>>>>>>>>>>>>>>>>>>>> earlier reply... >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 16 ???? 2019 ???? 12:02 ?.?., ?/? >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Cecile Madjar ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Dear Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you for reaching out. Since your email >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> was already organized in points, I will reply directly below your questions >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> below. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 1) What do we do when the StudyUID is blank >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> on the header? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/minor/docs/AppendixA-Troubleshooting_guideline.md >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> There solution provided at the table 3 does not guide us how to find the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> information ( is possible ). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The StudyUID is the field used in our >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> pipeline at the moment to check whether a DICOM study was already inserted >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> into LORIS with that same StudyUID since it is supposed to be unique for >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> every single study. Currently, we do not support insertion of DICOM studies >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> if they do not have a StudyUID associated with them. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Is there a specific reason why the StudyUID >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> is blank in the DICOM headers in your DICOM files? Did they go through some >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> processes before upload to LORIS? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 2) When i am about to upload a non-phanton >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> case i need a 'Visit Label'. Is there already a script that can create a >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> new visit label for a specific Candidate, so i can provide it as input >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> afterwards to the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> batch_uploads_imageuploader ( See option 5.1.3 https://github.com/aces/Loris-MRI/blob/minor/docs/05-PipelineLaunchOptions.md ) >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I am not sure if the front-end allows for it >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> but if you use batch_uploads_imageuploader, the insertion scripts could >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> create the visit label for you. However, it does need to be included in the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> patient name in order for the script to know which label it should use. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> For example: you upload V02 for MTL0123 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> (DCCID: 456789) but V02 was not yet created for MTL0123; the insertion >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> scripts will create a V02 visit for MTL0123 if the PatientName field for >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the dataset is MTL0123_456789_V02 with Stage marked as "Not Started". >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> However, *note that for the script to create >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the visit for the candidate, you have to make sure that all the visit label >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> of your projects were inserted in the Visit_Windows table* >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> (otherwise, the visit will never be created as they were not specified as >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> being part of the list of visit label to expect). So in the example above, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> you should have one row in Visit_Windows with Visit_label="V02" set. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 3) Section 4.3 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/minor/docs/04-Scripts.md >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> What do we do when the folder contains multiple mnc files? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> This is a case by case. Most of the time, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the MINC files that failed insertion into the imaging browser end up in the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> MRI violation module where you can see what went wrong with the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> acquisitions not inserted. If you notice that the MINC file should be >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> inserted as a specific protocol, you can force the insertion as explained >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in section 4.3. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> In your case, I have a feeling that you want >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> to be able to insert MINC files that did not go through the whole pipeline >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> insertion (DICOM archival, then dcm2mnc, then protocol identification, then >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> insertion...). In theory, you could call >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl on any MINC file, provided >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> you have at least the following information: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - path to the MINC file >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - uploadID associated with the MINC files or >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DICOM archive path from which those MINC files were created from >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Then the minc_insertion.pl script will do >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the subject information and protocol validation etc... >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> If all the MINC files come from the same >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> uploadID or TarchiveID, then you could run a loop in bash calling the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl script like this for files >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> deriving from uploadID=1: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ls /path/to/mnc/folder/* | while read f; do >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl -profile prod -uploadID 1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -mincPath $f; done >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helped! >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> -- >>>>>>>>>>> >>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>> >>>>>>>>>> >>>>>>>>> >>>>>>>>> -- >>>>>>>>> >>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>> Montreal Neurological Institute >>>>>>>>> McGill University | Montreal | Canada >>>>>>>>> >>>>>>>> _______________________________________________ >>>>>>> Loris-dev mailing list >>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>> >>>>>> >>>>>> >>>>>> -- >>>>>> >>>>>> christine.rogers at mcgill.ca >>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>> Montreal Neurological Institute >>>>>> McGill University | Montreal | Canada >>>>>> >>>>> _______________________________________________ >>>>> Loris-dev mailing list >>>>> Loris-dev at bic.mni.mcgill.ca >>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>> >>>> >>>> >>>> -- >>>> >>>> christine.rogers at mcgill.ca >>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>> Montreal Neurological Institute >>>> McGill University | Montreal | Canada >>>> _______________________________________________ >>>> Loris-dev mailing list >>>> Loris-dev at bic.mni.mcgill.ca >>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>> >>> >>> >>> -- >>> >>> christine.rogers at mcgill.ca >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>> Montreal Neurological Institute >>> McGill University | Montreal | Canada >>> >> _______________________________________________ >> Loris-dev mailing list >> Loris-dev at bic.mni.mcgill.ca >> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >> > > > -- > Shen Wang > Loris Developer > Montreal Neurological Institute > McGill University > > -- Shen Wang Loris Developer Montreal Neurological Institute McGill University -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 78176 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 20518 bytes Desc: not available URL: From sotirisnik at gmail.com Tue Aug 27 19:20:20 2019 From: sotirisnik at gmail.com (Sotirios Nikoloutsopoulos) Date: Wed, 28 Aug 2019 02:20:20 +0300 Subject: [Loris-dev] Import mri - scripts In-Reply-To: References: <65ad2b70c3084ffdb1e4a9dcdad948cd@YTOPR0101MB1803.CANPRD01.PROD.OUTLOOK.COM> Message-ID: Ok that fixed the install.sh problem. Now it doesn't show loris to the browser, although everything seems right ( also /etc/apache2/sites-enabled/000-default.conf was replaced by loris.config ). And apache is running lorisadmin at loris-VirtualBox:/var/www/loris/htdocs$ sudo systemctl status apache2[sudo] password for lorisadmin: ? apache2.service - LSB: Apache2 web server Loaded: loaded (/etc/init.d/apache2; bad; vendor preset: enabled) Drop-In: /lib/systemd/system/apache2.service.d ??apache2-systemd.conf Active: active (running) since ??? 2019-08-28 02:15:12 EEST; 3min 34s ago [image: image.png] ???? ???, 27 ??? 2019 ???? 9:42 ?.?., ?/? Shen Wang ??????: > Hi, > This is a bug for install.sh file, we will fix it later. > Thank for letting me know your Loris install situation. > regards > Shen > > > On Tue, 27 Aug 2019 at 14:28, Shen Wang wrote: > >> Hi, >> Please remove "set -euo pipefail" line 10 in the install.sh file. >> Then try again. >> >> >> >> On Tue, 27 Aug 2019 at 14:05, Sotirios Nikoloutsopoulos < >> sotirisnik at gmail.com> wrote: >> >>> Hi, >>> >>> i still haven't resolved the previous issue. Also i tried to install >>> Loris to a new virtual machine and when i execute install.sh i get the >>> following error >>> >>> lorisadmin at loris-VirtualBox:/var/www/loris/tools$ ./install.sh >>> LORIS Installation Script starting at 2019-08-27T21:00:42 >>> The log for this session will be stored in file >>> /var/www/loris/tools/logs/install-2019-08-27T21:00:42.log >>> --------------------------------------------------------------------- >>> LORIS Installation Script >>> --------------------------------------------------------------------- >>> >>> PHP appears to be installed. >>> >>> PHP Composer appears to be installed. >>> >>> This install script will ask you to provide inputs for different steps. >>> Please ensure you have the following information ready (if applicable): >>> >>> 1) Your project directory name. >>> (Will be used to modify the paths for Imaging data in the generated >>> config.xml file for LORIS, and may also be used to automatically >>> create/install apache config files.) If unsure, a default like >>> "LORIS" >>> should be acceptable. >>> >>> Please also consult the Loris WIKI on GitHub for more information on >>> these >>> Install Script input parameters. >>> >>> Ready to continue? [yn] y >>> >>> ./install.sh: line 132: projectname: unbound variable >>> >>> Thanks >>> >>> ???? ???, 6 ??? 2019 ???? 5:09 ?.?., ?/? Christine Rogers, Ms. < >>> christine.rogers at mcgill.ca> ??????: >>> >>>> Hi Sotirios, >>>> Could you also let us know -- on which pages is content visible, and on >>>> which pages/modules is content not visible for you? >>>> Thanks, >>>> Christine >>>> >>>> On Tue, Aug 6, 2019 at 9:54 AM Christine Rogers, Ms. < >>>> christine.rogers at mcgill.ca> wrote: >>>> >>>>> Thanks Sotirios, >>>>> That's good to know. It sounds like you've checked that your >>>>> /var/www/loris/project/config.xml file get populated properly. >>>>> >>>>> Please send us the last few errors you're seeing in your apache error >>>>> log file, and your config paths and we can see what's happening with your >>>>> front end -- >>>>> Run these Troubleshooting Queries >>>>> >>>>> to get your config path settings, given your front end is not displaying >>>>> fully. >>>>> >>>>> The Loris-MRI repo >>>>> 21 >>>>> install/upgrade would then be your next steps. >>>>> Best, >>>>> Christine >>>>> >>>>> On Tue, Aug 6, 2019 at 7:53 AM Sotirios Nikoloutsopoulos < >>>>> sotirisnik at gmail.com> wrote: >>>>> >>>>>> I am using a VM. What i did was: >>>>>> 1) Download the files from https://github.com/aces/Loris and replace >>>>>> them to my existing /vaw/www/loris folder. >>>>>> 2) Execute the composer install --no-dev and then composer >>>>>> dump-autoload as mentioned here >>>>>> https://github.com/aces/Loris/wiki/Updating-your-LORIS. >>>>>> 3) Execute install.sh from /var/www/loris/tools and because LORIS >>>>>> already existed i moved a .config file, then re-executed the install.sh >>>>>> successfully >>>>>> 4 ) As for the database, i dropped the schema and i executed the >>>>>> installdb.php >>>>>> >>>>>> ???? ???, 5 ??? 2019 ???? 5:22 ?.?., ?/? Christine Rogers, Ms. < >>>>>> christine.rogers at mcgill.ca> ??????: >>>>>> >>>>>>> Hi Sotorios, >>>>>>> >>>>>>> Thanks - when you re-installed did you start on a fresh root path / >>>>>>> VM or might some of your old system setting still apply? >>>>>>> (And if you did any steps similar to an upgrade, did you follow the >>>>>>> Upgrade steps in the Release Notes, from both repos?) >>>>>>> >>>>>>> About the TR_range column - it was recently split (MRI pr339 >>>>>>> ) split into TR_min and >>>>>>> _max columns. Given the code was trying to query TR_range which does not >>>>>>> exist in your mri_protocol table, double-check which version of the Loris >>>>>>> repo (tables) and the Loris-MRI repo (code) you have installed to ensure >>>>>>> they match. >>>>>>> >>>>>>> Christine >>>>>>> >>>>>>> >>>>>>> On Mon, Aug 5, 2019 at 9:06 AM Sotirios Nikoloutsopoulos < >>>>>>> sotirisnik at gmail.com> wrote: >>>>>>> >>>>>>>> I reinstalled LORIS to 21 version and now the content is not >>>>>>>> visible at all at most pages. >>>>>>>> >>>>>>>> [image: image.png] >>>>>>>> >>>>>>>> ???? ???, 5 ??? 2019 ???? 3:19 ?.?., ?/? Sotirios Nikoloutsopoulos < >>>>>>>> sotirisnik at gmail.com> ??????: >>>>>>>> >>>>>>>>> Hi, >>>>>>>>> >>>>>>>>> Is it easy to upgrade to Loris 21? Also the following fails >>>>>>>>> because the line 1985 of NeuroDB/MRIProcessingUtility.pm query mri_protocol >>>>>>>>> which doesn't have TR_range >>>>>>>>> https://github.com/aces/Loris/blob/21.0-release/SQL/0000-00-00-schema.sql#L556 >>>>>>>>> >>>>>>>>> [image: image.png] >>>>>>>>> >>>>>>>>> lorisadmin at hbp:/data/loris/bin/mri$ ./batch_uploads_imageuploader >>>>>>>>> -profile prod < ~/Desktop/input.txt > log.txt >>>>>>>>> Use of uninitialized value $_ in pattern match (m//) at >>>>>>>>> ./batch_uploads_imageuploader line 147. >>>>>>>>> base is DCC0000_258024_V1 >>>>>>>>> path is /data/incoming/ >>>>>>>>> type is .tar.gz >>>>>>>>> fullpath is /data/incoming/DCC0000_258024_V1.tar.gz >>>>>>>>> DBD::mysql::st execute failed: Unknown column 'TR_range' in 'where >>>>>>>>> clause' at >>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line 1985. >>>>>>>>> DBD::mysql::st fetchrow_array failed: fetch() without execute() at >>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line 1986. >>>>>>>>> Use of uninitialized value $count_mri_protocol in numeric gt (>) >>>>>>>>> at /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line >>>>>>>>> 1995. >>>>>>>>> DBD::mysql::st execute failed: Unknown column 'TR_range' in 'field >>>>>>>>> list' at /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 562. >>>>>>>>> Can't exec "mail": No such file or directory at >>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 721. >>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 722. >>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 723. >>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 724. >>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 725. >>>>>>>>> >>>>>>>>> No Mincs inserted >>>>>>>>> >>>>>>>>> Thanks, >>>>>>>>> >>>>>>>>> Sotirios >>>>>>>>> >>>>>>>>> ???? ???, 3 ??? 2019 ???? 1:08 ?.?., ?/? Christine Rogers, Ms. < >>>>>>>>> christine.rogers at mcgill.ca> ??????: >>>>>>>>> >>>>>>>>>> Hi Sotirios, >>>>>>>>>> >>>>>>>>>> First, just a note: we've released LORIS 21 this week with some >>>>>>>>>> major new features and cleanup -- especially if you are early in your setup >>>>>>>>>> phase, check out the Release notes for both the LORIS >>>>>>>>>> and >>>>>>>>>> Loris-MRI >>>>>>>>>> repos. >>>>>>>>>> >>>>>>>>>> Thanks for your screenshots -- your empty mri_protocol table >>>>>>>>>> should be at the root of these issues : >>>>>>>>>> >>>>>>>>>> The mri_protocol table must be populated >>>>>>>>>> >>>>>>>>>> in order for your scans to be registered in LORIS -- it serves as a >>>>>>>>>> whitelist for the insertion pipeline which filters out scans that aren't >>>>>>>>>> identified or matched to scan types in this table. >>>>>>>>>> >>>>>>>>>> By default, this table is populated with entries for t1, t2, fMRI >>>>>>>>>> and DTI (Insert statements for 21 release branch are here >>>>>>>>>> >>>>>>>>>> ) >>>>>>>>>> Feel free to restore our default records and broaden their >>>>>>>>>> parameters to match all your scan types. >>>>>>>>>> >>>>>>>>>> re Defaced, native, selected -- these filter the scans displayed >>>>>>>>>> as you move to the next page (View Session), instead of viewing "all types" >>>>>>>>>> of scans from a given session : >>>>>>>>>> >>>>>>>>>> - "defaced" means that a defacing script >>>>>>>>>> >>>>>>>>>> has masked the subject's face in the volume (for patient privacy) >>>>>>>>>> - "native" means that no pre-processing has been performed on >>>>>>>>>> the scan (it's raw data), >>>>>>>>>> - "selected" will show only volumes that have been QC'd and >>>>>>>>>> "selected" as the best of their type -- used to display only the best >>>>>>>>>> quality T1 image instead of all T1s acquired in a session, e.g. >>>>>>>>>> >>>>>>>>>> re QC Comments -- >>>>>>>>>> Once you have successfully loaded scans (matched to the >>>>>>>>>> mri_protocol table), you'll be able to use the Imaging Browser's View >>>>>>>>>> Session subpage to enter/view QC comments on each volume, or for each >>>>>>>>>> visit. >>>>>>>>>> These are stored directly in the database, and linked to each >>>>>>>>>> scan. (Table name: feedback_mri_comments) >>>>>>>>>> (Visit-level QC comments are linked to the session.) >>>>>>>>>> >>>>>>>>>> For a walkthrough of the Imaging setup - please see the Imaging >>>>>>>>>> Setup guide >>>>>>>>>> >>>>>>>>>> - >>>>>>>>>> >>>>>>>>>> An old LORIS walkthrough video >>>>>>>>>> can also walk you >>>>>>>>>> through some of the Imaging front-end features, starting at 8:00 >>>>>>>>>> LORIS' imaging modules have been updated many times since this >>>>>>>>>> video, but the functionality and workflow is similar. >>>>>>>>>> >>>>>>>>>> Let us know how it goes once you have entries in your >>>>>>>>>> mri_protocol table - >>>>>>>>>> Best, >>>>>>>>>> Christine >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> On Fri, Aug 2, 2019 at 7:58 AM Sotirios Nikoloutsopoulos < >>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>> >>>>>>>>>>> Hi Christine, >>>>>>>>>>> >>>>>>>>>>> In the candidate_list page i can see this patient >>>>>>>>>>> >>>>>>>>>>> [image: image.png] >>>>>>>>>>> >>>>>>>>>>> If i press the link under PSCID i get to see >>>>>>>>>>> [image: image.png] >>>>>>>>>>> >>>>>>>>>>> and if i press the link under Scan Done it redirects me to >>>>>>>>>>> imaging_browser >>>>>>>>>>> >>>>>>>>>>> [image: image.png] >>>>>>>>>>> >>>>>>>>>>> At the mri_violations page i also see No results ( neither on >>>>>>>>>>> resolved / not resolved ). >>>>>>>>>>> >>>>>>>>>>> At the imaging_uploader i can see the record that failed. >>>>>>>>>>> >>>>>>>>>>> [image: image.png] >>>>>>>>>>> >>>>>>>>>>> If i click on the tarchive info i get to see the Protocol Name >>>>>>>>>>> which i think is the acquisition we wanted? >>>>>>>>>>> [image: image.png] >>>>>>>>>>> >>>>>>>>>>> Also my mri_protocol table is empty. >>>>>>>>>>> >>>>>>>>>>> Furthermore i would like to ask about the defaced, native, >>>>>>>>>>> selected. What exactly is native and selected? And where are the qc >>>>>>>>>>> comments stored? >>>>>>>>>>> >>>>>>>>>>> [image: image.png] >>>>>>>>>>> >>>>>>>>>>> Finally a walkthrough would be helpful. >>>>>>>>>>> >>>>>>>>>>> Thanks, >>>>>>>>>>> >>>>>>>>>>> Sotirios >>>>>>>>>>> >>>>>>>>>>> ???? ???, 30 ???? 2019 ???? 8:29 ?.?., ?/? Christine Rogers, Ms. >>>>>>>>>>> ??????: >>>>>>>>>>> >>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>> Glad to hear you're making progress with the visit labels. To >>>>>>>>>>>> follow up on your last few emails: >>>>>>>>>>>> >>>>>>>>>>>> a- The Wiki's Setup Guide contains Sample insert statements >>>>>>>>>>>> for the Visit Windows table >>>>>>>>>>>> >>>>>>>>>>>> . >>>>>>>>>>>> >>>>>>>>>>>> As Cecile mentioned, the consistency of visit label format is >>>>>>>>>>>> important: V01, v01, V1, 01 -- whichever you select to use is fine; we use >>>>>>>>>>>> V01 by default across all documentation. >>>>>>>>>>>> >>>>>>>>>>>> b- For Password reset, there is a script in the tools/ >>>>>>>>>>>> directory so that a back-end administrator can reset any front-end user >>>>>>>>>>>> password, including Admin. (See info on setting up / resetting User >>>>>>>>>>>> passwords in the Wiki's Setup Guide >>>>>>>>>>>> >>>>>>>>>>>> ) >>>>>>>>>>>> >>>>>>>>>>>> c- The minc file not being registered -- due to >>>>>>>>>>>> AcquisitionProtocol unknown. >>>>>>>>>>>> This means the SeriesDescription (Acquisition Protocol) in you >>>>>>>>>>>> Dicom header was not matched to any scan listed in the mri_protocol >>>>>>>>>>>> database table. >>>>>>>>>>>> (In the online Loris-MRI Troubleshooting Guide, >>>>>>>>>>>> this >>>>>>>>>>>> is Table 3, 2nd-last item "no MINCs inserted"). >>>>>>>>>>>> >>>>>>>>>>>> The MRI Violations module (Readme here) >>>>>>>>>>>> will show >>>>>>>>>>>> you the details of this mismatch -- >>>>>>>>>>>> Go to the module (under the Imaging menu), find your scan and >>>>>>>>>>>> click the link "Could not identify scan type" -- in the next subpage you >>>>>>>>>>>> can compare the scan's actual parameters against the mri_protocol table. >>>>>>>>>>>> >>>>>>>>>>>> To resolve this, adjust your mri_protocol table values or >>>>>>>>>>>> perhaps ensure your DICOMs are labelled consistently. >>>>>>>>>>>> >>>>>>>>>>>> Let us know if this works for you -- we can also walk you >>>>>>>>>>>> through an example of non-identified scans on Demo.loris.ca >>>>>>>>>>>> (MRI Violations module). >>>>>>>>>>>> >>>>>>>>>>>> Best, >>>>>>>>>>>> Christine >>>>>>>>>>>> >>>>>>>>>>>> The LORIS team >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> On Tue, Jul 30, 2019 at 10:47 AM Sotirios Nikoloutsopoulos < >>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>> >>>>>>>>>>>>> I hope this is sufficient as the error for the visit label >>>>>>>>>>>>> disappeared. >>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>> >>>>>>>>>>>>> Please see the attached file. Also something i found. >>>>>>>>>>>>> >>>>>>>>>>>>> lorisadmin at hbp:/data/loris/bin/mri$ cat >>>>>>>>>>>>> /data/loris/data//logs/TarLoad-17-39-xubBdv.log >>>>>>>>>>>>> >>>>>>>>>>>>> ==> Loading file from disk >>>>>>>>>>>>> /tmp/TarLoad-17-39-UyQcG2/dcc0000_258024_v1_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>> >>>>>>>>>>>>> --> mapping DICOM parameter for >>>>>>>>>>>>> /tmp/TarLoad-17-39-UyQcG2/dcc0000_258024_v1_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>> >>>>>>>>>>>>> ==> computing md5 hash for MINC body. >>>>>>>>>>>>> >>>>>>>>>>>>> --> md5: 6b1202fd63e29de4c9be1cd9925888a5 >>>>>>>>>>>>> >>>>>>>>>>>>> ==> verifying acquisition protocol >>>>>>>>>>>>> >>>>>>>>>>>>> Acquisition protocol is unknown >>>>>>>>>>>>> >>>>>>>>>>>>> --> The minc file cannot be registered since the >>>>>>>>>>>>> AcquisitionProtocol is unknown >>>>>>>>>>>>> >>>>>>>>>>>>> ???? ???, 30 ???? 2019 ???? 4:58 ?.?., ?/? Sotirios >>>>>>>>>>>>> Nikoloutsopoulos ??????: >>>>>>>>>>>>> >>>>>>>>>>>>>> Ok I fixed the login problem by using a known hash and by >>>>>>>>>>>>>> deleting the rows from the login_history i was able to login. >>>>>>>>>>>>>> >>>>>>>>>>>>>> ???? ???, 30 ???? 2019 ???? 4:50 ?.?., ?/? Sotirios >>>>>>>>>>>>>> Nikoloutsopoulos ??????: >>>>>>>>>>>>>> >>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> there was no visit label 01 in the Visit_Windows table and i >>>>>>>>>>>>>>> don't know how to insert it because the record requires lots of attributes. >>>>>>>>>>>>>>> Also the system for a reason asked me to update my password and now i don't >>>>>>>>>>>>>>> remember it and my account got suspended. Is there a way to reset it or set >>>>>>>>>>>>>>> a simple password? I updated the password hash in the users table by using >>>>>>>>>>>>>>> the hash from another LORIS setup we had and i still couldn't login ( also >>>>>>>>>>>>>>> the attribute password is always NULL and the expiration date is 1999-01-01 >>>>>>>>>>>>>>> for some reason ). >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> Thanks >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> ???? ???, 29 ???? 2019 ???? 5:21 ?.?., ?/? Cecile Madjar < >>>>>>>>>>>>>>> cecile.madjar at mcin.ca> ??????: >>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Can you try adding the visit label v01 to the Visit_Windows >>>>>>>>>>>>>>>> table? >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> However, I noticed that in a previous dataset, the label >>>>>>>>>>>>>>>> was V1. Does that refer to the same visit? If so, you might want to >>>>>>>>>>>>>>>> harmonize the visit labels so they are all the same across datasets for a >>>>>>>>>>>>>>>> given timepoint, meaning you will need to relabel scans when the visit >>>>>>>>>>>>>>>> label is different but referring to the same visit label (v01 = V1 etc...). >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Hope this helps, >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> On Mon, Jul 29, 2019 at 10:15 AM Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Could you help me with the "Visit label does not exist"? I >>>>>>>>>>>>>>>>> had changed $subjectID{'createVisitLabel'} to 1 as you had suggested but >>>>>>>>>>>>>>>>> it appears that this problem hasn't been resolved yet. >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> lorisadmin at hbp:/data/loris/bin/mri$ cat >>>>>>>>>>>>>>>>> /data/loris/data//logs/TarLoad-14-58-9Xog7H.log >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> ==> Loading file from disk >>>>>>>>>>>>>>>>> /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> --> mapping DICOM parameter for >>>>>>>>>>>>>>>>> /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> --> using user-defined filterParameters for >>>>>>>>>>>>>>>>> /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Candidate Mismatch Error is Visit label does not exist >>>>>>>>>>>>>>>>> -> WARNING: This candidate was invalid. Logging to >>>>>>>>>>>>>>>>> MRICandidateErrors table with reason Visit >>>>>>>>>>>>>>>>> label does not exist >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> ???? ???, 26 ???? 2019 ???? 3:02 ?.?., ?/? Sotirios >>>>>>>>>>>>>>>>> Nikoloutsopoulos ??????: >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Hi Cecile, >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> The Center error was fixed. Still the insertion of mincs >>>>>>>>>>>>>>>>>> fails. Please see the output.txt file i attached. Also is there something >>>>>>>>>>>>>>>>>> else i need to change at the paths configuration? >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> ???? ???, 25 ???? 2019 ???? 6:55 ?.?., ?/? Cecile Madjar < >>>>>>>>>>>>>>>>>> cecile.madjar at mcin.ca> ??????: >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> We are making progress! >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> I have a feeling this error comes from the fact that >>>>>>>>>>>>>>>>>>> your psc table does not have the MRI_alias populated for the DCC site. >>>>>>>>>>>>>>>>>>> Running the following query in the mysql database should fix this: >>>>>>>>>>>>>>>>>>> UPDATE psc SET MRI_alias="DCC", Alias="DCC" WHERE >>>>>>>>>>>>>>>>>>> Name="Data Coordinating Center"; >>>>>>>>>>>>>>>>>>> Repeat the same with all your sites (make sure to change >>>>>>>>>>>>>>>>>>> the Aliases between sites, they should all be unique). >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Let me know how it goes! >>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> On Thu, Jul 25, 2019 at 11:43 AM Sotirios >>>>>>>>>>>>>>>>>>> Nikoloutsopoulos wrote: >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Dear Cecile, >>>>>>>>>>>>>>>>>>>> You were right about your guesses. I did the >>>>>>>>>>>>>>>>>>>> modifications you suggested, i still get the "no mincs inserted" error, now >>>>>>>>>>>>>>>>>>>> i am getting the "No center found this candidate" error ( how do i fix >>>>>>>>>>>>>>>>>>>> that? from what i see the .dcm files contains a 'Institution Name', is that >>>>>>>>>>>>>>>>>>>> the center? ), so i guess that's why the validation fails, but i changed >>>>>>>>>>>>>>>>>>>> the force variable of tarchiveLoader to 1, shouldn't it have inserted the >>>>>>>>>>>>>>>>>>>> mincs then? Also it is optional to have a mail server, right? ( from what i >>>>>>>>>>>>>>>>>>>> see the mail error does not affect the $valid_study, so i assume we are >>>>>>>>>>>>>>>>>>>> okay with that ) >>>>>>>>>>>>>>>>>>>> Thank you a lot, >>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> ???? ???, 25 ???? 2019 ???? 5:48 ?.?., ?/? Cecile >>>>>>>>>>>>>>>>>>>> Madjar ??????: >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> From what I understand, I believe you just need to >>>>>>>>>>>>>>>>>>>>> update a few config settings from the frontend in the Config module (under >>>>>>>>>>>>>>>>>>>>> the Admin menu). >>>>>>>>>>>>>>>>>>>>> [image: Screen Shot 2019-07-25 at 10.31.35 AM.png] >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> Then go to the Paths section of the config module and >>>>>>>>>>>>>>>>>>>>> update the "LORIS-MRI code" config setting to /data/loris/bin/mri (my guess >>>>>>>>>>>>>>>>>>>>> is that currently, it is set to /data/LORIS/data) and click on the submit >>>>>>>>>>>>>>>>>>>>> button. >>>>>>>>>>>>>>>>>>>>> [image: Screen Shot 2019-07-25 at 10.32.50 AM.png] >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> Then, go to Imaging Pipeline section of the >>>>>>>>>>>>>>>>>>>>> Configuration module and update the "Loris-MRI Data Directory" to >>>>>>>>>>>>>>>>>>>>> /data/loris/data/ (my guess is that it is empty at the moment in your >>>>>>>>>>>>>>>>>>>>> database which is why $data_dir is not defined when you run the >>>>>>>>>>>>>>>>>>>>> tarchiveLoader step of the insertion pipeline). >>>>>>>>>>>>>>>>>>>>> [image: Screen Shot 2019-07-25 at 10.40.52 AM.png] >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> Finally, I took a look at your environment file and it >>>>>>>>>>>>>>>>>>>>> might be a good idea to update your PERL5LIB variable to the following (it >>>>>>>>>>>>>>>>>>>>> has been added to the code a few releases ago as we realized this was >>>>>>>>>>>>>>>>>>>>> needed for the libraries. Not sure which version of LORIS-MRI you are using >>>>>>>>>>>>>>>>>>>>> but it does not hurt to update this variable to what I suggest below): >>>>>>>>>>>>>>>>>>>>> export >>>>>>>>>>>>>>>>>>>>> PERL5LIB=/data/loris/bin/mri/uploadNeuroDB:/data/loris/bin/mri/dicom-archive:$PERL5LIB >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> Hope this helps. Sorry you are experiencing so much >>>>>>>>>>>>>>>>>>>>> trouble setting things up. We probably need to update our WIKI. >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> On Thu, Jul 25, 2019 at 9:48 AM Sotirios >>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos wrote: >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> The "Loris-MRI Data Directory" should be in the >>>>>>>>>>>>>>>>>>>>>> environment file? >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> ???? ???, 25 ???? 2019 ???? 12:59 ?.?., ?/? Sotirios >>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos ??????: >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> The scripts are located in /data/loris/bin/mri/. >>>>>>>>>>>>>>>>>>>>>>> Somewhere I might have messed something up but i remember following the >>>>>>>>>>>>>>>>>>>>>>> instructions in the wiki.For example when i tried to execute the >>>>>>>>>>>>>>>>>>>>>>> batch_uploads_imageuploader perl script the line >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> my $command = "$bin_dir/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl " >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> was pointing to an invalid path, for example: it was >>>>>>>>>>>>>>>>>>>>>>> repeating a pattern and had LORIS instead of loris ( i think the mistake >>>>>>>>>>>>>>>>>>>>>>> was that in the wiki it suggested to use $PROJECT for the name of the >>>>>>>>>>>>>>>>>>>>>>> folder and i choosed 'loris' >>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris/wiki/Imaging-Database >>>>>>>>>>>>>>>>>>>>>>> ). See also the in image for the modification i did. Also i didn't find the >>>>>>>>>>>>>>>>>>>>>>> section to config the $data_dir variable. >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> ???? ???, 24 ???? 2019 ???? 6:05 ?.?., ?/? Cecile >>>>>>>>>>>>>>>>>>>>>>> Madjar ??????: >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> It looks like you have one Config setting not set >>>>>>>>>>>>>>>>>>>>>>>> (based on the first error message you got when running it the first time). >>>>>>>>>>>>>>>>>>>>>>>> You need to set a value for "Loris-MRI Data Directory" in the Config module >>>>>>>>>>>>>>>>>>>>>>>> under the Imaging pipeline section (from what I can see, it would be >>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/ for your setup). >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> The reason you got that error message the second >>>>>>>>>>>>>>>>>>>>>>>> time is that the pipeline checks if the DICOM study was already inserted in >>>>>>>>>>>>>>>>>>>>>>>> the tarchive table. Since you ran the study once already, the study is >>>>>>>>>>>>>>>>>>>>>>>> inserted into the tarchive, hence the message. However, the pipeline did >>>>>>>>>>>>>>>>>>>>>>>> not complete as the MINC files were not created and inserted into the >>>>>>>>>>>>>>>>>>>>>>>> files/parameter_file table. In order to continue the insertion, you will >>>>>>>>>>>>>>>>>>>>>>>> then need to run the tarchiveLoader command suggested in the terminal >>>>>>>>>>>>>>>>>>>>>>>> during the second run: >>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader >>>>>>>>>>>>>>>>>>>>>>>> -globLocation -profile prod >>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive//2012/DCM_2012-12-05_ImagingUpload-17-43-ZUEFjb.tar >>>>>>>>>>>>>>>>>>>>>>>> -verbose >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> Finally, I am a bit confused by your setup. Where >>>>>>>>>>>>>>>>>>>>>>>> are the scripts located? In /data/loris/bin/mri or /data/loris/data? It >>>>>>>>>>>>>>>>>>>>>>>> feels like the Config setting "LORIS-MRI code" in the Paths section was set >>>>>>>>>>>>>>>>>>>>>>>> to "/data/LORIS/data" but it should have been set to the directory where >>>>>>>>>>>>>>>>>>>>>>>> the scripts are located (most probably /data/loris/bin/mri). >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> Hope this helps, >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> On Wed, Jul 24, 2019 at 10:55 AM Sotirios >>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos wrote: >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> Ok first i execute this command: >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> "lorisadmin at hbp:/data/loris/bin/mri$ >>>>>>>>>>>>>>>>>>>>>>>>> ./batch_uploads_imageuploader -profile prod < ~/Desktop/input.txt > log.txt >>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at ./batch_uploads_imageuploader line 143. >>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at ./batch_uploads_imageuploader line 143. >>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $_ in pattern match >>>>>>>>>>>>>>>>>>>>>>>>> (m//) at ./batch_uploads_imageuploader line 147. >>>>>>>>>>>>>>>>>>>>>>>>> base is DCC0000_258024_V01 >>>>>>>>>>>>>>>>>>>>>>>>> path is /data/incoming/ >>>>>>>>>>>>>>>>>>>>>>>>> type is .tar.gz >>>>>>>>>>>>>>>>>>>>>>>>> fullpath is >>>>>>>>>>>>>>>>>>>>>>>>> /data/incoming/DCC0000_258024_V01.tar.gz >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> source /tmp/ImagingUpload-17-43-ZUEFjb >>>>>>>>>>>>>>>>>>>>>>>>> targetlocation /data/loris/data/tarchive >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 256. >>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 284. >>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at /data/loris/bin/mri/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>> tarchive_validation.pl line 219. >>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at /data/loris/bin/mri/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl line 270. >>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 711. >>>>>>>>>>>>>>>>>>>>>>>>> Can't exec "mail": No such file or directory at >>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 721. >>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 722. >>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 723. >>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 724. >>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 724. >>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 725. >>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 735. >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> No Mincs inserted >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> The tarchiveLoader insertion script has failed. >>>>>>>>>>>>>>>>>>>>>>>>> Running now the following command: >>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl -profile prod -upload_id 3 >>>>>>>>>>>>>>>>>>>>>>>>> /data/incoming/DCC0000_258024_V01.tar.gz -verbose" >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> I inserted the VisitLabel, but still the Mincs are >>>>>>>>>>>>>>>>>>>>>>>>> not inserted and i am getting this error >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> "lorisadmin at hbp:/data/loris/bin/mri$ >>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl -profile prod -upload_id 3 >>>>>>>>>>>>>>>>>>>>>>>>> /data/incoming/DCC0000_258024_V01.tar.gz -verbose >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> find -path \/tmp\/ImagingUpload\-17\-45\-5MsWEd >>>>>>>>>>>>>>>>>>>>>>>>> -name '__MACOSX' -delete >>>>>>>>>>>>>>>>>>>>>>>>> Spool message is: >>>>>>>>>>>>>>>>>>>>>>>>> The Scan for the uploadID 3 has already been run >>>>>>>>>>>>>>>>>>>>>>>>> with tarchiveID: 7. >>>>>>>>>>>>>>>>>>>>>>>>> To continue with the rest of the insertion >>>>>>>>>>>>>>>>>>>>>>>>> pipeline, please run tarchiveLoader from a terminal as follows: >>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader -globLocation -profile prod >>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive//2012/DCM_2012-12-05_ImagingUpload-17-43-ZUEFjb.tar >>>>>>>>>>>>>>>>>>>>>>>>> -verbose" >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> Which files should i delete? I thought that >>>>>>>>>>>>>>>>>>>>>>>>> deleting the files from the tarchive was enough. And i executed the last >>>>>>>>>>>>>>>>>>>>>>>>> proposed command to continue to rest of the insertion pipeline ( check the >>>>>>>>>>>>>>>>>>>>>>>>> image ). >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> Thank you >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 24 ???? 2019 ???? 5:05 ?.?., ?/? Cecile >>>>>>>>>>>>>>>>>>>>>>>>> Madjar ??????: >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> Sorry I was not clear before. Every visits of >>>>>>>>>>>>>>>>>>>>>>>>>> candidates are created in the session table with one entry per >>>>>>>>>>>>>>>>>>>>>>>>>> CandID/VisitLabel. So if the imaging pipeline created visits in the session >>>>>>>>>>>>>>>>>>>>>>>>>> table (that are not attached to instruments) and you want to clean your >>>>>>>>>>>>>>>>>>>>>>>>>> database completely, you can delete entries in that table as well. >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> Regarding your point 2, the imaging pipeline can >>>>>>>>>>>>>>>>>>>>>>>>>> create the visit in the session table as long as the visit label is present >>>>>>>>>>>>>>>>>>>>>>>>>> in the Visit_Windows table (which means the visit label stored in the >>>>>>>>>>>>>>>>>>>>>>>>>> PatientName is a valid visit label). >>>>>>>>>>>>>>>>>>>>>>>>>> However, in your prod file, if the >>>>>>>>>>>>>>>>>>>>>>>>>> variable $subjectID{'createVisitLabel'} is set to 1 for candidates, the >>>>>>>>>>>>>>>>>>>>>>>>>> visit label should be created in the Visit_Windows table I believe. Here >>>>>>>>>>>>>>>>>>>>>>>>>> is the line of the prod file you would need to change >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> . >>>>>>>>>>>>>>>>>>>>>>>>>> In general, we prefer populating the >>>>>>>>>>>>>>>>>>>>>>>>>> Visit_Windows table and set the $subjectID{'createVisitLabel'} to 0 for >>>>>>>>>>>>>>>>>>>>>>>>>> candidate data to avoid insertion of badly labelled MRI data that are >>>>>>>>>>>>>>>>>>>>>>>>>> complex to relabel. >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> Finally, regarding the candidate creation, if you >>>>>>>>>>>>>>>>>>>>>>>>>> execute the following steps, the pipeline should be able to create >>>>>>>>>>>>>>>>>>>>>>>>>> candidates: >>>>>>>>>>>>>>>>>>>>>>>>>> - set in the Imaging Pipeline section of the >>>>>>>>>>>>>>>>>>>>>>>>>> config module the config setting "Upload creation of candidates" to Yes >>>>>>>>>>>>>>>>>>>>>>>>>> - manually transfer the scans to the LORIS server >>>>>>>>>>>>>>>>>>>>>>>>>> instead of uploading it via the imaging browser >>>>>>>>>>>>>>>>>>>>>>>>>> - run batch_imaging_upload.pl as you did until >>>>>>>>>>>>>>>>>>>>>>>>>> now. >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helps! >>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> On Wed, Jul 24, 2019 at 8:47 AM Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos wrote: >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> About my second question i replaced the name of >>>>>>>>>>>>>>>>>>>>>>>>>>> the patient in the .dcm files and now i am getting an error that the visit >>>>>>>>>>>>>>>>>>>>>>>>>>> label does not exist. >>>>>>>>>>>>>>>>>>>>>>>>>>> I thought it was supposed to be automatically >>>>>>>>>>>>>>>>>>>>>>>>>>> created. >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> "Done adding archive info into database >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader >>>>>>>>>>>>>>>>>>>>>>>>>>> -globLocation -profile prod >>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive//DCM_2012-12-05_ImagingUpload-15-42-yUwQQV.tar >>>>>>>>>>>>>>>>>>>>>>>>>>> -verbose >>>>>>>>>>>>>>>>>>>>>>>>>>> md5sum >>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive/DCM_2012-12-05_ImagingUpload-15-42-yUwQQV.tar >>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>> candidate id 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> => No Visit labelVisit label does not exist >>>>>>>>>>>>>>>>>>>>>>>>>>> Set centerID = 1 >>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> Number of MINC files that will be considered for >>>>>>>>>>>>>>>>>>>>>>>>>>> inserting into the database: 1 >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> log dir is /logs and log file is >>>>>>>>>>>>>>>>>>>>>>>>>>> /logs/TarLoad-15-42-L6pocU.log >>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>> candidate id 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> => No Visit label >>>>>>>>>>>>>>>>>>>>>>>>>>> Cleaning up temp files: rm -rf >>>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-15-42-J2rQms/ImagingUpload-15-42-yUwQQV*" >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 24 ???? 2019 ???? 3:38 ?.?., ?/? >>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos >>>>>>>>>>>>>>>>>>>>>>>>>>> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> 1) What are the records in the session table? >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> 2) I tried to upload a non-phantom file like >>>>>>>>>>>>>>>>>>>>>>>>>>>> this >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> input_file.txt: >>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/incoming/DCC0000_258024_V1.tar.gz N >>>>>>>>>>>>>>>>>>>>>>>>>>>> DCC0000_258024_V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> Terminal: >>>>>>>>>>>>>>>>>>>>>>>>>>>> ./batch_uploads_imageuploader -profile prod < >>>>>>>>>>>>>>>>>>>>>>>>>>>> ~/Desktop/input.txt > log.txt >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> and i get the following error in the log.txt >>>>>>>>>>>>>>>>>>>>>>>>>>>> file >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> "Running now the following command: >>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl -profile prod >>>>>>>>>>>>>>>>>>>>>>>>>>>> -upload_id 7 /data/incoming/DCC0000_258024_V1.tar.gz -verbose >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> find -path >>>>>>>>>>>>>>>>>>>>>>>>>>>> \/tmp\/ImagingUpload\-14\-56\-FeLCB4 -name '__MACOSX' -delete >>>>>>>>>>>>>>>>>>>>>>>>>>>> Spool message is: >>>>>>>>>>>>>>>>>>>>>>>>>>>> The PatientName read from the DICOM header does >>>>>>>>>>>>>>>>>>>>>>>>>>>> not start with DCC0000_258024_V1 from the mri_upload table >>>>>>>>>>>>>>>>>>>>>>>>>>>> " >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> and the spool message is repeated for each .dcm >>>>>>>>>>>>>>>>>>>>>>>>>>>> file. Should i preprocess every .dcm file and change the PatientName to >>>>>>>>>>>>>>>>>>>>>>>>>>>> "DCC0000_258024_V1"? >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> 3) As far as it concerns the candidate profile >>>>>>>>>>>>>>>>>>>>>>>>>>>> i have to create a new one each time before i try to upload a file? Is >>>>>>>>>>>>>>>>>>>>>>>>>>>> there already a way to create a candidate profile and get the DCCID and >>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID without the user interface? >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 18 ???? 2019 ???? 5:00 ?.?., ?/? >>>>>>>>>>>>>>>>>>>>>>>>>>>> Cecile Madjar ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> See answers to your questions below. >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> About the 1st case we had a dicom with a blank >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> studyUID, maybe someone accidentally removed it. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> That is strange. Something must have been done >>>>>>>>>>>>>>>>>>>>>>>>>>>>> to the DICOM files. I have never seen a study with no StudyUID out of the >>>>>>>>>>>>>>>>>>>>>>>>>>>>> scanner. Usually, you need to manually erase it with some tool. However, >>>>>>>>>>>>>>>>>>>>>>>>>>>>> DICOMs never cease to surprise me... >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Some other questions: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 1) What are the steps to remove all of my >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> patients and uploads?: because i want to try to reupload all the testing >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> dicoms we had with a clean database. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Release 21.0 of LORIS-MRI will offer a script >>>>>>>>>>>>>>>>>>>>>>>>>>>>> to remove all the entries and files specific to an upload. However, this >>>>>>>>>>>>>>>>>>>>>>>>>>>>> release is not yet out. Hopefully in the next few weeks. >>>>>>>>>>>>>>>>>>>>>>>>>>>>> In the meantime, since your case is particular >>>>>>>>>>>>>>>>>>>>>>>>>>>>> and that you just want to start with a clean database, the following >>>>>>>>>>>>>>>>>>>>>>>>>>>>> deletes should work (hopefully I won't forget any tables): >>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from mri_violations_log; >>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from mri_protocol_violated_scans; >>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from MRICandidateErrors; >>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from parameter_file; >>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from files_qcstatus; # (if you played >>>>>>>>>>>>>>>>>>>>>>>>>>>>> with the QC part of the imaging browser for testing) >>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from feedback_mri_comments; # (if you >>>>>>>>>>>>>>>>>>>>>>>>>>>>> played with the QC part of the imaging browser for testing) >>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from tarchive_series; >>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from tarchive_files; >>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from mri_upload; >>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from tarchive; >>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from mri_scanner; >>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from candidate where PSCID="scanner"; >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> I don't know if you want to also delete >>>>>>>>>>>>>>>>>>>>>>>>>>>>> entries in the session and candidate table too? >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> 2) We do not need to create the profile of a >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> patient ( are the patients stored in the candidate table? because i can't >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> see the ghosts ), because will it automatically be created when importing a >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> dicom? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> I am not sure I understand fully this >>>>>>>>>>>>>>>>>>>>>>>>>>>>> question. All candidates are stored in the candidate table. The phantom >>>>>>>>>>>>>>>>>>>>>>>>>>>>> scans however are attached to a scanner candidate depending on where the >>>>>>>>>>>>>>>>>>>>>>>>>>>>> scan happened. It is a bit of a weird concept that we have to redesign >>>>>>>>>>>>>>>>>>>>>>>>>>>>> eventually but never got a chance to get to it. >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hopefully this answered your question, >>>>>>>>>>>>>>>>>>>>>>>>>>>>> otherwise, don't hesitate to let me know. >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> 3) What is the difference between uploading a >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> dicom as phantom instead of importing as PSCCID_DCCID_VisitLabel? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> When you upload the scan as >>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID_DCCID_VisitLabel, there is a check that makes sure the candidate IDs >>>>>>>>>>>>>>>>>>>>>>>>>>>>> and visit label are valid at the time of upload. >>>>>>>>>>>>>>>>>>>>>>>>>>>>> When you upload a scan as phantom, it expects >>>>>>>>>>>>>>>>>>>>>>>>>>>>> that the DICOM field PatientName and uploaded filename contains the string >>>>>>>>>>>>>>>>>>>>>>>>>>>>> "phantom". We enforced this behaviour on the imaging uploader side in >>>>>>>>>>>>>>>>>>>>>>>>>>>>> recent releases but I can't remember which one. Probably the upcoming 21.0 >>>>>>>>>>>>>>>>>>>>>>>>>>>>> release. >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> All those verifications might seem cumbersome >>>>>>>>>>>>>>>>>>>>>>>>>>>>> but they are here to ensure that the files inserted are all valid and >>>>>>>>>>>>>>>>>>>>>>>>>>>>> labelled properly as it is a bit messy to have to delete files that were >>>>>>>>>>>>>>>>>>>>>>>>>>>>> wrongly labelled. At least, the delete script present in release 21.0 will >>>>>>>>>>>>>>>>>>>>>>>>>>>>> make this process easier but it is still good practice to verify those >>>>>>>>>>>>>>>>>>>>>>>>>>>>> things. >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> With pleasure. Hopefully the answers to your >>>>>>>>>>>>>>>>>>>>>>>>>>>>> questions will be helpful. >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> PS: loris-dev mailing list: you will find the >>>>>>>>>>>>>>>>>>>>>>>>>>>>> initial answer I gave Sotirios below. I forgot to cc the loris-dev in my >>>>>>>>>>>>>>>>>>>>>>>>>>>>> earlier reply... >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 16 ???? 2019 ???? 12:02 ?.?., ?/? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Cecile Madjar ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Dear Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you for reaching out. Since your email >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> was already organized in points, I will reply directly below your questions >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> below. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 1) What do we do when the StudyUID is blank >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> on the header? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/minor/docs/AppendixA-Troubleshooting_guideline.md >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> There solution provided at the table 3 does not guide us how to find the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> information ( is possible ). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The StudyUID is the field used in our >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> pipeline at the moment to check whether a DICOM study was already inserted >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> into LORIS with that same StudyUID since it is supposed to be unique for >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> every single study. Currently, we do not support insertion of DICOM studies >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> if they do not have a StudyUID associated with them. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Is there a specific reason why the StudyUID >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> is blank in the DICOM headers in your DICOM files? Did they go through some >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> processes before upload to LORIS? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 2) When i am about to upload a non-phanton >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> case i need a 'Visit Label'. Is there already a script that can create a >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> new visit label for a specific Candidate, so i can provide it as input >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> afterwards to the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> batch_uploads_imageuploader ( See option 5.1.3 https://github.com/aces/Loris-MRI/blob/minor/docs/05-PipelineLaunchOptions.md ) >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I am not sure if the front-end allows for it >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> but if you use batch_uploads_imageuploader, the insertion scripts could >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> create the visit label for you. However, it does need to be included in the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> patient name in order for the script to know which label it should use. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> For example: you upload V02 for MTL0123 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> (DCCID: 456789) but V02 was not yet created for MTL0123; the insertion >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> scripts will create a V02 visit for MTL0123 if the PatientName field for >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the dataset is MTL0123_456789_V02 with Stage marked as "Not Started". >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> However, *note that for the script to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> create the visit for the candidate, you have to make sure that all the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit label of your projects were inserted in the Visit_Windows table* >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> (otherwise, the visit will never be created as they were not specified as >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> being part of the list of visit label to expect). So in the example above, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> you should have one row in Visit_Windows with Visit_label="V02" set. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 3) Section 4.3 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/minor/docs/04-Scripts.md >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> What do we do when the folder contains multiple mnc files? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> This is a case by case. Most of the time, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the MINC files that failed insertion into the imaging browser end up in the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> MRI violation module where you can see what went wrong with the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> acquisitions not inserted. If you notice that the MINC file should be >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> inserted as a specific protocol, you can force the insertion as explained >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in section 4.3. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> In your case, I have a feeling that you want >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> to be able to insert MINC files that did not go through the whole pipeline >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> insertion (DICOM archival, then dcm2mnc, then protocol identification, then >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> insertion...). In theory, you could call >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl on any MINC file, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> provided you have at least the following information: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - path to the MINC file >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - uploadID associated with the MINC files or >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DICOM archive path from which those MINC files were created from >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Then the minc_insertion.pl script will do >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the subject information and protocol validation etc... >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> If all the MINC files come from the same >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> uploadID or TarchiveID, then you could run a loop in bash calling the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl script like this for >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> files deriving from uploadID=1: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ls /path/to/mnc/folder/* | while read f; do >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl -profile prod -uploadID 1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -mincPath $f; done >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helped! >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> -- >>>>>>>>>>>> >>>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>> >>>>>>>>>> -- >>>>>>>>>> >>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>> Montreal Neurological Institute >>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>> >>>>>>>>> _______________________________________________ >>>>>>>> Loris-dev mailing list >>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>> >>>>>>> >>>>>>> >>>>>>> -- >>>>>>> >>>>>>> christine.rogers at mcgill.ca >>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>> Montreal Neurological Institute >>>>>>> McGill University | Montreal | Canada >>>>>>> >>>>>> _______________________________________________ >>>>>> Loris-dev mailing list >>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>> >>>>> >>>>> >>>>> -- >>>>> >>>>> christine.rogers at mcgill.ca >>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>> Montreal Neurological Institute >>>>> McGill University | Montreal | Canada >>>>> _______________________________________________ >>>>> Loris-dev mailing list >>>>> Loris-dev at bic.mni.mcgill.ca >>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>> >>>> >>>> >>>> -- >>>> >>>> christine.rogers at mcgill.ca >>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>> Montreal Neurological Institute >>>> McGill University | Montreal | Canada >>>> >>> _______________________________________________ >>> Loris-dev mailing list >>> Loris-dev at bic.mni.mcgill.ca >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>> >> >> >> -- >> Shen Wang >> Loris Developer >> Montreal Neurological Institute >> McGill University >> >> > > -- > Shen Wang > Loris Developer > Montreal Neurological Institute > McGill University > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 78176 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 20518 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 354645 bytes Desc: not available URL: From sotirisnik at gmail.com Tue Aug 27 19:30:46 2019 From: sotirisnik at gmail.com (Sotirios Nikoloutsopoulos) Date: Wed, 28 Aug 2019 02:30:46 +0300 Subject: [Loris-dev] Import mri - scripts In-Reply-To: References: <65ad2b70c3084ffdb1e4a9dcdad948cd@YTOPR0101MB1803.CANPRD01.PROD.OUTLOOK.COM> Message-ID: Also to mention that in the picture i opened the 000-default.conf which is just a copy of loris.conf by using cp ???? ???, 28 ??? 2019 ???? 2:20 ?.?., ?/? Sotirios Nikoloutsopoulos < sotirisnik at gmail.com> ??????: > Ok that fixed the install.sh problem. Now it doesn't show loris to the > browser, although everything seems right ( also > > /etc/apache2/sites-enabled/000-default.conf was replaced by loris.config ). > > > And apache is running > lorisadmin at loris-VirtualBox:/var/www/loris/htdocs$ sudo systemctl status > apache2[sudo] password for lorisadmin: > ? apache2.service - LSB: Apache2 web server > Loaded: loaded (/etc/init.d/apache2; bad; vendor preset: enabled) > Drop-In: /lib/systemd/system/apache2.service.d > ??apache2-systemd.conf > Active: active (running) since ??? 2019-08-28 02:15:12 EEST; 3min 34s > ago > > [image: image.png] > > ???? ???, 27 ??? 2019 ???? 9:42 ?.?., ?/? Shen Wang < > wangshen.mcin at gmail.com> ??????: > >> Hi, >> This is a bug for install.sh file, we will fix it later. >> Thank for letting me know your Loris install situation. >> regards >> Shen >> >> >> On Tue, 27 Aug 2019 at 14:28, Shen Wang wrote: >> >>> Hi, >>> Please remove "set -euo pipefail" line 10 in the install.sh file. >>> Then try again. >>> >>> >>> >>> On Tue, 27 Aug 2019 at 14:05, Sotirios Nikoloutsopoulos < >>> sotirisnik at gmail.com> wrote: >>> >>>> Hi, >>>> >>>> i still haven't resolved the previous issue. Also i tried to install >>>> Loris to a new virtual machine and when i execute install.sh i get the >>>> following error >>>> >>>> lorisadmin at loris-VirtualBox:/var/www/loris/tools$ ./install.sh >>>> LORIS Installation Script starting at 2019-08-27T21:00:42 >>>> The log for this session will be stored in file >>>> /var/www/loris/tools/logs/install-2019-08-27T21:00:42.log >>>> --------------------------------------------------------------------- >>>> LORIS Installation Script >>>> --------------------------------------------------------------------- >>>> >>>> PHP appears to be installed. >>>> >>>> PHP Composer appears to be installed. >>>> >>>> This install script will ask you to provide inputs for different steps. >>>> Please ensure you have the following information ready (if applicable): >>>> >>>> 1) Your project directory name. >>>> (Will be used to modify the paths for Imaging data in the generated >>>> config.xml file for LORIS, and may also be used to automatically >>>> create/install apache config files.) If unsure, a default like >>>> "LORIS" >>>> should be acceptable. >>>> >>>> Please also consult the Loris WIKI on GitHub for more information on >>>> these >>>> Install Script input parameters. >>>> >>>> Ready to continue? [yn] y >>>> >>>> ./install.sh: line 132: projectname: unbound variable >>>> >>>> Thanks >>>> >>>> ???? ???, 6 ??? 2019 ???? 5:09 ?.?., ?/? Christine Rogers, Ms. < >>>> christine.rogers at mcgill.ca> ??????: >>>> >>>>> Hi Sotirios, >>>>> Could you also let us know -- on which pages is content visible, and >>>>> on which pages/modules is content not visible for you? >>>>> Thanks, >>>>> Christine >>>>> >>>>> On Tue, Aug 6, 2019 at 9:54 AM Christine Rogers, Ms. < >>>>> christine.rogers at mcgill.ca> wrote: >>>>> >>>>>> Thanks Sotirios, >>>>>> That's good to know. It sounds like you've checked that your >>>>>> /var/www/loris/project/config.xml file get populated properly. >>>>>> >>>>>> Please send us the last few errors you're seeing in your apache error >>>>>> log file, and your config paths and we can see what's happening with your >>>>>> front end -- >>>>>> Run these Troubleshooting Queries >>>>>> >>>>>> to get your config path settings, given your front end is not displaying >>>>>> fully. >>>>>> >>>>>> The Loris-MRI repo >>>>>> 21 >>>>>> install/upgrade would then be your next steps. >>>>>> Best, >>>>>> Christine >>>>>> >>>>>> On Tue, Aug 6, 2019 at 7:53 AM Sotirios Nikoloutsopoulos < >>>>>> sotirisnik at gmail.com> wrote: >>>>>> >>>>>>> I am using a VM. What i did was: >>>>>>> 1) Download the files from https://github.com/aces/Loris and >>>>>>> replace them to my existing /vaw/www/loris folder. >>>>>>> 2) Execute the composer install --no-dev and then composer >>>>>>> dump-autoload as mentioned here >>>>>>> https://github.com/aces/Loris/wiki/Updating-your-LORIS. >>>>>>> 3) Execute install.sh from /var/www/loris/tools and because LORIS >>>>>>> already existed i moved a .config file, then re-executed the install.sh >>>>>>> successfully >>>>>>> 4 ) As for the database, i dropped the schema and i executed the >>>>>>> installdb.php >>>>>>> >>>>>>> ???? ???, 5 ??? 2019 ???? 5:22 ?.?., ?/? Christine Rogers, Ms. < >>>>>>> christine.rogers at mcgill.ca> ??????: >>>>>>> >>>>>>>> Hi Sotorios, >>>>>>>> >>>>>>>> Thanks - when you re-installed did you start on a fresh root path / >>>>>>>> VM or might some of your old system setting still apply? >>>>>>>> (And if you did any steps similar to an upgrade, did you follow the >>>>>>>> Upgrade steps in the Release Notes, from both repos?) >>>>>>>> >>>>>>>> About the TR_range column - it was recently split (MRI pr339 >>>>>>>> ) split into TR_min >>>>>>>> and _max columns. Given the code was trying to query TR_range which does >>>>>>>> not exist in your mri_protocol table, double-check which version of the >>>>>>>> Loris repo (tables) and the Loris-MRI repo (code) you have installed to >>>>>>>> ensure they match. >>>>>>>> >>>>>>>> Christine >>>>>>>> >>>>>>>> >>>>>>>> On Mon, Aug 5, 2019 at 9:06 AM Sotirios Nikoloutsopoulos < >>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>> >>>>>>>>> I reinstalled LORIS to 21 version and now the content is not >>>>>>>>> visible at all at most pages. >>>>>>>>> >>>>>>>>> [image: image.png] >>>>>>>>> >>>>>>>>> ???? ???, 5 ??? 2019 ???? 3:19 ?.?., ?/? Sotirios Nikoloutsopoulos >>>>>>>>> ??????: >>>>>>>>> >>>>>>>>>> Hi, >>>>>>>>>> >>>>>>>>>> Is it easy to upgrade to Loris 21? Also the following fails >>>>>>>>>> because the line 1985 of NeuroDB/MRIProcessingUtility.pm query mri_protocol >>>>>>>>>> which doesn't have TR_range >>>>>>>>>> https://github.com/aces/Loris/blob/21.0-release/SQL/0000-00-00-schema.sql#L556 >>>>>>>>>> >>>>>>>>>> [image: image.png] >>>>>>>>>> >>>>>>>>>> lorisadmin at hbp:/data/loris/bin/mri$ >>>>>>>>>> ./batch_uploads_imageuploader -profile prod < ~/Desktop/input.txt > log.txt >>>>>>>>>> Use of uninitialized value $_ in pattern match (m//) at >>>>>>>>>> ./batch_uploads_imageuploader line 147. >>>>>>>>>> base is DCC0000_258024_V1 >>>>>>>>>> path is /data/incoming/ >>>>>>>>>> type is .tar.gz >>>>>>>>>> fullpath is /data/incoming/DCC0000_258024_V1.tar.gz >>>>>>>>>> DBD::mysql::st execute failed: Unknown column 'TR_range' in >>>>>>>>>> 'where clause' at >>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line 1985. >>>>>>>>>> DBD::mysql::st fetchrow_array failed: fetch() without execute() >>>>>>>>>> at /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line >>>>>>>>>> 1986. >>>>>>>>>> Use of uninitialized value $count_mri_protocol in numeric gt (>) >>>>>>>>>> at /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line >>>>>>>>>> 1995. >>>>>>>>>> DBD::mysql::st execute failed: Unknown column 'TR_range' in >>>>>>>>>> 'field list' at /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 562. >>>>>>>>>> Can't exec "mail": No such file or directory at >>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 721. >>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 722. >>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 723. >>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 724. >>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 725. >>>>>>>>>> >>>>>>>>>> No Mincs inserted >>>>>>>>>> >>>>>>>>>> Thanks, >>>>>>>>>> >>>>>>>>>> Sotirios >>>>>>>>>> >>>>>>>>>> ???? ???, 3 ??? 2019 ???? 1:08 ?.?., ?/? Christine Rogers, Ms. < >>>>>>>>>> christine.rogers at mcgill.ca> ??????: >>>>>>>>>> >>>>>>>>>>> Hi Sotirios, >>>>>>>>>>> >>>>>>>>>>> First, just a note: we've released LORIS 21 this week with some >>>>>>>>>>> major new features and cleanup -- especially if you are early in your setup >>>>>>>>>>> phase, check out the Release notes for both the LORIS >>>>>>>>>>> and >>>>>>>>>>> Loris-MRI >>>>>>>>>>> repos. >>>>>>>>>>> >>>>>>>>>>> Thanks for your screenshots -- your empty mri_protocol table >>>>>>>>>>> should be at the root of these issues : >>>>>>>>>>> >>>>>>>>>>> The mri_protocol table must be populated >>>>>>>>>>> >>>>>>>>>>> in order for your scans to be registered in LORIS -- it serves as a >>>>>>>>>>> whitelist for the insertion pipeline which filters out scans that aren't >>>>>>>>>>> identified or matched to scan types in this table. >>>>>>>>>>> >>>>>>>>>>> By default, this table is populated with entries for t1, t2, >>>>>>>>>>> fMRI and DTI (Insert statements for 21 release branch are here >>>>>>>>>>> >>>>>>>>>>> ) >>>>>>>>>>> Feel free to restore our default records and broaden their >>>>>>>>>>> parameters to match all your scan types. >>>>>>>>>>> >>>>>>>>>>> re Defaced, native, selected -- these filter the scans displayed >>>>>>>>>>> as you move to the next page (View Session), instead of viewing "all types" >>>>>>>>>>> of scans from a given session : >>>>>>>>>>> >>>>>>>>>>> - "defaced" means that a defacing script >>>>>>>>>>> >>>>>>>>>>> has masked the subject's face in the volume (for patient privacy) >>>>>>>>>>> - "native" means that no pre-processing has been performed >>>>>>>>>>> on the scan (it's raw data), >>>>>>>>>>> - "selected" will show only volumes that have been QC'd and >>>>>>>>>>> "selected" as the best of their type -- used to display only the best >>>>>>>>>>> quality T1 image instead of all T1s acquired in a session, e.g. >>>>>>>>>>> >>>>>>>>>>> re QC Comments -- >>>>>>>>>>> Once you have successfully loaded scans (matched to the >>>>>>>>>>> mri_protocol table), you'll be able to use the Imaging Browser's View >>>>>>>>>>> Session subpage to enter/view QC comments on each volume, or for each >>>>>>>>>>> visit. >>>>>>>>>>> These are stored directly in the database, and linked to each >>>>>>>>>>> scan. (Table name: feedback_mri_comments) >>>>>>>>>>> (Visit-level QC comments are linked to the session.) >>>>>>>>>>> >>>>>>>>>>> For a walkthrough of the Imaging setup - please see the Imaging >>>>>>>>>>> Setup guide >>>>>>>>>>> >>>>>>>>>>> - >>>>>>>>>>> >>>>>>>>>>> An old LORIS walkthrough video >>>>>>>>>>> can also walk you >>>>>>>>>>> through some of the Imaging front-end features, starting at 8:00 >>>>>>>>>>> LORIS' imaging modules have been updated many times since this >>>>>>>>>>> video, but the functionality and workflow is similar. >>>>>>>>>>> >>>>>>>>>>> Let us know how it goes once you have entries in your >>>>>>>>>>> mri_protocol table - >>>>>>>>>>> Best, >>>>>>>>>>> Christine >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> On Fri, Aug 2, 2019 at 7:58 AM Sotirios Nikoloutsopoulos < >>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>> >>>>>>>>>>>> Hi Christine, >>>>>>>>>>>> >>>>>>>>>>>> In the candidate_list page i can see this patient >>>>>>>>>>>> >>>>>>>>>>>> [image: image.png] >>>>>>>>>>>> >>>>>>>>>>>> If i press the link under PSCID i get to see >>>>>>>>>>>> [image: image.png] >>>>>>>>>>>> >>>>>>>>>>>> and if i press the link under Scan Done it redirects me to >>>>>>>>>>>> imaging_browser >>>>>>>>>>>> >>>>>>>>>>>> [image: image.png] >>>>>>>>>>>> >>>>>>>>>>>> At the mri_violations page i also see No results ( neither on >>>>>>>>>>>> resolved / not resolved ). >>>>>>>>>>>> >>>>>>>>>>>> At the imaging_uploader i can see the record that failed. >>>>>>>>>>>> >>>>>>>>>>>> [image: image.png] >>>>>>>>>>>> >>>>>>>>>>>> If i click on the tarchive info i get to see the Protocol Name >>>>>>>>>>>> which i think is the acquisition we wanted? >>>>>>>>>>>> [image: image.png] >>>>>>>>>>>> >>>>>>>>>>>> Also my mri_protocol table is empty. >>>>>>>>>>>> >>>>>>>>>>>> Furthermore i would like to ask about the defaced, native, >>>>>>>>>>>> selected. What exactly is native and selected? And where are the qc >>>>>>>>>>>> comments stored? >>>>>>>>>>>> >>>>>>>>>>>> [image: image.png] >>>>>>>>>>>> >>>>>>>>>>>> Finally a walkthrough would be helpful. >>>>>>>>>>>> >>>>>>>>>>>> Thanks, >>>>>>>>>>>> >>>>>>>>>>>> Sotirios >>>>>>>>>>>> >>>>>>>>>>>> ???? ???, 30 ???? 2019 ???? 8:29 ?.?., ?/? Christine Rogers, >>>>>>>>>>>> Ms. ??????: >>>>>>>>>>>> >>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>> Glad to hear you're making progress with the visit labels. To >>>>>>>>>>>>> follow up on your last few emails: >>>>>>>>>>>>> >>>>>>>>>>>>> a- The Wiki's Setup Guide contains Sample insert statements >>>>>>>>>>>>> for the Visit Windows table >>>>>>>>>>>>> >>>>>>>>>>>>> . >>>>>>>>>>>>> >>>>>>>>>>>>> As Cecile mentioned, the consistency of visit label format is >>>>>>>>>>>>> important: V01, v01, V1, 01 -- whichever you select to use is fine; we use >>>>>>>>>>>>> V01 by default across all documentation. >>>>>>>>>>>>> >>>>>>>>>>>>> b- For Password reset, there is a script in the tools/ >>>>>>>>>>>>> directory so that a back-end administrator can reset any front-end user >>>>>>>>>>>>> password, including Admin. (See info on setting up / resetting User >>>>>>>>>>>>> passwords in the Wiki's Setup Guide >>>>>>>>>>>>> >>>>>>>>>>>>> ) >>>>>>>>>>>>> >>>>>>>>>>>>> c- The minc file not being registered -- due to >>>>>>>>>>>>> AcquisitionProtocol unknown. >>>>>>>>>>>>> This means the SeriesDescription (Acquisition Protocol) in you >>>>>>>>>>>>> Dicom header was not matched to any scan listed in the mri_protocol >>>>>>>>>>>>> database table. >>>>>>>>>>>>> (In the online Loris-MRI Troubleshooting Guide, >>>>>>>>>>>>> this >>>>>>>>>>>>> is Table 3, 2nd-last item "no MINCs inserted"). >>>>>>>>>>>>> >>>>>>>>>>>>> The MRI Violations module (Readme here) >>>>>>>>>>>>> will show >>>>>>>>>>>>> you the details of this mismatch -- >>>>>>>>>>>>> Go to the module (under the Imaging menu), find your scan and >>>>>>>>>>>>> click the link "Could not identify scan type" -- in the next subpage you >>>>>>>>>>>>> can compare the scan's actual parameters against the mri_protocol table. >>>>>>>>>>>>> >>>>>>>>>>>>> To resolve this, adjust your mri_protocol table values or >>>>>>>>>>>>> perhaps ensure your DICOMs are labelled consistently. >>>>>>>>>>>>> >>>>>>>>>>>>> Let us know if this works for you -- we can also walk you >>>>>>>>>>>>> through an example of non-identified scans on Demo.loris.ca >>>>>>>>>>>>> (MRI Violations module). >>>>>>>>>>>>> >>>>>>>>>>>>> Best, >>>>>>>>>>>>> Christine >>>>>>>>>>>>> >>>>>>>>>>>>> The LORIS team >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> On Tue, Jul 30, 2019 at 10:47 AM Sotirios Nikoloutsopoulos < >>>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>> >>>>>>>>>>>>>> I hope this is sufficient as the error for the visit label >>>>>>>>>>>>>> disappeared. >>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>> >>>>>>>>>>>>>> Please see the attached file. Also something i found. >>>>>>>>>>>>>> >>>>>>>>>>>>>> lorisadmin at hbp:/data/loris/bin/mri$ cat >>>>>>>>>>>>>> /data/loris/data//logs/TarLoad-17-39-xubBdv.log >>>>>>>>>>>>>> >>>>>>>>>>>>>> ==> Loading file from disk >>>>>>>>>>>>>> /tmp/TarLoad-17-39-UyQcG2/dcc0000_258024_v1_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>> >>>>>>>>>>>>>> --> mapping DICOM parameter for >>>>>>>>>>>>>> /tmp/TarLoad-17-39-UyQcG2/dcc0000_258024_v1_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>> >>>>>>>>>>>>>> ==> computing md5 hash for MINC body. >>>>>>>>>>>>>> >>>>>>>>>>>>>> --> md5: 6b1202fd63e29de4c9be1cd9925888a5 >>>>>>>>>>>>>> >>>>>>>>>>>>>> ==> verifying acquisition protocol >>>>>>>>>>>>>> >>>>>>>>>>>>>> Acquisition protocol is unknown >>>>>>>>>>>>>> >>>>>>>>>>>>>> --> The minc file cannot be registered since the >>>>>>>>>>>>>> AcquisitionProtocol is unknown >>>>>>>>>>>>>> >>>>>>>>>>>>>> ???? ???, 30 ???? 2019 ???? 4:58 ?.?., ?/? Sotirios >>>>>>>>>>>>>> Nikoloutsopoulos ??????: >>>>>>>>>>>>>> >>>>>>>>>>>>>>> Ok I fixed the login problem by using a known hash and by >>>>>>>>>>>>>>> deleting the rows from the login_history i was able to login. >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> ???? ???, 30 ???? 2019 ???? 4:50 ?.?., ?/? Sotirios >>>>>>>>>>>>>>> Nikoloutsopoulos ??????: >>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> there was no visit label 01 in the Visit_Windows table and >>>>>>>>>>>>>>>> i don't know how to insert it because the record requires lots of >>>>>>>>>>>>>>>> attributes. Also the system for a reason asked me to update my password and >>>>>>>>>>>>>>>> now i don't remember it and my account got suspended. Is there a way to >>>>>>>>>>>>>>>> reset it or set a simple password? I updated the password hash in the >>>>>>>>>>>>>>>> users table by using the hash from another LORIS setup we had and i still >>>>>>>>>>>>>>>> couldn't login ( also the attribute password is always NULL and the >>>>>>>>>>>>>>>> expiration date is 1999-01-01 for some reason ). >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Thanks >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> ???? ???, 29 ???? 2019 ???? 5:21 ?.?., ?/? Cecile Madjar < >>>>>>>>>>>>>>>> cecile.madjar at mcin.ca> ??????: >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Can you try adding the visit label v01 to the >>>>>>>>>>>>>>>>> Visit_Windows table? >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> However, I noticed that in a previous dataset, the label >>>>>>>>>>>>>>>>> was V1. Does that refer to the same visit? If so, you might want to >>>>>>>>>>>>>>>>> harmonize the visit labels so they are all the same across datasets for a >>>>>>>>>>>>>>>>> given timepoint, meaning you will need to relabel scans when the visit >>>>>>>>>>>>>>>>> label is different but referring to the same visit label (v01 = V1 etc...). >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Hope this helps, >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> On Mon, Jul 29, 2019 at 10:15 AM Sotirios Nikoloutsopoulos >>>>>>>>>>>>>>>>> wrote: >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Could you help me with the "Visit label does not exist"? >>>>>>>>>>>>>>>>>> I had changed $subjectID{'createVisitLabel'} to 1 as you had suggested but >>>>>>>>>>>>>>>>>> it appears that this problem hasn't been resolved yet. >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> lorisadmin at hbp:/data/loris/bin/mri$ cat >>>>>>>>>>>>>>>>>> /data/loris/data//logs/TarLoad-14-58-9Xog7H.log >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> ==> Loading file from disk >>>>>>>>>>>>>>>>>> /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> --> mapping DICOM parameter for >>>>>>>>>>>>>>>>>> /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> --> using user-defined filterParameters for >>>>>>>>>>>>>>>>>> /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Candidate Mismatch Error is Visit label does not exist >>>>>>>>>>>>>>>>>> -> WARNING: This candidate was invalid. Logging to >>>>>>>>>>>>>>>>>> MRICandidateErrors table with reason Visit >>>>>>>>>>>>>>>>>> label does not exist >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> ???? ???, 26 ???? 2019 ???? 3:02 ?.?., ?/? Sotirios >>>>>>>>>>>>>>>>>> Nikoloutsopoulos ??????: >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Hi Cecile, >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> The Center error was fixed. Still the insertion of mincs >>>>>>>>>>>>>>>>>>> fails. Please see the output.txt file i attached. Also is there something >>>>>>>>>>>>>>>>>>> else i need to change at the paths configuration? >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> ???? ???, 25 ???? 2019 ???? 6:55 ?.?., ?/? Cecile Madjar >>>>>>>>>>>>>>>>>>> ??????: >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> We are making progress! >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> I have a feeling this error comes from the fact that >>>>>>>>>>>>>>>>>>>> your psc table does not have the MRI_alias populated for the DCC site. >>>>>>>>>>>>>>>>>>>> Running the following query in the mysql database should fix this: >>>>>>>>>>>>>>>>>>>> UPDATE psc SET MRI_alias="DCC", Alias="DCC" WHERE >>>>>>>>>>>>>>>>>>>> Name="Data Coordinating Center"; >>>>>>>>>>>>>>>>>>>> Repeat the same with all your sites (make sure to >>>>>>>>>>>>>>>>>>>> change the Aliases between sites, they should all be unique). >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Let me know how it goes! >>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> On Thu, Jul 25, 2019 at 11:43 AM Sotirios >>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos wrote: >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> Dear Cecile, >>>>>>>>>>>>>>>>>>>>> You were right about your guesses. I did the >>>>>>>>>>>>>>>>>>>>> modifications you suggested, i still get the "no mincs inserted" error, now >>>>>>>>>>>>>>>>>>>>> i am getting the "No center found this candidate" error ( how do i fix >>>>>>>>>>>>>>>>>>>>> that? from what i see the .dcm files contains a 'Institution Name', is that >>>>>>>>>>>>>>>>>>>>> the center? ), so i guess that's why the validation fails, but i changed >>>>>>>>>>>>>>>>>>>>> the force variable of tarchiveLoader to 1, shouldn't it have inserted the >>>>>>>>>>>>>>>>>>>>> mincs then? Also it is optional to have a mail server, right? ( from what i >>>>>>>>>>>>>>>>>>>>> see the mail error does not affect the $valid_study, so i assume we are >>>>>>>>>>>>>>>>>>>>> okay with that ) >>>>>>>>>>>>>>>>>>>>> Thank you a lot, >>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> ???? ???, 25 ???? 2019 ???? 5:48 ?.?., ?/? Cecile >>>>>>>>>>>>>>>>>>>>> Madjar ??????: >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> From what I understand, I believe you just need to >>>>>>>>>>>>>>>>>>>>>> update a few config settings from the frontend in the Config module (under >>>>>>>>>>>>>>>>>>>>>> the Admin menu). >>>>>>>>>>>>>>>>>>>>>> [image: Screen Shot 2019-07-25 at 10.31.35 AM.png] >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> Then go to the Paths section of the config module and >>>>>>>>>>>>>>>>>>>>>> update the "LORIS-MRI code" config setting to /data/loris/bin/mri (my guess >>>>>>>>>>>>>>>>>>>>>> is that currently, it is set to /data/LORIS/data) and click on the submit >>>>>>>>>>>>>>>>>>>>>> button. >>>>>>>>>>>>>>>>>>>>>> [image: Screen Shot 2019-07-25 at 10.32.50 AM.png] >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> Then, go to Imaging Pipeline section of the >>>>>>>>>>>>>>>>>>>>>> Configuration module and update the "Loris-MRI Data Directory" to >>>>>>>>>>>>>>>>>>>>>> /data/loris/data/ (my guess is that it is empty at the moment in your >>>>>>>>>>>>>>>>>>>>>> database which is why $data_dir is not defined when you run the >>>>>>>>>>>>>>>>>>>>>> tarchiveLoader step of the insertion pipeline). >>>>>>>>>>>>>>>>>>>>>> [image: Screen Shot 2019-07-25 at 10.40.52 AM.png] >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> Finally, I took a look at your environment file and >>>>>>>>>>>>>>>>>>>>>> it might be a good idea to update your PERL5LIB variable to the following >>>>>>>>>>>>>>>>>>>>>> (it has been added to the code a few releases ago as we realized this was >>>>>>>>>>>>>>>>>>>>>> needed for the libraries. Not sure which version of LORIS-MRI you are using >>>>>>>>>>>>>>>>>>>>>> but it does not hurt to update this variable to what I suggest below): >>>>>>>>>>>>>>>>>>>>>> export >>>>>>>>>>>>>>>>>>>>>> PERL5LIB=/data/loris/bin/mri/uploadNeuroDB:/data/loris/bin/mri/dicom-archive:$PERL5LIB >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> Hope this helps. Sorry you are experiencing so much >>>>>>>>>>>>>>>>>>>>>> trouble setting things up. We probably need to update our WIKI. >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> On Thu, Jul 25, 2019 at 9:48 AM Sotirios >>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos wrote: >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> The "Loris-MRI Data Directory" should be in the >>>>>>>>>>>>>>>>>>>>>>> environment file? >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> ???? ???, 25 ???? 2019 ???? 12:59 ?.?., ?/? Sotirios >>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos ??????: >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> The scripts are located in /data/loris/bin/mri/. >>>>>>>>>>>>>>>>>>>>>>>> Somewhere I might have messed something up but i remember following the >>>>>>>>>>>>>>>>>>>>>>>> instructions in the wiki.For example when i tried to execute the >>>>>>>>>>>>>>>>>>>>>>>> batch_uploads_imageuploader perl script the line >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> my $command = "$bin_dir/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl " >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> was pointing to an invalid path, for example: it >>>>>>>>>>>>>>>>>>>>>>>> was repeating a pattern and had LORIS instead of loris ( i think the >>>>>>>>>>>>>>>>>>>>>>>> mistake was that in the wiki it suggested to use $PROJECT for the name of >>>>>>>>>>>>>>>>>>>>>>>> the folder and i choosed 'loris' >>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris/wiki/Imaging-Database >>>>>>>>>>>>>>>>>>>>>>>> ). See also the in image for the modification i did. Also i didn't find the >>>>>>>>>>>>>>>>>>>>>>>> section to config the $data_dir variable. >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 24 ???? 2019 ???? 6:05 ?.?., ?/? Cecile >>>>>>>>>>>>>>>>>>>>>>>> Madjar ??????: >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> It looks like you have one Config setting not set >>>>>>>>>>>>>>>>>>>>>>>>> (based on the first error message you got when running it the first time). >>>>>>>>>>>>>>>>>>>>>>>>> You need to set a value for "Loris-MRI Data Directory" in the Config module >>>>>>>>>>>>>>>>>>>>>>>>> under the Imaging pipeline section (from what I can see, it would be >>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/ for your setup). >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> The reason you got that error message the second >>>>>>>>>>>>>>>>>>>>>>>>> time is that the pipeline checks if the DICOM study was already inserted in >>>>>>>>>>>>>>>>>>>>>>>>> the tarchive table. Since you ran the study once already, the study is >>>>>>>>>>>>>>>>>>>>>>>>> inserted into the tarchive, hence the message. However, the pipeline did >>>>>>>>>>>>>>>>>>>>>>>>> not complete as the MINC files were not created and inserted into the >>>>>>>>>>>>>>>>>>>>>>>>> files/parameter_file table. In order to continue the insertion, you will >>>>>>>>>>>>>>>>>>>>>>>>> then need to run the tarchiveLoader command suggested in the terminal >>>>>>>>>>>>>>>>>>>>>>>>> during the second run: >>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader >>>>>>>>>>>>>>>>>>>>>>>>> -globLocation -profile prod >>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive//2012/DCM_2012-12-05_ImagingUpload-17-43-ZUEFjb.tar >>>>>>>>>>>>>>>>>>>>>>>>> -verbose >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> Finally, I am a bit confused by your setup. Where >>>>>>>>>>>>>>>>>>>>>>>>> are the scripts located? In /data/loris/bin/mri or /data/loris/data? It >>>>>>>>>>>>>>>>>>>>>>>>> feels like the Config setting "LORIS-MRI code" in the Paths section was set >>>>>>>>>>>>>>>>>>>>>>>>> to "/data/LORIS/data" but it should have been set to the directory where >>>>>>>>>>>>>>>>>>>>>>>>> the scripts are located (most probably /data/loris/bin/mri). >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> Hope this helps, >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> On Wed, Jul 24, 2019 at 10:55 AM Sotirios >>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos wrote: >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> Ok first i execute this command: >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> "lorisadmin at hbp:/data/loris/bin/mri$ >>>>>>>>>>>>>>>>>>>>>>>>>> ./batch_uploads_imageuploader -profile prod < ~/Desktop/input.txt > log.txt >>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at ./batch_uploads_imageuploader line 143. >>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at ./batch_uploads_imageuploader line 143. >>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $_ in pattern match >>>>>>>>>>>>>>>>>>>>>>>>>> (m//) at ./batch_uploads_imageuploader line 147. >>>>>>>>>>>>>>>>>>>>>>>>>> base is DCC0000_258024_V01 >>>>>>>>>>>>>>>>>>>>>>>>>> path is /data/incoming/ >>>>>>>>>>>>>>>>>>>>>>>>>> type is .tar.gz >>>>>>>>>>>>>>>>>>>>>>>>>> fullpath is >>>>>>>>>>>>>>>>>>>>>>>>>> /data/incoming/DCC0000_258024_V01.tar.gz >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> source /tmp/ImagingUpload-17-43-ZUEFjb >>>>>>>>>>>>>>>>>>>>>>>>>> targetlocation /data/loris/data/tarchive >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 256. >>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 284. >>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at /data/loris/bin/mri/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>> tarchive_validation.pl line 219. >>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at /data/loris/bin/mri/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl line 270. >>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 711. >>>>>>>>>>>>>>>>>>>>>>>>>> Can't exec "mail": No such file or directory at >>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 721. >>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 722. >>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 723. >>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 724. >>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 724. >>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 725. >>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 735. >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> No Mincs inserted >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> The tarchiveLoader insertion script has failed. >>>>>>>>>>>>>>>>>>>>>>>>>> Running now the following command: >>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl -profile prod -upload_id >>>>>>>>>>>>>>>>>>>>>>>>>> 3 /data/incoming/DCC0000_258024_V01.tar.gz -verbose" >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> I inserted the VisitLabel, but still the Mincs >>>>>>>>>>>>>>>>>>>>>>>>>> are not inserted and i am getting this error >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> "lorisadmin at hbp:/data/loris/bin/mri$ >>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl -profile prod -upload_id >>>>>>>>>>>>>>>>>>>>>>>>>> 3 /data/incoming/DCC0000_258024_V01.tar.gz -verbose >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> find -path \/tmp\/ImagingUpload\-17\-45\-5MsWEd >>>>>>>>>>>>>>>>>>>>>>>>>> -name '__MACOSX' -delete >>>>>>>>>>>>>>>>>>>>>>>>>> Spool message is: >>>>>>>>>>>>>>>>>>>>>>>>>> The Scan for the uploadID 3 has already been run >>>>>>>>>>>>>>>>>>>>>>>>>> with tarchiveID: 7. >>>>>>>>>>>>>>>>>>>>>>>>>> To continue with the rest of the insertion >>>>>>>>>>>>>>>>>>>>>>>>>> pipeline, please run tarchiveLoader from a terminal as follows: >>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader -globLocation -profile prod >>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive//2012/DCM_2012-12-05_ImagingUpload-17-43-ZUEFjb.tar >>>>>>>>>>>>>>>>>>>>>>>>>> -verbose" >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> Which files should i delete? I thought that >>>>>>>>>>>>>>>>>>>>>>>>>> deleting the files from the tarchive was enough. And i executed the last >>>>>>>>>>>>>>>>>>>>>>>>>> proposed command to continue to rest of the insertion pipeline ( check the >>>>>>>>>>>>>>>>>>>>>>>>>> image ). >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> Thank you >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 24 ???? 2019 ???? 5:05 ?.?., ?/? Cecile >>>>>>>>>>>>>>>>>>>>>>>>>> Madjar ??????: >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> Sorry I was not clear before. Every visits of >>>>>>>>>>>>>>>>>>>>>>>>>>> candidates are created in the session table with one entry per >>>>>>>>>>>>>>>>>>>>>>>>>>> CandID/VisitLabel. So if the imaging pipeline created visits in the session >>>>>>>>>>>>>>>>>>>>>>>>>>> table (that are not attached to instruments) and you want to clean your >>>>>>>>>>>>>>>>>>>>>>>>>>> database completely, you can delete entries in that table as well. >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> Regarding your point 2, the imaging pipeline can >>>>>>>>>>>>>>>>>>>>>>>>>>> create the visit in the session table as long as the visit label is present >>>>>>>>>>>>>>>>>>>>>>>>>>> in the Visit_Windows table (which means the visit label stored in the >>>>>>>>>>>>>>>>>>>>>>>>>>> PatientName is a valid visit label). >>>>>>>>>>>>>>>>>>>>>>>>>>> However, in your prod file, if the >>>>>>>>>>>>>>>>>>>>>>>>>>> variable $subjectID{'createVisitLabel'} is set to 1 for candidates, the >>>>>>>>>>>>>>>>>>>>>>>>>>> visit label should be created in the Visit_Windows table I believe. Here >>>>>>>>>>>>>>>>>>>>>>>>>>> is the line of the prod file you would need to change >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> . >>>>>>>>>>>>>>>>>>>>>>>>>>> In general, we prefer populating the >>>>>>>>>>>>>>>>>>>>>>>>>>> Visit_Windows table and set the $subjectID{'createVisitLabel'} to 0 for >>>>>>>>>>>>>>>>>>>>>>>>>>> candidate data to avoid insertion of badly labelled MRI data that are >>>>>>>>>>>>>>>>>>>>>>>>>>> complex to relabel. >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> Finally, regarding the candidate creation, if >>>>>>>>>>>>>>>>>>>>>>>>>>> you execute the following steps, the pipeline should be able to create >>>>>>>>>>>>>>>>>>>>>>>>>>> candidates: >>>>>>>>>>>>>>>>>>>>>>>>>>> - set in the Imaging Pipeline section of the >>>>>>>>>>>>>>>>>>>>>>>>>>> config module the config setting "Upload creation of candidates" to Yes >>>>>>>>>>>>>>>>>>>>>>>>>>> - manually transfer the scans to the LORIS >>>>>>>>>>>>>>>>>>>>>>>>>>> server instead of uploading it via the imaging browser >>>>>>>>>>>>>>>>>>>>>>>>>>> - run batch_imaging_upload.pl as you did until >>>>>>>>>>>>>>>>>>>>>>>>>>> now. >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helps! >>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> On Wed, Jul 24, 2019 at 8:47 AM Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos wrote: >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> About my second question i replaced the name of >>>>>>>>>>>>>>>>>>>>>>>>>>>> the patient in the .dcm files and now i am getting an error that the visit >>>>>>>>>>>>>>>>>>>>>>>>>>>> label does not exist. >>>>>>>>>>>>>>>>>>>>>>>>>>>> I thought it was supposed to be automatically >>>>>>>>>>>>>>>>>>>>>>>>>>>> created. >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> "Done adding archive info into database >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader >>>>>>>>>>>>>>>>>>>>>>>>>>>> -globLocation -profile prod >>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive//DCM_2012-12-05_ImagingUpload-15-42-yUwQQV.tar >>>>>>>>>>>>>>>>>>>>>>>>>>>> -verbose >>>>>>>>>>>>>>>>>>>>>>>>>>>> md5sum >>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive/DCM_2012-12-05_ImagingUpload-15-42-yUwQQV.tar >>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>> candidate id 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> => No Visit labelVisit label does not exist >>>>>>>>>>>>>>>>>>>>>>>>>>>> Set centerID = 1 >>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> Number of MINC files that will be considered >>>>>>>>>>>>>>>>>>>>>>>>>>>> for inserting into the database: 1 >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> log dir is /logs and log file is >>>>>>>>>>>>>>>>>>>>>>>>>>>> /logs/TarLoad-15-42-L6pocU.log >>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>> candidate id 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> => No Visit label >>>>>>>>>>>>>>>>>>>>>>>>>>>> Cleaning up temp files: rm -rf >>>>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-15-42-J2rQms/ImagingUpload-15-42-yUwQQV*" >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 24 ???? 2019 ???? 3:38 ?.?., ?/? >>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos >>>>>>>>>>>>>>>>>>>>>>>>>>>> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> 1) What are the records in the session table? >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> 2) I tried to upload a non-phantom file like >>>>>>>>>>>>>>>>>>>>>>>>>>>>> this >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> input_file.txt: >>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/incoming/DCC0000_258024_V1.tar.gz N >>>>>>>>>>>>>>>>>>>>>>>>>>>>> DCC0000_258024_V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Terminal: >>>>>>>>>>>>>>>>>>>>>>>>>>>>> ./batch_uploads_imageuploader -profile prod < >>>>>>>>>>>>>>>>>>>>>>>>>>>>> ~/Desktop/input.txt > log.txt >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> and i get the following error in the log.txt >>>>>>>>>>>>>>>>>>>>>>>>>>>>> file >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> "Running now the following command: >>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl -profile prod >>>>>>>>>>>>>>>>>>>>>>>>>>>>> -upload_id 7 /data/incoming/DCC0000_258024_V1.tar.gz -verbose >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> find -path >>>>>>>>>>>>>>>>>>>>>>>>>>>>> \/tmp\/ImagingUpload\-14\-56\-FeLCB4 -name '__MACOSX' -delete >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Spool message is: >>>>>>>>>>>>>>>>>>>>>>>>>>>>> The PatientName read from the DICOM header >>>>>>>>>>>>>>>>>>>>>>>>>>>>> does not start with DCC0000_258024_V1 from the mri_upload table >>>>>>>>>>>>>>>>>>>>>>>>>>>>> " >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> and the spool message is repeated for each >>>>>>>>>>>>>>>>>>>>>>>>>>>>> .dcm file. Should i preprocess every .dcm file and change the PatientName >>>>>>>>>>>>>>>>>>>>>>>>>>>>> to "DCC0000_258024_V1"? >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> 3) As far as it concerns the candidate profile >>>>>>>>>>>>>>>>>>>>>>>>>>>>> i have to create a new one each time before i try to upload a file? Is >>>>>>>>>>>>>>>>>>>>>>>>>>>>> there already a way to create a candidate profile and get the DCCID and >>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID without the user interface? >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 18 ???? 2019 ???? 5:00 ?.?., ?/? >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Cecile Madjar ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> See answers to your questions below. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> About the 1st case we had a dicom with a >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> blank studyUID, maybe someone accidentally removed it. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> That is strange. Something must have been >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> done to the DICOM files. I have never seen a study with no StudyUID out of >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the scanner. Usually, you need to manually erase it with some tool. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> However, DICOMs never cease to surprise me... >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Some other questions: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 1) What are the steps to remove all of my >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> patients and uploads?: because i want to try to reupload all the testing >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> dicoms we had with a clean database. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Release 21.0 of LORIS-MRI will offer a script >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> to remove all the entries and files specific to an upload. However, this >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> release is not yet out. Hopefully in the next few weeks. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> In the meantime, since your case is >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> particular and that you just want to start with a clean database, the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> following deletes should work (hopefully I won't forget any tables): >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from mri_violations_log; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from mri_protocol_violated_scans; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from MRICandidateErrors; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from parameter_file; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from files_qcstatus; # (if you played >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> with the QC part of the imaging browser for testing) >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from feedback_mri_comments; # (if you >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> played with the QC part of the imaging browser for testing) >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from tarchive_series; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from tarchive_files; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from mri_upload; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from tarchive; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from mri_scanner; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from candidate where PSCID="scanner"; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I don't know if you want to also delete >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> entries in the session and candidate table too? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 2) We do not need to create the profile of a >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> patient ( are the patients stored in the candidate table? because i can't >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> see the ghosts ), because will it automatically be created when importing a >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> dicom? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I am not sure I understand fully this >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> question. All candidates are stored in the candidate table. The phantom >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> scans however are attached to a scanner candidate depending on where the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> scan happened. It is a bit of a weird concept that we have to redesign >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> eventually but never got a chance to get to it. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hopefully this answered your question, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> otherwise, don't hesitate to let me know. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 3) What is the difference between uploading a >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> dicom as phantom instead of importing as PSCCID_DCCID_VisitLabel? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> When you upload the scan as >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID_DCCID_VisitLabel, there is a check that makes sure the candidate IDs >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and visit label are valid at the time of upload. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> When you upload a scan as phantom, it expects >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> that the DICOM field PatientName and uploaded filename contains the string >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> "phantom". We enforced this behaviour on the imaging uploader side in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> recent releases but I can't remember which one. Probably the upcoming 21.0 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> release. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> All those verifications might seem cumbersome >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> but they are here to ensure that the files inserted are all valid and >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> labelled properly as it is a bit messy to have to delete files that were >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> wrongly labelled. At least, the delete script present in release 21.0 will >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> make this process easier but it is still good practice to verify those >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> things. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> With pleasure. Hopefully the answers to your >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> questions will be helpful. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PS: loris-dev mailing list: you will find the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> initial answer I gave Sotirios below. I forgot to cc the loris-dev in my >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> earlier reply... >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 16 ???? 2019 ???? 12:02 ?.?., ?/? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Cecile Madjar >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Dear Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you for reaching out. Since your >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> email was already organized in points, I will reply directly below your >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> questions below. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 1) What do we do when the StudyUID is blank >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> on the header? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/minor/docs/AppendixA-Troubleshooting_guideline.md >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> There solution provided at the table 3 does not guide us how to find the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> information ( is possible ). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The StudyUID is the field used in our >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> pipeline at the moment to check whether a DICOM study was already inserted >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> into LORIS with that same StudyUID since it is supposed to be unique for >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> every single study. Currently, we do not support insertion of DICOM studies >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> if they do not have a StudyUID associated with them. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Is there a specific reason why the StudyUID >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> is blank in the DICOM headers in your DICOM files? Did they go through some >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> processes before upload to LORIS? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 2) When i am about to upload a non-phanton >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> case i need a 'Visit Label'. Is there already a script that can create a >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> new visit label for a specific Candidate, so i can provide it as input >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> afterwards to the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> batch_uploads_imageuploader ( See option 5.1.3 https://github.com/aces/Loris-MRI/blob/minor/docs/05-PipelineLaunchOptions.md ) >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I am not sure if the front-end allows for >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> it but if you use batch_uploads_imageuploader, the insertion scripts could >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> create the visit label for you. However, it does need to be included in the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> patient name in order for the script to know which label it should use. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> For example: you upload V02 for MTL0123 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> (DCCID: 456789) but V02 was not yet created for MTL0123; the insertion >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> scripts will create a V02 visit for MTL0123 if the PatientName field for >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the dataset is MTL0123_456789_V02 with Stage marked as "Not Started". >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> However, *note that for the script to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> create the visit for the candidate, you have to make sure that all the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit label of your projects were inserted in the Visit_Windows table* >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> (otherwise, the visit will never be created as they were not specified as >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> being part of the list of visit label to expect). So in the example above, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> you should have one row in Visit_Windows with Visit_label="V02" set. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 3) Section 4.3 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/minor/docs/04-Scripts.md >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> What do we do when the folder contains multiple mnc files? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> This is a case by case. Most of the time, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the MINC files that failed insertion into the imaging browser end up in the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> MRI violation module where you can see what went wrong with the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> acquisitions not inserted. If you notice that the MINC file should be >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> inserted as a specific protocol, you can force the insertion as explained >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in section 4.3. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> In your case, I have a feeling that you >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> want to be able to insert MINC files that did not go through the whole >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> pipeline insertion (DICOM archival, then dcm2mnc, then protocol >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> identification, then insertion...). In theory, you could call >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl on any MINC file, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> provided you have at least the following information: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - path to the MINC file >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - uploadID associated with the MINC files >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> or DICOM archive path from which those MINC files were created from >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Then the minc_insertion.pl script will do >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the subject information and protocol validation etc... >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> If all the MINC files come from the same >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> uploadID or TarchiveID, then you could run a loop in bash calling the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl script like this for >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> files deriving from uploadID=1: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ls /path/to/mnc/folder/* | while read f; do >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl -profile prod -uploadID >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 1 -mincPath $f; done >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helped! >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> -- >>>>>>>>>>>>> >>>>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> -- >>>>>>>>>>> >>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>> >>>>>>>>>> _______________________________________________ >>>>>>>>> Loris-dev mailing list >>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> -- >>>>>>>> >>>>>>>> christine.rogers at mcgill.ca >>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>> Montreal Neurological Institute >>>>>>>> McGill University | Montreal | Canada >>>>>>>> >>>>>>> _______________________________________________ >>>>>>> Loris-dev mailing list >>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>> >>>>>> >>>>>> >>>>>> -- >>>>>> >>>>>> christine.rogers at mcgill.ca >>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>> Montreal Neurological Institute >>>>>> McGill University | Montreal | Canada >>>>>> _______________________________________________ >>>>>> Loris-dev mailing list >>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>> >>>>> >>>>> >>>>> -- >>>>> >>>>> christine.rogers at mcgill.ca >>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>> Montreal Neurological Institute >>>>> McGill University | Montreal | Canada >>>>> >>>> _______________________________________________ >>>> Loris-dev mailing list >>>> Loris-dev at bic.mni.mcgill.ca >>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>> >>> >>> >>> -- >>> Shen Wang >>> Loris Developer >>> Montreal Neurological Institute >>> McGill University >>> >>> >> >> -- >> Shen Wang >> Loris Developer >> Montreal Neurological Institute >> McGill University >> >> -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 78176 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 20518 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 354645 bytes Desc: not available URL: From sotirisnik at gmail.com Wed Aug 28 21:29:40 2019 From: sotirisnik at gmail.com (Sotirios Nikoloutsopoulos) Date: Thu, 29 Aug 2019 04:29:40 +0300 Subject: [Loris-dev] Import mri - scripts In-Reply-To: References: <65ad2b70c3084ffdb1e4a9dcdad948cd@YTOPR0101MB1803.CANPRD01.PROD.OUTLOOK.COM> Message-ID: Any suggestion why Loris is not showing up in the browser? Thanks ???? ???, 28 ??? 2019 ???? 2:30 ?.?., ?/? Sotirios Nikoloutsopoulos < sotirisnik at gmail.com> ??????: > Also to mention that in the picture i opened the 000-default.conf which is > just a copy of loris.conf by using cp > > ???? ???, 28 ??? 2019 ???? 2:20 ?.?., ?/? Sotirios Nikoloutsopoulos < > sotirisnik at gmail.com> ??????: > >> Ok that fixed the install.sh problem. Now it doesn't show loris to the >> browser, although everything seems right ( also >> >> /etc/apache2/sites-enabled/000-default.conf was replaced by loris.config ). >> >> >> And apache is running >> lorisadmin at loris-VirtualBox:/var/www/loris/htdocs$ sudo systemctl status >> apache2[sudo] password for lorisadmin: >> ? apache2.service - LSB: Apache2 web server >> Loaded: loaded (/etc/init.d/apache2; bad; vendor preset: enabled) >> Drop-In: /lib/systemd/system/apache2.service.d >> ??apache2-systemd.conf >> Active: active (running) since ??? 2019-08-28 02:15:12 EEST; 3min 34s >> ago >> >> [image: image.png] >> >> ???? ???, 27 ??? 2019 ???? 9:42 ?.?., ?/? Shen Wang < >> wangshen.mcin at gmail.com> ??????: >> >>> Hi, >>> This is a bug for install.sh file, we will fix it later. >>> Thank for letting me know your Loris install situation. >>> regards >>> Shen >>> >>> >>> On Tue, 27 Aug 2019 at 14:28, Shen Wang wrote: >>> >>>> Hi, >>>> Please remove "set -euo pipefail" line 10 in the install.sh file. >>>> Then try again. >>>> >>>> >>>> >>>> On Tue, 27 Aug 2019 at 14:05, Sotirios Nikoloutsopoulos < >>>> sotirisnik at gmail.com> wrote: >>>> >>>>> Hi, >>>>> >>>>> i still haven't resolved the previous issue. Also i tried to install >>>>> Loris to a new virtual machine and when i execute install.sh i get the >>>>> following error >>>>> >>>>> lorisadmin at loris-VirtualBox:/var/www/loris/tools$ ./install.sh >>>>> LORIS Installation Script starting at 2019-08-27T21:00:42 >>>>> The log for this session will be stored in file >>>>> /var/www/loris/tools/logs/install-2019-08-27T21:00:42.log >>>>> --------------------------------------------------------------------- >>>>> LORIS Installation Script >>>>> --------------------------------------------------------------------- >>>>> >>>>> PHP appears to be installed. >>>>> >>>>> PHP Composer appears to be installed. >>>>> >>>>> This install script will ask you to provide inputs for different steps. >>>>> Please ensure you have the following information ready (if applicable): >>>>> >>>>> 1) Your project directory name. >>>>> (Will be used to modify the paths for Imaging data in the >>>>> generated >>>>> config.xml file for LORIS, and may also be used to automatically >>>>> create/install apache config files.) If unsure, a default like >>>>> "LORIS" >>>>> should be acceptable. >>>>> >>>>> Please also consult the Loris WIKI on GitHub for more information on >>>>> these >>>>> Install Script input parameters. >>>>> >>>>> Ready to continue? [yn] y >>>>> >>>>> ./install.sh: line 132: projectname: unbound variable >>>>> >>>>> Thanks >>>>> >>>>> ???? ???, 6 ??? 2019 ???? 5:09 ?.?., ?/? Christine Rogers, Ms. < >>>>> christine.rogers at mcgill.ca> ??????: >>>>> >>>>>> Hi Sotirios, >>>>>> Could you also let us know -- on which pages is content visible, and >>>>>> on which pages/modules is content not visible for you? >>>>>> Thanks, >>>>>> Christine >>>>>> >>>>>> On Tue, Aug 6, 2019 at 9:54 AM Christine Rogers, Ms. < >>>>>> christine.rogers at mcgill.ca> wrote: >>>>>> >>>>>>> Thanks Sotirios, >>>>>>> That's good to know. It sounds like you've checked that your >>>>>>> /var/www/loris/project/config.xml file get populated properly. >>>>>>> >>>>>>> Please send us the last few errors you're seeing in your apache >>>>>>> error log file, and your config paths and we can see what's happening with >>>>>>> your front end -- >>>>>>> Run these Troubleshooting Queries >>>>>>> >>>>>>> to get your config path settings, given your front end is not displaying >>>>>>> fully. >>>>>>> >>>>>>> The Loris-MRI repo >>>>>>> 21 >>>>>>> install/upgrade would then be your next steps. >>>>>>> Best, >>>>>>> Christine >>>>>>> >>>>>>> On Tue, Aug 6, 2019 at 7:53 AM Sotirios Nikoloutsopoulos < >>>>>>> sotirisnik at gmail.com> wrote: >>>>>>> >>>>>>>> I am using a VM. What i did was: >>>>>>>> 1) Download the files from https://github.com/aces/Loris and >>>>>>>> replace them to my existing /vaw/www/loris folder. >>>>>>>> 2) Execute the composer install --no-dev and then composer >>>>>>>> dump-autoload as mentioned here >>>>>>>> https://github.com/aces/Loris/wiki/Updating-your-LORIS. >>>>>>>> 3) Execute install.sh from /var/www/loris/tools and because LORIS >>>>>>>> already existed i moved a .config file, then re-executed the install.sh >>>>>>>> successfully >>>>>>>> 4 ) As for the database, i dropped the schema and i executed the >>>>>>>> installdb.php >>>>>>>> >>>>>>>> ???? ???, 5 ??? 2019 ???? 5:22 ?.?., ?/? Christine Rogers, Ms. < >>>>>>>> christine.rogers at mcgill.ca> ??????: >>>>>>>> >>>>>>>>> Hi Sotorios, >>>>>>>>> >>>>>>>>> Thanks - when you re-installed did you start on a fresh root path >>>>>>>>> / VM or might some of your old system setting still apply? >>>>>>>>> (And if you did any steps similar to an upgrade, did you follow >>>>>>>>> the Upgrade steps in the Release Notes, from both repos?) >>>>>>>>> >>>>>>>>> About the TR_range column - it was recently split (MRI pr339 >>>>>>>>> ) split into TR_min >>>>>>>>> and _max columns. Given the code was trying to query TR_range which does >>>>>>>>> not exist in your mri_protocol table, double-check which version of the >>>>>>>>> Loris repo (tables) and the Loris-MRI repo (code) you have installed to >>>>>>>>> ensure they match. >>>>>>>>> >>>>>>>>> Christine >>>>>>>>> >>>>>>>>> >>>>>>>>> On Mon, Aug 5, 2019 at 9:06 AM Sotirios Nikoloutsopoulos < >>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>> >>>>>>>>>> I reinstalled LORIS to 21 version and now the content is not >>>>>>>>>> visible at all at most pages. >>>>>>>>>> >>>>>>>>>> [image: image.png] >>>>>>>>>> >>>>>>>>>> ???? ???, 5 ??? 2019 ???? 3:19 ?.?., ?/? Sotirios >>>>>>>>>> Nikoloutsopoulos ??????: >>>>>>>>>> >>>>>>>>>>> Hi, >>>>>>>>>>> >>>>>>>>>>> Is it easy to upgrade to Loris 21? Also the following fails >>>>>>>>>>> because the line 1985 of NeuroDB/MRIProcessingUtility.pm query mri_protocol >>>>>>>>>>> which doesn't have TR_range >>>>>>>>>>> https://github.com/aces/Loris/blob/21.0-release/SQL/0000-00-00-schema.sql#L556 >>>>>>>>>>> >>>>>>>>>>> [image: image.png] >>>>>>>>>>> >>>>>>>>>>> lorisadmin at hbp:/data/loris/bin/mri$ >>>>>>>>>>> ./batch_uploads_imageuploader -profile prod < ~/Desktop/input.txt > log.txt >>>>>>>>>>> Use of uninitialized value $_ in pattern match (m//) at >>>>>>>>>>> ./batch_uploads_imageuploader line 147. >>>>>>>>>>> base is DCC0000_258024_V1 >>>>>>>>>>> path is /data/incoming/ >>>>>>>>>>> type is .tar.gz >>>>>>>>>>> fullpath is /data/incoming/DCC0000_258024_V1.tar.gz >>>>>>>>>>> DBD::mysql::st execute failed: Unknown column 'TR_range' in >>>>>>>>>>> 'where clause' at >>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line 1985. >>>>>>>>>>> DBD::mysql::st fetchrow_array failed: fetch() without execute() >>>>>>>>>>> at /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line >>>>>>>>>>> 1986. >>>>>>>>>>> Use of uninitialized value $count_mri_protocol in numeric gt (>) >>>>>>>>>>> at /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line >>>>>>>>>>> 1995. >>>>>>>>>>> DBD::mysql::st execute failed: Unknown column 'TR_range' in >>>>>>>>>>> 'field list' at /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 562. >>>>>>>>>>> Can't exec "mail": No such file or directory at >>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 721. >>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 722. >>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 723. >>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 724. >>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 725. >>>>>>>>>>> >>>>>>>>>>> No Mincs inserted >>>>>>>>>>> >>>>>>>>>>> Thanks, >>>>>>>>>>> >>>>>>>>>>> Sotirios >>>>>>>>>>> >>>>>>>>>>> ???? ???, 3 ??? 2019 ???? 1:08 ?.?., ?/? Christine Rogers, Ms. < >>>>>>>>>>> christine.rogers at mcgill.ca> ??????: >>>>>>>>>>> >>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>> >>>>>>>>>>>> First, just a note: we've released LORIS 21 this week with >>>>>>>>>>>> some major new features and cleanup -- especially if you are early in your >>>>>>>>>>>> setup phase, check out the Release notes for both the LORIS >>>>>>>>>>>> and >>>>>>>>>>>> Loris-MRI >>>>>>>>>>>> >>>>>>>>>>>> repos. >>>>>>>>>>>> >>>>>>>>>>>> Thanks for your screenshots -- your empty mri_protocol table >>>>>>>>>>>> should be at the root of these issues : >>>>>>>>>>>> >>>>>>>>>>>> The mri_protocol table must be populated >>>>>>>>>>>> >>>>>>>>>>>> in order for your scans to be registered in LORIS -- it serves as a >>>>>>>>>>>> whitelist for the insertion pipeline which filters out scans that aren't >>>>>>>>>>>> identified or matched to scan types in this table. >>>>>>>>>>>> >>>>>>>>>>>> By default, this table is populated with entries for t1, t2, >>>>>>>>>>>> fMRI and DTI (Insert statements for 21 release branch are here >>>>>>>>>>>> >>>>>>>>>>>> ) >>>>>>>>>>>> Feel free to restore our default records and broaden their >>>>>>>>>>>> parameters to match all your scan types. >>>>>>>>>>>> >>>>>>>>>>>> re Defaced, native, selected -- these filter the scans >>>>>>>>>>>> displayed as you move to the next page (View Session), instead of viewing >>>>>>>>>>>> "all types" of scans from a given session : >>>>>>>>>>>> >>>>>>>>>>>> - "defaced" means that a defacing script >>>>>>>>>>>> >>>>>>>>>>>> has masked the subject's face in the volume (for patient privacy) >>>>>>>>>>>> - "native" means that no pre-processing has been performed >>>>>>>>>>>> on the scan (it's raw data), >>>>>>>>>>>> - "selected" will show only volumes that have been QC'd >>>>>>>>>>>> and "selected" as the best of their type -- used to display only the best >>>>>>>>>>>> quality T1 image instead of all T1s acquired in a session, e.g. >>>>>>>>>>>> >>>>>>>>>>>> re QC Comments -- >>>>>>>>>>>> Once you have successfully loaded scans (matched to the >>>>>>>>>>>> mri_protocol table), you'll be able to use the Imaging Browser's View >>>>>>>>>>>> Session subpage to enter/view QC comments on each volume, or for each >>>>>>>>>>>> visit. >>>>>>>>>>>> These are stored directly in the database, and linked to each >>>>>>>>>>>> scan. (Table name: feedback_mri_comments) >>>>>>>>>>>> (Visit-level QC comments are linked to the session.) >>>>>>>>>>>> >>>>>>>>>>>> For a walkthrough of the Imaging setup - please see the Imaging >>>>>>>>>>>> Setup guide >>>>>>>>>>>> >>>>>>>>>>>> - >>>>>>>>>>>> >>>>>>>>>>>> An old LORIS walkthrough video >>>>>>>>>>>> can also walk >>>>>>>>>>>> you through some of the Imaging front-end features, starting at 8:00 >>>>>>>>>>>> LORIS' imaging modules have been updated many times since this >>>>>>>>>>>> video, but the functionality and workflow is similar. >>>>>>>>>>>> >>>>>>>>>>>> Let us know how it goes once you have entries in your >>>>>>>>>>>> mri_protocol table - >>>>>>>>>>>> Best, >>>>>>>>>>>> Christine >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> On Fri, Aug 2, 2019 at 7:58 AM Sotirios Nikoloutsopoulos < >>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>> >>>>>>>>>>>>> Hi Christine, >>>>>>>>>>>>> >>>>>>>>>>>>> In the candidate_list page i can see this patient >>>>>>>>>>>>> >>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>> >>>>>>>>>>>>> If i press the link under PSCID i get to see >>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>> >>>>>>>>>>>>> and if i press the link under Scan Done it redirects me to >>>>>>>>>>>>> imaging_browser >>>>>>>>>>>>> >>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>> >>>>>>>>>>>>> At the mri_violations page i also see No results ( neither on >>>>>>>>>>>>> resolved / not resolved ). >>>>>>>>>>>>> >>>>>>>>>>>>> At the imaging_uploader i can see the record that failed. >>>>>>>>>>>>> >>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>> >>>>>>>>>>>>> If i click on the tarchive info i get to see the Protocol Name >>>>>>>>>>>>> which i think is the acquisition we wanted? >>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>> >>>>>>>>>>>>> Also my mri_protocol table is empty. >>>>>>>>>>>>> >>>>>>>>>>>>> Furthermore i would like to ask about the defaced, native, >>>>>>>>>>>>> selected. What exactly is native and selected? And where are the qc >>>>>>>>>>>>> comments stored? >>>>>>>>>>>>> >>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>> >>>>>>>>>>>>> Finally a walkthrough would be helpful. >>>>>>>>>>>>> >>>>>>>>>>>>> Thanks, >>>>>>>>>>>>> >>>>>>>>>>>>> Sotirios >>>>>>>>>>>>> >>>>>>>>>>>>> ???? ???, 30 ???? 2019 ???? 8:29 ?.?., ?/? Christine Rogers, >>>>>>>>>>>>> Ms. ??????: >>>>>>>>>>>>> >>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>> Glad to hear you're making progress with the visit labels. >>>>>>>>>>>>>> To follow up on your last few emails: >>>>>>>>>>>>>> >>>>>>>>>>>>>> a- The Wiki's Setup Guide contains Sample insert statements >>>>>>>>>>>>>> for the Visit Windows table >>>>>>>>>>>>>> >>>>>>>>>>>>>> . >>>>>>>>>>>>>> >>>>>>>>>>>>>> As Cecile mentioned, the consistency of visit label format is >>>>>>>>>>>>>> important: V01, v01, V1, 01 -- whichever you select to use is fine; we use >>>>>>>>>>>>>> V01 by default across all documentation. >>>>>>>>>>>>>> >>>>>>>>>>>>>> b- For Password reset, there is a script in the tools/ >>>>>>>>>>>>>> directory so that a back-end administrator can reset any front-end user >>>>>>>>>>>>>> password, including Admin. (See info on setting up / resetting User >>>>>>>>>>>>>> passwords in the Wiki's Setup Guide >>>>>>>>>>>>>> >>>>>>>>>>>>>> ) >>>>>>>>>>>>>> >>>>>>>>>>>>>> c- The minc file not being registered -- due to >>>>>>>>>>>>>> AcquisitionProtocol unknown. >>>>>>>>>>>>>> This means the SeriesDescription (Acquisition Protocol) in >>>>>>>>>>>>>> you Dicom header was not matched to any scan listed in the mri_protocol >>>>>>>>>>>>>> database table. >>>>>>>>>>>>>> (In the online Loris-MRI Troubleshooting Guide, >>>>>>>>>>>>>> this >>>>>>>>>>>>>> is Table 3, 2nd-last item "no MINCs inserted"). >>>>>>>>>>>>>> >>>>>>>>>>>>>> The MRI Violations module (Readme here) >>>>>>>>>>>>>> will show >>>>>>>>>>>>>> you the details of this mismatch -- >>>>>>>>>>>>>> Go to the module (under the Imaging menu), find your scan and >>>>>>>>>>>>>> click the link "Could not identify scan type" -- in the next subpage you >>>>>>>>>>>>>> can compare the scan's actual parameters against the mri_protocol table. >>>>>>>>>>>>>> >>>>>>>>>>>>>> To resolve this, adjust your mri_protocol table values or >>>>>>>>>>>>>> perhaps ensure your DICOMs are labelled consistently. >>>>>>>>>>>>>> >>>>>>>>>>>>>> Let us know if this works for you -- we can also walk you >>>>>>>>>>>>>> through an example of non-identified scans on Demo.loris.ca >>>>>>>>>>>>>> (MRI Violations module). >>>>>>>>>>>>>> >>>>>>>>>>>>>> Best, >>>>>>>>>>>>>> Christine >>>>>>>>>>>>>> >>>>>>>>>>>>>> The LORIS team >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> On Tue, Jul 30, 2019 at 10:47 AM Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>> >>>>>>>>>>>>>>> I hope this is sufficient as the error for the visit label >>>>>>>>>>>>>>> disappeared. >>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> Please see the attached file. Also something i found. >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> lorisadmin at hbp:/data/loris/bin/mri$ cat >>>>>>>>>>>>>>> /data/loris/data//logs/TarLoad-17-39-xubBdv.log >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> ==> Loading file from disk >>>>>>>>>>>>>>> /tmp/TarLoad-17-39-UyQcG2/dcc0000_258024_v1_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> --> mapping DICOM parameter for >>>>>>>>>>>>>>> /tmp/TarLoad-17-39-UyQcG2/dcc0000_258024_v1_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> ==> computing md5 hash for MINC body. >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> --> md5: 6b1202fd63e29de4c9be1cd9925888a5 >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> ==> verifying acquisition protocol >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> Acquisition protocol is unknown >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> --> The minc file cannot be registered since the >>>>>>>>>>>>>>> AcquisitionProtocol is unknown >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> ???? ???, 30 ???? 2019 ???? 4:58 ?.?., ?/? Sotirios >>>>>>>>>>>>>>> Nikoloutsopoulos ??????: >>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Ok I fixed the login problem by using a known hash and by >>>>>>>>>>>>>>>> deleting the rows from the login_history i was able to login. >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> ???? ???, 30 ???? 2019 ???? 4:50 ?.?., ?/? Sotirios >>>>>>>>>>>>>>>> Nikoloutsopoulos ??????: >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> there was no visit label 01 in the Visit_Windows table and >>>>>>>>>>>>>>>>> i don't know how to insert it because the record requires lots of >>>>>>>>>>>>>>>>> attributes. Also the system for a reason asked me to update my password and >>>>>>>>>>>>>>>>> now i don't remember it and my account got suspended. Is there a way to >>>>>>>>>>>>>>>>> reset it or set a simple password? I updated the password hash in the >>>>>>>>>>>>>>>>> users table by using the hash from another LORIS setup we had and i still >>>>>>>>>>>>>>>>> couldn't login ( also the attribute password is always NULL and the >>>>>>>>>>>>>>>>> expiration date is 1999-01-01 for some reason ). >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Thanks >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> ???? ???, 29 ???? 2019 ???? 5:21 ?.?., ?/? Cecile Madjar < >>>>>>>>>>>>>>>>> cecile.madjar at mcin.ca> ??????: >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Can you try adding the visit label v01 to the >>>>>>>>>>>>>>>>>> Visit_Windows table? >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> However, I noticed that in a previous dataset, the label >>>>>>>>>>>>>>>>>> was V1. Does that refer to the same visit? If so, you might want to >>>>>>>>>>>>>>>>>> harmonize the visit labels so they are all the same across datasets for a >>>>>>>>>>>>>>>>>> given timepoint, meaning you will need to relabel scans when the visit >>>>>>>>>>>>>>>>>> label is different but referring to the same visit label (v01 = V1 etc...). >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Hope this helps, >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> On Mon, Jul 29, 2019 at 10:15 AM Sotirios >>>>>>>>>>>>>>>>>> Nikoloutsopoulos wrote: >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Could you help me with the "Visit label does not exist"? >>>>>>>>>>>>>>>>>>> I had changed $subjectID{'createVisitLabel'} to 1 as you had suggested but >>>>>>>>>>>>>>>>>>> it appears that this problem hasn't been resolved yet. >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> lorisadmin at hbp:/data/loris/bin/mri$ cat >>>>>>>>>>>>>>>>>>> /data/loris/data//logs/TarLoad-14-58-9Xog7H.log >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> ==> Loading file from disk >>>>>>>>>>>>>>>>>>> /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> --> mapping DICOM parameter for >>>>>>>>>>>>>>>>>>> /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> --> using user-defined filterParameters for >>>>>>>>>>>>>>>>>>> /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Candidate Mismatch Error is Visit label does not exist >>>>>>>>>>>>>>>>>>> -> WARNING: This candidate was invalid. Logging to >>>>>>>>>>>>>>>>>>> MRICandidateErrors table with reason Visit >>>>>>>>>>>>>>>>>>> label does not exist >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> ???? ???, 26 ???? 2019 ???? 3:02 ?.?., ?/? Sotirios >>>>>>>>>>>>>>>>>>> Nikoloutsopoulos ??????: >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Hi Cecile, >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> The Center error was fixed. Still the insertion of >>>>>>>>>>>>>>>>>>>> mincs fails. Please see the output.txt file i attached. Also is there >>>>>>>>>>>>>>>>>>>> something else i need to change at the paths configuration? >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> ???? ???, 25 ???? 2019 ???? 6:55 ?.?., ?/? Cecile >>>>>>>>>>>>>>>>>>>> Madjar ??????: >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> We are making progress! >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> I have a feeling this error comes from the fact that >>>>>>>>>>>>>>>>>>>>> your psc table does not have the MRI_alias populated for the DCC site. >>>>>>>>>>>>>>>>>>>>> Running the following query in the mysql database should fix this: >>>>>>>>>>>>>>>>>>>>> UPDATE psc SET MRI_alias="DCC", Alias="DCC" WHERE >>>>>>>>>>>>>>>>>>>>> Name="Data Coordinating Center"; >>>>>>>>>>>>>>>>>>>>> Repeat the same with all your sites (make sure to >>>>>>>>>>>>>>>>>>>>> change the Aliases between sites, they should all be unique). >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> Let me know how it goes! >>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> On Thu, Jul 25, 2019 at 11:43 AM Sotirios >>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos wrote: >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> Dear Cecile, >>>>>>>>>>>>>>>>>>>>>> You were right about your guesses. I did the >>>>>>>>>>>>>>>>>>>>>> modifications you suggested, i still get the "no mincs inserted" error, now >>>>>>>>>>>>>>>>>>>>>> i am getting the "No center found this candidate" error ( how do i fix >>>>>>>>>>>>>>>>>>>>>> that? from what i see the .dcm files contains a 'Institution Name', is that >>>>>>>>>>>>>>>>>>>>>> the center? ), so i guess that's why the validation fails, but i changed >>>>>>>>>>>>>>>>>>>>>> the force variable of tarchiveLoader to 1, shouldn't it have inserted the >>>>>>>>>>>>>>>>>>>>>> mincs then? Also it is optional to have a mail server, right? ( from what i >>>>>>>>>>>>>>>>>>>>>> see the mail error does not affect the $valid_study, so i assume we are >>>>>>>>>>>>>>>>>>>>>> okay with that ) >>>>>>>>>>>>>>>>>>>>>> Thank you a lot, >>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> ???? ???, 25 ???? 2019 ???? 5:48 ?.?., ?/? Cecile >>>>>>>>>>>>>>>>>>>>>> Madjar ??????: >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> From what I understand, I believe you just need to >>>>>>>>>>>>>>>>>>>>>>> update a few config settings from the frontend in the Config module (under >>>>>>>>>>>>>>>>>>>>>>> the Admin menu). >>>>>>>>>>>>>>>>>>>>>>> [image: Screen Shot 2019-07-25 at 10.31.35 AM.png] >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> Then go to the Paths section of the config module >>>>>>>>>>>>>>>>>>>>>>> and update the "LORIS-MRI code" config setting to /data/loris/bin/mri (my >>>>>>>>>>>>>>>>>>>>>>> guess is that currently, it is set to /data/LORIS/data) and click on the >>>>>>>>>>>>>>>>>>>>>>> submit button. >>>>>>>>>>>>>>>>>>>>>>> [image: Screen Shot 2019-07-25 at 10.32.50 AM.png] >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> Then, go to Imaging Pipeline section of the >>>>>>>>>>>>>>>>>>>>>>> Configuration module and update the "Loris-MRI Data Directory" to >>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/ (my guess is that it is empty at the moment in your >>>>>>>>>>>>>>>>>>>>>>> database which is why $data_dir is not defined when you run the >>>>>>>>>>>>>>>>>>>>>>> tarchiveLoader step of the insertion pipeline). >>>>>>>>>>>>>>>>>>>>>>> [image: Screen Shot 2019-07-25 at 10.40.52 AM.png] >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> Finally, I took a look at your environment file and >>>>>>>>>>>>>>>>>>>>>>> it might be a good idea to update your PERL5LIB variable to the following >>>>>>>>>>>>>>>>>>>>>>> (it has been added to the code a few releases ago as we realized this was >>>>>>>>>>>>>>>>>>>>>>> needed for the libraries. Not sure which version of LORIS-MRI you are using >>>>>>>>>>>>>>>>>>>>>>> but it does not hurt to update this variable to what I suggest below): >>>>>>>>>>>>>>>>>>>>>>> export >>>>>>>>>>>>>>>>>>>>>>> PERL5LIB=/data/loris/bin/mri/uploadNeuroDB:/data/loris/bin/mri/dicom-archive:$PERL5LIB >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> Hope this helps. Sorry you are experiencing so much >>>>>>>>>>>>>>>>>>>>>>> trouble setting things up. We probably need to update our WIKI. >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> On Thu, Jul 25, 2019 at 9:48 AM Sotirios >>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos wrote: >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> The "Loris-MRI Data Directory" should be in the >>>>>>>>>>>>>>>>>>>>>>>> environment file? >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 25 ???? 2019 ???? 12:59 ?.?., ?/? >>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos >>>>>>>>>>>>>>>>>>>>>>>> ??????: >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> The scripts are located in /data/loris/bin/mri/. >>>>>>>>>>>>>>>>>>>>>>>>> Somewhere I might have messed something up but i remember following the >>>>>>>>>>>>>>>>>>>>>>>>> instructions in the wiki.For example when i tried to execute the >>>>>>>>>>>>>>>>>>>>>>>>> batch_uploads_imageuploader perl script the line >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> my $command = "$bin_dir/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl " >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> was pointing to an invalid path, for example: it >>>>>>>>>>>>>>>>>>>>>>>>> was repeating a pattern and had LORIS instead of loris ( i think the >>>>>>>>>>>>>>>>>>>>>>>>> mistake was that in the wiki it suggested to use $PROJECT for the name of >>>>>>>>>>>>>>>>>>>>>>>>> the folder and i choosed 'loris' >>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris/wiki/Imaging-Database >>>>>>>>>>>>>>>>>>>>>>>>> ). See also the in image for the modification i did. Also i didn't find the >>>>>>>>>>>>>>>>>>>>>>>>> section to config the $data_dir variable. >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 24 ???? 2019 ???? 6:05 ?.?., ?/? Cecile >>>>>>>>>>>>>>>>>>>>>>>>> Madjar ??????: >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> It looks like you have one Config setting not set >>>>>>>>>>>>>>>>>>>>>>>>>> (based on the first error message you got when running it the first time). >>>>>>>>>>>>>>>>>>>>>>>>>> You need to set a value for "Loris-MRI Data Directory" in the Config module >>>>>>>>>>>>>>>>>>>>>>>>>> under the Imaging pipeline section (from what I can see, it would be >>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/ for your setup). >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> The reason you got that error message the second >>>>>>>>>>>>>>>>>>>>>>>>>> time is that the pipeline checks if the DICOM study was already inserted in >>>>>>>>>>>>>>>>>>>>>>>>>> the tarchive table. Since you ran the study once already, the study is >>>>>>>>>>>>>>>>>>>>>>>>>> inserted into the tarchive, hence the message. However, the pipeline did >>>>>>>>>>>>>>>>>>>>>>>>>> not complete as the MINC files were not created and inserted into the >>>>>>>>>>>>>>>>>>>>>>>>>> files/parameter_file table. In order to continue the insertion, you will >>>>>>>>>>>>>>>>>>>>>>>>>> then need to run the tarchiveLoader command suggested in the terminal >>>>>>>>>>>>>>>>>>>>>>>>>> during the second run: >>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader >>>>>>>>>>>>>>>>>>>>>>>>>> -globLocation -profile prod >>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive//2012/DCM_2012-12-05_ImagingUpload-17-43-ZUEFjb.tar >>>>>>>>>>>>>>>>>>>>>>>>>> -verbose >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> Finally, I am a bit confused by your setup. Where >>>>>>>>>>>>>>>>>>>>>>>>>> are the scripts located? In /data/loris/bin/mri or /data/loris/data? It >>>>>>>>>>>>>>>>>>>>>>>>>> feels like the Config setting "LORIS-MRI code" in the Paths section was set >>>>>>>>>>>>>>>>>>>>>>>>>> to "/data/LORIS/data" but it should have been set to the directory where >>>>>>>>>>>>>>>>>>>>>>>>>> the scripts are located (most probably /data/loris/bin/mri). >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helps, >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> On Wed, Jul 24, 2019 at 10:55 AM Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos wrote: >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> Ok first i execute this command: >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> "lorisadmin at hbp:/data/loris/bin/mri$ >>>>>>>>>>>>>>>>>>>>>>>>>>> ./batch_uploads_imageuploader -profile prod < ~/Desktop/input.txt > log.txt >>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at ./batch_uploads_imageuploader line 143. >>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at ./batch_uploads_imageuploader line 143. >>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $_ in pattern match >>>>>>>>>>>>>>>>>>>>>>>>>>> (m//) at ./batch_uploads_imageuploader line 147. >>>>>>>>>>>>>>>>>>>>>>>>>>> base is DCC0000_258024_V01 >>>>>>>>>>>>>>>>>>>>>>>>>>> path is /data/incoming/ >>>>>>>>>>>>>>>>>>>>>>>>>>> type is .tar.gz >>>>>>>>>>>>>>>>>>>>>>>>>>> fullpath is >>>>>>>>>>>>>>>>>>>>>>>>>>> /data/incoming/DCC0000_258024_V01.tar.gz >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> source /tmp/ImagingUpload-17-43-ZUEFjb >>>>>>>>>>>>>>>>>>>>>>>>>>> targetlocation /data/loris/data/tarchive >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 256. >>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 284. >>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at /data/loris/bin/mri/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>> tarchive_validation.pl line 219. >>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at /data/loris/bin/mri/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl line 270. >>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 711. >>>>>>>>>>>>>>>>>>>>>>>>>>> Can't exec "mail": No such file or directory at >>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 721. >>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 722. >>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 723. >>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 724. >>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 724. >>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 725. >>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 735. >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> No Mincs inserted >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> The tarchiveLoader insertion script has failed. >>>>>>>>>>>>>>>>>>>>>>>>>>> Running now the following command: >>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl -profile prod -upload_id >>>>>>>>>>>>>>>>>>>>>>>>>>> 3 /data/incoming/DCC0000_258024_V01.tar.gz -verbose" >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> I inserted the VisitLabel, but still the Mincs >>>>>>>>>>>>>>>>>>>>>>>>>>> are not inserted and i am getting this error >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> "lorisadmin at hbp:/data/loris/bin/mri$ >>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl -profile prod -upload_id >>>>>>>>>>>>>>>>>>>>>>>>>>> 3 /data/incoming/DCC0000_258024_V01.tar.gz -verbose >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> find -path \/tmp\/ImagingUpload\-17\-45\-5MsWEd >>>>>>>>>>>>>>>>>>>>>>>>>>> -name '__MACOSX' -delete >>>>>>>>>>>>>>>>>>>>>>>>>>> Spool message is: >>>>>>>>>>>>>>>>>>>>>>>>>>> The Scan for the uploadID 3 has already been run >>>>>>>>>>>>>>>>>>>>>>>>>>> with tarchiveID: 7. >>>>>>>>>>>>>>>>>>>>>>>>>>> To continue with the rest of the insertion >>>>>>>>>>>>>>>>>>>>>>>>>>> pipeline, please run tarchiveLoader from a terminal as follows: >>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader -globLocation -profile prod >>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive//2012/DCM_2012-12-05_ImagingUpload-17-43-ZUEFjb.tar >>>>>>>>>>>>>>>>>>>>>>>>>>> -verbose" >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> Which files should i delete? I thought that >>>>>>>>>>>>>>>>>>>>>>>>>>> deleting the files from the tarchive was enough. And i executed the last >>>>>>>>>>>>>>>>>>>>>>>>>>> proposed command to continue to rest of the insertion pipeline ( check the >>>>>>>>>>>>>>>>>>>>>>>>>>> image ). >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 24 ???? 2019 ???? 5:05 ?.?., ?/? >>>>>>>>>>>>>>>>>>>>>>>>>>> Cecile Madjar ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> Sorry I was not clear before. Every visits of >>>>>>>>>>>>>>>>>>>>>>>>>>>> candidates are created in the session table with one entry per >>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID/VisitLabel. So if the imaging pipeline created visits in the session >>>>>>>>>>>>>>>>>>>>>>>>>>>> table (that are not attached to instruments) and you want to clean your >>>>>>>>>>>>>>>>>>>>>>>>>>>> database completely, you can delete entries in that table as well. >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> Regarding your point 2, the imaging pipeline >>>>>>>>>>>>>>>>>>>>>>>>>>>> can create the visit in the session table as long as the visit label is >>>>>>>>>>>>>>>>>>>>>>>>>>>> present in the Visit_Windows table (which means the visit label stored in >>>>>>>>>>>>>>>>>>>>>>>>>>>> the PatientName is a valid visit label). >>>>>>>>>>>>>>>>>>>>>>>>>>>> However, in your prod file, if the >>>>>>>>>>>>>>>>>>>>>>>>>>>> variable $subjectID{'createVisitLabel'} is set to 1 for candidates, the >>>>>>>>>>>>>>>>>>>>>>>>>>>> visit label should be created in the Visit_Windows table I believe. Here >>>>>>>>>>>>>>>>>>>>>>>>>>>> is the line of the prod file you would need to change >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> . >>>>>>>>>>>>>>>>>>>>>>>>>>>> In general, we prefer populating the >>>>>>>>>>>>>>>>>>>>>>>>>>>> Visit_Windows table and set the $subjectID{'createVisitLabel'} to 0 for >>>>>>>>>>>>>>>>>>>>>>>>>>>> candidate data to avoid insertion of badly labelled MRI data that are >>>>>>>>>>>>>>>>>>>>>>>>>>>> complex to relabel. >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> Finally, regarding the candidate creation, if >>>>>>>>>>>>>>>>>>>>>>>>>>>> you execute the following steps, the pipeline should be able to create >>>>>>>>>>>>>>>>>>>>>>>>>>>> candidates: >>>>>>>>>>>>>>>>>>>>>>>>>>>> - set in the Imaging Pipeline section of the >>>>>>>>>>>>>>>>>>>>>>>>>>>> config module the config setting "Upload creation of candidates" to Yes >>>>>>>>>>>>>>>>>>>>>>>>>>>> - manually transfer the scans to the LORIS >>>>>>>>>>>>>>>>>>>>>>>>>>>> server instead of uploading it via the imaging browser >>>>>>>>>>>>>>>>>>>>>>>>>>>> - run batch_imaging_upload.pl as you did until >>>>>>>>>>>>>>>>>>>>>>>>>>>> now. >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helps! >>>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> On Wed, Jul 24, 2019 at 8:47 AM Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos wrote: >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> About my second question i replaced the name >>>>>>>>>>>>>>>>>>>>>>>>>>>>> of the patient in the .dcm files and now i am getting an error that the >>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit label does not exist. >>>>>>>>>>>>>>>>>>>>>>>>>>>>> I thought it was supposed to be automatically >>>>>>>>>>>>>>>>>>>>>>>>>>>>> created. >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> "Done adding archive info into database >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader >>>>>>>>>>>>>>>>>>>>>>>>>>>>> -globLocation -profile prod >>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive//DCM_2012-12-05_ImagingUpload-15-42-yUwQQV.tar >>>>>>>>>>>>>>>>>>>>>>>>>>>>> -verbose >>>>>>>>>>>>>>>>>>>>>>>>>>>>> md5sum >>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive/DCM_2012-12-05_ImagingUpload-15-42-yUwQQV.tar >>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>> candidate id 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> => No Visit labelVisit label does not exist >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Set centerID = 1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Number of MINC files that will be considered >>>>>>>>>>>>>>>>>>>>>>>>>>>>> for inserting into the database: 1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> log dir is /logs and log file is >>>>>>>>>>>>>>>>>>>>>>>>>>>>> /logs/TarLoad-15-42-L6pocU.log >>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>> candidate id 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> => No Visit label >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Cleaning up temp files: rm -rf >>>>>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-15-42-J2rQms/ImagingUpload-15-42-yUwQQV*" >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 24 ???? 2019 ???? 3:38 ?.?., ?/? >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 1) What are the records in the session table? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 2) I tried to upload a non-phantom file like >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> this >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> input_file.txt: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/incoming/DCC0000_258024_V1.tar.gz N >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DCC0000_258024_V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Terminal: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ./batch_uploads_imageuploader -profile prod >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> < ~/Desktop/input.txt > log.txt >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and i get the following error in the log.txt >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> file >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> "Running now the following command: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl -profile prod >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -upload_id 7 /data/incoming/DCC0000_258024_V1.tar.gz -verbose >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> find -path >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> \/tmp\/ImagingUpload\-14\-56\-FeLCB4 -name '__MACOSX' -delete >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Spool message is: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The PatientName read from the DICOM header >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> does not start with DCC0000_258024_V1 from the mri_upload table >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> " >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and the spool message is repeated for each >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> .dcm file. Should i preprocess every .dcm file and change the PatientName >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> to "DCC0000_258024_V1"? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 3) As far as it concerns the candidate >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> profile i have to create a new one each time before i try to upload a file? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Is there already a way to create a candidate profile and get the DCCID and >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID without the user interface? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 18 ???? 2019 ???? 5:00 ?.?., ?/? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Cecile Madjar ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> See answers to your questions below. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> About the 1st case we had a dicom with a >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> blank studyUID, maybe someone accidentally removed it. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> That is strange. Something must have been >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> done to the DICOM files. I have never seen a study with no StudyUID out of >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the scanner. Usually, you need to manually erase it with some tool. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> However, DICOMs never cease to surprise me... >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Some other questions: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 1) What are the steps to remove all of my >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> patients and uploads?: because i want to try to reupload all the testing >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> dicoms we had with a clean database. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Release 21.0 of LORIS-MRI will offer a >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> script to remove all the entries and files specific to an upload. However, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> this release is not yet out. Hopefully in the next few weeks. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> In the meantime, since your case is >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> particular and that you just want to start with a clean database, the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> following deletes should work (hopefully I won't forget any tables): >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from mri_violations_log; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from mri_protocol_violated_scans; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from MRICandidateErrors; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from parameter_file; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from files_qcstatus; # (if you played >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> with the QC part of the imaging browser for testing) >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from feedback_mri_comments; # (if you >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> played with the QC part of the imaging browser for testing) >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from tarchive_series; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from tarchive_files; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from mri_upload; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from tarchive; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from mri_scanner; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from candidate where PSCID="scanner"; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I don't know if you want to also delete >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> entries in the session and candidate table too? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 2) We do not need to create the profile of a >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> patient ( are the patients stored in the candidate table? because i can't >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> see the ghosts ), because will it automatically be created when importing a >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> dicom? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I am not sure I understand fully this >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> question. All candidates are stored in the candidate table. The phantom >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> scans however are attached to a scanner candidate depending on where the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> scan happened. It is a bit of a weird concept that we have to redesign >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> eventually but never got a chance to get to it. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hopefully this answered your question, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> otherwise, don't hesitate to let me know. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 3) What is the difference between uploading >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> a dicom as phantom instead of importing as PSCCID_DCCID_VisitLabel? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> When you upload the scan as >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID_DCCID_VisitLabel, there is a check that makes sure the candidate IDs >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and visit label are valid at the time of upload. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> When you upload a scan as phantom, it >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> expects that the DICOM field PatientName and uploaded filename contains the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> string "phantom". We enforced this behaviour on the imaging uploader side >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in recent releases but I can't remember which one. Probably the upcoming >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 21.0 release. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> All those verifications might seem >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> cumbersome but they are here to ensure that the files inserted are all >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> valid and labelled properly as it is a bit messy to have to delete files >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> that were wrongly labelled. At least, the delete script present in release >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 21.0 will make this process easier but it is still good practice to verify >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> those things. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> With pleasure. Hopefully the answers to your >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> questions will be helpful. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PS: loris-dev mailing list: you will find >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the initial answer I gave Sotirios below. I forgot to cc the loris-dev in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> my earlier reply... >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 16 ???? 2019 ???? 12:02 ?.?., ?/? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Cecile Madjar >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Dear Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you for reaching out. Since your >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> email was already organized in points, I will reply directly below your >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> questions below. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 1) What do we do when the StudyUID is >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> blank on the header? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/minor/docs/AppendixA-Troubleshooting_guideline.md >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> There solution provided at the table 3 does not guide us how to find the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> information ( is possible ). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The StudyUID is the field used in our >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> pipeline at the moment to check whether a DICOM study was already inserted >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> into LORIS with that same StudyUID since it is supposed to be unique for >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> every single study. Currently, we do not support insertion of DICOM studies >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> if they do not have a StudyUID associated with them. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Is there a specific reason why the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> StudyUID is blank in the DICOM headers in your DICOM files? Did they go >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> through some processes before upload to LORIS? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 2) When i am about to upload a non-phanton >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> case i need a 'Visit Label'. Is there already a script that can create a >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> new visit label for a specific Candidate, so i can provide it as input >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> afterwards to the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> batch_uploads_imageuploader ( See option 5.1.3 https://github.com/aces/Loris-MRI/blob/minor/docs/05-PipelineLaunchOptions.md ) >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I am not sure if the front-end allows for >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> it but if you use batch_uploads_imageuploader, the insertion scripts could >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> create the visit label for you. However, it does need to be included in the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> patient name in order for the script to know which label it should use. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> For example: you upload V02 for MTL0123 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> (DCCID: 456789) but V02 was not yet created for MTL0123; the insertion >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> scripts will create a V02 visit for MTL0123 if the PatientName field for >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the dataset is MTL0123_456789_V02 with Stage marked as "Not Started". >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> However, *note that for the script to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> create the visit for the candidate, you have to make sure that all the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit label of your projects were inserted in the Visit_Windows table* >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> (otherwise, the visit will never be created as they were not specified as >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> being part of the list of visit label to expect). So in the example above, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> you should have one row in Visit_Windows with Visit_label="V02" set. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 3) Section 4.3 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/minor/docs/04-Scripts.md >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> What do we do when the folder contains multiple mnc files? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> This is a case by case. Most of the time, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the MINC files that failed insertion into the imaging browser end up in the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> MRI violation module where you can see what went wrong with the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> acquisitions not inserted. If you notice that the MINC file should be >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> inserted as a specific protocol, you can force the insertion as explained >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in section 4.3. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> In your case, I have a feeling that you >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> want to be able to insert MINC files that did not go through the whole >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> pipeline insertion (DICOM archival, then dcm2mnc, then protocol >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> identification, then insertion...). In theory, you could call >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl on any MINC file, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> provided you have at least the following information: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - path to the MINC file >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - uploadID associated with the MINC files >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> or DICOM archive path from which those MINC files were created from >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Then the minc_insertion.pl script will do >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the subject information and protocol validation etc... >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> If all the MINC files come from the same >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> uploadID or TarchiveID, then you could run a loop in bash calling the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl script like this for >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> files deriving from uploadID=1: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ls /path/to/mnc/folder/* | while read f; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> do minc_insertion.pl -profile prod >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -uploadID 1 -mincPath $f; done >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helped! >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> -- >>>>>>>>>>>>>> >>>>>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> -- >>>>>>>>>>>> >>>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>>> >>>>>>>>>>> _______________________________________________ >>>>>>>>>> Loris-dev mailing list >>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> -- >>>>>>>>> >>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>> Montreal Neurological Institute >>>>>>>>> McGill University | Montreal | Canada >>>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> Loris-dev mailing list >>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>> >>>>>>> >>>>>>> >>>>>>> -- >>>>>>> >>>>>>> christine.rogers at mcgill.ca >>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>> Montreal Neurological Institute >>>>>>> McGill University | Montreal | Canada >>>>>>> _______________________________________________ >>>>>>> Loris-dev mailing list >>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>> >>>>>> >>>>>> >>>>>> -- >>>>>> >>>>>> christine.rogers at mcgill.ca >>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>> Montreal Neurological Institute >>>>>> McGill University | Montreal | Canada >>>>>> >>>>> _______________________________________________ >>>>> Loris-dev mailing list >>>>> Loris-dev at bic.mni.mcgill.ca >>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>> >>>> >>>> >>>> -- >>>> Shen Wang >>>> Loris Developer >>>> Montreal Neurological Institute >>>> McGill University >>>> >>>> >>> >>> -- >>> Shen Wang >>> Loris Developer >>> Montreal Neurological Institute >>> McGill University >>> >>> -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 78176 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 20518 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 354645 bytes Desc: not available URL: From christine.rogers at mcgill.ca Thu Aug 29 09:04:30 2019 From: christine.rogers at mcgill.ca (Christine Rogers, Ms.) Date: Thu, 29 Aug 2019 13:04:30 +0000 Subject: [Loris-dev] Import mri - scripts In-Reply-To: Message-ID: Hi Sotirios, > Any suggestion why Loris is not showing up in the browser? - What are the last few lines of your loris-access and loris-error apache logs? - What are the URL and host in your Config table? (run these queries from the wiki) - Are you using https, are the certificates in place, etc? - Do any of the wiki's Troubleshooting steps help? Best, Christine On Wed, Aug 28, 2019 at 9:30 PM Sotirios Nikoloutsopoulos > wrote: Any suggestion why Loris is not showing up in the browser? Thanks ???? ???, 28 ??? 2019 ???? 2:30 ?.?., ?/? Sotirios Nikoloutsopoulos > ??????: Also to mention that in the picture i opened the 000-default.conf which is just a copy of loris.conf by using cp ???? ???, 28 ??? 2019 ???? 2:20 ?.?., ?/? Sotirios Nikoloutsopoulos > ??????: Ok that fixed the install.sh problem. Now it doesn't show loris to the browser, although everything seems right ( also /etc/apache2/sites-enabled/000-default.conf was replaced by loris.config ). And apache is running lorisadmin at loris-VirtualBox:/var/www/loris/htdocs$ sudo systemctl status apache2[sudo] password for lorisadmin: ? apache2.service - LSB: Apache2 web server Loaded: loaded (/etc/init.d/apache2; bad; vendor preset: enabled) Drop-In: /lib/systemd/system/apache2.service.d ??apache2-systemd.conf Active: active (running) since ??? 2019-08-28 02:15:12 EEST; 3min 34s ago [image.png] ???? ???, 27 ??? 2019 ???? 9:42 ?.?., ?/? Shen Wang > ??????: Hi, This is a bug for install.sh file, we will fix it later. Thank for letting me know your Loris install situation. regards Shen On Tue, 27 Aug 2019 at 14:28, Shen Wang > wrote: Hi, Please remove "set -euo pipefail" line 10 in the install.sh file. Then try again. On Tue, 27 Aug 2019 at 14:05, Sotirios Nikoloutsopoulos > wrote: Hi, i still haven't resolved the previous issue. Also i tried to install Loris to a new virtual machine and when i execute install.sh i get the following error lorisadmin at loris-VirtualBox:/var/www/loris/tools$ ./install.sh LORIS Installation Script starting at 2019-08-27T21:00:42 The log for this session will be stored in file /var/www/loris/tools/logs/install-2019-08-27T21:00:42.log --------------------------------------------------------------------- LORIS Installation Script --------------------------------------------------------------------- PHP appears to be installed. PHP Composer appears to be installed. This install script will ask you to provide inputs for different steps. Please ensure you have the following information ready (if applicable): 1) Your project directory name. (Will be used to modify the paths for Imaging data in the generated config.xml file for LORIS, and may also be used to automatically create/install apache config files.) If unsure, a default like "LORIS" should be acceptable. Please also consult the Loris WIKI on GitHub for more information on these Install Script input parameters. Ready to continue? [yn] y ./install.sh: line 132: projectname: unbound variable Thanks ???? ???, 6 ??? 2019 ???? 5:09 ?.?., ?/? Christine Rogers, Ms. > ??????: Hi Sotirios, Could you also let us know -- on which pages is content visible, and on which pages/modules is content not visible for you? Thanks, Christine On Tue, Aug 6, 2019 at 9:54 AM Christine Rogers, Ms. > wrote: Thanks Sotirios, That's good to know. It sounds like you've checked that your /var/www/loris/project/config.xml file get populated properly. Please send us the last few errors you're seeing in your apache error log file, and your config paths and we can see what's happening with your front end -- Run these Troubleshooting Queries to get your config path settings, given your front end is not displaying fully. The Loris-MRI repo 21 install/upgrade would then be your next steps. Best, Christine On Tue, Aug 6, 2019 at 7:53 AM Sotirios Nikoloutsopoulos > wrote: I am using a VM. What i did was: 1) Download the files from https://github.com/aces/Loris and replace them to my existing /vaw/www/loris folder. 2) Execute the composer install --no-dev and then composer dump-autoload as mentioned here https://github.com/aces/Loris/wiki/Updating-your-LORIS. 3) Execute install.sh from /var/www/loris/tools and because LORIS already existed i moved a .config file, then re-executed the install.sh successfully 4 ) As for the database, i dropped the schema and i executed the installdb.php ???? ???, 5 ??? 2019 ???? 5:22 ?.?., ?/? Christine Rogers, Ms. > ??????: Hi Sotorios, Thanks - when you re-installed did you start on a fresh root path / VM or might some of your old system setting still apply? (And if you did any steps similar to an upgrade, did you follow the Upgrade steps in the Release Notes, from both repos?) About the TR_range column - it was recently split (MRI pr339) split into TR_min and _max columns. Given the code was trying to query TR_range which does not exist in your mri_protocol table, double-check which version of the Loris repo (tables) and the Loris-MRI repo (code) you have installed to ensure they match. Christine On Mon, Aug 5, 2019 at 9:06 AM Sotirios Nikoloutsopoulos > wrote: I reinstalled LORIS to 21 version and now the content is not visible at all at most pages. [image.png] ???? ???, 5 ??? 2019 ???? 3:19 ?.?., ?/? Sotirios Nikoloutsopoulos > ??????: Hi, Is it easy to upgrade to Loris 21? Also the following fails because the line 1985 of NeuroDB/MRIProcessingUtility.pm query mri_protocol which doesn't have TR_range https://github.com/aces/Loris/blob/21.0-release/SQL/0000-00-00-schema.sql#L556 [image.png] lorisadmin at hbp:/data/loris/bin/mri$ ./batch_uploads_imageuploader -profile prod < ~/Desktop/input.txt > log.txt Use of uninitialized value $_ in pattern match (m//) at ./batch_uploads_imageuploader line 147. base is DCC0000_258024_V1 path is /data/incoming/ type is .tar.gz fullpath is /data/incoming/DCC0000_258024_V1.tar.gz DBD::mysql::st execute failed: Unknown column 'TR_range' in 'where clause' at /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line 1985. DBD::mysql::st fetchrow_array failed: fetch() without execute() at /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line 1986. Use of uninitialized value $count_mri_protocol in numeric gt (>) at /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line 1995. DBD::mysql::st execute failed: Unknown column 'TR_range' in 'field list' at /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 562. Can't exec "mail": No such file or directory at /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 721. print() on closed filehandle MAIL at /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 722. print() on closed filehandle MAIL at /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 723. print() on closed filehandle MAIL at /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 724. print() on closed filehandle MAIL at /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 725. No Mincs inserted Thanks, Sotirios ???? ???, 3 ??? 2019 ???? 1:08 ?.?., ?/? Christine Rogers, Ms. > ??????: Hi Sotirios, First, just a note: we've released LORIS 21 this week with some major new features and cleanup -- especially if you are early in your setup phase, check out the Release notes for both the LORIS and Loris-MRI repos. Thanks for your screenshots -- your empty mri_protocol table should be at the root of these issues : The mri_protocol table must be populated in order for your scans to be registered in LORIS -- it serves as a whitelist for the insertion pipeline which filters out scans that aren't identified or matched to scan types in this table. By default, this table is populated with entries for t1, t2, fMRI and DTI (Insert statements for 21 release branch are here) Feel free to restore our default records and broaden their parameters to match all your scan types. re Defaced, native, selected -- these filter the scans displayed as you move to the next page (View Session), instead of viewing "all types" of scans from a given session : * "defaced" means that a defacing script has masked the subject's face in the volume (for patient privacy) * "native" means that no pre-processing has been performed on the scan (it's raw data), * "selected" will show only volumes that have been QC'd and "selected" as the best of their type -- used to display only the best quality T1 image instead of all T1s acquired in a session, e.g. re QC Comments -- Once you have successfully loaded scans (matched to the mri_protocol table), you'll be able to use the Imaging Browser's View Session subpage to enter/view QC comments on each volume, or for each visit. These are stored directly in the database, and linked to each scan. (Table name: feedback_mri_comments) (Visit-level QC comments are linked to the session.) For a walkthrough of the Imaging setup - please see the Imaging Setup guide - An old LORIS walkthrough video can also walk you through some of the Imaging front-end features, starting at 8:00 LORIS' imaging modules have been updated many times since this video, but the functionality and workflow is similar. Let us know how it goes once you have entries in your mri_protocol table - Best, Christine On Fri, Aug 2, 2019 at 7:58 AM Sotirios Nikoloutsopoulos > wrote: Hi Christine, In the candidate_list page i can see this patient [image.png] If i press the link under PSCID i get to see [image.png] and if i press the link under Scan Done it redirects me to imaging_browser [image.png] At the mri_violations page i also see No results ( neither on resolved / not resolved ). At the imaging_uploader i can see the record that failed. [image.png] If i click on the tarchive info i get to see the Protocol Name which i think is the acquisition we wanted? [image.png] Also my mri_protocol table is empty. Furthermore i would like to ask about the defaced, native, selected. What exactly is native and selected? And where are the qc comments stored? [image.png] Finally a walkthrough would be helpful. Thanks, Sotirios ???? ???, 30 ???? 2019 ???? 8:29 ?.?., ?/? Christine Rogers, Ms. > ??????: Hi Sotirios, Glad to hear you're making progress with the visit labels. To follow up on your last few emails: a- The Wiki's Setup Guide contains Sample insert statements for the Visit Windows table. As Cecile mentioned, the consistency of visit label format is important: V01, v01, V1, 01 -- whichever you select to use is fine; we use V01 by default across all documentation. b- For Password reset, there is a script in the tools/ directory so that a back-end administrator can reset any front-end user password, including Admin. (See info on setting up / resetting User passwords in the Wiki's Setup Guide) c- The minc file not being registered -- due to AcquisitionProtocol unknown. This means the SeriesDescription (Acquisition Protocol) in you Dicom header was not matched to any scan listed in the mri_protocol database table. (In the online Loris-MRI Troubleshooting Guide, this is Table 3, 2nd-last item "no MINCs inserted"). The MRI Violations module (Readme here) will show you the details of this mismatch -- Go to the module (under the Imaging menu), find your scan and click the link "Could not identify scan type" -- in the next subpage you can compare the scan's actual parameters against the mri_protocol table. To resolve this, adjust your mri_protocol table values or perhaps ensure your DICOMs are labelled consistently. Let us know if this works for you -- we can also walk you through an example of non-identified scans on Demo.loris.ca (MRI Violations module). Best, Christine The LORIS team On Tue, Jul 30, 2019 at 10:47 AM Sotirios Nikoloutsopoulos > wrote: I hope this is sufficient as the error for the visit label disappeared. [image.png] Please see the attached file. Also something i found. lorisadmin at hbp:/data/loris/bin/mri$ cat /data/loris/data//logs/TarLoad-17-39-xubBdv.log ==> Loading file from disk /tmp/TarLoad-17-39-UyQcG2/dcc0000_258024_v1_20121205_102108_501e1_mri.mnc --> mapping DICOM parameter for /tmp/TarLoad-17-39-UyQcG2/dcc0000_258024_v1_20121205_102108_501e1_mri.mnc ==> computing md5 hash for MINC body. --> md5: 6b1202fd63e29de4c9be1cd9925888a5 ==> verifying acquisition protocol Acquisition protocol is unknown --> The minc file cannot be registered since the AcquisitionProtocol is unknown ???? ???, 30 ???? 2019 ???? 4:58 ?.?., ?/? Sotirios Nikoloutsopoulos > ??????: Ok I fixed the login problem by using a known hash and by deleting the rows from the login_history i was able to login. ???? ???, 30 ???? 2019 ???? 4:50 ?.?., ?/? Sotirios Nikoloutsopoulos > ??????: Hi, there was no visit label 01 in the Visit_Windows table and i don't know how to insert it because the record requires lots of attributes. Also the system for a reason asked me to update my password and now i don't remember it and my account got suspended. Is there a way to reset it or set a simple password? I updated the password hash in the users table by using the hash from another LORIS setup we had and i still couldn't login ( also the attribute password is always NULL and the expiration date is 1999-01-01 for some reason ). Thanks ???? ???, 29 ???? 2019 ???? 5:21 ?.?., ?/? Cecile Madjar > ??????: Hi Sotirios, Can you try adding the visit label v01 to the Visit_Windows table? However, I noticed that in a previous dataset, the label was V1. Does that refer to the same visit? If so, you might want to harmonize the visit labels so they are all the same across datasets for a given timepoint, meaning you will need to relabel scans when the visit label is different but referring to the same visit label (v01 = V1 etc...). Hope this helps, C?cile On Mon, Jul 29, 2019 at 10:15 AM Sotirios Nikoloutsopoulos > wrote: Hi, Could you help me with the "Visit label does not exist"? I had changed $subjectID{'createVisitLabel'} to 1 as you had suggested but it appears that this problem hasn't been resolved yet. lorisadmin at hbp:/data/loris/bin/mri$ cat /data/loris/data//logs/TarLoad-14-58-9Xog7H.log ==> Loading file from disk /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc --> mapping DICOM parameter for /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc --> using user-defined filterParameters for /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc Candidate Mismatch Error is Visit label does not exist -> WARNING: This candidate was invalid. Logging to MRICandidateErrors table with reason Visit label does not exist Thank you, Sotirios ???? ???, 26 ???? 2019 ???? 3:02 ?.?., ?/? Sotirios Nikoloutsopoulos > ??????: Hi Cecile, The Center error was fixed. Still the insertion of mincs fails. Please see the output.txt file i attached. Also is there something else i need to change at the paths configuration? Thank you, Sotirios ???? ???, 25 ???? 2019 ???? 6:55 ?.?., ?/? Cecile Madjar > ??????: Hi Sotirios, We are making progress! I have a feeling this error comes from the fact that your psc table does not have the MRI_alias populated for the DCC site. Running the following query in the mysql database should fix this: UPDATE psc SET MRI_alias="DCC", Alias="DCC" WHERE Name="Data Coordinating Center"; Repeat the same with all your sites (make sure to change the Aliases between sites, they should all be unique). Let me know how it goes! Best, C?cile On Thu, Jul 25, 2019 at 11:43 AM Sotirios Nikoloutsopoulos > wrote: Dear Cecile, You were right about your guesses. I did the modifications you suggested, i still get the "no mincs inserted" error, now i am getting the "No center found this candidate" error ( how do i fix that? from what i see the .dcm files contains a 'Institution Name', is that the center? ), so i guess that's why the validation fails, but i changed the force variable of tarchiveLoader to 1, shouldn't it have inserted the mincs then? Also it is optional to have a mail server, right? ( from what i see the mail error does not affect the $valid_study, so i assume we are okay with that ) Thank you a lot, Sotirios ???? ???, 25 ???? 2019 ???? 5:48 ?.?., ?/? Cecile Madjar > ??????: Hi Sotirios, From what I understand, I believe you just need to update a few config settings from the frontend in the Config module (under the Admin menu). [Screen Shot 2019-07-25 at 10.31.35 AM.png] Then go to the Paths section of the config module and update the "LORIS-MRI code" config setting to /data/loris/bin/mri (my guess is that currently, it is set to /data/LORIS/data) and click on the submit button. [Screen Shot 2019-07-25 at 10.32.50 AM.png] Then, go to Imaging Pipeline section of the Configuration module and update the "Loris-MRI Data Directory" to /data/loris/data/ (my guess is that it is empty at the moment in your database which is why $data_dir is not defined when you run the tarchiveLoader step of the insertion pipeline). [Screen Shot 2019-07-25 at 10.40.52 AM.png] Finally, I took a look at your environment file and it might be a good idea to update your PERL5LIB variable to the following (it has been added to the code a few releases ago as we realized this was needed for the libraries. Not sure which version of LORIS-MRI you are using but it does not hurt to update this variable to what I suggest below): export PERL5LIB=/data/loris/bin/mri/uploadNeuroDB:/data/loris/bin/mri/dicom-archive:$PERL5LIB Hope this helps. Sorry you are experiencing so much trouble setting things up. We probably need to update our WIKI. Best, C?cile On Thu, Jul 25, 2019 at 9:48 AM Sotirios Nikoloutsopoulos > wrote: The "Loris-MRI Data Directory" should be in the environment file? ???? ???, 25 ???? 2019 ???? 12:59 ?.?., ?/? Sotirios Nikoloutsopoulos > ??????: The scripts are located in /data/loris/bin/mri/. Somewhere I might have messed something up but i remember following the instructions in the wiki.For example when i tried to execute the batch_uploads_imageuploader perl script the line my $command = "$bin_dir/uploadNeuroDB/imaging_upload_file.pl " was pointing to an invalid path, for example: it was repeating a pattern and had LORIS instead of loris ( i think the mistake was that in the wiki it suggested to use $PROJECT for the name of the folder and i choosed 'loris' https://github.com/aces/Loris/wiki/Imaging-Database ). See also the in image for the modification i did. Also i didn't find the section to config the $data_dir variable. Thank you, Sotirios ???? ???, 24 ???? 2019 ???? 6:05 ?.?., ?/? Cecile Madjar > ??????: Hi Sotirios, It looks like you have one Config setting not set (based on the first error message you got when running it the first time). You need to set a value for "Loris-MRI Data Directory" in the Config module under the Imaging pipeline section (from what I can see, it would be /data/loris/data/ for your setup). The reason you got that error message the second time is that the pipeline checks if the DICOM study was already inserted in the tarchive table. Since you ran the study once already, the study is inserted into the tarchive, hence the message. However, the pipeline did not complete as the MINC files were not created and inserted into the files/parameter_file table. In order to continue the insertion, you will then need to run the tarchiveLoader command suggested in the terminal during the second run: /data/LORIS/data//uploadNeuroDB/tarchiveLoader -globLocation -profile prod /data/loris/data/tarchive//2012/DCM_2012-12-05_ImagingUpload-17-43-ZUEFjb.tar -verbose Finally, I am a bit confused by your setup. Where are the scripts located? In /data/loris/bin/mri or /data/loris/data? It feels like the Config setting "LORIS-MRI code" in the Paths section was set to "/data/LORIS/data" but it should have been set to the directory where the scripts are located (most probably /data/loris/bin/mri). Hope this helps, C?cile On Wed, Jul 24, 2019 at 10:55 AM Sotirios Nikoloutsopoulos > wrote: Ok first i execute this command: "lorisadmin at hbp:/data/loris/bin/mri$ ./batch_uploads_imageuploader -profile prod < ~/Desktop/input.txt > log.txt Use of uninitialized value $data_dir in concatenation (.) or string at ./batch_uploads_imageuploader line 143. Use of uninitialized value $data_dir in concatenation (.) or string at ./batch_uploads_imageuploader line 143. Use of uninitialized value $_ in pattern match (m//) at ./batch_uploads_imageuploader line 147. base is DCC0000_258024_V01 path is /data/incoming/ type is .tar.gz fullpath is /data/incoming/DCC0000_258024_V01.tar.gz source /tmp/ImagingUpload-17-43-ZUEFjb targetlocation /data/loris/data/tarchive Use of uninitialized value $data_dir in concatenation (.) or string at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 256. Use of uninitialized value $data_dir in concatenation (.) or string at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 284. Use of uninitialized value $data_dir in concatenation (.) or string at /data/loris/bin/mri/uploadNeuroDB/tarchive_validation.pl line 219. Use of uninitialized value $data_dir in concatenation (.) or string at /data/loris/bin/mri/uploadNeuroDB/minc_insertion.pl line 270. Use of uninitialized value $data_dir in concatenation (.) or string at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 711. Can't exec "mail": No such file or directory at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 721. print() on closed filehandle MAIL at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 722. print() on closed filehandle MAIL at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 723. Use of uninitialized value $data_dir in concatenation (.) or string at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 724. print() on closed filehandle MAIL at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 724. print() on closed filehandle MAIL at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 725. Use of uninitialized value $data_dir in concatenation (.) or string at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 735. No Mincs inserted The tarchiveLoader insertion script has failed. Running now the following command: /data/loris/data/uploadNeuroDB/imaging_upload_file.pl -profile prod -upload_id 3 /data/incoming/DCC0000_258024_V01.tar.gz -verbose" I inserted the VisitLabel, but still the Mincs are not inserted and i am getting this error "lorisadmin at hbp:/data/loris/bin/mri$ /data/loris/data/uploadNeuroDB/imaging_upload_file.pl -profile prod -upload_id 3 /data/incoming/DCC0000_258024_V01.tar.gz -verbose find -path \/tmp\/ImagingUpload\-17\-45\-5MsWEd -name '__MACOSX' -delete Spool message is: The Scan for the uploadID 3 has already been run with tarchiveID: 7. To continue with the rest of the insertion pipeline, please run tarchiveLoader from a terminal as follows: /data/LORIS/data//uploadNeuroDB/tarchiveLoader -globLocation -profile prod /data/loris/data/tarchive//2012/DCM_2012-12-05_ImagingUpload-17-43-ZUEFjb.tar -verbose" Which files should i delete? I thought that deleting the files from the tarchive was enough. And i executed the last proposed command to continue to rest of the insertion pipeline ( check the image ). Thank you ???? ???, 24 ???? 2019 ???? 5:05 ?.?., ?/? Cecile Madjar > ??????: Hi Sotirios, Sorry I was not clear before. Every visits of candidates are created in the session table with one entry per CandID/VisitLabel. So if the imaging pipeline created visits in the session table (that are not attached to instruments) and you want to clean your database completely, you can delete entries in that table as well. Regarding your point 2, the imaging pipeline can create the visit in the session table as long as the visit label is present in the Visit_Windows table (which means the visit label stored in the PatientName is a valid visit label). However, in your prod file, if the variable $subjectID{'createVisitLabel'} is set to 1 for candidates, the visit label should be created in the Visit_Windows table I believe. Here is the line of the prod file you would need to change. In general, we prefer populating the Visit_Windows table and set the $subjectID{'createVisitLabel'} to 0 for candidate data to avoid insertion of badly labelled MRI data that are complex to relabel. Finally, regarding the candidate creation, if you execute the following steps, the pipeline should be able to create candidates: - set in the Imaging Pipeline section of the config module the config setting "Upload creation of candidates" to Yes - manually transfer the scans to the LORIS server instead of uploading it via the imaging browser - run batch_imaging_upload.pl as you did until now. Hope this helps! Best, C?cile On Wed, Jul 24, 2019 at 8:47 AM Sotirios Nikoloutsopoulos > wrote: About my second question i replaced the name of the patient in the .dcm files and now i am getting an error that the visit label does not exist. I thought it was supposed to be automatically created. "Done adding archive info into database /data/LORIS/data//uploadNeuroDB/tarchiveLoader -globLocation -profile prod /data/loris/data/tarchive//DCM_2012-12-05_ImagingUpload-15-42-yUwQQV.tar -verbose md5sum /data/loris/data/tarchive/DCM_2012-12-05_ImagingUpload-15-42-yUwQQV.tar PSCID is: DCC0000 CandID id: 258024 visit_label is: V1 PSCID is: DCC0000 CandID id: 258024 visit_label is: V1 candidate id 258024 => No Visit labelVisit label does not exist Set centerID = 1 PSCID is: DCC0000 CandID id: 258024 visit_label is: V1 PSCID is: DCC0000 CandID id: 258024 visit_label is: V1 Number of MINC files that will be considered for inserting into the database: 1 log dir is /logs and log file is /logs/TarLoad-15-42-L6pocU.log PSCID is: DCC0000 CandID id: 258024 visit_label is: V1 PSCID is: DCC0000 CandID id: 258024 visit_label is: V1 candidate id 258024 => No Visit label Cleaning up temp files: rm -rf /tmp/TarLoad-15-42-J2rQms/ImagingUpload-15-42-yUwQQV*" ???? ???, 24 ???? 2019 ???? 3:38 ?.?., ?/? Sotirios Nikoloutsopoulos > ??????: Hi, 1) What are the records in the session table? 2) I tried to upload a non-phantom file like this input_file.txt: /data/incoming/DCC0000_258024_V1.tar.gz N DCC0000_258024_V1 Terminal: ./batch_uploads_imageuploader -profile prod < ~/Desktop/input.txt > log.txt and i get the following error in the log.txt file "Running now the following command: /data/loris/data/uploadNeuroDB/imaging_upload_file.pl -profile prod -upload_id 7 /data/incoming/DCC0000_258024_V1.tar.gz -verbose find -path \/tmp\/ImagingUpload\-14\-56\-FeLCB4 -name '__MACOSX' -delete Spool message is: The PatientName read from the DICOM header does not start with DCC0000_258024_V1 from the mri_upload table " and the spool message is repeated for each .dcm file. Should i preprocess every .dcm file and change the PatientName to "DCC0000_258024_V1"? 3) As far as it concerns the candidate profile i have to create a new one each time before i try to upload a file? Is there already a way to create a candidate profile and get the DCCID and PSCID without the user interface? Thank you, Sotirios ???? ???, 18 ???? 2019 ???? 5:00 ?.?., ?/? Cecile Madjar > ??????: Hi Sotirios, See answers to your questions below. About the 1st case we had a dicom with a blank studyUID, maybe someone accidentally removed it. That is strange. Something must have been done to the DICOM files. I have never seen a study with no StudyUID out of the scanner. Usually, you need to manually erase it with some tool. However, DICOMs never cease to surprise me... Some other questions: 1) What are the steps to remove all of my patients and uploads?: because i want to try to reupload all the testing dicoms we had with a clean database. Release 21.0 of LORIS-MRI will offer a script to remove all the entries and files specific to an upload. However, this release is not yet out. Hopefully in the next few weeks. In the meantime, since your case is particular and that you just want to start with a clean database, the following deletes should work (hopefully I won't forget any tables): delete from mri_violations_log; delete from mri_protocol_violated_scans; delete from MRICandidateErrors; delete from parameter_file; delete from files_qcstatus; # (if you played with the QC part of the imaging browser for testing) delete from feedback_mri_comments; # (if you played with the QC part of the imaging browser for testing) delete from tarchive_series; delete from tarchive_files; delete from mri_upload; delete from tarchive; delete from mri_scanner; delete from candidate where PSCID="scanner"; I don't know if you want to also delete entries in the session and candidate table too? 2) We do not need to create the profile of a patient ( are the patients stored in the candidate table? because i can't see the ghosts ), because will it automatically be created when importing a dicom? I am not sure I understand fully this question. All candidates are stored in the candidate table. The phantom scans however are attached to a scanner candidate depending on where the scan happened. It is a bit of a weird concept that we have to redesign eventually but never got a chance to get to it. Hopefully this answered your question, otherwise, don't hesitate to let me know. 3) What is the difference between uploading a dicom as phantom instead of importing as PSCCID_DCCID_VisitLabel? When you upload the scan as PSCID_DCCID_VisitLabel, there is a check that makes sure the candidate IDs and visit label are valid at the time of upload. When you upload a scan as phantom, it expects that the DICOM field PatientName and uploaded filename contains the string "phantom". We enforced this behaviour on the imaging uploader side in recent releases but I can't remember which one. Probably the upcoming 21.0 release. All those verifications might seem cumbersome but they are here to ensure that the files inserted are all valid and labelled properly as it is a bit messy to have to delete files that were wrongly labelled. At least, the delete script present in release 21.0 will make this process easier but it is still good practice to verify those things. Thank you, With pleasure. Hopefully the answers to your questions will be helpful. Best, C?cile PS: loris-dev mailing list: you will find the initial answer I gave Sotirios below. I forgot to cc the loris-dev in my earlier reply... ???? ???, 16 ???? 2019 ???? 12:02 ?.?., ?/? Cecile Madjar > ??????: Dear Sotirios, Thank you for reaching out. Since your email was already organized in points, I will reply directly below your questions below. Best, C?cile 1) What do we do when the StudyUID is blank on the header? https://github.com/aces/Loris-MRI/blob/minor/docs/AppendixA-Troubleshooting_guideline.md There solution provided at the table 3 does not guide us how to find the information ( is possible ). The StudyUID is the field used in our pipeline at the moment to check whether a DICOM study was already inserted into LORIS with that same StudyUID since it is supposed to be unique for every single study. Currently, we do not support insertion of DICOM studies if they do not have a StudyUID associated with them. Is there a specific reason why the StudyUID is blank in the DICOM headers in your DICOM files? Did they go through some processes before upload to LORIS? 2) When i am about to upload a non-phanton case i need a 'Visit Label'. Is there already a script that can create a new visit label for a specific Candidate, so i can provide it as input afterwards to the batch_uploads_imageuploader ( See option 5.1.3 https://github.com/aces/Loris-MRI/blob/minor/docs/05-PipelineLaunchOptions.md ) I am not sure if the front-end allows for it but if you use batch_uploads_imageuploader, the insertion scripts could create the visit label for you. However, it does need to be included in the patient name in order for the script to know which label it should use. For example: you upload V02 for MTL0123 (DCCID: 456789) but V02 was not yet created for MTL0123; the insertion scripts will create a V02 visit for MTL0123 if the PatientName field for the dataset is MTL0123_456789_V02 with Stage marked as "Not Started". However, note that for the script to create the visit for the candidate, you have to make sure that all the visit label of your projects were inserted in the Visit_Windows table (otherwise, the visit will never be created as they were not specified as being part of the list of visit label to expect). So in the example above, you should have one row in Visit_Windows with Visit_label="V02" set. 3) Section 4.3 https://github.com/aces/Loris-MRI/blob/minor/docs/04-Scripts.md What do we do when the folder contains multiple mnc files? This is a case by case. Most of the time, the MINC files that failed insertion into the imaging browser end up in the MRI violation module where you can see what went wrong with the acquisitions not inserted. If you notice that the MINC file should be inserted as a specific protocol, you can force the insertion as explained in section 4.3. In your case, I have a feeling that you want to be able to insert MINC files that did not go through the whole pipeline insertion (DICOM archival, then dcm2mnc, then protocol identification, then insertion...). In theory, you could call minc_insertion.pl on any MINC file, provided you have at least the following information: - path to the MINC file - uploadID associated with the MINC files or DICOM archive path from which those MINC files were created from Then the minc_insertion.pl script will do the subject information and protocol validation etc... If all the MINC files come from the same uploadID or TarchiveID, then you could run a loop in bash calling the minc_insertion.pl script like this for files deriving from uploadID=1: ls /path/to/mnc/folder/* | while read f; do minc_insertion.pl -profile prod -uploadID 1 -mincPath $f; done Thank you, Hope this helped! _______________________________________________ Loris-dev mailing list Loris-dev at bic.mni.mcgill.ca https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev -- christine.rogers at mcgill.ca McGill Centre for Integrative Neuroscience | MCIN.ca Montreal Neurological Institute McGill University | Montreal | Canada -- christine.rogers at mcgill.ca McGill Centre for Integrative Neuroscience | MCIN.ca Montreal Neurological Institute McGill University | Montreal | Canada _______________________________________________ Loris-dev mailing list Loris-dev at bic.mni.mcgill.ca https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev -- christine.rogers at mcgill.ca McGill Centre for Integrative Neuroscience | MCIN.ca Montreal Neurological Institute McGill University | Montreal | Canada _______________________________________________ Loris-dev mailing list Loris-dev at bic.mni.mcgill.ca https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev -- christine.rogers at mcgill.ca McGill Centre for Integrative Neuroscience | MCIN.ca Montreal Neurological Institute McGill University | Montreal | Canada _______________________________________________ Loris-dev mailing list Loris-dev at bic.mni.mcgill.ca https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev -- christine.rogers at mcgill.ca McGill Centre for Integrative Neuroscience | MCIN.ca Montreal Neurological Institute McGill University | Montreal | Canada _______________________________________________ Loris-dev mailing list Loris-dev at bic.mni.mcgill.ca https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev -- Shen Wang Loris Developer Montreal Neurological Institute McGill University -- Shen Wang Loris Developer Montreal Neurological Institute McGill University _______________________________________________ Loris-dev mailing list Loris-dev at bic.mni.mcgill.ca https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev -- christine.rogers at mcgill.ca McGill Centre for Integrative Neuroscience | MCIN.ca Montreal Neurological Institute McGill University | Montreal | Canada -------------- next part -------------- An HTML attachment was scrubbed... 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Name: image.png Type: image/png Size: 354645 bytes Desc: image.png URL: From sotirisnik at gmail.com Thu Aug 29 19:46:35 2019 From: sotirisnik at gmail.com (Sotirios Nikoloutsopoulos) Date: Fri, 30 Aug 2019 02:46:35 +0300 Subject: [Loris-dev] Import mri - scripts In-Reply-To: References: Message-ID: Hi, loris-access.log reports HTTP 500 error and loris-error reports that some files are missing e.x. autoload.php from /var/www/loris/htdocs/../vendor/autoload.php ( https://github.com/aces/Loris/tree/minor/htdocs/vendor and as i can verify those files do not exist in the github folder ) Thanks ???? ???, 29 ??? 2019 ???? 4:04 ?.?., ?/? Christine Rogers, Ms. < christine.rogers at mcgill.ca> ??????: > Hi Sotirios, > > > Any suggestion why Loris is not showing up in the browser? > > > - What are the last few lines of your loris-access and loris-error apache > logs? > > - What are the URL and host in your Config table? (run these queries > from the wiki > > ) > > - Are you using https, are the certificates in place, etc? > > - Do any of the wiki's Troubleshooting steps > > help? > > Best, > Christine > > On Wed, Aug 28, 2019 at 9:30 PM Sotirios Nikoloutsopoulos < > sotirisnik at gmail.com> wrote: > >> Any suggestion why Loris is not showing up in the browser? >> >> Thanks >> >> >> ???? ???, 28 ??? 2019 ???? 2:30 ?.?., ?/? Sotirios Nikoloutsopoulos < >> sotirisnik at gmail.com> ??????: >> >>> Also to mention that in the picture i opened the 000-default.conf which >>> is just a copy of loris.conf by using cp >>> >>> ???? ???, 28 ??? 2019 ???? 2:20 ?.?., ?/? Sotirios Nikoloutsopoulos < >>> sotirisnik at gmail.com> ??????: >>> >>>> Ok that fixed the install.sh problem. Now it doesn't show loris to the >>>> browser, although everything seems right ( also >>>> >>>> /etc/apache2/sites-enabled/000-default.conf was replaced by loris.config ). >>>> >>>> >>>> And apache is running >>>> lorisadmin at loris-VirtualBox:/var/www/loris/htdocs$ sudo systemctl >>>> status apache2[sudo] password for lorisadmin: >>>> ? apache2.service - LSB: Apache2 web server >>>> Loaded: loaded (/etc/init.d/apache2; bad; vendor preset: enabled) >>>> Drop-In: /lib/systemd/system/apache2.service.d >>>> ??apache2-systemd.conf >>>> Active: active (running) since ??? 2019-08-28 02:15:12 EEST; 3min >>>> 34s ago >>>> >>>> [image: image.png] >>>> >>>> ???? ???, 27 ??? 2019 ???? 9:42 ?.?., ?/? Shen Wang < >>>> wangshen.mcin at gmail.com> ??????: >>>> >>>>> Hi, >>>>> This is a bug for install.sh file, we will fix it later. >>>>> Thank for letting me know your Loris install situation. >>>>> regards >>>>> Shen >>>>> >>>>> >>>>> On Tue, 27 Aug 2019 at 14:28, Shen Wang >>>>> wrote: >>>>> >>>>>> Hi, >>>>>> Please remove "set -euo pipefail" line 10 in the install.sh file. >>>>>> Then try again. >>>>>> >>>>>> >>>>>> >>>>>> On Tue, 27 Aug 2019 at 14:05, Sotirios Nikoloutsopoulos < >>>>>> sotirisnik at gmail.com> wrote: >>>>>> >>>>>>> Hi, >>>>>>> >>>>>>> i still haven't resolved the previous issue. Also i tried to install >>>>>>> Loris to a new virtual machine and when i execute install.sh i get the >>>>>>> following error >>>>>>> >>>>>>> lorisadmin at loris-VirtualBox:/var/www/loris/tools$ ./install.sh >>>>>>> LORIS Installation Script starting at 2019-08-27T21:00:42 >>>>>>> The log for this session will be stored in file >>>>>>> /var/www/loris/tools/logs/install-2019-08-27T21:00:42.log >>>>>>> --------------------------------------------------------------------- >>>>>>> LORIS Installation Script >>>>>>> --------------------------------------------------------------------- >>>>>>> >>>>>>> PHP appears to be installed. >>>>>>> >>>>>>> PHP Composer appears to be installed. >>>>>>> >>>>>>> This install script will ask you to provide inputs for different >>>>>>> steps. >>>>>>> Please ensure you have the following information ready (if >>>>>>> applicable): >>>>>>> >>>>>>> 1) Your project directory name. >>>>>>> (Will be used to modify the paths for Imaging data in the >>>>>>> generated >>>>>>> config.xml file for LORIS, and may also be used to automatically >>>>>>> create/install apache config files.) If unsure, a default like >>>>>>> "LORIS" >>>>>>> should be acceptable. >>>>>>> >>>>>>> Please also consult the Loris WIKI on GitHub for more information on >>>>>>> these >>>>>>> Install Script input parameters. >>>>>>> >>>>>>> Ready to continue? [yn] y >>>>>>> >>>>>>> ./install.sh: line 132: projectname: unbound variable >>>>>>> >>>>>>> Thanks >>>>>>> >>>>>>> ???? ???, 6 ??? 2019 ???? 5:09 ?.?., ?/? Christine Rogers, Ms. < >>>>>>> christine.rogers at mcgill.ca> ??????: >>>>>>> >>>>>>>> Hi Sotirios, >>>>>>>> Could you also let us know -- on which pages is content visible, >>>>>>>> and on which pages/modules is content not visible for you? >>>>>>>> Thanks, >>>>>>>> Christine >>>>>>>> >>>>>>>> On Tue, Aug 6, 2019 at 9:54 AM Christine Rogers, Ms. < >>>>>>>> christine.rogers at mcgill.ca> wrote: >>>>>>>> >>>>>>>>> Thanks Sotirios, >>>>>>>>> That's good to know. It sounds like you've checked that your >>>>>>>>> /var/www/loris/project/config.xml file get populated properly. >>>>>>>>> >>>>>>>>> Please send us the last few errors you're seeing in your apache >>>>>>>>> error log file, and your config paths and we can see what's happening with >>>>>>>>> your front end -- >>>>>>>>> Run these Troubleshooting Queries >>>>>>>>> >>>>>>>>> to get your config path settings, given your front end is not displaying >>>>>>>>> fully. >>>>>>>>> >>>>>>>>> The Loris-MRI repo >>>>>>>>> 21 >>>>>>>>> install/upgrade would then be your next steps. >>>>>>>>> Best, >>>>>>>>> Christine >>>>>>>>> >>>>>>>>> On Tue, Aug 6, 2019 at 7:53 AM Sotirios Nikoloutsopoulos < >>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>> >>>>>>>>>> I am using a VM. What i did was: >>>>>>>>>> 1) Download the files from https://github.com/aces/Loris and >>>>>>>>>> replace them to my existing /vaw/www/loris folder. >>>>>>>>>> 2) Execute the composer install --no-dev and then composer >>>>>>>>>> dump-autoload as mentioned here >>>>>>>>>> https://github.com/aces/Loris/wiki/Updating-your-LORIS. >>>>>>>>>> 3) Execute install.sh from /var/www/loris/tools and because >>>>>>>>>> LORIS already existed i moved a .config file, then re-executed the >>>>>>>>>> install.sh successfully >>>>>>>>>> 4 ) As for the database, i dropped the schema and i executed the >>>>>>>>>> installdb.php >>>>>>>>>> >>>>>>>>>> ???? ???, 5 ??? 2019 ???? 5:22 ?.?., ?/? Christine Rogers, Ms. < >>>>>>>>>> christine.rogers at mcgill.ca> ??????: >>>>>>>>>> >>>>>>>>>>> Hi Sotorios, >>>>>>>>>>> >>>>>>>>>>> Thanks - when you re-installed did you start on a fresh root >>>>>>>>>>> path / VM or might some of your old system setting still apply? >>>>>>>>>>> (And if you did any steps similar to an upgrade, did you follow >>>>>>>>>>> the Upgrade steps in the Release Notes, from both repos?) >>>>>>>>>>> >>>>>>>>>>> About the TR_range column - it was recently split (MRI pr339 >>>>>>>>>>> ) split into TR_min >>>>>>>>>>> and _max columns. Given the code was trying to query TR_range which does >>>>>>>>>>> not exist in your mri_protocol table, double-check which version of the >>>>>>>>>>> Loris repo (tables) and the Loris-MRI repo (code) you have installed to >>>>>>>>>>> ensure they match. >>>>>>>>>>> >>>>>>>>>>> Christine >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> On Mon, Aug 5, 2019 at 9:06 AM Sotirios Nikoloutsopoulos < >>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>> >>>>>>>>>>>> I reinstalled LORIS to 21 version and now the content is not >>>>>>>>>>>> visible at all at most pages. >>>>>>>>>>>> >>>>>>>>>>>> [image: image.png] >>>>>>>>>>>> >>>>>>>>>>>> ???? ???, 5 ??? 2019 ???? 3:19 ?.?., ?/? Sotirios >>>>>>>>>>>> Nikoloutsopoulos ??????: >>>>>>>>>>>> >>>>>>>>>>>>> Hi, >>>>>>>>>>>>> >>>>>>>>>>>>> Is it easy to upgrade to Loris 21? Also the following fails >>>>>>>>>>>>> because the line 1985 of NeuroDB/MRIProcessingUtility.pm query mri_protocol >>>>>>>>>>>>> which doesn't have TR_range >>>>>>>>>>>>> https://github.com/aces/Loris/blob/21.0-release/SQL/0000-00-00-schema.sql#L556 >>>>>>>>>>>>> >>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>> >>>>>>>>>>>>> lorisadmin at hbp:/data/loris/bin/mri$ >>>>>>>>>>>>> ./batch_uploads_imageuploader -profile prod < ~/Desktop/input.txt > log.txt >>>>>>>>>>>>> Use of uninitialized value $_ in pattern match (m//) at >>>>>>>>>>>>> ./batch_uploads_imageuploader line 147. >>>>>>>>>>>>> base is DCC0000_258024_V1 >>>>>>>>>>>>> path is /data/incoming/ >>>>>>>>>>>>> type is .tar.gz >>>>>>>>>>>>> fullpath is /data/incoming/DCC0000_258024_V1.tar.gz >>>>>>>>>>>>> DBD::mysql::st execute failed: Unknown column 'TR_range' in >>>>>>>>>>>>> 'where clause' at >>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line 1985. >>>>>>>>>>>>> DBD::mysql::st fetchrow_array failed: fetch() without >>>>>>>>>>>>> execute() at >>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line 1986. >>>>>>>>>>>>> Use of uninitialized value $count_mri_protocol in numeric gt >>>>>>>>>>>>> (>) at /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm >>>>>>>>>>>>> line 1995. >>>>>>>>>>>>> DBD::mysql::st execute failed: Unknown column 'TR_range' in >>>>>>>>>>>>> 'field list' at /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 562. >>>>>>>>>>>>> Can't exec "mail": No such file or directory at >>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 721. >>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 722. >>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 723. >>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 724. >>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 725. >>>>>>>>>>>>> >>>>>>>>>>>>> No Mincs inserted >>>>>>>>>>>>> >>>>>>>>>>>>> Thanks, >>>>>>>>>>>>> >>>>>>>>>>>>> Sotirios >>>>>>>>>>>>> >>>>>>>>>>>>> ???? ???, 3 ??? 2019 ???? 1:08 ?.?., ?/? Christine Rogers, Ms. >>>>>>>>>>>>> ??????: >>>>>>>>>>>>> >>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>> >>>>>>>>>>>>>> First, just a note: we've released LORIS 21 this week with >>>>>>>>>>>>>> some major new features and cleanup -- especially if you are early in your >>>>>>>>>>>>>> setup phase, check out the Release notes for both the LORIS >>>>>>>>>>>>>> and >>>>>>>>>>>>>> Loris-MRI >>>>>>>>>>>>>> >>>>>>>>>>>>>> repos. >>>>>>>>>>>>>> >>>>>>>>>>>>>> Thanks for your screenshots -- your empty mri_protocol table >>>>>>>>>>>>>> should be at the root of these issues : >>>>>>>>>>>>>> >>>>>>>>>>>>>> The mri_protocol table must be populated >>>>>>>>>>>>>> >>>>>>>>>>>>>> in order for your scans to be registered in LORIS -- it serves as a >>>>>>>>>>>>>> whitelist for the insertion pipeline which filters out scans that aren't >>>>>>>>>>>>>> identified or matched to scan types in this table. >>>>>>>>>>>>>> >>>>>>>>>>>>>> By default, this table is populated with entries for t1, t2, >>>>>>>>>>>>>> fMRI and DTI (Insert statements for 21 release branch are >>>>>>>>>>>>>> here >>>>>>>>>>>>>> >>>>>>>>>>>>>> ) >>>>>>>>>>>>>> Feel free to restore our default records and broaden their >>>>>>>>>>>>>> parameters to match all your scan types. >>>>>>>>>>>>>> >>>>>>>>>>>>>> re Defaced, native, selected -- these filter the scans >>>>>>>>>>>>>> displayed as you move to the next page (View Session), instead of viewing >>>>>>>>>>>>>> "all types" of scans from a given session : >>>>>>>>>>>>>> >>>>>>>>>>>>>> - "defaced" means that a defacing script >>>>>>>>>>>>>> >>>>>>>>>>>>>> has masked the subject's face in the volume (for patient privacy) >>>>>>>>>>>>>> - "native" means that no pre-processing has been >>>>>>>>>>>>>> performed on the scan (it's raw data), >>>>>>>>>>>>>> - "selected" will show only volumes that have been QC'd >>>>>>>>>>>>>> and "selected" as the best of their type -- used to display only the best >>>>>>>>>>>>>> quality T1 image instead of all T1s acquired in a session, e.g. >>>>>>>>>>>>>> >>>>>>>>>>>>>> re QC Comments -- >>>>>>>>>>>>>> Once you have successfully loaded scans (matched to the >>>>>>>>>>>>>> mri_protocol table), you'll be able to use the Imaging Browser's View >>>>>>>>>>>>>> Session subpage to enter/view QC comments on each volume, or for each >>>>>>>>>>>>>> visit. >>>>>>>>>>>>>> These are stored directly in the database, and linked to each >>>>>>>>>>>>>> scan. (Table name: feedback_mri_comments) >>>>>>>>>>>>>> (Visit-level QC comments are linked to the session.) >>>>>>>>>>>>>> >>>>>>>>>>>>>> For a walkthrough of the Imaging setup - please see the Imaging >>>>>>>>>>>>>> Setup guide >>>>>>>>>>>>>> >>>>>>>>>>>>>> - >>>>>>>>>>>>>> >>>>>>>>>>>>>> An old LORIS walkthrough video >>>>>>>>>>>>>> can also walk >>>>>>>>>>>>>> you through some of the Imaging front-end features, starting at 8:00 >>>>>>>>>>>>>> LORIS' imaging modules have been updated many times since >>>>>>>>>>>>>> this video, but the functionality and workflow is similar. >>>>>>>>>>>>>> >>>>>>>>>>>>>> Let us know how it goes once you have entries in your >>>>>>>>>>>>>> mri_protocol table - >>>>>>>>>>>>>> Best, >>>>>>>>>>>>>> Christine >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> On Fri, Aug 2, 2019 at 7:58 AM Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>> >>>>>>>>>>>>>>> Hi Christine, >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> In the candidate_list page i can see this patient >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> If i press the link under PSCID i get to see >>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> and if i press the link under Scan Done it redirects me to >>>>>>>>>>>>>>> imaging_browser >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> At the mri_violations page i also see No results ( neither >>>>>>>>>>>>>>> on resolved / not resolved ). >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> At the imaging_uploader i can see the record that failed. >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> If i click on the tarchive info i get to see the Protocol >>>>>>>>>>>>>>> Name which i think is the acquisition we wanted? >>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> Also my mri_protocol table is empty. >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> Furthermore i would like to ask about the defaced, native, >>>>>>>>>>>>>>> selected. What exactly is native and selected? And where are the qc >>>>>>>>>>>>>>> comments stored? >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> Finally a walkthrough would be helpful. >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> Thanks, >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> ???? ???, 30 ???? 2019 ???? 8:29 ?.?., ?/? Christine Rogers, >>>>>>>>>>>>>>> Ms. ??????: >>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>> Glad to hear you're making progress with the visit labels. >>>>>>>>>>>>>>>> To follow up on your last few emails: >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> a- The Wiki's Setup Guide contains Sample insert >>>>>>>>>>>>>>>> statements for the Visit Windows table >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> . >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> As Cecile mentioned, the consistency of visit label format >>>>>>>>>>>>>>>> is important: V01, v01, V1, 01 -- whichever you select to use is fine; we >>>>>>>>>>>>>>>> use V01 by default across all documentation. >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> b- For Password reset, there is a script in the tools/ >>>>>>>>>>>>>>>> directory so that a back-end administrator can reset any front-end user >>>>>>>>>>>>>>>> password, including Admin. (See info on setting up / resetting User >>>>>>>>>>>>>>>> passwords in the Wiki's Setup Guide >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> ) >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> c- The minc file not being registered -- due to >>>>>>>>>>>>>>>> AcquisitionProtocol unknown. >>>>>>>>>>>>>>>> This means the SeriesDescription (Acquisition Protocol) in >>>>>>>>>>>>>>>> you Dicom header was not matched to any scan listed in the mri_protocol >>>>>>>>>>>>>>>> database table. >>>>>>>>>>>>>>>> (In the online Loris-MRI Troubleshooting Guide, >>>>>>>>>>>>>>>> this >>>>>>>>>>>>>>>> is Table 3, 2nd-last item "no MINCs inserted"). >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> The MRI Violations module (Readme here) >>>>>>>>>>>>>>>> will show >>>>>>>>>>>>>>>> you the details of this mismatch -- >>>>>>>>>>>>>>>> Go to the module (under the Imaging menu), find your scan >>>>>>>>>>>>>>>> and click the link "Could not identify scan type" -- in the next subpage >>>>>>>>>>>>>>>> you can compare the scan's actual parameters against the mri_protocol >>>>>>>>>>>>>>>> table. >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> To resolve this, adjust your mri_protocol table values or >>>>>>>>>>>>>>>> perhaps ensure your DICOMs are labelled consistently. >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Let us know if this works for you -- we can also walk you >>>>>>>>>>>>>>>> through an example of non-identified scans on Demo.loris.ca >>>>>>>>>>>>>>>> (MRI Violations module). >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>> Christine >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> The LORIS team >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> On Tue, Jul 30, 2019 at 10:47 AM Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> I hope this is sufficient as the error for the visit label >>>>>>>>>>>>>>>>> disappeared. >>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Please see the attached file. Also something i found. >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> lorisadmin at hbp:/data/loris/bin/mri$ cat >>>>>>>>>>>>>>>>> /data/loris/data//logs/TarLoad-17-39-xubBdv.log >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> ==> Loading file from disk >>>>>>>>>>>>>>>>> /tmp/TarLoad-17-39-UyQcG2/dcc0000_258024_v1_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> --> mapping DICOM parameter for >>>>>>>>>>>>>>>>> /tmp/TarLoad-17-39-UyQcG2/dcc0000_258024_v1_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> ==> computing md5 hash for MINC body. >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> --> md5: 6b1202fd63e29de4c9be1cd9925888a5 >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> ==> verifying acquisition protocol >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Acquisition protocol is unknown >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> --> The minc file cannot be registered since the >>>>>>>>>>>>>>>>> AcquisitionProtocol is unknown >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> ???? ???, 30 ???? 2019 ???? 4:58 ?.?., ?/? Sotirios >>>>>>>>>>>>>>>>> Nikoloutsopoulos ??????: >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Ok I fixed the login problem by using a known hash and by >>>>>>>>>>>>>>>>>> deleting the rows from the login_history i was able to login. >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> ???? ???, 30 ???? 2019 ???? 4:50 ?.?., ?/? Sotirios >>>>>>>>>>>>>>>>>> Nikoloutsopoulos ??????: >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> there was no visit label 01 in the Visit_Windows table >>>>>>>>>>>>>>>>>>> and i don't know how to insert it because the record requires lots of >>>>>>>>>>>>>>>>>>> attributes. Also the system for a reason asked me to update my password and >>>>>>>>>>>>>>>>>>> now i don't remember it and my account got suspended. Is there a way to >>>>>>>>>>>>>>>>>>> reset it or set a simple password? I updated the password hash in the >>>>>>>>>>>>>>>>>>> users table by using the hash from another LORIS setup we had and i still >>>>>>>>>>>>>>>>>>> couldn't login ( also the attribute password is always NULL and the >>>>>>>>>>>>>>>>>>> expiration date is 1999-01-01 for some reason ). >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Thanks >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> ???? ???, 29 ???? 2019 ???? 5:21 ?.?., ?/? Cecile Madjar >>>>>>>>>>>>>>>>>>> ??????: >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Can you try adding the visit label v01 to the >>>>>>>>>>>>>>>>>>>> Visit_Windows table? >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> However, I noticed that in a previous dataset, the >>>>>>>>>>>>>>>>>>>> label was V1. Does that refer to the same visit? If so, you might want to >>>>>>>>>>>>>>>>>>>> harmonize the visit labels so they are all the same across datasets for a >>>>>>>>>>>>>>>>>>>> given timepoint, meaning you will need to relabel scans when the visit >>>>>>>>>>>>>>>>>>>> label is different but referring to the same visit label (v01 = V1 etc...). >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Hope this helps, >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> On Mon, Jul 29, 2019 at 10:15 AM Sotirios >>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos wrote: >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> Could you help me with the "Visit label does not >>>>>>>>>>>>>>>>>>>>> exist"? I had changed $subjectID{'createVisitLabel'} to 1 as you had >>>>>>>>>>>>>>>>>>>>> suggested but it appears that this problem hasn't been resolved yet. >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> lorisadmin at hbp:/data/loris/bin/mri$ cat >>>>>>>>>>>>>>>>>>>>> /data/loris/data//logs/TarLoad-14-58-9Xog7H.log >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> ==> Loading file from disk >>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> --> mapping DICOM parameter for >>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> --> using user-defined filterParameters for >>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> Candidate Mismatch Error is Visit label does not exist >>>>>>>>>>>>>>>>>>>>> -> WARNING: This candidate was invalid. Logging to >>>>>>>>>>>>>>>>>>>>> MRICandidateErrors table with reason >>>>>>>>>>>>>>>>>>>>> Visit label does not exist >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> ???? ???, 26 ???? 2019 ???? 3:02 ?.?., ?/? Sotirios >>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos ??????: >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> Hi Cecile, >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> The Center error was fixed. Still the insertion of >>>>>>>>>>>>>>>>>>>>>> mincs fails. Please see the output.txt file i attached. Also is there >>>>>>>>>>>>>>>>>>>>>> something else i need to change at the paths configuration? >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> ???? ???, 25 ???? 2019 ???? 6:55 ?.?., ?/? Cecile >>>>>>>>>>>>>>>>>>>>>> Madjar ??????: >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> We are making progress! >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> I have a feeling this error comes from the fact that >>>>>>>>>>>>>>>>>>>>>>> your psc table does not have the MRI_alias populated for the DCC site. >>>>>>>>>>>>>>>>>>>>>>> Running the following query in the mysql database should fix this: >>>>>>>>>>>>>>>>>>>>>>> UPDATE psc SET MRI_alias="DCC", Alias="DCC" WHERE >>>>>>>>>>>>>>>>>>>>>>> Name="Data Coordinating Center"; >>>>>>>>>>>>>>>>>>>>>>> Repeat the same with all your sites (make sure to >>>>>>>>>>>>>>>>>>>>>>> change the Aliases between sites, they should all be unique). >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> Let me know how it goes! >>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> On Thu, Jul 25, 2019 at 11:43 AM Sotirios >>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos wrote: >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> Dear Cecile, >>>>>>>>>>>>>>>>>>>>>>>> You were right about your guesses. I did the >>>>>>>>>>>>>>>>>>>>>>>> modifications you suggested, i still get the "no mincs inserted" error, now >>>>>>>>>>>>>>>>>>>>>>>> i am getting the "No center found this candidate" error ( how do i fix >>>>>>>>>>>>>>>>>>>>>>>> that? from what i see the .dcm files contains a 'Institution Name', is that >>>>>>>>>>>>>>>>>>>>>>>> the center? ), so i guess that's why the validation fails, but i changed >>>>>>>>>>>>>>>>>>>>>>>> the force variable of tarchiveLoader to 1, shouldn't it have inserted the >>>>>>>>>>>>>>>>>>>>>>>> mincs then? Also it is optional to have a mail server, right? ( from what i >>>>>>>>>>>>>>>>>>>>>>>> see the mail error does not affect the $valid_study, so i assume we are >>>>>>>>>>>>>>>>>>>>>>>> okay with that ) >>>>>>>>>>>>>>>>>>>>>>>> Thank you a lot, >>>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 25 ???? 2019 ???? 5:48 ?.?., ?/? Cecile >>>>>>>>>>>>>>>>>>>>>>>> Madjar ??????: >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> From what I understand, I believe you just need to >>>>>>>>>>>>>>>>>>>>>>>>> update a few config settings from the frontend in the Config module (under >>>>>>>>>>>>>>>>>>>>>>>>> the Admin menu). >>>>>>>>>>>>>>>>>>>>>>>>> [image: Screen Shot 2019-07-25 at 10.31.35 AM.png] >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> Then go to the Paths section of the config module >>>>>>>>>>>>>>>>>>>>>>>>> and update the "LORIS-MRI code" config setting to /data/loris/bin/mri (my >>>>>>>>>>>>>>>>>>>>>>>>> guess is that currently, it is set to /data/LORIS/data) and click on the >>>>>>>>>>>>>>>>>>>>>>>>> submit button. >>>>>>>>>>>>>>>>>>>>>>>>> [image: Screen Shot 2019-07-25 at 10.32.50 AM.png] >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> Then, go to Imaging Pipeline section of the >>>>>>>>>>>>>>>>>>>>>>>>> Configuration module and update the "Loris-MRI Data Directory" to >>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/ (my guess is that it is empty at the moment in your >>>>>>>>>>>>>>>>>>>>>>>>> database which is why $data_dir is not defined when you run the >>>>>>>>>>>>>>>>>>>>>>>>> tarchiveLoader step of the insertion pipeline). >>>>>>>>>>>>>>>>>>>>>>>>> [image: Screen Shot 2019-07-25 at 10.40.52 AM.png] >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> Finally, I took a look at your environment file >>>>>>>>>>>>>>>>>>>>>>>>> and it might be a good idea to update your PERL5LIB variable to the >>>>>>>>>>>>>>>>>>>>>>>>> following (it has been added to the code a few releases ago as we realized >>>>>>>>>>>>>>>>>>>>>>>>> this was needed for the libraries. Not sure which version of LORIS-MRI you >>>>>>>>>>>>>>>>>>>>>>>>> are using but it does not hurt to update this variable to what I suggest >>>>>>>>>>>>>>>>>>>>>>>>> below): >>>>>>>>>>>>>>>>>>>>>>>>> export >>>>>>>>>>>>>>>>>>>>>>>>> PERL5LIB=/data/loris/bin/mri/uploadNeuroDB:/data/loris/bin/mri/dicom-archive:$PERL5LIB >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> Hope this helps. Sorry you are experiencing so >>>>>>>>>>>>>>>>>>>>>>>>> much trouble setting things up. We probably need to update our WIKI. >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> On Thu, Jul 25, 2019 at 9:48 AM Sotirios >>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos wrote: >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> The "Loris-MRI Data Directory" should be in the >>>>>>>>>>>>>>>>>>>>>>>>>> environment file? >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 25 ???? 2019 ???? 12:59 ?.?., ?/? >>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos >>>>>>>>>>>>>>>>>>>>>>>>>> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> The scripts are located in >>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/. Somewhere I might have messed something up but i >>>>>>>>>>>>>>>>>>>>>>>>>>> remember following the instructions in the wiki.For example when i tried to >>>>>>>>>>>>>>>>>>>>>>>>>>> execute the batch_uploads_imageuploader perl script the line >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> my $command = "$bin_dir/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl " >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> was pointing to an invalid path, for example: it >>>>>>>>>>>>>>>>>>>>>>>>>>> was repeating a pattern and had LORIS instead of loris ( i think the >>>>>>>>>>>>>>>>>>>>>>>>>>> mistake was that in the wiki it suggested to use $PROJECT for the name of >>>>>>>>>>>>>>>>>>>>>>>>>>> the folder and i choosed 'loris' >>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris/wiki/Imaging-Database >>>>>>>>>>>>>>>>>>>>>>>>>>> ). See also the in image for the modification i did. Also i didn't find the >>>>>>>>>>>>>>>>>>>>>>>>>>> section to config the $data_dir variable. >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 24 ???? 2019 ???? 6:05 ?.?., ?/? >>>>>>>>>>>>>>>>>>>>>>>>>>> Cecile Madjar ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> It looks like you have one Config setting not >>>>>>>>>>>>>>>>>>>>>>>>>>>> set (based on the first error message you got when running it the first >>>>>>>>>>>>>>>>>>>>>>>>>>>> time). You need to set a value for "Loris-MRI Data Directory" in the Config >>>>>>>>>>>>>>>>>>>>>>>>>>>> module under the Imaging pipeline section (from what I can see, it would be >>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/ for your setup). >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> The reason you got that error message the >>>>>>>>>>>>>>>>>>>>>>>>>>>> second time is that the pipeline checks if the DICOM study was already >>>>>>>>>>>>>>>>>>>>>>>>>>>> inserted in the tarchive table. Since you ran the study once already, the >>>>>>>>>>>>>>>>>>>>>>>>>>>> study is inserted into the tarchive, hence the message. However, the >>>>>>>>>>>>>>>>>>>>>>>>>>>> pipeline did not complete as the MINC files were not created and inserted >>>>>>>>>>>>>>>>>>>>>>>>>>>> into the files/parameter_file table. In order to continue the insertion, >>>>>>>>>>>>>>>>>>>>>>>>>>>> you will then need to run the tarchiveLoader command suggested in the >>>>>>>>>>>>>>>>>>>>>>>>>>>> terminal during the second run: >>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader >>>>>>>>>>>>>>>>>>>>>>>>>>>> -globLocation -profile prod >>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive//2012/DCM_2012-12-05_ImagingUpload-17-43-ZUEFjb.tar >>>>>>>>>>>>>>>>>>>>>>>>>>>> -verbose >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> Finally, I am a bit confused by your setup. >>>>>>>>>>>>>>>>>>>>>>>>>>>> Where are the scripts located? In /data/loris/bin/mri or /data/loris/data? >>>>>>>>>>>>>>>>>>>>>>>>>>>> It feels like the Config setting "LORIS-MRI code" in the Paths section was >>>>>>>>>>>>>>>>>>>>>>>>>>>> set to "/data/LORIS/data" but it should have been set to the directory >>>>>>>>>>>>>>>>>>>>>>>>>>>> where the scripts are located (most probably /data/loris/bin/mri). >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helps, >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> On Wed, Jul 24, 2019 at 10:55 AM Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos wrote: >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Ok first i execute this command: >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> "lorisadmin at hbp:/data/loris/bin/mri$ >>>>>>>>>>>>>>>>>>>>>>>>>>>>> ./batch_uploads_imageuploader -profile prod < ~/Desktop/input.txt > log.txt >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at ./batch_uploads_imageuploader line 143. >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at ./batch_uploads_imageuploader line 143. >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $_ in pattern match >>>>>>>>>>>>>>>>>>>>>>>>>>>>> (m//) at ./batch_uploads_imageuploader line 147. >>>>>>>>>>>>>>>>>>>>>>>>>>>>> base is DCC0000_258024_V01 >>>>>>>>>>>>>>>>>>>>>>>>>>>>> path is /data/incoming/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>> type is .tar.gz >>>>>>>>>>>>>>>>>>>>>>>>>>>>> fullpath is >>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/incoming/DCC0000_258024_V01.tar.gz >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> source /tmp/ImagingUpload-17-43-ZUEFjb >>>>>>>>>>>>>>>>>>>>>>>>>>>>> targetlocation /data/loris/data/tarchive >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 256. >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 284. >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at /data/loris/bin/mri/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>> tarchive_validation.pl line 219. >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at /data/loris/bin/mri/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl line 270. >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 711. >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Can't exec "mail": No such file or directory >>>>>>>>>>>>>>>>>>>>>>>>>>>>> at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 721. >>>>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 722. >>>>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 723. >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 724. >>>>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 724. >>>>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 725. >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 735. >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> No Mincs inserted >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> The tarchiveLoader insertion script has failed. >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Running now the following command: >>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl -profile prod >>>>>>>>>>>>>>>>>>>>>>>>>>>>> -upload_id 3 /data/incoming/DCC0000_258024_V01.tar.gz -verbose" >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> I inserted the VisitLabel, but still the Mincs >>>>>>>>>>>>>>>>>>>>>>>>>>>>> are not inserted and i am getting this error >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> "lorisadmin at hbp:/data/loris/bin/mri$ >>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl -profile prod >>>>>>>>>>>>>>>>>>>>>>>>>>>>> -upload_id 3 /data/incoming/DCC0000_258024_V01.tar.gz -verbose >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> find -path >>>>>>>>>>>>>>>>>>>>>>>>>>>>> \/tmp\/ImagingUpload\-17\-45\-5MsWEd -name '__MACOSX' -delete >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Spool message is: >>>>>>>>>>>>>>>>>>>>>>>>>>>>> The Scan for the uploadID 3 has already been >>>>>>>>>>>>>>>>>>>>>>>>>>>>> run with tarchiveID: 7. >>>>>>>>>>>>>>>>>>>>>>>>>>>>> To continue with the rest of the insertion >>>>>>>>>>>>>>>>>>>>>>>>>>>>> pipeline, please run tarchiveLoader from a terminal as follows: >>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader -globLocation -profile prod >>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive//2012/DCM_2012-12-05_ImagingUpload-17-43-ZUEFjb.tar >>>>>>>>>>>>>>>>>>>>>>>>>>>>> -verbose" >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Which files should i delete? I thought that >>>>>>>>>>>>>>>>>>>>>>>>>>>>> deleting the files from the tarchive was enough. And i executed the last >>>>>>>>>>>>>>>>>>>>>>>>>>>>> proposed command to continue to rest of the insertion pipeline ( check the >>>>>>>>>>>>>>>>>>>>>>>>>>>>> image ). >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 24 ???? 2019 ???? 5:05 ?.?., ?/? >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Cecile Madjar ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sorry I was not clear before. Every visits of >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> candidates are created in the session table with one entry per >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID/VisitLabel. So if the imaging pipeline created visits in the session >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> table (that are not attached to instruments) and you want to clean your >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> database completely, you can delete entries in that table as well. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Regarding your point 2, the imaging pipeline >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> can create the visit in the session table as long as the visit label is >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> present in the Visit_Windows table (which means the visit label stored in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the PatientName is a valid visit label). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> However, in your prod file, if the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> variable $subjectID{'createVisitLabel'} is set to 1 for candidates, the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit label should be created in the Visit_Windows table I believe. Here >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> is the line of the prod file you would need to change >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> . >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> In general, we prefer populating the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Visit_Windows table and set the $subjectID{'createVisitLabel'} to 0 for >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> candidate data to avoid insertion of badly labelled MRI data that are >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> complex to relabel. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Finally, regarding the candidate creation, if >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> you execute the following steps, the pipeline should be able to create >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> candidates: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - set in the Imaging Pipeline section of the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> config module the config setting "Upload creation of candidates" to Yes >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - manually transfer the scans to the LORIS >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> server instead of uploading it via the imaging browser >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - run batch_imaging_upload.pl as you did >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> until now. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helps! >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> On Wed, Jul 24, 2019 at 8:47 AM Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> wrote: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> About my second question i replaced the name >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> of the patient in the .dcm files and now i am getting an error that the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit label does not exist. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I thought it was supposed to be >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> automatically created. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> "Done adding archive info into database >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -globLocation -profile prod >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive//DCM_2012-12-05_ImagingUpload-15-42-yUwQQV.tar >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -verbose >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> md5sum >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive/DCM_2012-12-05_ImagingUpload-15-42-yUwQQV.tar >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> candidate id 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> => No Visit labelVisit label does not exist >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Set centerID = 1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Number of MINC files that will be considered >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> for inserting into the database: 1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> log dir is /logs and log file is >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /logs/TarLoad-15-42-L6pocU.log >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> candidate id 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> => No Visit label >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Cleaning up temp files: rm -rf >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-15-42-J2rQms/ImagingUpload-15-42-yUwQQV*" >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 24 ???? 2019 ???? 3:38 ?.?., ?/? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 1) What are the records in the session >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> table? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 2) I tried to upload a non-phantom file >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> like this >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> input_file.txt: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/incoming/DCC0000_258024_V1.tar.gz N >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DCC0000_258024_V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Terminal: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ./batch_uploads_imageuploader -profile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> prod < ~/Desktop/input.txt > log.txt >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and i get the following error in the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> log.txt file >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> "Running now the following command: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl -profile prod >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -upload_id 7 /data/incoming/DCC0000_258024_V1.tar.gz -verbose >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> find -path >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> \/tmp\/ImagingUpload\-14\-56\-FeLCB4 -name '__MACOSX' -delete >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Spool message is: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The PatientName read from the DICOM header >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> does not start with DCC0000_258024_V1 from the mri_upload table >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> " >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and the spool message is repeated for each >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> .dcm file. Should i preprocess every .dcm file and change the PatientName >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> to "DCC0000_258024_V1"? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 3) As far as it concerns the candidate >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> profile i have to create a new one each time before i try to upload a file? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Is there already a way to create a candidate profile and get the DCCID and >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID without the user interface? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 18 ???? 2019 ???? 5:00 ?.?., ?/? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Cecile Madjar >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> See answers to your questions below. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> About the 1st case we had a dicom with a >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> blank studyUID, maybe someone accidentally removed it. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> That is strange. Something must have been >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> done to the DICOM files. I have never seen a study with no StudyUID out of >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the scanner. Usually, you need to manually erase it with some tool. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> However, DICOMs never cease to surprise me... >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Some other questions: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 1) What are the steps to remove all of my >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> patients and uploads?: because i want to try to reupload all the testing >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> dicoms we had with a clean database. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Release 21.0 of LORIS-MRI will offer a >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> script to remove all the entries and files specific to an upload. However, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> this release is not yet out. Hopefully in the next few weeks. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> In the meantime, since your case is >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> particular and that you just want to start with a clean database, the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> following deletes should work (hopefully I won't forget any tables): >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from mri_violations_log; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from mri_protocol_violated_scans; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from MRICandidateErrors; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from parameter_file; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from files_qcstatus; # (if you >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> played with the QC part of the imaging browser for testing) >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from feedback_mri_comments; # (if >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> you played with the QC part of the imaging browser for testing) >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from tarchive_series; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from tarchive_files; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from mri_upload; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from tarchive; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from mri_scanner; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from candidate where >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID="scanner"; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I don't know if you want to also delete >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> entries in the session and candidate table too? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 2) We do not need to create the profile of >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> a patient ( are the patients stored in the candidate table? because i can't >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> see the ghosts ), because will it automatically be created when importing a >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> dicom? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I am not sure I understand fully this >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> question. All candidates are stored in the candidate table. The phantom >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> scans however are attached to a scanner candidate depending on where the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> scan happened. It is a bit of a weird concept that we have to redesign >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> eventually but never got a chance to get to it. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hopefully this answered your question, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> otherwise, don't hesitate to let me know. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 3) What is the difference between >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> uploading a dicom as phantom instead of importing as >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCCID_DCCID_VisitLabel? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> When you upload the scan as >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID_DCCID_VisitLabel, there is a check that makes sure the candidate IDs >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and visit label are valid at the time of upload. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> When you upload a scan as phantom, it >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> expects that the DICOM field PatientName and uploaded filename contains the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> string "phantom". We enforced this behaviour on the imaging uploader side >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in recent releases but I can't remember which one. Probably the upcoming >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 21.0 release. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> All those verifications might seem >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> cumbersome but they are here to ensure that the files inserted are all >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> valid and labelled properly as it is a bit messy to have to delete files >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> that were wrongly labelled. At least, the delete script present in release >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 21.0 will make this process easier but it is still good practice to verify >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> those things. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> With pleasure. Hopefully the answers to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> your questions will be helpful. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PS: loris-dev mailing list: you will find >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the initial answer I gave Sotirios below. I forgot to cc the loris-dev in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> my earlier reply... >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 16 ???? 2019 ???? 12:02 ?.?., >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ?/? Cecile Madjar >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Dear Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you for reaching out. Since your >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> email was already organized in points, I will reply directly below your >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> questions below. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 1) What do we do when the StudyUID is >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> blank on the header? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/minor/docs/AppendixA-Troubleshooting_guideline.md >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> There solution provided at the table 3 does not guide us how to find the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> information ( is possible ). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The StudyUID is the field used in our >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> pipeline at the moment to check whether a DICOM study was already inserted >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> into LORIS with that same StudyUID since it is supposed to be unique for >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> every single study. Currently, we do not support insertion of DICOM studies >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> if they do not have a StudyUID associated with them. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Is there a specific reason why the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> StudyUID is blank in the DICOM headers in your DICOM files? Did they go >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> through some processes before upload to LORIS? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 2) When i am about to upload a >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> non-phanton case i need a 'Visit Label'. Is there already a script that can >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> create a new visit label for a specific Candidate, so i can provide it as >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> input afterwards to the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> batch_uploads_imageuploader ( See option 5.1.3 https://github.com/aces/Loris-MRI/blob/minor/docs/05-PipelineLaunchOptions.md ) >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I am not sure if the front-end allows >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> for it but if you use batch_uploads_imageuploader, the insertion scripts >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> could create the visit label for you. However, it does need to be included >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in the patient name in order for the script to know which label it should >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> use. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> For example: you upload V02 for MTL0123 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> (DCCID: 456789) but V02 was not yet created for MTL0123; the insertion >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> scripts will create a V02 visit for MTL0123 if the PatientName field for >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the dataset is MTL0123_456789_V02 with Stage marked as "Not Started". >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> However, *note that for the script to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> create the visit for the candidate, you have to make sure that all the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit label of your projects were inserted in the Visit_Windows table* >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> (otherwise, the visit will never be created as they were not specified as >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> being part of the list of visit label to expect). So in the example above, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> you should have one row in Visit_Windows with Visit_label="V02" set. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 3) Section 4.3 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/minor/docs/04-Scripts.md >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> What do we do when the folder contains multiple mnc files? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> This is a case by case. Most of the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> time, the MINC files that failed insertion into the imaging browser end up >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in the MRI violation module where you can see what went wrong with the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> acquisitions not inserted. If you notice that the MINC file should be >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> inserted as a specific protocol, you can force the insertion as explained >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in section 4.3. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> In your case, I have a feeling that you >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> want to be able to insert MINC files that did not go through the whole >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> pipeline insertion (DICOM archival, then dcm2mnc, then protocol >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> identification, then insertion...). In theory, you could call >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl on any MINC file, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> provided you have at least the following information: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - path to the MINC file >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - uploadID associated with the MINC >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> files or DICOM archive path from which those MINC files were created from >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Then the minc_insertion.pl script will >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> do the subject information and protocol validation etc... >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> If all the MINC files come from the same >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> uploadID or TarchiveID, then you could run a loop in bash calling the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl script like this for >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> files deriving from uploadID=1: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ls /path/to/mnc/folder/* | while read f; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> do minc_insertion.pl -profile prod >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -uploadID 1 -mincPath $f; done >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helped! >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> -- >>>>>>>>>>>>>> >>>>>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>>>>> >>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> -- >>>>>>>>>>> >>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>> >>>>>>>>>> _______________________________________________ >>>>>>>>>> Loris-dev mailing list >>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> -- >>>>>>>>> >>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>> Montreal Neurological Institute >>>>>>>>> McGill University | Montreal | Canada >>>>>>>>> _______________________________________________ >>>>>>>>> Loris-dev mailing list >>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> -- >>>>>>>> >>>>>>>> christine.rogers at mcgill.ca >>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>> Montreal Neurological Institute >>>>>>>> McGill University | Montreal | Canada >>>>>>>> >>>>>>> _______________________________________________ >>>>>>> Loris-dev mailing list >>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>> >>>>>> >>>>>> >>>>>> -- >>>>>> Shen Wang >>>>>> Loris Developer >>>>>> Montreal Neurological Institute >>>>>> McGill University >>>>>> >>>>>> >>>>> >>>>> -- >>>>> Shen Wang >>>>> Loris Developer >>>>> Montreal Neurological Institute >>>>> McGill University >>>>> >>>>> _______________________________________________ >> Loris-dev mailing list >> Loris-dev at bic.mni.mcgill.ca >> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >> > > > -- > > christine.rogers at mcgill.ca > McGill Centre for Integrative Neuroscience | MCIN.ca > Montreal Neurological Institute > McGill University | Montreal | Canada > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: lorris-error.log Type: text/x-log Size: 21570 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: loris-access.log Type: text/x-log Size: 5703 bytes Desc: not available URL: From AMORALESPINZON at bwh.harvard.edu Thu Aug 29 21:46:13 2019 From: AMORALESPINZON at bwh.harvard.edu (Morales Pinzon, Alfredo) Date: Fri, 30 Aug 2019 01:46:13 +0000 Subject: [Loris-dev] Error "not a unique file" inserting segmentation files in LORIS Message-ID: Dear DevLoris Team, I started the uploading process of processed files, segmentations and transformations, using the file "register_processed_data.pl" but some files are not being uploaded. The error reported in "data/logs/registerProcessed" show the following log for one of the files that could not be inserted: ------------------------------------------------------------------------------- ==> Successfully connected to database Log file, 2019-08-29_19:08:17 ==>Mapped DICOM parameters -> using user-defined filterParameters for /xxx/w024/gvf_ISPC-stx152lsq6.mnc.gz ==> Verifying acquisition center - Center Name : UNKN - CenterID : 0 -> Set ScannerID to 0. ==> Data found for candidate : 123456 - Visit: w024 -> Set SessionID to 28269. -> Set SourceFileID to 49598. -> Set AcquisitionProtocolID to 1013. -> Set CoordinateSpace to stx152lsq6. -> Set SourcePipeline to ConsensusGd. -> Set PipelineDate to 2019-08-29. -> Set OutputType to gvf. -> Set md5hash to b877648ed0ef9a7458ad4931f4dbfd11. ==> NeuroDB::File=HASH(0x136baa8) is not a unique file and will not be added to database. ------------------------------------------------------------------------------- I checked the md5hash for a previous uploaded file, which is different from the previous, but the same "md5hash" was calculated. See the following log: ------------------------------------------------------------------------------- ==> Successfully connected to database Log file, 2019-08-19_10:11:53 ==>Mapped DICOM parameters -> using user-defined filterParameters for ==> Verifying acquisition center - Center Name : UNKN - CenterID : 0 -> Set ScannerID to 0. ==> Data found for candidate : 123456 - Visit: baseline -> Set SessionID to 28268. -> Set SourceFileID to 49593. -> Set AcquisitionProtocolID to 1013. -> Set CoordinateSpace to stx152lsq6. -> Set SourcePipeline to T2Vol. -> Set PipelineDate to 2019-08-19. -> Set OutputType to gvf. -> Set md5hash to b877648ed0ef9a7458ad4931f4dbfd11. File /xxx/baseline/gvf_ISPC-stx152lsq6.mnc.gz moved to: /yyy/data/assembly/123456/baseline/mri/processed/T2Vol/IPMSA_123456_baseline_t1c_001_gvf_001.mnc.gz ==> FAILED TO INSERT INTERMEDIARY FILES FOR 112945! Making JIV ==> Registered /data_/ipmsa/loris_data/IPMSA/data/assembly/307024/baseline/mri/processed/T2Vol/IPMSA_307024_baseline_t1c_001_gvf_001.mnc.gz in database, given FileID: 112945 ------------------------------------------------------------------------------- Here are the corresponding md5 for each file calculated using the command md5sum: /xxx/w024/gvf_ISPC-stx152lsq6.mnc.gz 7306010346c4614d8e338595b386ca5c /xxx/baseline/gvf_ISPC-stx152lsq6.mnc.gz 22107253f8b87c9918ac7f82fdc22c36 Could you please help me inserting those files which are different in size and md5 from previous uploaded files? The only similarity between the previous uploaded files and the ones that could not be uploaded is the filename. Let me know if you need more information. Regards, Alfredo. The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -------------- next part -------------- An HTML attachment was scrubbed... URL: From wangshen.mcin at gmail.com Fri Aug 30 11:13:16 2019 From: wangshen.mcin at gmail.com (Shen Wang) Date: Fri, 30 Aug 2019 11:13:16 -0400 Subject: [Loris-dev] Import mri - scripts In-Reply-To: References: Message-ID: Hi Sotirios, You should not use our minor branch (only for developing), we have published the 21.0-release officially, it is a stable version of Loris. After checking your error logs, you're missing is running composer install, which will import your packages and create the vendor folder, along with the autoload script. Regards Shen On Thu, 29 Aug 2019 at 19:46, Sotirios Nikoloutsopoulos < sotirisnik at gmail.com> wrote: > Hi, > > loris-access.log reports HTTP 500 error and loris-error reports that some > files are missing e.x. autoload.php from > /var/www/loris/htdocs/../vendor/autoload.php ( > https://github.com/aces/Loris/tree/minor/htdocs/vendor and as i can > verify those files do not exist in the github folder ) > > Thanks > > > > ???? ???, 29 ??? 2019 ???? 4:04 ?.?., ?/? Christine Rogers, Ms. < > christine.rogers at mcgill.ca> ??????: > >> Hi Sotirios, >> >> > Any suggestion why Loris is not showing up in the browser? >> >> >> - What are the last few lines of your loris-access and loris-error apache >> logs? >> >> - What are the URL and host in your Config table? (run these queries >> from the wiki >> >> ) >> >> - Are you using https, are the certificates in place, etc? >> >> - Do any of the wiki's Troubleshooting steps >> >> help? >> >> Best, >> Christine >> >> On Wed, Aug 28, 2019 at 9:30 PM Sotirios Nikoloutsopoulos < >> sotirisnik at gmail.com> wrote: >> >>> Any suggestion why Loris is not showing up in the browser? >>> >>> Thanks >>> >>> >>> ???? ???, 28 ??? 2019 ???? 2:30 ?.?., ?/? Sotirios Nikoloutsopoulos < >>> sotirisnik at gmail.com> ??????: >>> >>>> Also to mention that in the picture i opened the 000-default.conf which >>>> is just a copy of loris.conf by using cp >>>> >>>> ???? ???, 28 ??? 2019 ???? 2:20 ?.?., ?/? Sotirios Nikoloutsopoulos < >>>> sotirisnik at gmail.com> ??????: >>>> >>>>> Ok that fixed the install.sh problem. Now it doesn't show loris to the >>>>> browser, although everything seems right ( also >>>>> >>>>> /etc/apache2/sites-enabled/000-default.conf was replaced by loris.config ). >>>>> >>>>> >>>>> And apache is running >>>>> lorisadmin at loris-VirtualBox:/var/www/loris/htdocs$ sudo systemctl >>>>> status apache2[sudo] password for lorisadmin: >>>>> ? apache2.service - LSB: Apache2 web server >>>>> Loaded: loaded (/etc/init.d/apache2; bad; vendor preset: enabled) >>>>> Drop-In: /lib/systemd/system/apache2.service.d >>>>> ??apache2-systemd.conf >>>>> Active: active (running) since ??? 2019-08-28 02:15:12 EEST; 3min >>>>> 34s ago >>>>> >>>>> [image: image.png] >>>>> >>>>> ???? ???, 27 ??? 2019 ???? 9:42 ?.?., ?/? Shen Wang < >>>>> wangshen.mcin at gmail.com> ??????: >>>>> >>>>>> Hi, >>>>>> This is a bug for install.sh file, we will fix it later. >>>>>> Thank for letting me know your Loris install situation. >>>>>> regards >>>>>> Shen >>>>>> >>>>>> >>>>>> On Tue, 27 Aug 2019 at 14:28, Shen Wang >>>>>> wrote: >>>>>> >>>>>>> Hi, >>>>>>> Please remove "set -euo pipefail" line 10 in the install.sh file. >>>>>>> Then try again. >>>>>>> >>>>>>> >>>>>>> >>>>>>> On Tue, 27 Aug 2019 at 14:05, Sotirios Nikoloutsopoulos < >>>>>>> sotirisnik at gmail.com> wrote: >>>>>>> >>>>>>>> Hi, >>>>>>>> >>>>>>>> i still haven't resolved the previous issue. Also i tried to >>>>>>>> install Loris to a new virtual machine and when i execute install.sh i get >>>>>>>> the following error >>>>>>>> >>>>>>>> lorisadmin at loris-VirtualBox:/var/www/loris/tools$ ./install.sh >>>>>>>> LORIS Installation Script starting at 2019-08-27T21:00:42 >>>>>>>> The log for this session will be stored in file >>>>>>>> /var/www/loris/tools/logs/install-2019-08-27T21:00:42.log >>>>>>>> >>>>>>>> --------------------------------------------------------------------- >>>>>>>> LORIS Installation Script >>>>>>>> >>>>>>>> --------------------------------------------------------------------- >>>>>>>> >>>>>>>> PHP appears to be installed. >>>>>>>> >>>>>>>> PHP Composer appears to be installed. >>>>>>>> >>>>>>>> This install script will ask you to provide inputs for different >>>>>>>> steps. >>>>>>>> Please ensure you have the following information ready (if >>>>>>>> applicable): >>>>>>>> >>>>>>>> 1) Your project directory name. >>>>>>>> (Will be used to modify the paths for Imaging data in the >>>>>>>> generated >>>>>>>> config.xml file for LORIS, and may also be used to >>>>>>>> automatically >>>>>>>> create/install apache config files.) If unsure, a default like >>>>>>>> "LORIS" >>>>>>>> should be acceptable. >>>>>>>> >>>>>>>> Please also consult the Loris WIKI on GitHub for more information >>>>>>>> on these >>>>>>>> Install Script input parameters. >>>>>>>> >>>>>>>> Ready to continue? [yn] y >>>>>>>> >>>>>>>> ./install.sh: line 132: projectname: unbound variable >>>>>>>> >>>>>>>> Thanks >>>>>>>> >>>>>>>> ???? ???, 6 ??? 2019 ???? 5:09 ?.?., ?/? Christine Rogers, Ms. < >>>>>>>> christine.rogers at mcgill.ca> ??????: >>>>>>>> >>>>>>>>> Hi Sotirios, >>>>>>>>> Could you also let us know -- on which pages is content visible, >>>>>>>>> and on which pages/modules is content not visible for you? >>>>>>>>> Thanks, >>>>>>>>> Christine >>>>>>>>> >>>>>>>>> On Tue, Aug 6, 2019 at 9:54 AM Christine Rogers, Ms. < >>>>>>>>> christine.rogers at mcgill.ca> wrote: >>>>>>>>> >>>>>>>>>> Thanks Sotirios, >>>>>>>>>> That's good to know. It sounds like you've checked that your >>>>>>>>>> /var/www/loris/project/config.xml file get populated properly. >>>>>>>>>> >>>>>>>>>> Please send us the last few errors you're seeing in your apache >>>>>>>>>> error log file, and your config paths and we can see what's happening with >>>>>>>>>> your front end -- >>>>>>>>>> Run these Troubleshooting Queries >>>>>>>>>> >>>>>>>>>> to get your config path settings, given your front end is not displaying >>>>>>>>>> fully. >>>>>>>>>> >>>>>>>>>> The Loris-MRI repo >>>>>>>>>> 21 >>>>>>>>>> install/upgrade would then be your next steps. >>>>>>>>>> Best, >>>>>>>>>> Christine >>>>>>>>>> >>>>>>>>>> On Tue, Aug 6, 2019 at 7:53 AM Sotirios Nikoloutsopoulos < >>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>> >>>>>>>>>>> I am using a VM. What i did was: >>>>>>>>>>> 1) Download the files from https://github.com/aces/Loris and >>>>>>>>>>> replace them to my existing /vaw/www/loris folder. >>>>>>>>>>> 2) Execute the composer install --no-dev and then composer >>>>>>>>>>> dump-autoload as mentioned here >>>>>>>>>>> https://github.com/aces/Loris/wiki/Updating-your-LORIS. >>>>>>>>>>> 3) Execute install.sh from /var/www/loris/tools and because >>>>>>>>>>> LORIS already existed i moved a .config file, then re-executed the >>>>>>>>>>> install.sh successfully >>>>>>>>>>> 4 ) As for the database, i dropped the schema and i executed the >>>>>>>>>>> installdb.php >>>>>>>>>>> >>>>>>>>>>> ???? ???, 5 ??? 2019 ???? 5:22 ?.?., ?/? Christine Rogers, Ms. < >>>>>>>>>>> christine.rogers at mcgill.ca> ??????: >>>>>>>>>>> >>>>>>>>>>>> Hi Sotorios, >>>>>>>>>>>> >>>>>>>>>>>> Thanks - when you re-installed did you start on a fresh root >>>>>>>>>>>> path / VM or might some of your old system setting still apply? >>>>>>>>>>>> (And if you did any steps similar to an upgrade, did you follow >>>>>>>>>>>> the Upgrade steps in the Release Notes, from both repos?) >>>>>>>>>>>> >>>>>>>>>>>> About the TR_range column - it was recently split (MRI pr339 >>>>>>>>>>>> ) split into >>>>>>>>>>>> TR_min and _max columns. Given the code was trying to query TR_range which >>>>>>>>>>>> does not exist in your mri_protocol table, double-check which version of >>>>>>>>>>>> the Loris repo (tables) and the Loris-MRI repo (code) you have installed to >>>>>>>>>>>> ensure they match. >>>>>>>>>>>> >>>>>>>>>>>> Christine >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> On Mon, Aug 5, 2019 at 9:06 AM Sotirios Nikoloutsopoulos < >>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>> >>>>>>>>>>>>> I reinstalled LORIS to 21 version and now the content is not >>>>>>>>>>>>> visible at all at most pages. >>>>>>>>>>>>> >>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>> >>>>>>>>>>>>> ???? ???, 5 ??? 2019 ???? 3:19 ?.?., ?/? Sotirios >>>>>>>>>>>>> Nikoloutsopoulos ??????: >>>>>>>>>>>>> >>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>> >>>>>>>>>>>>>> Is it easy to upgrade to Loris 21? Also the following fails >>>>>>>>>>>>>> because the line 1985 of NeuroDB/MRIProcessingUtility.pm query mri_protocol >>>>>>>>>>>>>> which doesn't have TR_range >>>>>>>>>>>>>> https://github.com/aces/Loris/blob/21.0-release/SQL/0000-00-00-schema.sql#L556 >>>>>>>>>>>>>> >>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>> >>>>>>>>>>>>>> lorisadmin at hbp:/data/loris/bin/mri$ >>>>>>>>>>>>>> ./batch_uploads_imageuploader -profile prod < ~/Desktop/input.txt > log.txt >>>>>>>>>>>>>> Use of uninitialized value $_ in pattern match (m//) at >>>>>>>>>>>>>> ./batch_uploads_imageuploader line 147. >>>>>>>>>>>>>> base is DCC0000_258024_V1 >>>>>>>>>>>>>> path is /data/incoming/ >>>>>>>>>>>>>> type is .tar.gz >>>>>>>>>>>>>> fullpath is /data/incoming/DCC0000_258024_V1.tar.gz >>>>>>>>>>>>>> DBD::mysql::st execute failed: Unknown column 'TR_range' in >>>>>>>>>>>>>> 'where clause' at >>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line 1985. >>>>>>>>>>>>>> DBD::mysql::st fetchrow_array failed: fetch() without >>>>>>>>>>>>>> execute() at >>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line 1986. >>>>>>>>>>>>>> Use of uninitialized value $count_mri_protocol in numeric gt >>>>>>>>>>>>>> (>) at /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm >>>>>>>>>>>>>> line 1995. >>>>>>>>>>>>>> DBD::mysql::st execute failed: Unknown column 'TR_range' in >>>>>>>>>>>>>> 'field list' at /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 562. >>>>>>>>>>>>>> Can't exec "mail": No such file or directory at >>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 721. >>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 722. >>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 723. >>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 724. >>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 725. >>>>>>>>>>>>>> >>>>>>>>>>>>>> No Mincs inserted >>>>>>>>>>>>>> >>>>>>>>>>>>>> Thanks, >>>>>>>>>>>>>> >>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>> >>>>>>>>>>>>>> ???? ???, 3 ??? 2019 ???? 1:08 ?.?., ?/? Christine Rogers, >>>>>>>>>>>>>> Ms. ??????: >>>>>>>>>>>>>> >>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> First, just a note: we've released LORIS 21 this week with >>>>>>>>>>>>>>> some major new features and cleanup -- especially if you are early in your >>>>>>>>>>>>>>> setup phase, check out the Release notes for both the LORIS >>>>>>>>>>>>>>> and >>>>>>>>>>>>>>> Loris-MRI >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> repos. >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> Thanks for your screenshots -- your empty mri_protocol table >>>>>>>>>>>>>>> should be at the root of these issues : >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> The mri_protocol table must be populated >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> in order for your scans to be registered in LORIS -- it serves as a >>>>>>>>>>>>>>> whitelist for the insertion pipeline which filters out scans that aren't >>>>>>>>>>>>>>> identified or matched to scan types in this table. >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> By default, this table is populated with entries for t1, t2, >>>>>>>>>>>>>>> fMRI and DTI (Insert statements for 21 release branch are >>>>>>>>>>>>>>> here >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> ) >>>>>>>>>>>>>>> Feel free to restore our default records and broaden their >>>>>>>>>>>>>>> parameters to match all your scan types. >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> re Defaced, native, selected -- these filter the scans >>>>>>>>>>>>>>> displayed as you move to the next page (View Session), instead of viewing >>>>>>>>>>>>>>> "all types" of scans from a given session : >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> - "defaced" means that a defacing script >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> has masked the subject's face in the volume (for patient privacy) >>>>>>>>>>>>>>> - "native" means that no pre-processing has been >>>>>>>>>>>>>>> performed on the scan (it's raw data), >>>>>>>>>>>>>>> - "selected" will show only volumes that have been QC'd >>>>>>>>>>>>>>> and "selected" as the best of their type -- used to display only the best >>>>>>>>>>>>>>> quality T1 image instead of all T1s acquired in a session, e.g. >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> re QC Comments -- >>>>>>>>>>>>>>> Once you have successfully loaded scans (matched to the >>>>>>>>>>>>>>> mri_protocol table), you'll be able to use the Imaging Browser's View >>>>>>>>>>>>>>> Session subpage to enter/view QC comments on each volume, or for each >>>>>>>>>>>>>>> visit. >>>>>>>>>>>>>>> These are stored directly in the database, and linked to >>>>>>>>>>>>>>> each scan. (Table name: feedback_mri_comments) >>>>>>>>>>>>>>> (Visit-level QC comments are linked to the session.) >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> For a walkthrough of the Imaging setup - please see the Imaging >>>>>>>>>>>>>>> Setup guide >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> - >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> An old LORIS walkthrough video >>>>>>>>>>>>>>> can also walk >>>>>>>>>>>>>>> you through some of the Imaging front-end features, starting at 8:00 >>>>>>>>>>>>>>> LORIS' imaging modules have been updated many times since >>>>>>>>>>>>>>> this video, but the functionality and workflow is similar. >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> Let us know how it goes once you have entries in your >>>>>>>>>>>>>>> mri_protocol table - >>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>> Christine >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> On Fri, Aug 2, 2019 at 7:58 AM Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Hi Christine, >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> In the candidate_list page i can see this patient >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> If i press the link under PSCID i get to see >>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> and if i press the link under Scan Done it redirects me to >>>>>>>>>>>>>>>> imaging_browser >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> At the mri_violations page i also see No results ( neither >>>>>>>>>>>>>>>> on resolved / not resolved ). >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> At the imaging_uploader i can see the record that failed. >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> If i click on the tarchive info i get to see the Protocol >>>>>>>>>>>>>>>> Name which i think is the acquisition we wanted? >>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Also my mri_protocol table is empty. >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Furthermore i would like to ask about the defaced, native, >>>>>>>>>>>>>>>> selected. What exactly is native and selected? And where are the qc >>>>>>>>>>>>>>>> comments stored? >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Finally a walkthrough would be helpful. >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Thanks, >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> ???? ???, 30 ???? 2019 ???? 8:29 ?.?., ?/? Christine >>>>>>>>>>>>>>>> Rogers, Ms. ??????: >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>> Glad to hear you're making progress with the visit >>>>>>>>>>>>>>>>> labels. To follow up on your last few emails: >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> a- The Wiki's Setup Guide contains Sample insert >>>>>>>>>>>>>>>>> statements for the Visit Windows table >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> . >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> As Cecile mentioned, the consistency of visit label format >>>>>>>>>>>>>>>>> is important: V01, v01, V1, 01 -- whichever you select to use is fine; we >>>>>>>>>>>>>>>>> use V01 by default across all documentation. >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> b- For Password reset, there is a script in the tools/ >>>>>>>>>>>>>>>>> directory so that a back-end administrator can reset any front-end user >>>>>>>>>>>>>>>>> password, including Admin. (See info on setting up / resetting User >>>>>>>>>>>>>>>>> passwords in the Wiki's Setup Guide >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> ) >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> c- The minc file not being registered -- due to >>>>>>>>>>>>>>>>> AcquisitionProtocol unknown. >>>>>>>>>>>>>>>>> This means the SeriesDescription (Acquisition Protocol) in >>>>>>>>>>>>>>>>> you Dicom header was not matched to any scan listed in the mri_protocol >>>>>>>>>>>>>>>>> database table. >>>>>>>>>>>>>>>>> (In the online Loris-MRI Troubleshooting Guide, >>>>>>>>>>>>>>>>> this >>>>>>>>>>>>>>>>> is Table 3, 2nd-last item "no MINCs inserted"). >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> The MRI Violations module (Readme here) >>>>>>>>>>>>>>>>> will show >>>>>>>>>>>>>>>>> you the details of this mismatch -- >>>>>>>>>>>>>>>>> Go to the module (under the Imaging menu), find your scan >>>>>>>>>>>>>>>>> and click the link "Could not identify scan type" -- in the next subpage >>>>>>>>>>>>>>>>> you can compare the scan's actual parameters against the mri_protocol >>>>>>>>>>>>>>>>> table. >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> To resolve this, adjust your mri_protocol table values or >>>>>>>>>>>>>>>>> perhaps ensure your DICOMs are labelled consistently. >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Let us know if this works for you -- we can also walk you >>>>>>>>>>>>>>>>> through an example of non-identified scans on >>>>>>>>>>>>>>>>> Demo.loris.ca (MRI Violations module). >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>> Christine >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> The LORIS team >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> On Tue, Jul 30, 2019 at 10:47 AM Sotirios Nikoloutsopoulos >>>>>>>>>>>>>>>>> wrote: >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> I hope this is sufficient as the error for the visit >>>>>>>>>>>>>>>>>> label disappeared. >>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Please see the attached file. Also something i found. >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> lorisadmin at hbp:/data/loris/bin/mri$ cat >>>>>>>>>>>>>>>>>> /data/loris/data//logs/TarLoad-17-39-xubBdv.log >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> ==> Loading file from disk >>>>>>>>>>>>>>>>>> /tmp/TarLoad-17-39-UyQcG2/dcc0000_258024_v1_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> --> mapping DICOM parameter for >>>>>>>>>>>>>>>>>> /tmp/TarLoad-17-39-UyQcG2/dcc0000_258024_v1_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> ==> computing md5 hash for MINC body. >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> --> md5: 6b1202fd63e29de4c9be1cd9925888a5 >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> ==> verifying acquisition protocol >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Acquisition protocol is unknown >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> --> The minc file cannot be registered since the >>>>>>>>>>>>>>>>>> AcquisitionProtocol is unknown >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> ???? ???, 30 ???? 2019 ???? 4:58 ?.?., ?/? Sotirios >>>>>>>>>>>>>>>>>> Nikoloutsopoulos ??????: >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Ok I fixed the login problem by using a known hash and >>>>>>>>>>>>>>>>>>> by deleting the rows from the login_history i was able to login. >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> ???? ???, 30 ???? 2019 ???? 4:50 ?.?., ?/? Sotirios >>>>>>>>>>>>>>>>>>> Nikoloutsopoulos ??????: >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> there was no visit label 01 in the Visit_Windows table >>>>>>>>>>>>>>>>>>>> and i don't know how to insert it because the record requires lots of >>>>>>>>>>>>>>>>>>>> attributes. Also the system for a reason asked me to update my password and >>>>>>>>>>>>>>>>>>>> now i don't remember it and my account got suspended. Is there a way to >>>>>>>>>>>>>>>>>>>> reset it or set a simple password? I updated the password hash in the >>>>>>>>>>>>>>>>>>>> users table by using the hash from another LORIS setup we had and i still >>>>>>>>>>>>>>>>>>>> couldn't login ( also the attribute password is always NULL and the >>>>>>>>>>>>>>>>>>>> expiration date is 1999-01-01 for some reason ). >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Thanks >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> ???? ???, 29 ???? 2019 ???? 5:21 ?.?., ?/? Cecile >>>>>>>>>>>>>>>>>>>> Madjar ??????: >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> Can you try adding the visit label v01 to the >>>>>>>>>>>>>>>>>>>>> Visit_Windows table? >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> However, I noticed that in a previous dataset, the >>>>>>>>>>>>>>>>>>>>> label was V1. Does that refer to the same visit? If so, you might want to >>>>>>>>>>>>>>>>>>>>> harmonize the visit labels so they are all the same across datasets for a >>>>>>>>>>>>>>>>>>>>> given timepoint, meaning you will need to relabel scans when the visit >>>>>>>>>>>>>>>>>>>>> label is different but referring to the same visit label (v01 = V1 etc...). >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> Hope this helps, >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> On Mon, Jul 29, 2019 at 10:15 AM Sotirios >>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos wrote: >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> Could you help me with the "Visit label does not >>>>>>>>>>>>>>>>>>>>>> exist"? I had changed $subjectID{'createVisitLabel'} to 1 as you had >>>>>>>>>>>>>>>>>>>>>> suggested but it appears that this problem hasn't been resolved yet. >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> lorisadmin at hbp:/data/loris/bin/mri$ cat >>>>>>>>>>>>>>>>>>>>>> /data/loris/data//logs/TarLoad-14-58-9Xog7H.log >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> ==> Loading file from disk >>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> --> mapping DICOM parameter for >>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> --> using user-defined filterParameters for >>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> Candidate Mismatch Error is Visit label does not exist >>>>>>>>>>>>>>>>>>>>>> -> WARNING: This candidate was invalid. Logging to >>>>>>>>>>>>>>>>>>>>>> MRICandidateErrors table with reason >>>>>>>>>>>>>>>>>>>>>> Visit label does not exist >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> ???? ???, 26 ???? 2019 ???? 3:02 ?.?., ?/? Sotirios >>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos ??????: >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> Hi Cecile, >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> The Center error was fixed. Still the insertion of >>>>>>>>>>>>>>>>>>>>>>> mincs fails. Please see the output.txt file i attached. Also is there >>>>>>>>>>>>>>>>>>>>>>> something else i need to change at the paths configuration? >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> ???? ???, 25 ???? 2019 ???? 6:55 ?.?., ?/? Cecile >>>>>>>>>>>>>>>>>>>>>>> Madjar ??????: >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> We are making progress! >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> I have a feeling this error comes from the fact >>>>>>>>>>>>>>>>>>>>>>>> that your psc table does not have the MRI_alias populated for the DCC site. >>>>>>>>>>>>>>>>>>>>>>>> Running the following query in the mysql database should fix this: >>>>>>>>>>>>>>>>>>>>>>>> UPDATE psc SET MRI_alias="DCC", Alias="DCC" WHERE >>>>>>>>>>>>>>>>>>>>>>>> Name="Data Coordinating Center"; >>>>>>>>>>>>>>>>>>>>>>>> Repeat the same with all your sites (make sure to >>>>>>>>>>>>>>>>>>>>>>>> change the Aliases between sites, they should all be unique). >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> Let me know how it goes! >>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> On Thu, Jul 25, 2019 at 11:43 AM Sotirios >>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos wrote: >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> Dear Cecile, >>>>>>>>>>>>>>>>>>>>>>>>> You were right about your guesses. I did the >>>>>>>>>>>>>>>>>>>>>>>>> modifications you suggested, i still get the "no mincs inserted" error, now >>>>>>>>>>>>>>>>>>>>>>>>> i am getting the "No center found this candidate" error ( how do i fix >>>>>>>>>>>>>>>>>>>>>>>>> that? from what i see the .dcm files contains a 'Institution Name', is that >>>>>>>>>>>>>>>>>>>>>>>>> the center? ), so i guess that's why the validation fails, but i changed >>>>>>>>>>>>>>>>>>>>>>>>> the force variable of tarchiveLoader to 1, shouldn't it have inserted the >>>>>>>>>>>>>>>>>>>>>>>>> mincs then? Also it is optional to have a mail server, right? ( from what i >>>>>>>>>>>>>>>>>>>>>>>>> see the mail error does not affect the $valid_study, so i assume we are >>>>>>>>>>>>>>>>>>>>>>>>> okay with that ) >>>>>>>>>>>>>>>>>>>>>>>>> Thank you a lot, >>>>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 25 ???? 2019 ???? 5:48 ?.?., ?/? Cecile >>>>>>>>>>>>>>>>>>>>>>>>> Madjar ??????: >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> From what I understand, I believe you just need >>>>>>>>>>>>>>>>>>>>>>>>>> to update a few config settings from the frontend in the Config module >>>>>>>>>>>>>>>>>>>>>>>>>> (under the Admin menu). >>>>>>>>>>>>>>>>>>>>>>>>>> [image: Screen Shot 2019-07-25 at 10.31.35 AM.png] >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> Then go to the Paths section of the config module >>>>>>>>>>>>>>>>>>>>>>>>>> and update the "LORIS-MRI code" config setting to /data/loris/bin/mri (my >>>>>>>>>>>>>>>>>>>>>>>>>> guess is that currently, it is set to /data/LORIS/data) and click on the >>>>>>>>>>>>>>>>>>>>>>>>>> submit button. >>>>>>>>>>>>>>>>>>>>>>>>>> [image: Screen Shot 2019-07-25 at 10.32.50 AM.png] >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> Then, go to Imaging Pipeline section of the >>>>>>>>>>>>>>>>>>>>>>>>>> Configuration module and update the "Loris-MRI Data Directory" to >>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/ (my guess is that it is empty at the moment in your >>>>>>>>>>>>>>>>>>>>>>>>>> database which is why $data_dir is not defined when you run the >>>>>>>>>>>>>>>>>>>>>>>>>> tarchiveLoader step of the insertion pipeline). >>>>>>>>>>>>>>>>>>>>>>>>>> [image: Screen Shot 2019-07-25 at 10.40.52 AM.png] >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> Finally, I took a look at your environment file >>>>>>>>>>>>>>>>>>>>>>>>>> and it might be a good idea to update your PERL5LIB variable to the >>>>>>>>>>>>>>>>>>>>>>>>>> following (it has been added to the code a few releases ago as we realized >>>>>>>>>>>>>>>>>>>>>>>>>> this was needed for the libraries. Not sure which version of LORIS-MRI you >>>>>>>>>>>>>>>>>>>>>>>>>> are using but it does not hurt to update this variable to what I suggest >>>>>>>>>>>>>>>>>>>>>>>>>> below): >>>>>>>>>>>>>>>>>>>>>>>>>> export >>>>>>>>>>>>>>>>>>>>>>>>>> PERL5LIB=/data/loris/bin/mri/uploadNeuroDB:/data/loris/bin/mri/dicom-archive:$PERL5LIB >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helps. Sorry you are experiencing so >>>>>>>>>>>>>>>>>>>>>>>>>> much trouble setting things up. We probably need to update our WIKI. >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> On Thu, Jul 25, 2019 at 9:48 AM Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos wrote: >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> The "Loris-MRI Data Directory" should be in the >>>>>>>>>>>>>>>>>>>>>>>>>>> environment file? >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 25 ???? 2019 ???? 12:59 ?.?., ?/? >>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos >>>>>>>>>>>>>>>>>>>>>>>>>>> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> The scripts are located in >>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/. Somewhere I might have messed something up but i >>>>>>>>>>>>>>>>>>>>>>>>>>>> remember following the instructions in the wiki.For example when i tried to >>>>>>>>>>>>>>>>>>>>>>>>>>>> execute the batch_uploads_imageuploader perl script the line >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> my $command = "$bin_dir/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl " >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> was pointing to an invalid path, for example: >>>>>>>>>>>>>>>>>>>>>>>>>>>> it was repeating a pattern and had LORIS instead of loris ( i think the >>>>>>>>>>>>>>>>>>>>>>>>>>>> mistake was that in the wiki it suggested to use $PROJECT for the name of >>>>>>>>>>>>>>>>>>>>>>>>>>>> the folder and i choosed 'loris' >>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris/wiki/Imaging-Database >>>>>>>>>>>>>>>>>>>>>>>>>>>> ). See also the in image for the modification i did. Also i didn't find the >>>>>>>>>>>>>>>>>>>>>>>>>>>> section to config the $data_dir variable. >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 24 ???? 2019 ???? 6:05 ?.?., ?/? >>>>>>>>>>>>>>>>>>>>>>>>>>>> Cecile Madjar ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> It looks like you have one Config setting not >>>>>>>>>>>>>>>>>>>>>>>>>>>>> set (based on the first error message you got when running it the first >>>>>>>>>>>>>>>>>>>>>>>>>>>>> time). You need to set a value for "Loris-MRI Data Directory" in the Config >>>>>>>>>>>>>>>>>>>>>>>>>>>>> module under the Imaging pipeline section (from what I can see, it would be >>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/ for your setup). >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> The reason you got that error message the >>>>>>>>>>>>>>>>>>>>>>>>>>>>> second time is that the pipeline checks if the DICOM study was already >>>>>>>>>>>>>>>>>>>>>>>>>>>>> inserted in the tarchive table. Since you ran the study once already, the >>>>>>>>>>>>>>>>>>>>>>>>>>>>> study is inserted into the tarchive, hence the message. However, the >>>>>>>>>>>>>>>>>>>>>>>>>>>>> pipeline did not complete as the MINC files were not created and inserted >>>>>>>>>>>>>>>>>>>>>>>>>>>>> into the files/parameter_file table. In order to continue the insertion, >>>>>>>>>>>>>>>>>>>>>>>>>>>>> you will then need to run the tarchiveLoader command suggested in the >>>>>>>>>>>>>>>>>>>>>>>>>>>>> terminal during the second run: >>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader >>>>>>>>>>>>>>>>>>>>>>>>>>>>> -globLocation -profile prod >>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive//2012/DCM_2012-12-05_ImagingUpload-17-43-ZUEFjb.tar >>>>>>>>>>>>>>>>>>>>>>>>>>>>> -verbose >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Finally, I am a bit confused by your setup. >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Where are the scripts located? In /data/loris/bin/mri or /data/loris/data? >>>>>>>>>>>>>>>>>>>>>>>>>>>>> It feels like the Config setting "LORIS-MRI code" in the Paths section was >>>>>>>>>>>>>>>>>>>>>>>>>>>>> set to "/data/LORIS/data" but it should have been set to the directory >>>>>>>>>>>>>>>>>>>>>>>>>>>>> where the scripts are located (most probably /data/loris/bin/mri). >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helps, >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> On Wed, Jul 24, 2019 at 10:55 AM Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos wrote: >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Ok first i execute this command: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> "lorisadmin at hbp:/data/loris/bin/mri$ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ./batch_uploads_imageuploader -profile prod < ~/Desktop/input.txt > log.txt >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at ./batch_uploads_imageuploader line 143. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at ./batch_uploads_imageuploader line 143. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $_ in pattern >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> match (m//) at ./batch_uploads_imageuploader line 147. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> base is DCC0000_258024_V01 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> path is /data/incoming/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> type is .tar.gz >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> fullpath is >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/incoming/DCC0000_258024_V01.tar.gz >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> source /tmp/ImagingUpload-17-43-ZUEFjb >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> targetlocation /data/loris/data/tarchive >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 256. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 284. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at /data/loris/bin/mri/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> tarchive_validation.pl line 219. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at /data/loris/bin/mri/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl line 270. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 711. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Can't exec "mail": No such file or directory >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 721. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 722. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 723. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 724. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 724. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 725. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 735. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> No Mincs inserted >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The tarchiveLoader insertion script has >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> failed. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Running now the following command: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl -profile prod >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -upload_id 3 /data/incoming/DCC0000_258024_V01.tar.gz -verbose" >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I inserted the VisitLabel, but still the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Mincs are not inserted and i am getting this error >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> "lorisadmin at hbp:/data/loris/bin/mri$ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl -profile prod >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -upload_id 3 /data/incoming/DCC0000_258024_V01.tar.gz -verbose >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> find -path >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> \/tmp\/ImagingUpload\-17\-45\-5MsWEd -name '__MACOSX' -delete >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Spool message is: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The Scan for the uploadID 3 has already been >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> run with tarchiveID: 7. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> To continue with the rest of the insertion >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> pipeline, please run tarchiveLoader from a terminal as follows: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader -globLocation -profile prod >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive//2012/DCM_2012-12-05_ImagingUpload-17-43-ZUEFjb.tar >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -verbose" >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Which files should i delete? I thought that >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> deleting the files from the tarchive was enough. And i executed the last >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> proposed command to continue to rest of the insertion pipeline ( check the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> image ). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 24 ???? 2019 ???? 5:05 ?.?., ?/? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Cecile Madjar ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sorry I was not clear before. Every visits >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> of candidates are created in the session table with one entry per >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID/VisitLabel. So if the imaging pipeline created visits in the session >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> table (that are not attached to instruments) and you want to clean your >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> database completely, you can delete entries in that table as well. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Regarding your point 2, the imaging pipeline >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> can create the visit in the session table as long as the visit label is >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> present in the Visit_Windows table (which means the visit label stored in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the PatientName is a valid visit label). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> However, in your prod file, if the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> variable $subjectID{'createVisitLabel'} is set to 1 for candidates, the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit label should be created in the Visit_Windows table I believe. Here >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> is the line of the prod file you would need to change >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> . >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> In general, we prefer populating the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Visit_Windows table and set the $subjectID{'createVisitLabel'} to 0 for >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> candidate data to avoid insertion of badly labelled MRI data that are >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> complex to relabel. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Finally, regarding the candidate creation, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> if you execute the following steps, the pipeline should be able to create >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> candidates: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - set in the Imaging Pipeline section of the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> config module the config setting "Upload creation of candidates" to Yes >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - manually transfer the scans to the LORIS >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> server instead of uploading it via the imaging browser >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - run batch_imaging_upload.pl as you did >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> until now. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helps! >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> On Wed, Jul 24, 2019 at 8:47 AM Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> wrote: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> About my second question i replaced the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> name of the patient in the .dcm files and now i am getting an error that >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the visit label does not exist. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I thought it was supposed to be >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> automatically created. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> "Done adding archive info into database >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -globLocation -profile prod >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive//DCM_2012-12-05_ImagingUpload-15-42-yUwQQV.tar >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -verbose >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> md5sum >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive/DCM_2012-12-05_ImagingUpload-15-42-yUwQQV.tar >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> candidate id 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> => No Visit labelVisit label does not exist >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Set centerID = 1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Number of MINC files that will be >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> considered for inserting into the database: 1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> log dir is /logs and log file is >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /logs/TarLoad-15-42-L6pocU.log >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> candidate id 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> => No Visit label >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Cleaning up temp files: rm -rf >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-15-42-J2rQms/ImagingUpload-15-42-yUwQQV*" >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 24 ???? 2019 ???? 3:38 ?.?., ?/? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 1) What are the records in the session >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> table? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 2) I tried to upload a non-phantom file >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> like this >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> input_file.txt: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/incoming/DCC0000_258024_V1.tar.gz N >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DCC0000_258024_V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Terminal: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ./batch_uploads_imageuploader -profile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> prod < ~/Desktop/input.txt > log.txt >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and i get the following error in the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> log.txt file >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> "Running now the following command: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl -profile prod >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -upload_id 7 /data/incoming/DCC0000_258024_V1.tar.gz -verbose >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> find -path >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> \/tmp\/ImagingUpload\-14\-56\-FeLCB4 -name '__MACOSX' -delete >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Spool message is: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The PatientName read from the DICOM header >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> does not start with DCC0000_258024_V1 from the mri_upload table >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> " >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and the spool message is repeated for each >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> .dcm file. Should i preprocess every .dcm file and change the PatientName >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> to "DCC0000_258024_V1"? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 3) As far as it concerns the candidate >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> profile i have to create a new one each time before i try to upload a file? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Is there already a way to create a candidate profile and get the DCCID and >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID without the user interface? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 18 ???? 2019 ???? 5:00 ?.?., ?/? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Cecile Madjar >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> See answers to your questions below. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> About the 1st case we had a dicom with a >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> blank studyUID, maybe someone accidentally removed it. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> That is strange. Something must have been >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> done to the DICOM files. I have never seen a study with no StudyUID out of >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the scanner. Usually, you need to manually erase it with some tool. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> However, DICOMs never cease to surprise me... >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Some other questions: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 1) What are the steps to remove all of >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> my patients and uploads?: because i want to try to reupload all the testing >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> dicoms we had with a clean database. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Release 21.0 of LORIS-MRI will offer a >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> script to remove all the entries and files specific to an upload. However, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> this release is not yet out. Hopefully in the next few weeks. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> In the meantime, since your case is >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> particular and that you just want to start with a clean database, the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> following deletes should work (hopefully I won't forget any tables): >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from mri_violations_log; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from mri_protocol_violated_scans; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from MRICandidateErrors; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from parameter_file; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from files_qcstatus; # (if you >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> played with the QC part of the imaging browser for testing) >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from feedback_mri_comments; # (if >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> you played with the QC part of the imaging browser for testing) >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from tarchive_series; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from tarchive_files; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from mri_upload; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from tarchive; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from mri_scanner; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from candidate where >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID="scanner"; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I don't know if you want to also delete >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> entries in the session and candidate table too? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 2) We do not need to create the profile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> of a patient ( are the patients stored in the candidate table? because i >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> can't see the ghosts ), because will it automatically be created when >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> importing a dicom? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I am not sure I understand fully this >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> question. All candidates are stored in the candidate table. The phantom >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> scans however are attached to a scanner candidate depending on where the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> scan happened. It is a bit of a weird concept that we have to redesign >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> eventually but never got a chance to get to it. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hopefully this answered your question, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> otherwise, don't hesitate to let me know. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 3) What is the difference between >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> uploading a dicom as phantom instead of importing as >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCCID_DCCID_VisitLabel? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> When you upload the scan as >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID_DCCID_VisitLabel, there is a check that makes sure the candidate IDs >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and visit label are valid at the time of upload. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> When you upload a scan as phantom, it >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> expects that the DICOM field PatientName and uploaded filename contains the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> string "phantom". We enforced this behaviour on the imaging uploader side >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in recent releases but I can't remember which one. Probably the upcoming >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 21.0 release. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> All those verifications might seem >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> cumbersome but they are here to ensure that the files inserted are all >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> valid and labelled properly as it is a bit messy to have to delete files >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> that were wrongly labelled. At least, the delete script present in release >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 21.0 will make this process easier but it is still good practice to verify >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> those things. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> With pleasure. Hopefully the answers to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> your questions will be helpful. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PS: loris-dev mailing list: you will find >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the initial answer I gave Sotirios below. I forgot to cc the loris-dev in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> my earlier reply... >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 16 ???? 2019 ???? 12:02 ?.?., >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ?/? Cecile Madjar >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Dear Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you for reaching out. Since your >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> email was already organized in points, I will reply directly below your >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> questions below. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 1) What do we do when the StudyUID is >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> blank on the header? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/minor/docs/AppendixA-Troubleshooting_guideline.md >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> There solution provided at the table 3 does not guide us how to find the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> information ( is possible ). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The StudyUID is the field used in our >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> pipeline at the moment to check whether a DICOM study was already inserted >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> into LORIS with that same StudyUID since it is supposed to be unique for >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> every single study. Currently, we do not support insertion of DICOM studies >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> if they do not have a StudyUID associated with them. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Is there a specific reason why the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> StudyUID is blank in the DICOM headers in your DICOM files? Did they go >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> through some processes before upload to LORIS? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 2) When i am about to upload a >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> non-phanton case i need a 'Visit Label'. Is there already a script that can >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> create a new visit label for a specific Candidate, so i can provide it as >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> input afterwards to the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> batch_uploads_imageuploader ( See option 5.1.3 https://github.com/aces/Loris-MRI/blob/minor/docs/05-PipelineLaunchOptions.md ) >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I am not sure if the front-end allows >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> for it but if you use batch_uploads_imageuploader, the insertion scripts >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> could create the visit label for you. However, it does need to be included >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in the patient name in order for the script to know which label it should >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> use. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> For example: you upload V02 for MTL0123 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> (DCCID: 456789) but V02 was not yet created for MTL0123; the insertion >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> scripts will create a V02 visit for MTL0123 if the PatientName field for >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the dataset is MTL0123_456789_V02 with Stage marked as "Not Started". >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> However, *note that for the script to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> create the visit for the candidate, you have to make sure that all the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit label of your projects were inserted in the Visit_Windows table* >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> (otherwise, the visit will never be created as they were not specified as >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> being part of the list of visit label to expect). So in the example above, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> you should have one row in Visit_Windows with Visit_label="V02" set. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 3) Section 4.3 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/minor/docs/04-Scripts.md >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> What do we do when the folder contains multiple mnc files? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> This is a case by case. Most of the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> time, the MINC files that failed insertion into the imaging browser end up >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in the MRI violation module where you can see what went wrong with the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> acquisitions not inserted. If you notice that the MINC file should be >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> inserted as a specific protocol, you can force the insertion as explained >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in section 4.3. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> In your case, I have a feeling that you >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> want to be able to insert MINC files that did not go through the whole >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> pipeline insertion (DICOM archival, then dcm2mnc, then protocol >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> identification, then insertion...). In theory, you could call >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl on any MINC file, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> provided you have at least the following information: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - path to the MINC file >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - uploadID associated with the MINC >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> files or DICOM archive path from which those MINC files were created from >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Then the minc_insertion.pl script will >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> do the subject information and protocol validation etc... >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> If all the MINC files come from the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> same uploadID or TarchiveID, then you could run a loop in bash calling the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl script like this for >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> files deriving from uploadID=1: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ls /path/to/mnc/folder/* | while read >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> f; do minc_insertion.pl -profile prod >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -uploadID 1 -mincPath $f; done >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helped! >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>>>>>> >>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> -- >>>>>>>>>>>> >>>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>>> >>>>>>>>>>> _______________________________________________ >>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> -- >>>>>>>>>> >>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>> Montreal Neurological Institute >>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>> _______________________________________________ >>>>>>>>>> Loris-dev mailing list >>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> -- >>>>>>>>> >>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>> Montreal Neurological Institute >>>>>>>>> McGill University | Montreal | Canada >>>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> Loris-dev mailing list >>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>> >>>>>>> >>>>>>> >>>>>>> -- >>>>>>> Shen Wang >>>>>>> Loris Developer >>>>>>> Montreal Neurological Institute >>>>>>> McGill University >>>>>>> >>>>>>> >>>>>> >>>>>> -- >>>>>> Shen Wang >>>>>> Loris Developer >>>>>> Montreal Neurological Institute >>>>>> McGill University >>>>>> >>>>>> _______________________________________________ >>> Loris-dev mailing list >>> Loris-dev at bic.mni.mcgill.ca >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>> >> >> >> -- >> >> christine.rogers at mcgill.ca >> McGill Centre for Integrative Neuroscience | MCIN.ca >> Montreal Neurological Institute >> McGill University | Montreal | Canada >> > -- Shen Wang Loris Developer Montreal Neurological Institute McGill University -------------- next part -------------- An HTML attachment was scrubbed... URL: From christine.rogers at mcgill.ca Fri Aug 30 11:17:20 2019 From: christine.rogers at mcgill.ca (Christine Rogers, Ms.) Date: Fri, 30 Aug 2019 15:17:20 +0000 Subject: [Loris-dev] Error "not a unique file" inserting segmentation files in LORIS In-Reply-To: References: Message-ID: Hi Alfredo, Could you please help me inserting those files which are different in size and md5 from previous uploaded files? The only similarity between the previous uploaded files and the ones that could not be uploaded is the filename. To provide a quick answer (since most of our imaging team is on vacation this week) : Yes the MD5hash seems to require a unique filename (* below). Can you use distinct filenames ? i.e. Are you are trying to load additional data for a participant session (i.e. same IDs and visit label) ? Or, are you trying to load more than one participant/session at a time? (*) This line in the actual MRIProcessingUtility library: (around Line 617) $md5hash = &NeuroDB::MRI::compute_hash(\$file); and my $unique = &NeuroDB::MRI::is_unique_hash(\$file); I'll check with other imaging devs to see if we have a workaround while our senior devs are away -- I think there must be some solution... Meanwhile, the MD5hash for imaging files is documented here (per this script documentation) : computeMd5Hash($file, $upload_id) Computes the MD5 hash of a file and makes sure it is unique. INPUTS: * $file : file to use to compute the MD5 hash * $upload_id: upload ID of the study RETURNS: 1 if the file is unique, 0 otherwise Best, Christine On Thu, Aug 29, 2019 at 9:46 PM Morales Pinzon, Alfredo > wrote: Dear DevLoris Team, I started the uploading process of processed files, segmentations and transformations, using the file "register_processed_data.pl" but some files are not being uploaded. The error reported in "data/logs/registerProcessed" show the following log for one of the files that could not be inserted: ------------------------------------------------------------------------------- ==> Successfully connected to database Log file, 2019-08-29_19:08:17 ==>Mapped DICOM parameters -> using user-defined filterParameters for /xxx/w024/gvf_ISPC-stx152lsq6.mnc.gz ==> Verifying acquisition center - Center Name : UNKN - CenterID : 0 -> Set ScannerID to 0. ==> Data found for candidate : 123456 - Visit: w024 -> Set SessionID to 28269. -> Set SourceFileID to 49598. -> Set AcquisitionProtocolID to 1013. -> Set CoordinateSpace to stx152lsq6. -> Set SourcePipeline to ConsensusGd. -> Set PipelineDate to 2019-08-29. -> Set OutputType to gvf. -> Set md5hash to b877648ed0ef9a7458ad4931f4dbfd11. ==> NeuroDB::File=HASH(0x136baa8) is not a unique file and will not be added to database. ------------------------------------------------------------------------------- I checked the md5hash for a previous uploaded file, which is different from the previous, but the same "md5hash" was calculated. See the following log: ------------------------------------------------------------------------------- ==> Successfully connected to database Log file, 2019-08-19_10:11:53 ==>Mapped DICOM parameters -> using user-defined filterParameters for ==> Verifying acquisition center - Center Name : UNKN - CenterID : 0 -> Set ScannerID to 0. ==> Data found for candidate : 123456 - Visit: baseline -> Set SessionID to 28268. -> Set SourceFileID to 49593. -> Set AcquisitionProtocolID to 1013. -> Set CoordinateSpace to stx152lsq6. -> Set SourcePipeline to T2Vol. -> Set PipelineDate to 2019-08-19. -> Set OutputType to gvf. -> Set md5hash to b877648ed0ef9a7458ad4931f4dbfd11. File /xxx/baseline/gvf_ISPC-stx152lsq6.mnc.gz moved to: /yyy/data/assembly/123456/baseline/mri/processed/T2Vol/IPMSA_123456_baseline_t1c_001_gvf_001.mnc.gz ==> FAILED TO INSERT INTERMEDIARY FILES FOR 112945! Making JIV ==> Registered /data_/ipmsa/loris_data/IPMSA/data/assembly/307024/baseline/mri/processed/T2Vol/IPMSA_307024_baseline_t1c_001_gvf_001.mnc.gz in database, given FileID: 112945 ------------------------------------------------------------------------------- Here are the corresponding md5 for each file calculated using the command md5sum: /xxx/w024/gvf_ISPC-stx152lsq6.mnc.gz 7306010346c4614d8e338595b386ca5c /xxx/baseline/gvf_ISPC-stx152lsq6.mnc.gz 22107253f8b87c9918ac7f82fdc22c36 Could you please help me inserting those files which are different in size and md5 from previous uploaded files? The only similarity between the previous uploaded files and the ones that could not be uploaded is the filename. Let me know if you need more information. Regards, Alfredo. The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. _______________________________________________ Loris-dev mailing list Loris-dev at bic.mni.mcgill.ca https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev -- christine.rogers at mcgill.ca McGill Centre for Integrative Neuroscience | MCIN.ca Montreal Neurological Institute McGill University | Montreal | Canada -------------- next part -------------- An HTML attachment was scrubbed... URL: From istvan.morocz at mcgill.ca Fri Aug 30 11:29:19 2019 From: istvan.morocz at mcgill.ca (Istvan Akos Imre Morocz, Dr) Date: Fri, 30 Aug 2019 15:29:19 +0000 Subject: [Loris-dev] Error "not a unique file" inserting segmentation files in LORIS In-Reply-To: References: Message-ID: in this particular case and clinical trial (ORATORIO) the filenames can be identical but their paths are not and are obvisouly unique. is this a problem for LORIS ? thanks for helping, bye, pisti On Fri, 30 Aug 2019, Christine Rogers, Ms. wrote: > Hi Alfredo,? > Could you please help me inserting those files which are different in size and md5 from previous uploaded files? > > ? > The only similarity between the previous uploaded files and the ones that could not be uploaded is the filename. > > > To provide a quick answer (since most of our imaging team is on vacation this week) :? > > Yes the MD5hash seems to require a unique filename (* below). > Can you use distinct filenames ?? i.e. Are you are trying to load additional data for a participant session (i.e. same IDs and visit label) ??? > Or, are you trying to load more than one participant/session at a time?? > > (*) This line in the actual MRIProcessingUtility library:? (around Line 617) > $md5hash = &NeuroDB::MRI::compute_hash(\$file); > > and > my $unique = &NeuroDB::MRI::is_unique_hash(\$file); > > > > I'll check with other imaging devs to see if we have a workaround while our senior devs are away -- I think there must be some solution...?? > Meanwhile, the MD5hash for imaging files is documented here (per this script documentation)? :? > > computeMd5Hash($file, $upload_id) > Computes the MD5 hash of a file and makes sure it is unique. > INPUTS: > o $file : file to use to compute the MD5 hash > o $upload_id: upload ID of the study > RETURNS: 1 if the file is unique, 0 otherwise > > > > Best,? > Christine? > > > > On Thu, Aug 29, 2019 at 9:46 PM Morales Pinzon, Alfredo wrote: > Dear DevLoris Team, > > I started the uploading process of processed files, segmentations and transformations, using the file "register_processed_data.pl" but some files are not being > uploaded. The error reported in "data/logs/registerProcessed" show the following log for one of the files that could not be inserted: > > ------------------------------------------------------------------------------- > ==> Successfully connected to database > Log file, 2019-08-29_19:08:17 > > > ==>Mapped DICOM parameters > ?-> using user-defined filterParameters for /xxx/w024/gvf_ISPC-stx152lsq6.mnc.gz > > ==> Verifying acquisition center > ?- Center Name ?: UNKN > ?- CenterID ? ? : 0 > ?-> Set ScannerID to 0. > > ==> Data found for candidate ? : 123456 - Visit: w024 > ?-> Set SessionID to 28269. > ?-> Set SourceFileID to 49598. > ?-> Set AcquisitionProtocolID to 1013. > ?-> Set CoordinateSpace to stx152lsq6. > ?-> Set SourcePipeline to ConsensusGd. > ?-> Set PipelineDate to 2019-08-29. > ?-> Set OutputType to gvf. > ?-> Set md5hash to b877648ed0ef9a7458ad4931f4dbfd11. > > ==> NeuroDB::File=HASH(0x136baa8) is not a unique file and will not be added to database. > ------------------------------------------------------------------------------- > > I checked the md5hash for a previous uploaded file, which is different from the previous, but the same "md5hash" was calculated. See the following log: > > ------------------------------------------------------------------------------- > > ==> Successfully connected to database > Log file, 2019-08-19_10:11:53 > > > ==>Mapped DICOM parameters > ?-> using user-defined filterParameters for > > ==> Verifying acquisition center > ?- Center Name ?: UNKN > ?- CenterID ? ? : 0 > ?-> Set ScannerID to 0. > > ==> Data found for candidate ? : 123456 - Visit: baseline > ?-> Set SessionID to 28268. > ?-> Set SourceFileID to 49593. > ?-> Set AcquisitionProtocolID to 1013. > ?-> Set CoordinateSpace to stx152lsq6. > ?-> Set SourcePipeline to T2Vol. > ?-> Set PipelineDate to 2019-08-19. > ?-> Set OutputType to gvf. > ?-> Set md5hash to b877648ed0ef9a7458ad4931f4dbfd11. > File /xxx/baseline/gvf_ISPC-stx152lsq6.mnc.gz > ?moved to: > ?/yyy/data/assembly/123456/baseline/mri/processed/T2Vol/IPMSA_123456_baseline_t1c_001_gvf_001.mnc.gz > > ==> FAILED TO INSERT INTERMEDIARY FILES FOR 112945! > > Making JIV > > ?==> Registered /data_/ipmsa/loris_data/IPMSA/data/assembly/307024/baseline/mri/processed/T2Vol/IPMSA_307024_baseline_t1c_001_gvf_001.mnc.gz in database, given > FileID: 112945 > ------------------------------------------------------------------------------- > > Here are the corresponding md5 for each file calculated using the command md5sum: > /xxx/w024/gvf_ISPC-stx152lsq6.mnc.gz ? 7306010346c4614d8e338595b386ca5c > /xxx/baseline/gvf_ISPC-stx152lsq6.mnc.gz 22107253f8b87c9918ac7f82fdc22c36 > > Could you please help me inserting those files which are different in size and md5 from previous uploaded files? The only similarity between the previous uploaded > files and the ones that could not be uploaded is the filename. > > Let me know if you need more information. > > Regards, > Alfredo. > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in error > but does not contain patient information, please contact the sender and properly > dispose of the e-mail. > > _______________________________________________ > Loris-dev mailing list > Loris-dev at bic.mni.mcgill.ca > https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > > > > -- > > christine.rogers at mcgill.ca > McGill Centre for Integrative Neuroscience | MCIN.ca > Montreal Neurological Institute > McGill University | Montreal | Canada > > ,-*~'`^`'~*-,._.,-*~'`^`'~*-,._ ' : istvan.morocz at mcgill.ca ` https://www.pistikem.org : pistikem at gmail.com : +1-514-927-1169 , https://noisis.com : istvan.morocz at noisis.com . `~*-,._.,-*~'`^`'~*-,._.,-*~'`" From AMORALESPINZON at bwh.harvard.edu Fri Aug 30 12:53:21 2019 From: AMORALESPINZON at bwh.harvard.edu (Morales Pinzon, Alfredo) Date: Fri, 30 Aug 2019 16:53:21 +0000 Subject: [Loris-dev] Error "not a unique file" inserting segmentation files in LORIS In-Reply-To: References: , Message-ID: Hi Christine, Thank you for your answer. Here are the answers to your questions: Can you use distinct filenames ? We could but we already have all the images, thousands, with a pre-defined convention. One solution could be to make a copy with a different name before uploading. Are you are trying to load additional data for a participant session (i.e. same IDs and visit label) ? Yes, we are uploading the result of a couple of pipelines for each participant for each label. Let me know if you can find a workaround, in the mean time I will check with Pisti if we can make a copy of the files with a different name before uploading. Best, Alfredo. ________________________________ From: Christine Rogers, Ms. Sent: Friday, August 30, 2019 11:17 AM To: Morales Pinzon, Alfredo Cc: loris-dev at bic.mni.mcgill.ca ; Cecile Madjar ; Sridar Narayanan, Dr. ; Rozie Arnaoutelis, Ms. ; Douglas Arnold, Dr. ; Guttmann, Charles,M.D. Subject: Re: [Loris-dev] Error "not a unique file" inserting segmentation files in LORIS External Email - Use Caution Hi Alfredo, Could you please help me inserting those files which are different in size and md5 from previous uploaded files? The only similarity between the previous uploaded files and the ones that could not be uploaded is the filename. To provide a quick answer (since most of our imaging team is on vacation this week) : Yes the MD5hash seems to require a unique filename (* below). Can you use distinct filenames ? i.e. Are you are trying to load additional data for a participant session (i.e. same IDs and visit label) ? Or, are you trying to load more than one participant/session at a time? (*) This line in the actual MRIProcessingUtility library: (around Line 617) $md5hash = &NeuroDB::MRI::compute_hash(\$file); and my $unique = &NeuroDB::MRI::is_unique_hash(\$file); I'll check with other imaging devs to see if we have a workaround while our senior devs are away -- I think there must be some solution... Meanwhile, the MD5hash for imaging files is documented here (per this script documentation) : computeMd5Hash($file, $upload_id) Computes the MD5 hash of a file and makes sure it is unique. INPUTS: * $file : file to use to compute the MD5 hash * $upload_id: upload ID of the study RETURNS: 1 if the file is unique, 0 otherwise Best, Christine On Thu, Aug 29, 2019 at 9:46 PM Morales Pinzon, Alfredo > wrote: Dear DevLoris Team, I started the uploading process of processed files, segmentations and transformations, using the file "register_processed_data.pl" but some files are not being uploaded. The error reported in "data/logs/registerProcessed" show the following log for one of the files that could not be inserted: ------------------------------------------------------------------------------- ==> Successfully connected to database Log file, 2019-08-29_19:08:17 ==>Mapped DICOM parameters -> using user-defined filterParameters for /xxx/w024/gvf_ISPC-stx152lsq6.mnc.gz ==> Verifying acquisition center - Center Name : UNKN - CenterID : 0 -> Set ScannerID to 0. ==> Data found for candidate : 123456 - Visit: w024 -> Set SessionID to 28269. -> Set SourceFileID to 49598. -> Set AcquisitionProtocolID to 1013. -> Set CoordinateSpace to stx152lsq6. -> Set SourcePipeline to ConsensusGd. -> Set PipelineDate to 2019-08-29. -> Set OutputType to gvf. -> Set md5hash to b877648ed0ef9a7458ad4931f4dbfd11. ==> NeuroDB::File=HASH(0x136baa8) is not a unique file and will not be added to database. ------------------------------------------------------------------------------- I checked the md5hash for a previous uploaded file, which is different from the previous, but the same "md5hash" was calculated. See the following log: ------------------------------------------------------------------------------- ==> Successfully connected to database Log file, 2019-08-19_10:11:53 ==>Mapped DICOM parameters -> using user-defined filterParameters for ==> Verifying acquisition center - Center Name : UNKN - CenterID : 0 -> Set ScannerID to 0. ==> Data found for candidate : 123456 - Visit: baseline -> Set SessionID to 28268. -> Set SourceFileID to 49593. -> Set AcquisitionProtocolID to 1013. -> Set CoordinateSpace to stx152lsq6. -> Set SourcePipeline to T2Vol. -> Set PipelineDate to 2019-08-19. -> Set OutputType to gvf. -> Set md5hash to b877648ed0ef9a7458ad4931f4dbfd11. File /xxx/baseline/gvf_ISPC-stx152lsq6.mnc.gz moved to: /yyy/data/assembly/123456/baseline/mri/processed/T2Vol/IPMSA_123456_baseline_t1c_001_gvf_001.mnc.gz ==> FAILED TO INSERT INTERMEDIARY FILES FOR 112945! Making JIV ==> Registered /data_/ipmsa/loris_data/IPMSA/data/assembly/307024/baseline/mri/processed/T2Vol/IPMSA_307024_baseline_t1c_001_gvf_001.mnc.gz in database, given FileID: 112945 ------------------------------------------------------------------------------- Here are the corresponding md5 for each file calculated using the command md5sum: /xxx/w024/gvf_ISPC-stx152lsq6.mnc.gz 7306010346c4614d8e338595b386ca5c /xxx/baseline/gvf_ISPC-stx152lsq6.mnc.gz 22107253f8b87c9918ac7f82fdc22c36 Could you please help me inserting those files which are different in size and md5 from previous uploaded files? The only similarity between the previous uploaded files and the ones that could not be uploaded is the filename. Let me know if you need more information. Regards, Alfredo. The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. _______________________________________________ Loris-dev mailing list Loris-dev at bic.mni.mcgill.ca https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev -- christine.rogers at mcgill.ca McGill Centre for Integrative Neuroscience | MCIN.ca Montreal Neurological Institute McGill University | Montreal | Canada -------------- next part -------------- An HTML attachment was scrubbed... URL: From christine.rogers at mcgill.ca Fri Aug 30 15:34:55 2019 From: christine.rogers at mcgill.ca (Christine Rogers, Ms.) Date: Fri, 30 Aug 2019 19:34:55 +0000 Subject: [Loris-dev] Error "not a unique file" inserting segmentation files in LORIS In-Reply-To: References: Message-ID: Hi Alfredo, Great, this is helpful to know. If I understand you - the filename is the same for all the packages of processed data you are trying to upload, for various subject-visits. e.g. you may have organized them in subdirectories like: $subject/$visit/processed_data.gz One solution could be to make a copy with a different name before uploading. Instead of making a copy (or renaming) -- try a unique soft-link for each package. I should think that would work (though can't confirm right now). e.g. Use a simple bash command to execute for each package: > ln -s $subject/$visit/processed_data.gz ./$subject_$visit_processed_data.gz (then tell the pipeline to load each $subject_$visit_processed_data.gz ) Again, this no-duplicate check exists to help ensure duplicate data isn't inserted, which is a protection we try to preserve as much as possible. Since all the code is customizable, this check could be manually bypassed, but ideally this workaround will help keep the error-proofing intact. Let us know how this goes - We'll be offline for Labour day weekend but back in the office next Tuesday. Best, Christine On Fri, Aug 30, 2019 at 12:53 PM Morales Pinzon, Alfredo > wrote: Hi Christine, Thank you for your answer. Here are the answers to your questions: Can you use distinct filenames ? We could but we already have all the images, thousands, with a pre-defined convention. One solution could be to make a copy with a different name before uploading. Are you are trying to load additional data for a participant session (i.e. same IDs and visit label) ? Yes, we are uploading the result of a couple of pipelines for each participant for each label. Let me know if you can find a workaround, in the mean time I will check with Pisti if we can make a copy of the files with a different name before uploading. Best, Alfredo. ________________________________ From: Christine Rogers, Ms. > Sent: Friday, August 30, 2019 11:17 AM To: Morales Pinzon, Alfredo > Cc: loris-dev at bic.mni.mcgill.ca >; Cecile Madjar >; Sridar Narayanan, Dr. >; Rozie Arnaoutelis, Ms. >; Douglas Arnold, Dr. >; Guttmann, Charles,M.D. > Subject: Re: [Loris-dev] Error "not a unique file" inserting segmentation files in LORIS External Email - Use Caution Hi Alfredo, Could you please help me inserting those files which are different in size and md5 from previous uploaded files? The only similarity between the previous uploaded files and the ones that could not be uploaded is the filename. To provide a quick answer (since most of our imaging team is on vacation this week) : Yes the MD5hash seems to require a unique filename (* below). Can you use distinct filenames ? i.e. Are you are trying to load additional data for a participant session (i.e. same IDs and visit label) ? Or, are you trying to load more than one participant/session at a time? (*) This line in the actual MRIProcessingUtility library: (around Line 617) $md5hash = &NeuroDB::MRI::compute_hash(\$file); and my $unique = &NeuroDB::MRI::is_unique_hash(\$file); I'll check with other imaging devs to see if we have a workaround while our senior devs are away -- I think there must be some solution... Meanwhile, the MD5hash for imaging files is documented here (per this script documentation) : computeMd5Hash($file, $upload_id) Computes the MD5 hash of a file and makes sure it is unique. INPUTS: * $file : file to use to compute the MD5 hash * $upload_id: upload ID of the study RETURNS: 1 if the file is unique, 0 otherwise Best, Christine On Thu, Aug 29, 2019 at 9:46 PM Morales Pinzon, Alfredo > wrote: Dear DevLoris Team, I started the uploading process of processed files, segmentations and transformations, using the file "register_processed_data.pl" but some files are not being uploaded. The error reported in "data/logs/registerProcessed" show the following log for one of the files that could not be inserted: ------------------------------------------------------------------------------- ==> Successfully connected to database Log file, 2019-08-29_19:08:17 ==>Mapped DICOM parameters -> using user-defined filterParameters for /xxx/w024/gvf_ISPC-stx152lsq6.mnc.gz ==> Verifying acquisition center - Center Name : UNKN - CenterID : 0 -> Set ScannerID to 0. ==> Data found for candidate : 123456 - Visit: w024 -> Set SessionID to 28269. -> Set SourceFileID to 49598. -> Set AcquisitionProtocolID to 1013. -> Set CoordinateSpace to stx152lsq6. -> Set SourcePipeline to ConsensusGd. -> Set PipelineDate to 2019-08-29. -> Set OutputType to gvf. -> Set md5hash to b877648ed0ef9a7458ad4931f4dbfd11. ==> NeuroDB::File=HASH(0x136baa8) is not a unique file and will not be added to database. ------------------------------------------------------------------------------- I checked the md5hash for a previous uploaded file, which is different from the previous, but the same "md5hash" was calculated. See the following log: ------------------------------------------------------------------------------- ==> Successfully connected to database Log file, 2019-08-19_10:11:53 ==>Mapped DICOM parameters -> using user-defined filterParameters for ==> Verifying acquisition center - Center Name : UNKN - CenterID : 0 -> Set ScannerID to 0. ==> Data found for candidate : 123456 - Visit: baseline -> Set SessionID to 28268. -> Set SourceFileID to 49593. -> Set AcquisitionProtocolID to 1013. -> Set CoordinateSpace to stx152lsq6. -> Set SourcePipeline to T2Vol. -> Set PipelineDate to 2019-08-19. -> Set OutputType to gvf. -> Set md5hash to b877648ed0ef9a7458ad4931f4dbfd11. File /xxx/baseline/gvf_ISPC-stx152lsq6.mnc.gz moved to: /yyy/data/assembly/123456/baseline/mri/processed/T2Vol/IPMSA_123456_baseline_t1c_001_gvf_001.mnc.gz ==> FAILED TO INSERT INTERMEDIARY FILES FOR 112945! Making JIV ==> Registered /data_/ipmsa/loris_data/IPMSA/data/assembly/307024/baseline/mri/processed/T2Vol/IPMSA_307024_baseline_t1c_001_gvf_001.mnc.gz in database, given FileID: 112945 ------------------------------------------------------------------------------- Here are the corresponding md5 for each file calculated using the command md5sum: /xxx/w024/gvf_ISPC-stx152lsq6.mnc.gz 7306010346c4614d8e338595b386ca5c /xxx/baseline/gvf_ISPC-stx152lsq6.mnc.gz 22107253f8b87c9918ac7f82fdc22c36 Could you please help me inserting those files which are different in size and md5 from previous uploaded files? The only similarity between the previous uploaded files and the ones that could not be uploaded is the filename. Let me know if you need more information. Regards, Alfredo. The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. _______________________________________________ Loris-dev mailing list Loris-dev at bic.mni.mcgill.ca https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev -- christine.rogers at mcgill.ca McGill Centre for Integrative Neuroscience | MCIN.ca Montreal Neurological Institute McGill University | Montreal | Canada _______________________________________________ Loris-dev mailing list Loris-dev at bic.mni.mcgill.ca https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev -- christine.rogers at mcgill.ca McGill Centre for Integrative Neuroscience | MCIN.ca Montreal Neurological Institute McGill University | Montreal | Canada -------------- next part -------------- An HTML attachment was scrubbed... URL: From rnair at caltech.edu Fri Aug 30 17:43:52 2019 From: rnair at caltech.edu (Remya Nair) Date: Fri, 30 Aug 2019 14:43:52 -0700 Subject: [Loris-dev] Questions regarding querying LORIS Message-ID: Hi, We have a couple of questions that we were hoping the LORIS developers might be able to help with. Apologies if this has been answered previously on this forum. 1. If we have data stored on several instruments within LORIS, is it possible to query, filter and export specific data that we need into a CSV file (or any spreadsheet) using the LORIS interface? If not, is this a feature currently being developed? 2. Currently we understand the way to do mass uploads of data into a LORIS instrument is via the database directly. Is there any way to upload data into an instrument directly from a CSV instead (or any spreadsheet format file)? Your take on the above questions would be greatly appreciated. Thank you in advance for your help. Best, Remya -- -------------- next part -------------- An HTML attachment was scrubbed... URL: From sotirisnik at gmail.com Fri Aug 30 19:31:20 2019 From: sotirisnik at gmail.com (Sotirios Nikoloutsopoulos) Date: Sat, 31 Aug 2019 02:31:20 +0300 Subject: [Loris-dev] Import mri - scripts In-Reply-To: References: Message-ID: Hi, Is the link below the stable release? wget https://github.com/aces/Loris/archive/v21.0.0.zip -O release.zip Also in the chown command i think that we need to add -R ( see chown file ) *sudo chown -**R **lorisadmin.lorisadmin /var/www/**l**oris* I runned composer install in /var/www/loris, please see the attached files. Thanks ???? ???, 30 ??? 2019 ???? 6:13 ?.?., ?/? Shen Wang ??????: > Hi Sotirios, > You should not use our minor branch (only for developing), we have > published the 21.0-release officially, it is a stable version of Loris. > After checking your error logs, you're missing is running composer > install, which will import your packages and create the vendor folder, > along with the autoload script. > Regards > Shen > > On Thu, 29 Aug 2019 at 19:46, Sotirios Nikoloutsopoulos < > sotirisnik at gmail.com> wrote: > >> Hi, >> >> loris-access.log reports HTTP 500 error and loris-error reports that some >> files are missing e.x. autoload.php from >> /var/www/loris/htdocs/../vendor/autoload.php ( >> https://github.com/aces/Loris/tree/minor/htdocs/vendor and as i can >> verify those files do not exist in the github folder ) >> >> Thanks >> >> >> >> ???? ???, 29 ??? 2019 ???? 4:04 ?.?., ?/? Christine Rogers, Ms. < >> christine.rogers at mcgill.ca> ??????: >> >>> Hi Sotirios, >>> >>> > Any suggestion why Loris is not showing up in the browser? >>> >>> >>> - What are the last few lines of your loris-access and loris-error >>> apache logs? >>> >>> - What are the URL and host in your Config table? (run these queries >>> from the wiki >>> >>> ) >>> >>> - Are you using https, are the certificates in place, etc? >>> >>> - Do any of the wiki's Troubleshooting steps >>> >>> help? >>> >>> Best, >>> Christine >>> >>> On Wed, Aug 28, 2019 at 9:30 PM Sotirios Nikoloutsopoulos < >>> sotirisnik at gmail.com> wrote: >>> >>>> Any suggestion why Loris is not showing up in the browser? >>>> >>>> Thanks >>>> >>>> >>>> ???? ???, 28 ??? 2019 ???? 2:30 ?.?., ?/? Sotirios Nikoloutsopoulos < >>>> sotirisnik at gmail.com> ??????: >>>> >>>>> Also to mention that in the picture i opened the 000-default.conf >>>>> which is just a copy of loris.conf by using cp >>>>> >>>>> ???? ???, 28 ??? 2019 ???? 2:20 ?.?., ?/? Sotirios Nikoloutsopoulos < >>>>> sotirisnik at gmail.com> ??????: >>>>> >>>>>> Ok that fixed the install.sh problem. Now it doesn't show loris to >>>>>> the browser, although everything seems right ( also >>>>>> >>>>>> /etc/apache2/sites-enabled/000-default.conf was replaced by loris.config ). >>>>>> >>>>>> >>>>>> And apache is running >>>>>> lorisadmin at loris-VirtualBox:/var/www/loris/htdocs$ sudo systemctl >>>>>> status apache2[sudo] password for lorisadmin: >>>>>> ? apache2.service - LSB: Apache2 web server >>>>>> Loaded: loaded (/etc/init.d/apache2; bad; vendor preset: enabled) >>>>>> Drop-In: /lib/systemd/system/apache2.service.d >>>>>> ??apache2-systemd.conf >>>>>> Active: active (running) since ??? 2019-08-28 02:15:12 EEST; 3min >>>>>> 34s ago >>>>>> >>>>>> [image: image.png] >>>>>> >>>>>> ???? ???, 27 ??? 2019 ???? 9:42 ?.?., ?/? Shen Wang < >>>>>> wangshen.mcin at gmail.com> ??????: >>>>>> >>>>>>> Hi, >>>>>>> This is a bug for install.sh file, we will fix it later. >>>>>>> Thank for letting me know your Loris install situation. >>>>>>> regards >>>>>>> Shen >>>>>>> >>>>>>> >>>>>>> On Tue, 27 Aug 2019 at 14:28, Shen Wang >>>>>>> wrote: >>>>>>> >>>>>>>> Hi, >>>>>>>> Please remove "set -euo pipefail" line 10 in the install.sh file. >>>>>>>> Then try again. >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> On Tue, 27 Aug 2019 at 14:05, Sotirios Nikoloutsopoulos < >>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>> >>>>>>>>> Hi, >>>>>>>>> >>>>>>>>> i still haven't resolved the previous issue. Also i tried to >>>>>>>>> install Loris to a new virtual machine and when i execute install.sh i get >>>>>>>>> the following error >>>>>>>>> >>>>>>>>> lorisadmin at loris-VirtualBox:/var/www/loris/tools$ ./install.sh >>>>>>>>> LORIS Installation Script starting at 2019-08-27T21:00:42 >>>>>>>>> The log for this session will be stored in file >>>>>>>>> /var/www/loris/tools/logs/install-2019-08-27T21:00:42.log >>>>>>>>> >>>>>>>>> --------------------------------------------------------------------- >>>>>>>>> LORIS Installation Script >>>>>>>>> >>>>>>>>> --------------------------------------------------------------------- >>>>>>>>> >>>>>>>>> PHP appears to be installed. >>>>>>>>> >>>>>>>>> PHP Composer appears to be installed. >>>>>>>>> >>>>>>>>> This install script will ask you to provide inputs for different >>>>>>>>> steps. >>>>>>>>> Please ensure you have the following information ready (if >>>>>>>>> applicable): >>>>>>>>> >>>>>>>>> 1) Your project directory name. >>>>>>>>> (Will be used to modify the paths for Imaging data in the >>>>>>>>> generated >>>>>>>>> config.xml file for LORIS, and may also be used to >>>>>>>>> automatically >>>>>>>>> create/install apache config files.) If unsure, a default >>>>>>>>> like "LORIS" >>>>>>>>> should be acceptable. >>>>>>>>> >>>>>>>>> Please also consult the Loris WIKI on GitHub for more information >>>>>>>>> on these >>>>>>>>> Install Script input parameters. >>>>>>>>> >>>>>>>>> Ready to continue? [yn] y >>>>>>>>> >>>>>>>>> ./install.sh: line 132: projectname: unbound variable >>>>>>>>> >>>>>>>>> Thanks >>>>>>>>> >>>>>>>>> ???? ???, 6 ??? 2019 ???? 5:09 ?.?., ?/? Christine Rogers, Ms. < >>>>>>>>> christine.rogers at mcgill.ca> ??????: >>>>>>>>> >>>>>>>>>> Hi Sotirios, >>>>>>>>>> Could you also let us know -- on which pages is content visible, >>>>>>>>>> and on which pages/modules is content not visible for you? >>>>>>>>>> Thanks, >>>>>>>>>> Christine >>>>>>>>>> >>>>>>>>>> On Tue, Aug 6, 2019 at 9:54 AM Christine Rogers, Ms. < >>>>>>>>>> christine.rogers at mcgill.ca> wrote: >>>>>>>>>> >>>>>>>>>>> Thanks Sotirios, >>>>>>>>>>> That's good to know. It sounds like you've checked that your >>>>>>>>>>> /var/www/loris/project/config.xml file get populated properly. >>>>>>>>>>> >>>>>>>>>>> Please send us the last few errors you're seeing in your apache >>>>>>>>>>> error log file, and your config paths and we can see what's happening with >>>>>>>>>>> your front end -- >>>>>>>>>>> Run these Troubleshooting Queries >>>>>>>>>>> >>>>>>>>>>> to get your config path settings, given your front end is not displaying >>>>>>>>>>> fully. >>>>>>>>>>> >>>>>>>>>>> The Loris-MRI repo >>>>>>>>>>> 21 >>>>>>>>>>> install/upgrade would then be your next steps. >>>>>>>>>>> Best, >>>>>>>>>>> Christine >>>>>>>>>>> >>>>>>>>>>> On Tue, Aug 6, 2019 at 7:53 AM Sotirios Nikoloutsopoulos < >>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>> >>>>>>>>>>>> I am using a VM. What i did was: >>>>>>>>>>>> 1) Download the files from https://github.com/aces/Loris and >>>>>>>>>>>> replace them to my existing /vaw/www/loris folder. >>>>>>>>>>>> 2) Execute the composer install --no-dev and then composer >>>>>>>>>>>> dump-autoload as mentioned here >>>>>>>>>>>> https://github.com/aces/Loris/wiki/Updating-your-LORIS. >>>>>>>>>>>> 3) Execute install.sh from /var/www/loris/tools and because >>>>>>>>>>>> LORIS already existed i moved a .config file, then re-executed the >>>>>>>>>>>> install.sh successfully >>>>>>>>>>>> 4 ) As for the database, i dropped the schema and i executed >>>>>>>>>>>> the installdb.php >>>>>>>>>>>> >>>>>>>>>>>> ???? ???, 5 ??? 2019 ???? 5:22 ?.?., ?/? Christine Rogers, Ms. < >>>>>>>>>>>> christine.rogers at mcgill.ca> ??????: >>>>>>>>>>>> >>>>>>>>>>>>> Hi Sotorios, >>>>>>>>>>>>> >>>>>>>>>>>>> Thanks - when you re-installed did you start on a fresh root >>>>>>>>>>>>> path / VM or might some of your old system setting still apply? >>>>>>>>>>>>> (And if you did any steps similar to an upgrade, did you >>>>>>>>>>>>> follow the Upgrade steps in the Release Notes, from both repos?) >>>>>>>>>>>>> >>>>>>>>>>>>> About the TR_range column - it was recently split (MRI pr339 >>>>>>>>>>>>> ) split into >>>>>>>>>>>>> TR_min and _max columns. Given the code was trying to query TR_range which >>>>>>>>>>>>> does not exist in your mri_protocol table, double-check which version of >>>>>>>>>>>>> the Loris repo (tables) and the Loris-MRI repo (code) you have installed to >>>>>>>>>>>>> ensure they match. >>>>>>>>>>>>> >>>>>>>>>>>>> Christine >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> On Mon, Aug 5, 2019 at 9:06 AM Sotirios Nikoloutsopoulos < >>>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>> >>>>>>>>>>>>>> I reinstalled LORIS to 21 version and now the content is not >>>>>>>>>>>>>> visible at all at most pages. >>>>>>>>>>>>>> >>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>> >>>>>>>>>>>>>> ???? ???, 5 ??? 2019 ???? 3:19 ?.?., ?/? Sotirios >>>>>>>>>>>>>> Nikoloutsopoulos ??????: >>>>>>>>>>>>>> >>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> Is it easy to upgrade to Loris 21? Also the following fails >>>>>>>>>>>>>>> because the line 1985 of NeuroDB/MRIProcessingUtility.pm query mri_protocol >>>>>>>>>>>>>>> which doesn't have TR_range >>>>>>>>>>>>>>> https://github.com/aces/Loris/blob/21.0-release/SQL/0000-00-00-schema.sql#L556 >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> lorisadmin at hbp:/data/loris/bin/mri$ >>>>>>>>>>>>>>> ./batch_uploads_imageuploader -profile prod < ~/Desktop/input.txt > log.txt >>>>>>>>>>>>>>> Use of uninitialized value $_ in pattern match (m//) at >>>>>>>>>>>>>>> ./batch_uploads_imageuploader line 147. >>>>>>>>>>>>>>> base is DCC0000_258024_V1 >>>>>>>>>>>>>>> path is /data/incoming/ >>>>>>>>>>>>>>> type is .tar.gz >>>>>>>>>>>>>>> fullpath is /data/incoming/DCC0000_258024_V1.tar.gz >>>>>>>>>>>>>>> DBD::mysql::st execute failed: Unknown column 'TR_range' in >>>>>>>>>>>>>>> 'where clause' at >>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line 1985. >>>>>>>>>>>>>>> DBD::mysql::st fetchrow_array failed: fetch() without >>>>>>>>>>>>>>> execute() at >>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line 1986. >>>>>>>>>>>>>>> Use of uninitialized value $count_mri_protocol in numeric gt >>>>>>>>>>>>>>> (>) at /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm >>>>>>>>>>>>>>> line 1995. >>>>>>>>>>>>>>> DBD::mysql::st execute failed: Unknown column 'TR_range' in >>>>>>>>>>>>>>> 'field list' at /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 562. >>>>>>>>>>>>>>> Can't exec "mail": No such file or directory at >>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 721. >>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 722. >>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 723. >>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 724. >>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 725. >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> No Mincs inserted >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> Thanks, >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> ???? ???, 3 ??? 2019 ???? 1:08 ?.?., ?/? Christine Rogers, >>>>>>>>>>>>>>> Ms. ??????: >>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> First, just a note: we've released LORIS 21 this week with >>>>>>>>>>>>>>>> some major new features and cleanup -- especially if you are early in your >>>>>>>>>>>>>>>> setup phase, check out the Release notes for both the LORIS >>>>>>>>>>>>>>>> and >>>>>>>>>>>>>>>> Loris-MRI >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> repos. >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Thanks for your screenshots -- your empty mri_protocol >>>>>>>>>>>>>>>> table should be at the root of these issues : >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> The mri_protocol table must be populated >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> in order for your scans to be registered in LORIS -- it serves as a >>>>>>>>>>>>>>>> whitelist for the insertion pipeline which filters out scans that aren't >>>>>>>>>>>>>>>> identified or matched to scan types in this table. >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> By default, this table is populated with entries for t1, >>>>>>>>>>>>>>>> t2, fMRI and DTI (Insert statements for 21 release branch >>>>>>>>>>>>>>>> are here >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> ) >>>>>>>>>>>>>>>> Feel free to restore our default records and broaden their >>>>>>>>>>>>>>>> parameters to match all your scan types. >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> re Defaced, native, selected -- these filter the scans >>>>>>>>>>>>>>>> displayed as you move to the next page (View Session), instead of viewing >>>>>>>>>>>>>>>> "all types" of scans from a given session : >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> - "defaced" means that a defacing script >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> has masked the subject's face in the volume (for patient privacy) >>>>>>>>>>>>>>>> - "native" means that no pre-processing has been >>>>>>>>>>>>>>>> performed on the scan (it's raw data), >>>>>>>>>>>>>>>> - "selected" will show only volumes that have been >>>>>>>>>>>>>>>> QC'd and "selected" as the best of their type -- used to display only the >>>>>>>>>>>>>>>> best quality T1 image instead of all T1s acquired in a session, e.g. >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> re QC Comments -- >>>>>>>>>>>>>>>> Once you have successfully loaded scans (matched to the >>>>>>>>>>>>>>>> mri_protocol table), you'll be able to use the Imaging Browser's View >>>>>>>>>>>>>>>> Session subpage to enter/view QC comments on each volume, or for each >>>>>>>>>>>>>>>> visit. >>>>>>>>>>>>>>>> These are stored directly in the database, and linked to >>>>>>>>>>>>>>>> each scan. (Table name: feedback_mri_comments) >>>>>>>>>>>>>>>> (Visit-level QC comments are linked to the session.) >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> For a walkthrough of the Imaging setup - please see the Imaging >>>>>>>>>>>>>>>> Setup guide >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> - >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> An old LORIS walkthrough video >>>>>>>>>>>>>>>> can also >>>>>>>>>>>>>>>> walk you through some of the Imaging front-end features, starting at 8:00 >>>>>>>>>>>>>>>> LORIS' imaging modules have been updated many times since >>>>>>>>>>>>>>>> this video, but the functionality and workflow is similar. >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Let us know how it goes once you have entries in your >>>>>>>>>>>>>>>> mri_protocol table - >>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>> Christine >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> On Fri, Aug 2, 2019 at 7:58 AM Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Hi Christine, >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> In the candidate_list page i can see this patient >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> If i press the link under PSCID i get to see >>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> and if i press the link under Scan Done it redirects me to >>>>>>>>>>>>>>>>> imaging_browser >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> At the mri_violations page i also see No results ( neither >>>>>>>>>>>>>>>>> on resolved / not resolved ). >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> At the imaging_uploader i can see the record that failed. >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> If i click on the tarchive info i get to see the Protocol >>>>>>>>>>>>>>>>> Name which i think is the acquisition we wanted? >>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Also my mri_protocol table is empty. >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Furthermore i would like to ask about the defaced, native, >>>>>>>>>>>>>>>>> selected. What exactly is native and selected? And where are the qc >>>>>>>>>>>>>>>>> comments stored? >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Finally a walkthrough would be helpful. >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Thanks, >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> ???? ???, 30 ???? 2019 ???? 8:29 ?.?., ?/? Christine >>>>>>>>>>>>>>>>> Rogers, Ms. ??????: >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>> Glad to hear you're making progress with the visit >>>>>>>>>>>>>>>>>> labels. To follow up on your last few emails: >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> a- The Wiki's Setup Guide contains Sample insert >>>>>>>>>>>>>>>>>> statements for the Visit Windows table >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> . >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> As Cecile mentioned, the consistency of visit label >>>>>>>>>>>>>>>>>> format is important: V01, v01, V1, 01 -- whichever you select to use is >>>>>>>>>>>>>>>>>> fine; we use V01 by default across all documentation. >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> b- For Password reset, there is a script in the tools/ >>>>>>>>>>>>>>>>>> directory so that a back-end administrator can reset any front-end user >>>>>>>>>>>>>>>>>> password, including Admin. (See info on setting up / resetting User >>>>>>>>>>>>>>>>>> passwords in the Wiki's Setup Guide >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> ) >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> c- The minc file not being registered -- due to >>>>>>>>>>>>>>>>>> AcquisitionProtocol unknown. >>>>>>>>>>>>>>>>>> This means the SeriesDescription (Acquisition Protocol) >>>>>>>>>>>>>>>>>> in you Dicom header was not matched to any scan listed in the mri_protocol >>>>>>>>>>>>>>>>>> database table. >>>>>>>>>>>>>>>>>> (In the online Loris-MRI Troubleshooting Guide, >>>>>>>>>>>>>>>>>> this >>>>>>>>>>>>>>>>>> is Table 3, 2nd-last item "no MINCs inserted"). >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> The MRI Violations module (Readme here) >>>>>>>>>>>>>>>>>> will show >>>>>>>>>>>>>>>>>> you the details of this mismatch -- >>>>>>>>>>>>>>>>>> Go to the module (under the Imaging menu), find your scan >>>>>>>>>>>>>>>>>> and click the link "Could not identify scan type" -- in the next subpage >>>>>>>>>>>>>>>>>> you can compare the scan's actual parameters against the mri_protocol >>>>>>>>>>>>>>>>>> table. >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> To resolve this, adjust your mri_protocol table values or >>>>>>>>>>>>>>>>>> perhaps ensure your DICOMs are labelled consistently. >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Let us know if this works for you -- we can also walk you >>>>>>>>>>>>>>>>>> through an example of non-identified scans on >>>>>>>>>>>>>>>>>> Demo.loris.ca (MRI Violations module). >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>> Christine >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> The LORIS team >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> On Tue, Jul 30, 2019 at 10:47 AM Sotirios >>>>>>>>>>>>>>>>>> Nikoloutsopoulos wrote: >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> I hope this is sufficient as the error for the visit >>>>>>>>>>>>>>>>>>> label disappeared. >>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Please see the attached file. Also something i found. >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> lorisadmin at hbp:/data/loris/bin/mri$ cat >>>>>>>>>>>>>>>>>>> /data/loris/data//logs/TarLoad-17-39-xubBdv.log >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> ==> Loading file from disk >>>>>>>>>>>>>>>>>>> /tmp/TarLoad-17-39-UyQcG2/dcc0000_258024_v1_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> --> mapping DICOM parameter for >>>>>>>>>>>>>>>>>>> /tmp/TarLoad-17-39-UyQcG2/dcc0000_258024_v1_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> ==> computing md5 hash for MINC body. >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> --> md5: 6b1202fd63e29de4c9be1cd9925888a5 >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> ==> verifying acquisition protocol >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Acquisition protocol is unknown >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> --> The minc file cannot be registered since the >>>>>>>>>>>>>>>>>>> AcquisitionProtocol is unknown >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> ???? ???, 30 ???? 2019 ???? 4:58 ?.?., ?/? Sotirios >>>>>>>>>>>>>>>>>>> Nikoloutsopoulos ??????: >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Ok I fixed the login problem by using a known hash and >>>>>>>>>>>>>>>>>>>> by deleting the rows from the login_history i was able to login. >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> ???? ???, 30 ???? 2019 ???? 4:50 ?.?., ?/? Sotirios >>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos ??????: >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> there was no visit label 01 in the Visit_Windows table >>>>>>>>>>>>>>>>>>>>> and i don't know how to insert it because the record requires lots of >>>>>>>>>>>>>>>>>>>>> attributes. Also the system for a reason asked me to update my password and >>>>>>>>>>>>>>>>>>>>> now i don't remember it and my account got suspended. Is there a way to >>>>>>>>>>>>>>>>>>>>> reset it or set a simple password? I updated the password hash in the >>>>>>>>>>>>>>>>>>>>> users table by using the hash from another LORIS setup we had and i still >>>>>>>>>>>>>>>>>>>>> couldn't login ( also the attribute password is always NULL and the >>>>>>>>>>>>>>>>>>>>> expiration date is 1999-01-01 for some reason ). >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> Thanks >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> ???? ???, 29 ???? 2019 ???? 5:21 ?.?., ?/? Cecile >>>>>>>>>>>>>>>>>>>>> Madjar ??????: >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> Can you try adding the visit label v01 to the >>>>>>>>>>>>>>>>>>>>>> Visit_Windows table? >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> However, I noticed that in a previous dataset, the >>>>>>>>>>>>>>>>>>>>>> label was V1. Does that refer to the same visit? If so, you might want to >>>>>>>>>>>>>>>>>>>>>> harmonize the visit labels so they are all the same across datasets for a >>>>>>>>>>>>>>>>>>>>>> given timepoint, meaning you will need to relabel scans when the visit >>>>>>>>>>>>>>>>>>>>>> label is different but referring to the same visit label (v01 = V1 etc...). >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> Hope this helps, >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> On Mon, Jul 29, 2019 at 10:15 AM Sotirios >>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos wrote: >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> Could you help me with the "Visit label does not >>>>>>>>>>>>>>>>>>>>>>> exist"? I had changed $subjectID{'createVisitLabel'} to 1 as you had >>>>>>>>>>>>>>>>>>>>>>> suggested but it appears that this problem hasn't been resolved yet. >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> lorisadmin at hbp:/data/loris/bin/mri$ cat >>>>>>>>>>>>>>>>>>>>>>> /data/loris/data//logs/TarLoad-14-58-9Xog7H.log >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> ==> Loading file from disk >>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> --> mapping DICOM parameter for >>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> --> using user-defined filterParameters for >>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> Candidate Mismatch Error is Visit label does not >>>>>>>>>>>>>>>>>>>>>>> exist >>>>>>>>>>>>>>>>>>>>>>> -> WARNING: This candidate was invalid. Logging to >>>>>>>>>>>>>>>>>>>>>>> MRICandidateErrors table with reason >>>>>>>>>>>>>>>>>>>>>>> Visit label does not exist >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> ???? ???, 26 ???? 2019 ???? 3:02 ?.?., ?/? Sotirios >>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos ??????: >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> Hi Cecile, >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> The Center error was fixed. Still the insertion of >>>>>>>>>>>>>>>>>>>>>>>> mincs fails. Please see the output.txt file i attached. Also is there >>>>>>>>>>>>>>>>>>>>>>>> something else i need to change at the paths configuration? >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 25 ???? 2019 ???? 6:55 ?.?., ?/? Cecile >>>>>>>>>>>>>>>>>>>>>>>> Madjar ??????: >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> We are making progress! >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> I have a feeling this error comes from the fact >>>>>>>>>>>>>>>>>>>>>>>>> that your psc table does not have the MRI_alias populated for the DCC site. >>>>>>>>>>>>>>>>>>>>>>>>> Running the following query in the mysql database should fix this: >>>>>>>>>>>>>>>>>>>>>>>>> UPDATE psc SET MRI_alias="DCC", Alias="DCC" WHERE >>>>>>>>>>>>>>>>>>>>>>>>> Name="Data Coordinating Center"; >>>>>>>>>>>>>>>>>>>>>>>>> Repeat the same with all your sites (make sure to >>>>>>>>>>>>>>>>>>>>>>>>> change the Aliases between sites, they should all be unique). >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> Let me know how it goes! >>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> On Thu, Jul 25, 2019 at 11:43 AM Sotirios >>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos wrote: >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> Dear Cecile, >>>>>>>>>>>>>>>>>>>>>>>>>> You were right about your guesses. I did the >>>>>>>>>>>>>>>>>>>>>>>>>> modifications you suggested, i still get the "no mincs inserted" error, now >>>>>>>>>>>>>>>>>>>>>>>>>> i am getting the "No center found this candidate" error ( how do i fix >>>>>>>>>>>>>>>>>>>>>>>>>> that? from what i see the .dcm files contains a 'Institution Name', is that >>>>>>>>>>>>>>>>>>>>>>>>>> the center? ), so i guess that's why the validation fails, but i changed >>>>>>>>>>>>>>>>>>>>>>>>>> the force variable of tarchiveLoader to 1, shouldn't it have inserted the >>>>>>>>>>>>>>>>>>>>>>>>>> mincs then? Also it is optional to have a mail server, right? ( from what i >>>>>>>>>>>>>>>>>>>>>>>>>> see the mail error does not affect the $valid_study, so i assume we are >>>>>>>>>>>>>>>>>>>>>>>>>> okay with that ) >>>>>>>>>>>>>>>>>>>>>>>>>> Thank you a lot, >>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 25 ???? 2019 ???? 5:48 ?.?., ?/? Cecile >>>>>>>>>>>>>>>>>>>>>>>>>> Madjar ??????: >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> From what I understand, I believe you just need >>>>>>>>>>>>>>>>>>>>>>>>>>> to update a few config settings from the frontend in the Config module >>>>>>>>>>>>>>>>>>>>>>>>>>> (under the Admin menu). >>>>>>>>>>>>>>>>>>>>>>>>>>> [image: Screen Shot 2019-07-25 at 10.31.35 >>>>>>>>>>>>>>>>>>>>>>>>>>> AM.png] >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> Then go to the Paths section of the config >>>>>>>>>>>>>>>>>>>>>>>>>>> module and update the "LORIS-MRI code" config setting to >>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri (my guess is that currently, it is set to >>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data) and click on the submit button. >>>>>>>>>>>>>>>>>>>>>>>>>>> [image: Screen Shot 2019-07-25 at 10.32.50 >>>>>>>>>>>>>>>>>>>>>>>>>>> AM.png] >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> Then, go to Imaging Pipeline section of the >>>>>>>>>>>>>>>>>>>>>>>>>>> Configuration module and update the "Loris-MRI Data Directory" to >>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/ (my guess is that it is empty at the moment in your >>>>>>>>>>>>>>>>>>>>>>>>>>> database which is why $data_dir is not defined when you run the >>>>>>>>>>>>>>>>>>>>>>>>>>> tarchiveLoader step of the insertion pipeline). >>>>>>>>>>>>>>>>>>>>>>>>>>> [image: Screen Shot 2019-07-25 at 10.40.52 >>>>>>>>>>>>>>>>>>>>>>>>>>> AM.png] >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> Finally, I took a look at your environment file >>>>>>>>>>>>>>>>>>>>>>>>>>> and it might be a good idea to update your PERL5LIB variable to the >>>>>>>>>>>>>>>>>>>>>>>>>>> following (it has been added to the code a few releases ago as we realized >>>>>>>>>>>>>>>>>>>>>>>>>>> this was needed for the libraries. Not sure which version of LORIS-MRI you >>>>>>>>>>>>>>>>>>>>>>>>>>> are using but it does not hurt to update this variable to what I suggest >>>>>>>>>>>>>>>>>>>>>>>>>>> below): >>>>>>>>>>>>>>>>>>>>>>>>>>> export >>>>>>>>>>>>>>>>>>>>>>>>>>> PERL5LIB=/data/loris/bin/mri/uploadNeuroDB:/data/loris/bin/mri/dicom-archive:$PERL5LIB >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helps. Sorry you are experiencing so >>>>>>>>>>>>>>>>>>>>>>>>>>> much trouble setting things up. We probably need to update our WIKI. >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> On Thu, Jul 25, 2019 at 9:48 AM Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos wrote: >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> The "Loris-MRI Data Directory" should be in the >>>>>>>>>>>>>>>>>>>>>>>>>>>> environment file? >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 25 ???? 2019 ???? 12:59 ?.?., ?/? >>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos >>>>>>>>>>>>>>>>>>>>>>>>>>>> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> The scripts are located in >>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/. Somewhere I might have messed something up but i >>>>>>>>>>>>>>>>>>>>>>>>>>>>> remember following the instructions in the wiki.For example when i tried to >>>>>>>>>>>>>>>>>>>>>>>>>>>>> execute the batch_uploads_imageuploader perl script the line >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> my $command = "$bin_dir/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl " >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> was pointing to an invalid path, for example: >>>>>>>>>>>>>>>>>>>>>>>>>>>>> it was repeating a pattern and had LORIS instead of loris ( i think the >>>>>>>>>>>>>>>>>>>>>>>>>>>>> mistake was that in the wiki it suggested to use $PROJECT for the name of >>>>>>>>>>>>>>>>>>>>>>>>>>>>> the folder and i choosed 'loris' >>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris/wiki/Imaging-Database >>>>>>>>>>>>>>>>>>>>>>>>>>>>> ). See also the in image for the modification i did. Also i didn't find the >>>>>>>>>>>>>>>>>>>>>>>>>>>>> section to config the $data_dir variable. >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 24 ???? 2019 ???? 6:05 ?.?., ?/? >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Cecile Madjar ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> It looks like you have one Config setting not >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> set (based on the first error message you got when running it the first >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> time). You need to set a value for "Loris-MRI Data Directory" in the Config >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> module under the Imaging pipeline section (from what I can see, it would be >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/ for your setup). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The reason you got that error message the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> second time is that the pipeline checks if the DICOM study was already >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> inserted in the tarchive table. Since you ran the study once already, the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> study is inserted into the tarchive, hence the message. However, the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> pipeline did not complete as the MINC files were not created and inserted >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> into the files/parameter_file table. In order to continue the insertion, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> you will then need to run the tarchiveLoader command suggested in the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> terminal during the second run: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -globLocation -profile prod >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive//2012/DCM_2012-12-05_ImagingUpload-17-43-ZUEFjb.tar >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -verbose >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Finally, I am a bit confused by your setup. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Where are the scripts located? In /data/loris/bin/mri or /data/loris/data? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> It feels like the Config setting "LORIS-MRI code" in the Paths section was >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> set to "/data/LORIS/data" but it should have been set to the directory >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> where the scripts are located (most probably /data/loris/bin/mri). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helps, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> On Wed, Jul 24, 2019 at 10:55 AM Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> wrote: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Ok first i execute this command: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> "lorisadmin at hbp:/data/loris/bin/mri$ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ./batch_uploads_imageuploader -profile prod < ~/Desktop/input.txt > log.txt >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at ./batch_uploads_imageuploader line 143. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at ./batch_uploads_imageuploader line 143. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $_ in pattern >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> match (m//) at ./batch_uploads_imageuploader line 147. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> base is DCC0000_258024_V01 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> path is /data/incoming/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> type is .tar.gz >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> fullpath is >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/incoming/DCC0000_258024_V01.tar.gz >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> source /tmp/ImagingUpload-17-43-ZUEFjb >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> targetlocation /data/loris/data/tarchive >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 256. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 284. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at /data/loris/bin/mri/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> tarchive_validation.pl line 219. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at /data/loris/bin/mri/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl line 270. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 711. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Can't exec "mail": No such file or directory >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 721. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 722. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 723. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 724. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 724. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 725. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 735. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> No Mincs inserted >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The tarchiveLoader insertion script has >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> failed. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Running now the following command: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl -profile prod >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -upload_id 3 /data/incoming/DCC0000_258024_V01.tar.gz -verbose" >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I inserted the VisitLabel, but still the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Mincs are not inserted and i am getting this error >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> "lorisadmin at hbp:/data/loris/bin/mri$ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl -profile prod >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -upload_id 3 /data/incoming/DCC0000_258024_V01.tar.gz -verbose >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> find -path >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> \/tmp\/ImagingUpload\-17\-45\-5MsWEd -name '__MACOSX' -delete >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Spool message is: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The Scan for the uploadID 3 has already been >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> run with tarchiveID: 7. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> To continue with the rest of the insertion >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> pipeline, please run tarchiveLoader from a terminal as follows: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader -globLocation -profile prod >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive//2012/DCM_2012-12-05_ImagingUpload-17-43-ZUEFjb.tar >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -verbose" >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Which files should i delete? I thought that >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> deleting the files from the tarchive was enough. And i executed the last >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> proposed command to continue to rest of the insertion pipeline ( check the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> image ). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 24 ???? 2019 ???? 5:05 ?.?., ?/? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Cecile Madjar >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sorry I was not clear before. Every visits >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> of candidates are created in the session table with one entry per >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID/VisitLabel. So if the imaging pipeline created visits in the session >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> table (that are not attached to instruments) and you want to clean your >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> database completely, you can delete entries in that table as well. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Regarding your point 2, the imaging >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> pipeline can create the visit in the session table as long as the visit >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> label is present in the Visit_Windows table (which means the visit label >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> stored in the PatientName is a valid visit label). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> However, in your prod file, if the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> variable $subjectID{'createVisitLabel'} is set to 1 for candidates, the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit label should be created in the Visit_Windows table I believe. Here >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> is the line of the prod file you would need to change >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> . >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> In general, we prefer populating the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Visit_Windows table and set the $subjectID{'createVisitLabel'} to 0 for >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> candidate data to avoid insertion of badly labelled MRI data that are >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> complex to relabel. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Finally, regarding the candidate creation, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> if you execute the following steps, the pipeline should be able to create >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> candidates: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - set in the Imaging Pipeline section of >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the config module the config setting "Upload creation of candidates" to Yes >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - manually transfer the scans to the LORIS >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> server instead of uploading it via the imaging browser >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - run batch_imaging_upload.pl as you did >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> until now. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helps! >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> On Wed, Jul 24, 2019 at 8:47 AM Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> wrote: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> About my second question i replaced the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> name of the patient in the .dcm files and now i am getting an error that >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the visit label does not exist. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I thought it was supposed to be >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> automatically created. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> "Done adding archive info into database >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -globLocation -profile prod >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive//DCM_2012-12-05_ImagingUpload-15-42-yUwQQV.tar >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -verbose >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> md5sum >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive/DCM_2012-12-05_ImagingUpload-15-42-yUwQQV.tar >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> candidate id 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> => No Visit labelVisit label does not >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> exist >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Set centerID = 1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Number of MINC files that will be >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> considered for inserting into the database: 1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> log dir is /logs and log file is >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /logs/TarLoad-15-42-L6pocU.log >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> candidate id 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> => No Visit label >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Cleaning up temp files: rm -rf >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-15-42-J2rQms/ImagingUpload-15-42-yUwQQV*" >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 24 ???? 2019 ???? 3:38 ?.?., ?/? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 1) What are the records in the session >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> table? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 2) I tried to upload a non-phantom file >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> like this >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> input_file.txt: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/incoming/DCC0000_258024_V1.tar.gz N >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DCC0000_258024_V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Terminal: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ./batch_uploads_imageuploader -profile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> prod < ~/Desktop/input.txt > log.txt >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and i get the following error in the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> log.txt file >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> "Running now the following command: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl -profile prod >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -upload_id 7 /data/incoming/DCC0000_258024_V1.tar.gz -verbose >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> find -path >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> \/tmp\/ImagingUpload\-14\-56\-FeLCB4 -name '__MACOSX' -delete >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Spool message is: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The PatientName read from the DICOM >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> header does not start with DCC0000_258024_V1 from the mri_upload table >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> " >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and the spool message is repeated for >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> each .dcm file. Should i preprocess every .dcm file and change the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PatientName to "DCC0000_258024_V1"? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 3) As far as it concerns the candidate >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> profile i have to create a new one each time before i try to upload a file? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Is there already a way to create a candidate profile and get the DCCID and >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID without the user interface? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 18 ???? 2019 ???? 5:00 ?.?., >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ?/? Cecile Madjar >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> See answers to your questions below. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> About the 1st case we had a dicom with a >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> blank studyUID, maybe someone accidentally removed it. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> That is strange. Something must have >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> been done to the DICOM files. I have never seen a study with no StudyUID >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> out of the scanner. Usually, you need to manually erase it with some tool. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> However, DICOMs never cease to surprise me... >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Some other questions: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 1) What are the steps to remove all of >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> my patients and uploads?: because i want to try to reupload all the testing >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> dicoms we had with a clean database. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Release 21.0 of LORIS-MRI will offer a >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> script to remove all the entries and files specific to an upload. However, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> this release is not yet out. Hopefully in the next few weeks. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> In the meantime, since your case is >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> particular and that you just want to start with a clean database, the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> following deletes should work (hopefully I won't forget any tables): >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from mri_violations_log; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from mri_protocol_violated_scans; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from MRICandidateErrors; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from parameter_file; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from files_qcstatus; # (if you >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> played with the QC part of the imaging browser for testing) >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from feedback_mri_comments; # (if >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> you played with the QC part of the imaging browser for testing) >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from tarchive_series; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from tarchive_files; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from mri_upload; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from tarchive; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from mri_scanner; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from candidate where >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID="scanner"; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I don't know if you want to also delete >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> entries in the session and candidate table too? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 2) We do not need to create the profile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> of a patient ( are the patients stored in the candidate table? because i >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> can't see the ghosts ), because will it automatically be created when >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> importing a dicom? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I am not sure I understand fully this >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> question. All candidates are stored in the candidate table. The phantom >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> scans however are attached to a scanner candidate depending on where the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> scan happened. It is a bit of a weird concept that we have to redesign >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> eventually but never got a chance to get to it. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hopefully this answered your question, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> otherwise, don't hesitate to let me know. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 3) What is the difference between >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> uploading a dicom as phantom instead of importing as >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCCID_DCCID_VisitLabel? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> When you upload the scan as >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID_DCCID_VisitLabel, there is a check that makes sure the candidate IDs >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and visit label are valid at the time of upload. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> When you upload a scan as phantom, it >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> expects that the DICOM field PatientName and uploaded filename contains the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> string "phantom". We enforced this behaviour on the imaging uploader side >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in recent releases but I can't remember which one. Probably the upcoming >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 21.0 release. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> All those verifications might seem >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> cumbersome but they are here to ensure that the files inserted are all >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> valid and labelled properly as it is a bit messy to have to delete files >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> that were wrongly labelled. At least, the delete script present in release >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 21.0 will make this process easier but it is still good practice to verify >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> those things. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> With pleasure. Hopefully the answers to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> your questions will be helpful. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PS: loris-dev mailing list: you will >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> find the initial answer I gave Sotirios below. I forgot to cc the loris-dev >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in my earlier reply... >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 16 ???? 2019 ???? 12:02 ?.?., >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ?/? Cecile Madjar < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> cecile.madjar at mcin.ca> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Dear Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you for reaching out. Since your >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> email was already organized in points, I will reply directly below your >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> questions below. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 1) What do we do when the StudyUID is >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> blank on the header? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/minor/docs/AppendixA-Troubleshooting_guideline.md >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> There solution provided at the table 3 does not guide us how to find the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> information ( is possible ). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The StudyUID is the field used in our >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> pipeline at the moment to check whether a DICOM study was already inserted >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> into LORIS with that same StudyUID since it is supposed to be unique for >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> every single study. Currently, we do not support insertion of DICOM studies >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> if they do not have a StudyUID associated with them. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Is there a specific reason why the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> StudyUID is blank in the DICOM headers in your DICOM files? Did they go >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> through some processes before upload to LORIS? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 2) When i am about to upload a >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> non-phanton case i need a 'Visit Label'. Is there already a script that can >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> create a new visit label for a specific Candidate, so i can provide it as >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> input afterwards to the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> batch_uploads_imageuploader ( See option 5.1.3 https://github.com/aces/Loris-MRI/blob/minor/docs/05-PipelineLaunchOptions.md ) >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I am not sure if the front-end allows >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> for it but if you use batch_uploads_imageuploader, the insertion scripts >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> could create the visit label for you. However, it does need to be included >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in the patient name in order for the script to know which label it should >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> use. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> For example: you upload V02 for >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> MTL0123 (DCCID: 456789) but V02 was not yet created for MTL0123; the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> insertion scripts will create a V02 visit for MTL0123 if the PatientName >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> field for the dataset is MTL0123_456789_V02 with Stage marked as "Not >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Started". >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> However, *note that for the script to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> create the visit for the candidate, you have to make sure that all the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit label of your projects were inserted in the Visit_Windows table* >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> (otherwise, the visit will never be created as they were not specified as >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> being part of the list of visit label to expect). So in the example above, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> you should have one row in Visit_Windows with Visit_label="V02" set. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 3) Section 4.3 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/minor/docs/04-Scripts.md >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> What do we do when the folder contains multiple mnc files? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> This is a case by case. Most of the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> time, the MINC files that failed insertion into the imaging browser end up >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in the MRI violation module where you can see what went wrong with the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> acquisitions not inserted. If you notice that the MINC file should be >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> inserted as a specific protocol, you can force the insertion as explained >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in section 4.3. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> In your case, I have a feeling that >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> you want to be able to insert MINC files that did not go through the whole >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> pipeline insertion (DICOM archival, then dcm2mnc, then protocol >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> identification, then insertion...). In theory, you could call >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl on any MINC file, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> provided you have at least the following information: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - path to the MINC file >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - uploadID associated with the MINC >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> files or DICOM archive path from which those MINC files were created from >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Then the minc_insertion.pl script >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> will do the subject information and protocol validation etc... >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> If all the MINC files come from the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> same uploadID or TarchiveID, then you could run a loop in bash calling the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl script like this >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> for files deriving from uploadID=1: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ls /path/to/mnc/folder/* | while read >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> f; do minc_insertion.pl -profile prod >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -uploadID 1 -mincPath $f; done >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helped! >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> -- >>>>>>>>>>>>> >>>>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>>>> >>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> -- >>>>>>>>>>> >>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>> _______________________________________________ >>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> -- >>>>>>>>>> >>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>> Montreal Neurological Institute >>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>> >>>>>>>>> _______________________________________________ >>>>>>>>> Loris-dev mailing list >>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> -- >>>>>>>> Shen Wang >>>>>>>> Loris Developer >>>>>>>> Montreal Neurological Institute >>>>>>>> McGill University >>>>>>>> >>>>>>>> >>>>>>> >>>>>>> -- >>>>>>> Shen Wang >>>>>>> Loris Developer >>>>>>> Montreal Neurological Institute >>>>>>> McGill University >>>>>>> >>>>>>> _______________________________________________ >>>> Loris-dev mailing list >>>> Loris-dev at bic.mni.mcgill.ca >>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>> >>> >>> >>> -- >>> >>> christine.rogers at mcgill.ca >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>> Montreal Neurological Institute >>> McGill University | Montreal | Canada >>> >> > > -- > Shen Wang > Loris Developer > Montreal Neurological Institute > McGill University > > -------------- next part -------------- An HTML attachment was scrubbed... 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Name: sudo_chown_correction Type: application/octet-stream Size: 2898 bytes Desc: not available URL: From wangshen.mcin at gmail.com Fri Aug 30 20:31:42 2019 From: wangshen.mcin at gmail.com (Shen Wang) Date: Fri, 30 Aug 2019 20:31:42 -0400 Subject: [Loris-dev] Import mri - scripts In-Reply-To: References: Message-ID: Hi, This file is correct. https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief [ change v18.0.4.zip to v21.0.0.zip ] This install guide is also works for 21.0.0. Which version of Composer do you use? The error of continue to break, should be fixed after running [ composer self-update ] , then do composer install. Regards Shen On Fri, 30 Aug 2019 at 19:31, Sotirios Nikoloutsopoulos < sotirisnik at gmail.com> wrote: > Hi, > > Is the link below the stable release? > > wget https://github.com/aces/Loris/archive/v21.0.0.zip -O release.zip > > Also in the chown command i think that we need to add -R ( see chown file ) > > *sudo chown -**R **lorisadmin.lorisadmin /var/www/**l**oris* > > I runned composer install in /var/www/loris, please see the attached files. > > Thanks > > ???? ???, 30 ??? 2019 ???? 6:13 ?.?., ?/? Shen Wang < > wangshen.mcin at gmail.com> ??????: > >> Hi Sotirios, >> You should not use our minor branch (only for developing), we have >> published the 21.0-release officially, it is a stable version of Loris. >> After checking your error logs, you're missing is running composer >> install, which will import your packages and create the vendor folder, >> along with the autoload script. >> Regards >> Shen >> >> On Thu, 29 Aug 2019 at 19:46, Sotirios Nikoloutsopoulos < >> sotirisnik at gmail.com> wrote: >> >>> Hi, >>> >>> loris-access.log reports HTTP 500 error and loris-error reports that >>> some files are missing e.x. autoload.php from >>> /var/www/loris/htdocs/../vendor/autoload.php ( >>> https://github.com/aces/Loris/tree/minor/htdocs/vendor and as i can >>> verify those files do not exist in the github folder ) >>> >>> Thanks >>> >>> >>> >>> ???? ???, 29 ??? 2019 ???? 4:04 ?.?., ?/? Christine Rogers, Ms. < >>> christine.rogers at mcgill.ca> ??????: >>> >>>> Hi Sotirios, >>>> >>>> > Any suggestion why Loris is not showing up in the browser? >>>> >>>> >>>> - What are the last few lines of your loris-access and loris-error >>>> apache logs? >>>> >>>> - What are the URL and host in your Config table? (run these queries >>>> from the wiki >>>> >>>> ) >>>> >>>> - Are you using https, are the certificates in place, etc? >>>> >>>> - Do any of the wiki's Troubleshooting steps >>>> >>>> help? >>>> >>>> Best, >>>> Christine >>>> >>>> On Wed, Aug 28, 2019 at 9:30 PM Sotirios Nikoloutsopoulos < >>>> sotirisnik at gmail.com> wrote: >>>> >>>>> Any suggestion why Loris is not showing up in the browser? >>>>> >>>>> Thanks >>>>> >>>>> >>>>> ???? ???, 28 ??? 2019 ???? 2:30 ?.?., ?/? Sotirios Nikoloutsopoulos < >>>>> sotirisnik at gmail.com> ??????: >>>>> >>>>>> Also to mention that in the picture i opened the 000-default.conf >>>>>> which is just a copy of loris.conf by using cp >>>>>> >>>>>> ???? ???, 28 ??? 2019 ???? 2:20 ?.?., ?/? Sotirios Nikoloutsopoulos < >>>>>> sotirisnik at gmail.com> ??????: >>>>>> >>>>>>> Ok that fixed the install.sh problem. Now it doesn't show loris to >>>>>>> the browser, although everything seems right ( also >>>>>>> >>>>>>> /etc/apache2/sites-enabled/000-default.conf was replaced by loris.config ). >>>>>>> >>>>>>> >>>>>>> And apache is running >>>>>>> lorisadmin at loris-VirtualBox:/var/www/loris/htdocs$ sudo systemctl >>>>>>> status apache2[sudo] password for lorisadmin: >>>>>>> ? apache2.service - LSB: Apache2 web server >>>>>>> Loaded: loaded (/etc/init.d/apache2; bad; vendor preset: enabled) >>>>>>> Drop-In: /lib/systemd/system/apache2.service.d >>>>>>> ??apache2-systemd.conf >>>>>>> Active: active (running) since ??? 2019-08-28 02:15:12 EEST; 3min >>>>>>> 34s ago >>>>>>> >>>>>>> [image: image.png] >>>>>>> >>>>>>> ???? ???, 27 ??? 2019 ???? 9:42 ?.?., ?/? Shen Wang < >>>>>>> wangshen.mcin at gmail.com> ??????: >>>>>>> >>>>>>>> Hi, >>>>>>>> This is a bug for install.sh file, we will fix it later. >>>>>>>> Thank for letting me know your Loris install situation. >>>>>>>> regards >>>>>>>> Shen >>>>>>>> >>>>>>>> >>>>>>>> On Tue, 27 Aug 2019 at 14:28, Shen Wang >>>>>>>> wrote: >>>>>>>> >>>>>>>>> Hi, >>>>>>>>> Please remove "set -euo pipefail" line 10 in the install.sh file. >>>>>>>>> Then try again. >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> On Tue, 27 Aug 2019 at 14:05, Sotirios Nikoloutsopoulos < >>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>> >>>>>>>>>> Hi, >>>>>>>>>> >>>>>>>>>> i still haven't resolved the previous issue. Also i tried to >>>>>>>>>> install Loris to a new virtual machine and when i execute install.sh i get >>>>>>>>>> the following error >>>>>>>>>> >>>>>>>>>> lorisadmin at loris-VirtualBox:/var/www/loris/tools$ ./install.sh >>>>>>>>>> LORIS Installation Script starting at 2019-08-27T21:00:42 >>>>>>>>>> The log for this session will be stored in file >>>>>>>>>> /var/www/loris/tools/logs/install-2019-08-27T21:00:42.log >>>>>>>>>> >>>>>>>>>> --------------------------------------------------------------------- >>>>>>>>>> LORIS Installation Script >>>>>>>>>> >>>>>>>>>> --------------------------------------------------------------------- >>>>>>>>>> >>>>>>>>>> PHP appears to be installed. >>>>>>>>>> >>>>>>>>>> PHP Composer appears to be installed. >>>>>>>>>> >>>>>>>>>> This install script will ask you to provide inputs for different >>>>>>>>>> steps. >>>>>>>>>> Please ensure you have the following information ready (if >>>>>>>>>> applicable): >>>>>>>>>> >>>>>>>>>> 1) Your project directory name. >>>>>>>>>> (Will be used to modify the paths for Imaging data in the >>>>>>>>>> generated >>>>>>>>>> config.xml file for LORIS, and may also be used to >>>>>>>>>> automatically >>>>>>>>>> create/install apache config files.) If unsure, a default >>>>>>>>>> like "LORIS" >>>>>>>>>> should be acceptable. >>>>>>>>>> >>>>>>>>>> Please also consult the Loris WIKI on GitHub for more information >>>>>>>>>> on these >>>>>>>>>> Install Script input parameters. >>>>>>>>>> >>>>>>>>>> Ready to continue? [yn] y >>>>>>>>>> >>>>>>>>>> ./install.sh: line 132: projectname: unbound variable >>>>>>>>>> >>>>>>>>>> Thanks >>>>>>>>>> >>>>>>>>>> ???? ???, 6 ??? 2019 ???? 5:09 ?.?., ?/? Christine Rogers, Ms. < >>>>>>>>>> christine.rogers at mcgill.ca> ??????: >>>>>>>>>> >>>>>>>>>>> Hi Sotirios, >>>>>>>>>>> Could you also let us know -- on which pages is content visible, >>>>>>>>>>> and on which pages/modules is content not visible for you? >>>>>>>>>>> Thanks, >>>>>>>>>>> Christine >>>>>>>>>>> >>>>>>>>>>> On Tue, Aug 6, 2019 at 9:54 AM Christine Rogers, Ms. < >>>>>>>>>>> christine.rogers at mcgill.ca> wrote: >>>>>>>>>>> >>>>>>>>>>>> Thanks Sotirios, >>>>>>>>>>>> That's good to know. It sounds like you've checked that your >>>>>>>>>>>> /var/www/loris/project/config.xml file get populated properly. >>>>>>>>>>>> >>>>>>>>>>>> Please send us the last few errors you're seeing in your apache >>>>>>>>>>>> error log file, and your config paths and we can see what's happening with >>>>>>>>>>>> your front end -- >>>>>>>>>>>> Run these Troubleshooting Queries >>>>>>>>>>>> >>>>>>>>>>>> to get your config path settings, given your front end is not displaying >>>>>>>>>>>> fully. >>>>>>>>>>>> >>>>>>>>>>>> The Loris-MRI repo >>>>>>>>>>>> 21 >>>>>>>>>>>> install/upgrade would then be your next steps. >>>>>>>>>>>> Best, >>>>>>>>>>>> Christine >>>>>>>>>>>> >>>>>>>>>>>> On Tue, Aug 6, 2019 at 7:53 AM Sotirios Nikoloutsopoulos < >>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>> >>>>>>>>>>>>> I am using a VM. What i did was: >>>>>>>>>>>>> 1) Download the files from https://github.com/aces/Loris and >>>>>>>>>>>>> replace them to my existing /vaw/www/loris folder. >>>>>>>>>>>>> 2) Execute the composer install --no-dev and then composer >>>>>>>>>>>>> dump-autoload as mentioned here >>>>>>>>>>>>> https://github.com/aces/Loris/wiki/Updating-your-LORIS. >>>>>>>>>>>>> 3) Execute install.sh from /var/www/loris/tools and because >>>>>>>>>>>>> LORIS already existed i moved a .config file, then re-executed the >>>>>>>>>>>>> install.sh successfully >>>>>>>>>>>>> 4 ) As for the database, i dropped the schema and i executed >>>>>>>>>>>>> the installdb.php >>>>>>>>>>>>> >>>>>>>>>>>>> ???? ???, 5 ??? 2019 ???? 5:22 ?.?., ?/? Christine Rogers, Ms. >>>>>>>>>>>>> ??????: >>>>>>>>>>>>> >>>>>>>>>>>>>> Hi Sotorios, >>>>>>>>>>>>>> >>>>>>>>>>>>>> Thanks - when you re-installed did you start on a fresh root >>>>>>>>>>>>>> path / VM or might some of your old system setting still apply? >>>>>>>>>>>>>> (And if you did any steps similar to an upgrade, did you >>>>>>>>>>>>>> follow the Upgrade steps in the Release Notes, from both repos?) >>>>>>>>>>>>>> >>>>>>>>>>>>>> About the TR_range column - it was recently split (MRI pr339 >>>>>>>>>>>>>> ) split into >>>>>>>>>>>>>> TR_min and _max columns. Given the code was trying to query TR_range which >>>>>>>>>>>>>> does not exist in your mri_protocol table, double-check which version of >>>>>>>>>>>>>> the Loris repo (tables) and the Loris-MRI repo (code) you have installed to >>>>>>>>>>>>>> ensure they match. >>>>>>>>>>>>>> >>>>>>>>>>>>>> Christine >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> On Mon, Aug 5, 2019 at 9:06 AM Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>> >>>>>>>>>>>>>>> I reinstalled LORIS to 21 version and now the content is not >>>>>>>>>>>>>>> visible at all at most pages. >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> ???? ???, 5 ??? 2019 ???? 3:19 ?.?., ?/? Sotirios >>>>>>>>>>>>>>> Nikoloutsopoulos ??????: >>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Is it easy to upgrade to Loris 21? Also the following fails >>>>>>>>>>>>>>>> because the line 1985 of NeuroDB/MRIProcessingUtility.pm query mri_protocol >>>>>>>>>>>>>>>> which doesn't have TR_range >>>>>>>>>>>>>>>> https://github.com/aces/Loris/blob/21.0-release/SQL/0000-00-00-schema.sql#L556 >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> lorisadmin at hbp:/data/loris/bin/mri$ >>>>>>>>>>>>>>>> ./batch_uploads_imageuploader -profile prod < ~/Desktop/input.txt > log.txt >>>>>>>>>>>>>>>> Use of uninitialized value $_ in pattern match (m//) at >>>>>>>>>>>>>>>> ./batch_uploads_imageuploader line 147. >>>>>>>>>>>>>>>> base is DCC0000_258024_V1 >>>>>>>>>>>>>>>> path is /data/incoming/ >>>>>>>>>>>>>>>> type is .tar.gz >>>>>>>>>>>>>>>> fullpath is /data/incoming/DCC0000_258024_V1.tar.gz >>>>>>>>>>>>>>>> DBD::mysql::st execute failed: Unknown column 'TR_range' in >>>>>>>>>>>>>>>> 'where clause' at >>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line 1985. >>>>>>>>>>>>>>>> DBD::mysql::st fetchrow_array failed: fetch() without >>>>>>>>>>>>>>>> execute() at >>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line 1986. >>>>>>>>>>>>>>>> Use of uninitialized value $count_mri_protocol in numeric >>>>>>>>>>>>>>>> gt (>) at /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm >>>>>>>>>>>>>>>> line 1995. >>>>>>>>>>>>>>>> DBD::mysql::st execute failed: Unknown column 'TR_range' in >>>>>>>>>>>>>>>> 'field list' at /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 562. >>>>>>>>>>>>>>>> Can't exec "mail": No such file or directory at >>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 721. >>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 722. >>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 723. >>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 724. >>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 725. >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> No Mincs inserted >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Thanks, >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> ???? ???, 3 ??? 2019 ???? 1:08 ?.?., ?/? Christine Rogers, >>>>>>>>>>>>>>>> Ms. ??????: >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> First, just a note: we've released LORIS 21 this week >>>>>>>>>>>>>>>>> with some major new features and cleanup -- especially if you are early in >>>>>>>>>>>>>>>>> your setup phase, check out the Release notes for both the >>>>>>>>>>>>>>>>> LORIS >>>>>>>>>>>>>>>>> and Loris-MRI >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> repos. >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Thanks for your screenshots -- your empty mri_protocol >>>>>>>>>>>>>>>>> table should be at the root of these issues : >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> The mri_protocol table must be populated >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> in order for your scans to be registered in LORIS -- it serves as a >>>>>>>>>>>>>>>>> whitelist for the insertion pipeline which filters out scans that aren't >>>>>>>>>>>>>>>>> identified or matched to scan types in this table. >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> By default, this table is populated with entries for t1, >>>>>>>>>>>>>>>>> t2, fMRI and DTI (Insert statements for 21 release branch >>>>>>>>>>>>>>>>> are here >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> ) >>>>>>>>>>>>>>>>> Feel free to restore our default records and broaden their >>>>>>>>>>>>>>>>> parameters to match all your scan types. >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> re Defaced, native, selected -- these filter the scans >>>>>>>>>>>>>>>>> displayed as you move to the next page (View Session), instead of viewing >>>>>>>>>>>>>>>>> "all types" of scans from a given session : >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> - "defaced" means that a defacing script >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> has masked the subject's face in the volume (for patient privacy) >>>>>>>>>>>>>>>>> - "native" means that no pre-processing has been >>>>>>>>>>>>>>>>> performed on the scan (it's raw data), >>>>>>>>>>>>>>>>> - "selected" will show only volumes that have been >>>>>>>>>>>>>>>>> QC'd and "selected" as the best of their type -- used to display only the >>>>>>>>>>>>>>>>> best quality T1 image instead of all T1s acquired in a session, e.g. >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> re QC Comments -- >>>>>>>>>>>>>>>>> Once you have successfully loaded scans (matched to the >>>>>>>>>>>>>>>>> mri_protocol table), you'll be able to use the Imaging Browser's View >>>>>>>>>>>>>>>>> Session subpage to enter/view QC comments on each volume, or for each >>>>>>>>>>>>>>>>> visit. >>>>>>>>>>>>>>>>> These are stored directly in the database, and linked to >>>>>>>>>>>>>>>>> each scan. (Table name: feedback_mri_comments) >>>>>>>>>>>>>>>>> (Visit-level QC comments are linked to the session.) >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> For a walkthrough of the Imaging setup - please see the Imaging >>>>>>>>>>>>>>>>> Setup guide >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> - >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> An old LORIS walkthrough video >>>>>>>>>>>>>>>>> can also >>>>>>>>>>>>>>>>> walk you through some of the Imaging front-end features, starting at 8:00 >>>>>>>>>>>>>>>>> LORIS' imaging modules have been updated many times since >>>>>>>>>>>>>>>>> this video, but the functionality and workflow is similar. >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Let us know how it goes once you have entries in your >>>>>>>>>>>>>>>>> mri_protocol table - >>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>> Christine >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> On Fri, Aug 2, 2019 at 7:58 AM Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Hi Christine, >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> In the candidate_list page i can see this patient >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> If i press the link under PSCID i get to see >>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> and if i press the link under Scan Done it redirects me >>>>>>>>>>>>>>>>>> to imaging_browser >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> At the mri_violations page i also see No results ( >>>>>>>>>>>>>>>>>> neither on resolved / not resolved ). >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> At the imaging_uploader i can see the record that failed. >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> If i click on the tarchive info i get to see the Protocol >>>>>>>>>>>>>>>>>> Name which i think is the acquisition we wanted? >>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Also my mri_protocol table is empty. >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Furthermore i would like to ask about the defaced, >>>>>>>>>>>>>>>>>> native, selected. What exactly is native and selected? And where are the qc >>>>>>>>>>>>>>>>>> comments stored? >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Finally a walkthrough would be helpful. >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Thanks, >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> ???? ???, 30 ???? 2019 ???? 8:29 ?.?., ?/? Christine >>>>>>>>>>>>>>>>>> Rogers, Ms. ??????: >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>> Glad to hear you're making progress with the visit >>>>>>>>>>>>>>>>>>> labels. To follow up on your last few emails: >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> a- The Wiki's Setup Guide contains Sample insert >>>>>>>>>>>>>>>>>>> statements for the Visit Windows table >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> . >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> As Cecile mentioned, the consistency of visit label >>>>>>>>>>>>>>>>>>> format is important: V01, v01, V1, 01 -- whichever you select to use is >>>>>>>>>>>>>>>>>>> fine; we use V01 by default across all documentation. >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> b- For Password reset, there is a script in the tools/ >>>>>>>>>>>>>>>>>>> directory so that a back-end administrator can reset any front-end user >>>>>>>>>>>>>>>>>>> password, including Admin. (See info on setting up / resetting User >>>>>>>>>>>>>>>>>>> passwords in the Wiki's Setup Guide >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> ) >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> c- The minc file not being registered -- due to >>>>>>>>>>>>>>>>>>> AcquisitionProtocol unknown. >>>>>>>>>>>>>>>>>>> This means the SeriesDescription (Acquisition Protocol) >>>>>>>>>>>>>>>>>>> in you Dicom header was not matched to any scan listed in the mri_protocol >>>>>>>>>>>>>>>>>>> database table. >>>>>>>>>>>>>>>>>>> (In the online Loris-MRI Troubleshooting Guide, >>>>>>>>>>>>>>>>>>> this >>>>>>>>>>>>>>>>>>> is Table 3, 2nd-last item "no MINCs inserted"). >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> The MRI Violations module (Readme here) >>>>>>>>>>>>>>>>>>> will show >>>>>>>>>>>>>>>>>>> you the details of this mismatch -- >>>>>>>>>>>>>>>>>>> Go to the module (under the Imaging menu), find your >>>>>>>>>>>>>>>>>>> scan and click the link "Could not identify scan type" -- in the next >>>>>>>>>>>>>>>>>>> subpage you can compare the scan's actual parameters against the >>>>>>>>>>>>>>>>>>> mri_protocol table. >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> To resolve this, adjust your mri_protocol table values >>>>>>>>>>>>>>>>>>> or perhaps ensure your DICOMs are labelled consistently. >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Let us know if this works for you -- we can also walk >>>>>>>>>>>>>>>>>>> you through an example of non-identified scans on >>>>>>>>>>>>>>>>>>> Demo.loris.ca (MRI Violations module). >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>> Christine >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> The LORIS team >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> On Tue, Jul 30, 2019 at 10:47 AM Sotirios >>>>>>>>>>>>>>>>>>> Nikoloutsopoulos wrote: >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> I hope this is sufficient as the error for the visit >>>>>>>>>>>>>>>>>>>> label disappeared. >>>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Please see the attached file. Also something i found. >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> lorisadmin at hbp:/data/loris/bin/mri$ cat >>>>>>>>>>>>>>>>>>>> /data/loris/data//logs/TarLoad-17-39-xubBdv.log >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> ==> Loading file from disk >>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-17-39-UyQcG2/dcc0000_258024_v1_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> --> mapping DICOM parameter for >>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-17-39-UyQcG2/dcc0000_258024_v1_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> ==> computing md5 hash for MINC body. >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> --> md5: 6b1202fd63e29de4c9be1cd9925888a5 >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> ==> verifying acquisition protocol >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Acquisition protocol is unknown >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> --> The minc file cannot be registered since the >>>>>>>>>>>>>>>>>>>> AcquisitionProtocol is unknown >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> ???? ???, 30 ???? 2019 ???? 4:58 ?.?., ?/? Sotirios >>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos ??????: >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> Ok I fixed the login problem by using a known hash and >>>>>>>>>>>>>>>>>>>>> by deleting the rows from the login_history i was able to login. >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> ???? ???, 30 ???? 2019 ???? 4:50 ?.?., ?/? Sotirios >>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos ??????: >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> there was no visit label 01 in the Visit_Windows >>>>>>>>>>>>>>>>>>>>>> table and i don't know how to insert it because the record requires lots of >>>>>>>>>>>>>>>>>>>>>> attributes. Also the system for a reason asked me to update my password and >>>>>>>>>>>>>>>>>>>>>> now i don't remember it and my account got suspended. Is there a way to >>>>>>>>>>>>>>>>>>>>>> reset it or set a simple password? I updated the password hash in the >>>>>>>>>>>>>>>>>>>>>> users table by using the hash from another LORIS setup we had and i still >>>>>>>>>>>>>>>>>>>>>> couldn't login ( also the attribute password is always NULL and the >>>>>>>>>>>>>>>>>>>>>> expiration date is 1999-01-01 for some reason ). >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> Thanks >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> ???? ???, 29 ???? 2019 ???? 5:21 ?.?., ?/? Cecile >>>>>>>>>>>>>>>>>>>>>> Madjar ??????: >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> Can you try adding the visit label v01 to the >>>>>>>>>>>>>>>>>>>>>>> Visit_Windows table? >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> However, I noticed that in a previous dataset, the >>>>>>>>>>>>>>>>>>>>>>> label was V1. Does that refer to the same visit? If so, you might want to >>>>>>>>>>>>>>>>>>>>>>> harmonize the visit labels so they are all the same across datasets for a >>>>>>>>>>>>>>>>>>>>>>> given timepoint, meaning you will need to relabel scans when the visit >>>>>>>>>>>>>>>>>>>>>>> label is different but referring to the same visit label (v01 = V1 etc...). >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> Hope this helps, >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> On Mon, Jul 29, 2019 at 10:15 AM Sotirios >>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos wrote: >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> Could you help me with the "Visit label does not >>>>>>>>>>>>>>>>>>>>>>>> exist"? I had changed $subjectID{'createVisitLabel'} to 1 as you had >>>>>>>>>>>>>>>>>>>>>>>> suggested but it appears that this problem hasn't been resolved yet. >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> lorisadmin at hbp:/data/loris/bin/mri$ cat >>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data//logs/TarLoad-14-58-9Xog7H.log >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> ==> Loading file from disk >>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> --> mapping DICOM parameter for >>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> --> using user-defined filterParameters for >>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> Candidate Mismatch Error is Visit label does not >>>>>>>>>>>>>>>>>>>>>>>> exist >>>>>>>>>>>>>>>>>>>>>>>> -> WARNING: This candidate was invalid. Logging to >>>>>>>>>>>>>>>>>>>>>>>> MRICandidateErrors table with reason >>>>>>>>>>>>>>>>>>>>>>>> Visit label does not exist >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 26 ???? 2019 ???? 3:02 ?.?., ?/? Sotirios >>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos ??????: >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> Hi Cecile, >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> The Center error was fixed. Still the insertion of >>>>>>>>>>>>>>>>>>>>>>>>> mincs fails. Please see the output.txt file i attached. Also is there >>>>>>>>>>>>>>>>>>>>>>>>> something else i need to change at the paths configuration? >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 25 ???? 2019 ???? 6:55 ?.?., ?/? Cecile >>>>>>>>>>>>>>>>>>>>>>>>> Madjar ??????: >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> We are making progress! >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> I have a feeling this error comes from the fact >>>>>>>>>>>>>>>>>>>>>>>>>> that your psc table does not have the MRI_alias populated for the DCC site. >>>>>>>>>>>>>>>>>>>>>>>>>> Running the following query in the mysql database should fix this: >>>>>>>>>>>>>>>>>>>>>>>>>> UPDATE psc SET MRI_alias="DCC", Alias="DCC" WHERE >>>>>>>>>>>>>>>>>>>>>>>>>> Name="Data Coordinating Center"; >>>>>>>>>>>>>>>>>>>>>>>>>> Repeat the same with all your sites (make sure to >>>>>>>>>>>>>>>>>>>>>>>>>> change the Aliases between sites, they should all be unique). >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> Let me know how it goes! >>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> On Thu, Jul 25, 2019 at 11:43 AM Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos wrote: >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> Dear Cecile, >>>>>>>>>>>>>>>>>>>>>>>>>>> You were right about your guesses. I did the >>>>>>>>>>>>>>>>>>>>>>>>>>> modifications you suggested, i still get the "no mincs inserted" error, now >>>>>>>>>>>>>>>>>>>>>>>>>>> i am getting the "No center found this candidate" error ( how do i fix >>>>>>>>>>>>>>>>>>>>>>>>>>> that? from what i see the .dcm files contains a 'Institution Name', is that >>>>>>>>>>>>>>>>>>>>>>>>>>> the center? ), so i guess that's why the validation fails, but i changed >>>>>>>>>>>>>>>>>>>>>>>>>>> the force variable of tarchiveLoader to 1, shouldn't it have inserted the >>>>>>>>>>>>>>>>>>>>>>>>>>> mincs then? Also it is optional to have a mail server, right? ( from what i >>>>>>>>>>>>>>>>>>>>>>>>>>> see the mail error does not affect the $valid_study, so i assume we are >>>>>>>>>>>>>>>>>>>>>>>>>>> okay with that ) >>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you a lot, >>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 25 ???? 2019 ???? 5:48 ?.?., ?/? >>>>>>>>>>>>>>>>>>>>>>>>>>> Cecile Madjar ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> From what I understand, I believe you just need >>>>>>>>>>>>>>>>>>>>>>>>>>>> to update a few config settings from the frontend in the Config module >>>>>>>>>>>>>>>>>>>>>>>>>>>> (under the Admin menu). >>>>>>>>>>>>>>>>>>>>>>>>>>>> [image: Screen Shot 2019-07-25 at 10.31.35 >>>>>>>>>>>>>>>>>>>>>>>>>>>> AM.png] >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> Then go to the Paths section of the config >>>>>>>>>>>>>>>>>>>>>>>>>>>> module and update the "LORIS-MRI code" config setting to >>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri (my guess is that currently, it is set to >>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data) and click on the submit button. >>>>>>>>>>>>>>>>>>>>>>>>>>>> [image: Screen Shot 2019-07-25 at 10.32.50 >>>>>>>>>>>>>>>>>>>>>>>>>>>> AM.png] >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> Then, go to Imaging Pipeline section of the >>>>>>>>>>>>>>>>>>>>>>>>>>>> Configuration module and update the "Loris-MRI Data Directory" to >>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/ (my guess is that it is empty at the moment in your >>>>>>>>>>>>>>>>>>>>>>>>>>>> database which is why $data_dir is not defined when you run the >>>>>>>>>>>>>>>>>>>>>>>>>>>> tarchiveLoader step of the insertion pipeline). >>>>>>>>>>>>>>>>>>>>>>>>>>>> [image: Screen Shot 2019-07-25 at 10.40.52 >>>>>>>>>>>>>>>>>>>>>>>>>>>> AM.png] >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> Finally, I took a look at your environment file >>>>>>>>>>>>>>>>>>>>>>>>>>>> and it might be a good idea to update your PERL5LIB variable to the >>>>>>>>>>>>>>>>>>>>>>>>>>>> following (it has been added to the code a few releases ago as we realized >>>>>>>>>>>>>>>>>>>>>>>>>>>> this was needed for the libraries. Not sure which version of LORIS-MRI you >>>>>>>>>>>>>>>>>>>>>>>>>>>> are using but it does not hurt to update this variable to what I suggest >>>>>>>>>>>>>>>>>>>>>>>>>>>> below): >>>>>>>>>>>>>>>>>>>>>>>>>>>> export >>>>>>>>>>>>>>>>>>>>>>>>>>>> PERL5LIB=/data/loris/bin/mri/uploadNeuroDB:/data/loris/bin/mri/dicom-archive:$PERL5LIB >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helps. Sorry you are experiencing so >>>>>>>>>>>>>>>>>>>>>>>>>>>> much trouble setting things up. We probably need to update our WIKI. >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> On Thu, Jul 25, 2019 at 9:48 AM Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos wrote: >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> The "Loris-MRI Data Directory" should be in >>>>>>>>>>>>>>>>>>>>>>>>>>>>> the environment file? >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 25 ???? 2019 ???? 12:59 ?.?., ?/? >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The scripts are located in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/. Somewhere I might have messed something up but i >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> remember following the instructions in the wiki.For example when i tried to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> execute the batch_uploads_imageuploader perl script the line >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> my $command = "$bin_dir/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl " >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> was pointing to an invalid path, for example: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> it was repeating a pattern and had LORIS instead of loris ( i think the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> mistake was that in the wiki it suggested to use $PROJECT for the name of >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the folder and i choosed 'loris' >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris/wiki/Imaging-Database >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ). See also the in image for the modification i did. Also i didn't find the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> section to config the $data_dir variable. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 24 ???? 2019 ???? 6:05 ?.?., ?/? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Cecile Madjar ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> It looks like you have one Config setting >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> not set (based on the first error message you got when running it the first >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> time). You need to set a value for "Loris-MRI Data Directory" in the Config >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> module under the Imaging pipeline section (from what I can see, it would be >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/ for your setup). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The reason you got that error message the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> second time is that the pipeline checks if the DICOM study was already >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> inserted in the tarchive table. Since you ran the study once already, the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> study is inserted into the tarchive, hence the message. However, the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> pipeline did not complete as the MINC files were not created and inserted >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> into the files/parameter_file table. In order to continue the insertion, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> you will then need to run the tarchiveLoader command suggested in the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> terminal during the second run: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -globLocation -profile prod >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive//2012/DCM_2012-12-05_ImagingUpload-17-43-ZUEFjb.tar >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -verbose >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Finally, I am a bit confused by your setup. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Where are the scripts located? In /data/loris/bin/mri or /data/loris/data? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> It feels like the Config setting "LORIS-MRI code" in the Paths section was >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> set to "/data/LORIS/data" but it should have been set to the directory >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> where the scripts are located (most probably /data/loris/bin/mri). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helps, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> On Wed, Jul 24, 2019 at 10:55 AM Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> wrote: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Ok first i execute this command: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> "lorisadmin at hbp:/data/loris/bin/mri$ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ./batch_uploads_imageuploader -profile prod < ~/Desktop/input.txt > log.txt >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at ./batch_uploads_imageuploader line 143. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at ./batch_uploads_imageuploader line 143. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $_ in pattern >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> match (m//) at ./batch_uploads_imageuploader line 147. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> base is DCC0000_258024_V01 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> path is /data/incoming/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> type is .tar.gz >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> fullpath is >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/incoming/DCC0000_258024_V01.tar.gz >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> source /tmp/ImagingUpload-17-43-ZUEFjb >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> targetlocation /data/loris/data/tarchive >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 256. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 284. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at /data/loris/bin/mri/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> tarchive_validation.pl line 219. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at /data/loris/bin/mri/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl line 270. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 711. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Can't exec "mail": No such file or >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> directory at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 721. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 722. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 723. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 724. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 724. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 725. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 735. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> No Mincs inserted >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The tarchiveLoader insertion script has >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> failed. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Running now the following command: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl -profile prod >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -upload_id 3 /data/incoming/DCC0000_258024_V01.tar.gz -verbose" >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I inserted the VisitLabel, but still the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Mincs are not inserted and i am getting this error >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> "lorisadmin at hbp:/data/loris/bin/mri$ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl -profile prod >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -upload_id 3 /data/incoming/DCC0000_258024_V01.tar.gz -verbose >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> find -path >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> \/tmp\/ImagingUpload\-17\-45\-5MsWEd -name '__MACOSX' -delete >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Spool message is: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The Scan for the uploadID 3 has already >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> been run with tarchiveID: 7. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> To continue with the rest of the insertion >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> pipeline, please run tarchiveLoader from a terminal as follows: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader -globLocation -profile prod >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive//2012/DCM_2012-12-05_ImagingUpload-17-43-ZUEFjb.tar >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -verbose" >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Which files should i delete? I thought that >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> deleting the files from the tarchive was enough. And i executed the last >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> proposed command to continue to rest of the insertion pipeline ( check the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> image ). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 24 ???? 2019 ???? 5:05 ?.?., ?/? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Cecile Madjar >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sorry I was not clear before. Every visits >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> of candidates are created in the session table with one entry per >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID/VisitLabel. So if the imaging pipeline created visits in the session >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> table (that are not attached to instruments) and you want to clean your >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> database completely, you can delete entries in that table as well. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Regarding your point 2, the imaging >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> pipeline can create the visit in the session table as long as the visit >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> label is present in the Visit_Windows table (which means the visit label >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> stored in the PatientName is a valid visit label). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> However, in your prod file, if the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> variable $subjectID{'createVisitLabel'} is set to 1 for candidates, the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit label should be created in the Visit_Windows table I believe. Here >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> is the line of the prod file you would need to change >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> . >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> In general, we prefer populating the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Visit_Windows table and set the $subjectID{'createVisitLabel'} to 0 for >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> candidate data to avoid insertion of badly labelled MRI data that are >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> complex to relabel. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Finally, regarding the candidate creation, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> if you execute the following steps, the pipeline should be able to create >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> candidates: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - set in the Imaging Pipeline section of >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the config module the config setting "Upload creation of candidates" to Yes >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - manually transfer the scans to the LORIS >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> server instead of uploading it via the imaging browser >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - run batch_imaging_upload.pl as you did >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> until now. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helps! >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> On Wed, Jul 24, 2019 at 8:47 AM Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> wrote: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> About my second question i replaced the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> name of the patient in the .dcm files and now i am getting an error that >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the visit label does not exist. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I thought it was supposed to be >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> automatically created. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> "Done adding archive info into database >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -globLocation -profile prod >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive//DCM_2012-12-05_ImagingUpload-15-42-yUwQQV.tar >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -verbose >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> md5sum >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive/DCM_2012-12-05_ImagingUpload-15-42-yUwQQV.tar >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> candidate id 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> => No Visit labelVisit label does not >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> exist >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Set centerID = 1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Number of MINC files that will be >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> considered for inserting into the database: 1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> log dir is /logs and log file is >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /logs/TarLoad-15-42-L6pocU.log >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> candidate id 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> => No Visit label >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Cleaning up temp files: rm -rf >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-15-42-J2rQms/ImagingUpload-15-42-yUwQQV*" >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 24 ???? 2019 ???? 3:38 ?.?., >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ?/? Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 1) What are the records in the session >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> table? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 2) I tried to upload a non-phantom file >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> like this >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> input_file.txt: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/incoming/DCC0000_258024_V1.tar.gz >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> N DCC0000_258024_V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Terminal: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ./batch_uploads_imageuploader -profile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> prod < ~/Desktop/input.txt > log.txt >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and i get the following error in the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> log.txt file >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> "Running now the following command: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl -profile prod >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -upload_id 7 /data/incoming/DCC0000_258024_V1.tar.gz -verbose >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> find -path >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> \/tmp\/ImagingUpload\-14\-56\-FeLCB4 -name '__MACOSX' -delete >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Spool message is: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The PatientName read from the DICOM >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> header does not start with DCC0000_258024_V1 from the mri_upload table >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> " >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and the spool message is repeated for >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> each .dcm file. Should i preprocess every .dcm file and change the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PatientName to "DCC0000_258024_V1"? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 3) As far as it concerns the candidate >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> profile i have to create a new one each time before i try to upload a file? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Is there already a way to create a candidate profile and get the DCCID and >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID without the user interface? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 18 ???? 2019 ???? 5:00 ?.?., >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ?/? Cecile Madjar >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> See answers to your questions below. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> About the 1st case we had a dicom with >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> a blank studyUID, maybe someone accidentally removed it. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> That is strange. Something must have >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> been done to the DICOM files. I have never seen a study with no StudyUID >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> out of the scanner. Usually, you need to manually erase it with some tool. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> However, DICOMs never cease to surprise me... >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Some other questions: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 1) What are the steps to remove all of >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> my patients and uploads?: because i want to try to reupload all the testing >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> dicoms we had with a clean database. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Release 21.0 of LORIS-MRI will offer a >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> script to remove all the entries and files specific to an upload. However, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> this release is not yet out. Hopefully in the next few weeks. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> In the meantime, since your case is >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> particular and that you just want to start with a clean database, the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> following deletes should work (hopefully I won't forget any tables): >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from mri_violations_log; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from mri_protocol_violated_scans; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from MRICandidateErrors; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from parameter_file; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from files_qcstatus; # (if you >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> played with the QC part of the imaging browser for testing) >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from feedback_mri_comments; # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> (if you played with the QC part of the imaging browser for testing) >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from tarchive_series; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from tarchive_files; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from mri_upload; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from tarchive; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from mri_scanner; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from candidate where >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID="scanner"; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I don't know if you want to also delete >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> entries in the session and candidate table too? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 2) We do not need to create the profile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> of a patient ( are the patients stored in the candidate table? because i >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> can't see the ghosts ), because will it automatically be created when >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> importing a dicom? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I am not sure I understand fully this >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> question. All candidates are stored in the candidate table. The phantom >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> scans however are attached to a scanner candidate depending on where the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> scan happened. It is a bit of a weird concept that we have to redesign >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> eventually but never got a chance to get to it. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hopefully this answered your question, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> otherwise, don't hesitate to let me know. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 3) What is the difference between >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> uploading a dicom as phantom instead of importing as >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCCID_DCCID_VisitLabel? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> When you upload the scan as >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID_DCCID_VisitLabel, there is a check that makes sure the candidate IDs >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and visit label are valid at the time of upload. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> When you upload a scan as phantom, it >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> expects that the DICOM field PatientName and uploaded filename contains the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> string "phantom". We enforced this behaviour on the imaging uploader side >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in recent releases but I can't remember which one. Probably the upcoming >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 21.0 release. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> All those verifications might seem >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> cumbersome but they are here to ensure that the files inserted are all >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> valid and labelled properly as it is a bit messy to have to delete files >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> that were wrongly labelled. At least, the delete script present in release >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 21.0 will make this process easier but it is still good practice to verify >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> those things. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> With pleasure. Hopefully the answers to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> your questions will be helpful. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PS: loris-dev mailing list: you will >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> find the initial answer I gave Sotirios below. I forgot to cc the loris-dev >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in my earlier reply... >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 16 ???? 2019 ???? 12:02 ?.?., >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ?/? Cecile Madjar < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> cecile.madjar at mcin.ca> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Dear Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you for reaching out. Since >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> your email was already organized in points, I will reply directly below >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> your questions below. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 1) What do we do when the StudyUID is >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> blank on the header? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/minor/docs/AppendixA-Troubleshooting_guideline.md >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> There solution provided at the table 3 does not guide us how to find the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> information ( is possible ). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The StudyUID is the field used in our >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> pipeline at the moment to check whether a DICOM study was already inserted >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> into LORIS with that same StudyUID since it is supposed to be unique for >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> every single study. Currently, we do not support insertion of DICOM studies >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> if they do not have a StudyUID associated with them. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Is there a specific reason why the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> StudyUID is blank in the DICOM headers in your DICOM files? Did they go >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> through some processes before upload to LORIS? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 2) When i am about to upload a >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> non-phanton case i need a 'Visit Label'. Is there already a script that can >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> create a new visit label for a specific Candidate, so i can provide it as >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> input afterwards to the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> batch_uploads_imageuploader ( See option 5.1.3 https://github.com/aces/Loris-MRI/blob/minor/docs/05-PipelineLaunchOptions.md ) >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I am not sure if the front-end allows >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> for it but if you use batch_uploads_imageuploader, the insertion scripts >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> could create the visit label for you. However, it does need to be included >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in the patient name in order for the script to know which label it should >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> use. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> For example: you upload V02 for >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> MTL0123 (DCCID: 456789) but V02 was not yet created for MTL0123; the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> insertion scripts will create a V02 visit for MTL0123 if the PatientName >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> field for the dataset is MTL0123_456789_V02 with Stage marked as "Not >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Started". >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> However, *note that for the script >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> to create the visit for the candidate, you have to make sure that all the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit label of your projects were inserted in the Visit_Windows table* >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> (otherwise, the visit will never be created as they were not specified as >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> being part of the list of visit label to expect). So in the example above, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> you should have one row in Visit_Windows with Visit_label="V02" set. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 3) Section 4.3 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/minor/docs/04-Scripts.md >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> What do we do when the folder contains multiple mnc files? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> This is a case by case. Most of the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> time, the MINC files that failed insertion into the imaging browser end up >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in the MRI violation module where you can see what went wrong with the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> acquisitions not inserted. If you notice that the MINC file should be >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> inserted as a specific protocol, you can force the insertion as explained >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in section 4.3. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> In your case, I have a feeling that >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> you want to be able to insert MINC files that did not go through the whole >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> pipeline insertion (DICOM archival, then dcm2mnc, then protocol >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> identification, then insertion...). In theory, you could call >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl on any MINC file, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> provided you have at least the following information: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - path to the MINC file >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - uploadID associated with the MINC >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> files or DICOM archive path from which those MINC files were created from >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Then the minc_insertion.pl script >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> will do the subject information and protocol validation etc... >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> If all the MINC files come from the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> same uploadID or TarchiveID, then you could run a loop in bash calling the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl script like this >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> for files deriving from uploadID=1: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ls /path/to/mnc/folder/* | while read >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> f; do minc_insertion.pl -profile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> prod -uploadID 1 -mincPath $f; done >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helped! >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> -- >>>>>>>>>>>>>> >>>>>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>>>>> >>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> -- >>>>>>>>>>>> >>>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> -- >>>>>>>>>>> >>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>> >>>>>>>>>> _______________________________________________ >>>>>>>>>> Loris-dev mailing list >>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> -- >>>>>>>>> Shen Wang >>>>>>>>> Loris Developer >>>>>>>>> Montreal Neurological Institute >>>>>>>>> McGill University >>>>>>>>> >>>>>>>>> >>>>>>>> >>>>>>>> -- >>>>>>>> Shen Wang >>>>>>>> Loris Developer >>>>>>>> Montreal Neurological Institute >>>>>>>> McGill University >>>>>>>> >>>>>>>> _______________________________________________ >>>>> Loris-dev mailing list >>>>> Loris-dev at bic.mni.mcgill.ca >>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>> >>>> >>>> >>>> -- >>>> >>>> christine.rogers at mcgill.ca >>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>> Montreal Neurological Institute >>>> McGill University | Montreal | Canada >>>> >>> >> >> -- >> Shen Wang >> Loris Developer >> Montreal Neurological Institute >> McGill University >> >> -- Shen Wang Loris Developer Montreal Neurological Institute McGill University -------------- next part -------------- An HTML attachment was scrubbed... URL: From sotirisnik at gmail.com Fri Aug 30 20:55:19 2019 From: sotirisnik at gmail.com (Sotirios Nikoloutsopoulos) Date: Sat, 31 Aug 2019 03:55:19 +0300 Subject: [Loris-dev] Import mri - scripts In-Reply-To: References: Message-ID: Which version of composer should i use? lorisadmin at loris-VirtualBox:/var/www/loris$ composer --version Composer version @package_branch_alias_version@ (1.0.0-beta2) 2016-03-27 16:00:34 lorisadmin at loris-VirtualBox:/var/www/loris$ composer self-update [InvalidArgumentException] Command "self-update" is not defined. ???? ???, 31 ??? 2019 ???? 3:31 ?.?., ?/? Shen Wang ??????: > Hi, > This file is correct. > https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief [ change > v18.0.4.zip to v21.0.0.zip > ] > This install guide is also works for 21.0.0. > Which version of Composer do you use? > The error of continue to break, should be fixed after running [ composer > self-update ] , then do composer install. > Regards > Shen > > On Fri, 30 Aug 2019 at 19:31, Sotirios Nikoloutsopoulos < > sotirisnik at gmail.com> wrote: > >> Hi, >> >> Is the link below the stable release? >> >> wget https://github.com/aces/Loris/archive/v21.0.0.zip -O release.zip >> >> Also in the chown command i think that we need to add -R ( see chown file >> ) >> >> *sudo chown -**R **lorisadmin.lorisadmin /var/www/**l**oris* >> >> I runned composer install in /var/www/loris, please see the attached >> files. >> >> Thanks >> >> ???? ???, 30 ??? 2019 ???? 6:13 ?.?., ?/? Shen Wang < >> wangshen.mcin at gmail.com> ??????: >> >>> Hi Sotirios, >>> You should not use our minor branch (only for developing), we have >>> published the 21.0-release officially, it is a stable version of Loris. >>> After checking your error logs, you're missing is running composer >>> install, which will import your packages and create the vendor folder, >>> along with the autoload script. >>> Regards >>> Shen >>> >>> On Thu, 29 Aug 2019 at 19:46, Sotirios Nikoloutsopoulos < >>> sotirisnik at gmail.com> wrote: >>> >>>> Hi, >>>> >>>> loris-access.log reports HTTP 500 error and loris-error reports that >>>> some files are missing e.x. autoload.php from >>>> /var/www/loris/htdocs/../vendor/autoload.php ( >>>> https://github.com/aces/Loris/tree/minor/htdocs/vendor and as i can >>>> verify those files do not exist in the github folder ) >>>> >>>> Thanks >>>> >>>> >>>> >>>> ???? ???, 29 ??? 2019 ???? 4:04 ?.?., ?/? Christine Rogers, Ms. < >>>> christine.rogers at mcgill.ca> ??????: >>>> >>>>> Hi Sotirios, >>>>> >>>>> > Any suggestion why Loris is not showing up in the browser? >>>>> >>>>> >>>>> - What are the last few lines of your loris-access and loris-error >>>>> apache logs? >>>>> >>>>> - What are the URL and host in your Config table? (run these queries >>>>> from the wiki >>>>> >>>>> ) >>>>> >>>>> - Are you using https, are the certificates in place, etc? >>>>> >>>>> - Do any of the wiki's Troubleshooting steps >>>>> >>>>> help? >>>>> >>>>> Best, >>>>> Christine >>>>> >>>>> On Wed, Aug 28, 2019 at 9:30 PM Sotirios Nikoloutsopoulos < >>>>> sotirisnik at gmail.com> wrote: >>>>> >>>>>> Any suggestion why Loris is not showing up in the browser? >>>>>> >>>>>> Thanks >>>>>> >>>>>> >>>>>> ???? ???, 28 ??? 2019 ???? 2:30 ?.?., ?/? Sotirios Nikoloutsopoulos < >>>>>> sotirisnik at gmail.com> ??????: >>>>>> >>>>>>> Also to mention that in the picture i opened the 000-default.conf >>>>>>> which is just a copy of loris.conf by using cp >>>>>>> >>>>>>> ???? ???, 28 ??? 2019 ???? 2:20 ?.?., ?/? Sotirios Nikoloutsopoulos < >>>>>>> sotirisnik at gmail.com> ??????: >>>>>>> >>>>>>>> Ok that fixed the install.sh problem. Now it doesn't show loris to >>>>>>>> the browser, although everything seems right ( also >>>>>>>> >>>>>>>> /etc/apache2/sites-enabled/000-default.conf was replaced by loris.config ). >>>>>>>> >>>>>>>> >>>>>>>> And apache is running >>>>>>>> lorisadmin at loris-VirtualBox:/var/www/loris/htdocs$ sudo systemctl >>>>>>>> status apache2[sudo] password for lorisadmin: >>>>>>>> ? apache2.service - LSB: Apache2 web server >>>>>>>> Loaded: loaded (/etc/init.d/apache2; bad; vendor preset: enabled) >>>>>>>> Drop-In: /lib/systemd/system/apache2.service.d >>>>>>>> ??apache2-systemd.conf >>>>>>>> Active: active (running) since ??? 2019-08-28 02:15:12 EEST; >>>>>>>> 3min 34s ago >>>>>>>> >>>>>>>> [image: image.png] >>>>>>>> >>>>>>>> ???? ???, 27 ??? 2019 ???? 9:42 ?.?., ?/? Shen Wang < >>>>>>>> wangshen.mcin at gmail.com> ??????: >>>>>>>> >>>>>>>>> Hi, >>>>>>>>> This is a bug for install.sh file, we will fix it later. >>>>>>>>> Thank for letting me know your Loris install situation. >>>>>>>>> regards >>>>>>>>> Shen >>>>>>>>> >>>>>>>>> >>>>>>>>> On Tue, 27 Aug 2019 at 14:28, Shen Wang >>>>>>>>> wrote: >>>>>>>>> >>>>>>>>>> Hi, >>>>>>>>>> Please remove "set -euo pipefail" line 10 in the install.sh file. >>>>>>>>>> Then try again. >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> On Tue, 27 Aug 2019 at 14:05, Sotirios Nikoloutsopoulos < >>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>> >>>>>>>>>>> Hi, >>>>>>>>>>> >>>>>>>>>>> i still haven't resolved the previous issue. Also i tried to >>>>>>>>>>> install Loris to a new virtual machine and when i execute install.sh i get >>>>>>>>>>> the following error >>>>>>>>>>> >>>>>>>>>>> lorisadmin at loris-VirtualBox:/var/www/loris/tools$ ./install.sh >>>>>>>>>>> LORIS Installation Script starting at 2019-08-27T21:00:42 >>>>>>>>>>> The log for this session will be stored in file >>>>>>>>>>> /var/www/loris/tools/logs/install-2019-08-27T21:00:42.log >>>>>>>>>>> >>>>>>>>>>> --------------------------------------------------------------------- >>>>>>>>>>> LORIS Installation Script >>>>>>>>>>> >>>>>>>>>>> --------------------------------------------------------------------- >>>>>>>>>>> >>>>>>>>>>> PHP appears to be installed. >>>>>>>>>>> >>>>>>>>>>> PHP Composer appears to be installed. >>>>>>>>>>> >>>>>>>>>>> This install script will ask you to provide inputs for different >>>>>>>>>>> steps. >>>>>>>>>>> Please ensure you have the following information ready (if >>>>>>>>>>> applicable): >>>>>>>>>>> >>>>>>>>>>> 1) Your project directory name. >>>>>>>>>>> (Will be used to modify the paths for Imaging data in the >>>>>>>>>>> generated >>>>>>>>>>> config.xml file for LORIS, and may also be used to >>>>>>>>>>> automatically >>>>>>>>>>> create/install apache config files.) If unsure, a default >>>>>>>>>>> like "LORIS" >>>>>>>>>>> should be acceptable. >>>>>>>>>>> >>>>>>>>>>> Please also consult the Loris WIKI on GitHub for more >>>>>>>>>>> information on these >>>>>>>>>>> Install Script input parameters. >>>>>>>>>>> >>>>>>>>>>> Ready to continue? [yn] y >>>>>>>>>>> >>>>>>>>>>> ./install.sh: line 132: projectname: unbound variable >>>>>>>>>>> >>>>>>>>>>> Thanks >>>>>>>>>>> >>>>>>>>>>> ???? ???, 6 ??? 2019 ???? 5:09 ?.?., ?/? Christine Rogers, Ms. < >>>>>>>>>>> christine.rogers at mcgill.ca> ??????: >>>>>>>>>>> >>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>> Could you also let us know -- on which pages is content >>>>>>>>>>>> visible, and on which pages/modules is content not visible for you? >>>>>>>>>>>> Thanks, >>>>>>>>>>>> Christine >>>>>>>>>>>> >>>>>>>>>>>> On Tue, Aug 6, 2019 at 9:54 AM Christine Rogers, Ms. < >>>>>>>>>>>> christine.rogers at mcgill.ca> wrote: >>>>>>>>>>>> >>>>>>>>>>>>> Thanks Sotirios, >>>>>>>>>>>>> That's good to know. It sounds like you've checked that your >>>>>>>>>>>>> /var/www/loris/project/config.xml file get populated properly. >>>>>>>>>>>>> >>>>>>>>>>>>> Please send us the last few errors you're seeing in your >>>>>>>>>>>>> apache error log file, and your config paths and we can see what's >>>>>>>>>>>>> happening with your front end -- >>>>>>>>>>>>> Run these Troubleshooting Queries >>>>>>>>>>>>> >>>>>>>>>>>>> to get your config path settings, given your front end is not displaying >>>>>>>>>>>>> fully. >>>>>>>>>>>>> >>>>>>>>>>>>> The Loris-MRI repo >>>>>>>>>>>>> 21 >>>>>>>>>>>>> install/upgrade would then be your next steps. >>>>>>>>>>>>> Best, >>>>>>>>>>>>> Christine >>>>>>>>>>>>> >>>>>>>>>>>>> On Tue, Aug 6, 2019 at 7:53 AM Sotirios Nikoloutsopoulos < >>>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>> >>>>>>>>>>>>>> I am using a VM. What i did was: >>>>>>>>>>>>>> 1) Download the files from https://github.com/aces/Loris and >>>>>>>>>>>>>> replace them to my existing /vaw/www/loris folder. >>>>>>>>>>>>>> 2) Execute the composer install --no-dev and then composer >>>>>>>>>>>>>> dump-autoload as mentioned here >>>>>>>>>>>>>> https://github.com/aces/Loris/wiki/Updating-your-LORIS. >>>>>>>>>>>>>> 3) Execute install.sh from /var/www/loris/tools and because >>>>>>>>>>>>>> LORIS already existed i moved a .config file, then re-executed the >>>>>>>>>>>>>> install.sh successfully >>>>>>>>>>>>>> 4 ) As for the database, i dropped the schema and i executed >>>>>>>>>>>>>> the installdb.php >>>>>>>>>>>>>> >>>>>>>>>>>>>> ???? ???, 5 ??? 2019 ???? 5:22 ?.?., ?/? Christine Rogers, >>>>>>>>>>>>>> Ms. ??????: >>>>>>>>>>>>>> >>>>>>>>>>>>>>> Hi Sotorios, >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> Thanks - when you re-installed did you start on a fresh root >>>>>>>>>>>>>>> path / VM or might some of your old system setting still apply? >>>>>>>>>>>>>>> (And if you did any steps similar to an upgrade, did you >>>>>>>>>>>>>>> follow the Upgrade steps in the Release Notes, from both repos?) >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> About the TR_range column - it was recently split (MRI pr339 >>>>>>>>>>>>>>> ) split into >>>>>>>>>>>>>>> TR_min and _max columns. Given the code was trying to query TR_range which >>>>>>>>>>>>>>> does not exist in your mri_protocol table, double-check which version of >>>>>>>>>>>>>>> the Loris repo (tables) and the Loris-MRI repo (code) you have installed to >>>>>>>>>>>>>>> ensure they match. >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> Christine >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> On Mon, Aug 5, 2019 at 9:06 AM Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> I reinstalled LORIS to 21 version and now the content is >>>>>>>>>>>>>>>> not visible at all at most pages. >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> ???? ???, 5 ??? 2019 ???? 3:19 ?.?., ?/? Sotirios >>>>>>>>>>>>>>>> Nikoloutsopoulos ??????: >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Is it easy to upgrade to Loris 21? Also the following >>>>>>>>>>>>>>>>> fails because the line 1985 of NeuroDB/MRIProcessingUtility.pm query >>>>>>>>>>>>>>>>> mri_protocol which doesn't have TR_range >>>>>>>>>>>>>>>>> https://github.com/aces/Loris/blob/21.0-release/SQL/0000-00-00-schema.sql#L556 >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> lorisadmin at hbp:/data/loris/bin/mri$ >>>>>>>>>>>>>>>>> ./batch_uploads_imageuploader -profile prod < ~/Desktop/input.txt > log.txt >>>>>>>>>>>>>>>>> Use of uninitialized value $_ in pattern match (m//) at >>>>>>>>>>>>>>>>> ./batch_uploads_imageuploader line 147. >>>>>>>>>>>>>>>>> base is DCC0000_258024_V1 >>>>>>>>>>>>>>>>> path is /data/incoming/ >>>>>>>>>>>>>>>>> type is .tar.gz >>>>>>>>>>>>>>>>> fullpath is /data/incoming/DCC0000_258024_V1.tar.gz >>>>>>>>>>>>>>>>> DBD::mysql::st execute failed: Unknown column 'TR_range' >>>>>>>>>>>>>>>>> in 'where clause' at >>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line 1985. >>>>>>>>>>>>>>>>> DBD::mysql::st fetchrow_array failed: fetch() without >>>>>>>>>>>>>>>>> execute() at >>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line 1986. >>>>>>>>>>>>>>>>> Use of uninitialized value $count_mri_protocol in numeric >>>>>>>>>>>>>>>>> gt (>) at /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm >>>>>>>>>>>>>>>>> line 1995. >>>>>>>>>>>>>>>>> DBD::mysql::st execute failed: Unknown column 'TR_range' >>>>>>>>>>>>>>>>> in 'field list' at /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line >>>>>>>>>>>>>>>>> 562. >>>>>>>>>>>>>>>>> Can't exec "mail": No such file or directory at >>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 721. >>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 722. >>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 723. >>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 724. >>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 725. >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> No Mincs inserted >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Thanks, >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> ???? ???, 3 ??? 2019 ???? 1:08 ?.?., ?/? Christine Rogers, >>>>>>>>>>>>>>>>> Ms. ??????: >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> First, just a note: we've released LORIS 21 this week >>>>>>>>>>>>>>>>>> with some major new features and cleanup -- especially if you are early in >>>>>>>>>>>>>>>>>> your setup phase, check out the Release notes for both the >>>>>>>>>>>>>>>>>> LORIS >>>>>>>>>>>>>>>>>> and >>>>>>>>>>>>>>>>>> Loris-MRI >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> repos. >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Thanks for your screenshots -- your empty mri_protocol >>>>>>>>>>>>>>>>>> table should be at the root of these issues : >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> The mri_protocol table must be populated >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> in order for your scans to be registered in LORIS -- it serves as a >>>>>>>>>>>>>>>>>> whitelist for the insertion pipeline which filters out scans that aren't >>>>>>>>>>>>>>>>>> identified or matched to scan types in this table. >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> By default, this table is populated with entries for t1, >>>>>>>>>>>>>>>>>> t2, fMRI and DTI (Insert statements for 21 release >>>>>>>>>>>>>>>>>> branch are here >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> ) >>>>>>>>>>>>>>>>>> Feel free to restore our default records and broaden >>>>>>>>>>>>>>>>>> their parameters to match all your scan types. >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> re Defaced, native, selected -- these filter the scans >>>>>>>>>>>>>>>>>> displayed as you move to the next page (View Session), instead of viewing >>>>>>>>>>>>>>>>>> "all types" of scans from a given session : >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> - "defaced" means that a defacing script >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> has masked the subject's face in the volume (for patient privacy) >>>>>>>>>>>>>>>>>> - "native" means that no pre-processing has been >>>>>>>>>>>>>>>>>> performed on the scan (it's raw data), >>>>>>>>>>>>>>>>>> - "selected" will show only volumes that have been >>>>>>>>>>>>>>>>>> QC'd and "selected" as the best of their type -- used to display only the >>>>>>>>>>>>>>>>>> best quality T1 image instead of all T1s acquired in a session, e.g. >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> re QC Comments -- >>>>>>>>>>>>>>>>>> Once you have successfully loaded scans (matched to the >>>>>>>>>>>>>>>>>> mri_protocol table), you'll be able to use the Imaging Browser's View >>>>>>>>>>>>>>>>>> Session subpage to enter/view QC comments on each volume, or for each >>>>>>>>>>>>>>>>>> visit. >>>>>>>>>>>>>>>>>> These are stored directly in the database, and linked to >>>>>>>>>>>>>>>>>> each scan. (Table name: feedback_mri_comments) >>>>>>>>>>>>>>>>>> (Visit-level QC comments are linked to the session.) >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> For a walkthrough of the Imaging setup - please see the Imaging >>>>>>>>>>>>>>>>>> Setup guide >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> - >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> An old LORIS walkthrough video >>>>>>>>>>>>>>>>>> can also >>>>>>>>>>>>>>>>>> walk you through some of the Imaging front-end features, starting at 8:00 >>>>>>>>>>>>>>>>>> LORIS' imaging modules have been updated many times since >>>>>>>>>>>>>>>>>> this video, but the functionality and workflow is similar. >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Let us know how it goes once you have entries in your >>>>>>>>>>>>>>>>>> mri_protocol table - >>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>> Christine >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> On Fri, Aug 2, 2019 at 7:58 AM Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Hi Christine, >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> In the candidate_list page i can see this patient >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> If i press the link under PSCID i get to see >>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> and if i press the link under Scan Done it redirects me >>>>>>>>>>>>>>>>>>> to imaging_browser >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> At the mri_violations page i also see No results ( >>>>>>>>>>>>>>>>>>> neither on resolved / not resolved ). >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> At the imaging_uploader i can see the record that failed. >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> If i click on the tarchive info i get to see the >>>>>>>>>>>>>>>>>>> Protocol Name which i think is the acquisition we wanted? >>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Also my mri_protocol table is empty. >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Furthermore i would like to ask about the defaced, >>>>>>>>>>>>>>>>>>> native, selected. What exactly is native and selected? And where are the qc >>>>>>>>>>>>>>>>>>> comments stored? >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Finally a walkthrough would be helpful. >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Thanks, >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> ???? ???, 30 ???? 2019 ???? 8:29 ?.?., ?/? Christine >>>>>>>>>>>>>>>>>>> Rogers, Ms. ??????: >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>> Glad to hear you're making progress with the visit >>>>>>>>>>>>>>>>>>>> labels. To follow up on your last few emails: >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> a- The Wiki's Setup Guide contains Sample insert >>>>>>>>>>>>>>>>>>>> statements for the Visit Windows table >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> . >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> As Cecile mentioned, the consistency of visit label >>>>>>>>>>>>>>>>>>>> format is important: V01, v01, V1, 01 -- whichever you select to use is >>>>>>>>>>>>>>>>>>>> fine; we use V01 by default across all documentation. >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> b- For Password reset, there is a script in the tools/ >>>>>>>>>>>>>>>>>>>> directory so that a back-end administrator can reset any front-end user >>>>>>>>>>>>>>>>>>>> password, including Admin. (See info on setting up / resetting User >>>>>>>>>>>>>>>>>>>> passwords in the Wiki's Setup Guide >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> ) >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> c- The minc file not being registered -- due to >>>>>>>>>>>>>>>>>>>> AcquisitionProtocol unknown. >>>>>>>>>>>>>>>>>>>> This means the SeriesDescription (Acquisition Protocol) >>>>>>>>>>>>>>>>>>>> in you Dicom header was not matched to any scan listed in the mri_protocol >>>>>>>>>>>>>>>>>>>> database table. >>>>>>>>>>>>>>>>>>>> (In the online Loris-MRI Troubleshooting Guide, >>>>>>>>>>>>>>>>>>>> this >>>>>>>>>>>>>>>>>>>> is Table 3, 2nd-last item "no MINCs inserted"). >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> The MRI Violations module (Readme here) >>>>>>>>>>>>>>>>>>>> will show >>>>>>>>>>>>>>>>>>>> you the details of this mismatch -- >>>>>>>>>>>>>>>>>>>> Go to the module (under the Imaging menu), find your >>>>>>>>>>>>>>>>>>>> scan and click the link "Could not identify scan type" -- in the next >>>>>>>>>>>>>>>>>>>> subpage you can compare the scan's actual parameters against the >>>>>>>>>>>>>>>>>>>> mri_protocol table. >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> To resolve this, adjust your mri_protocol table values >>>>>>>>>>>>>>>>>>>> or perhaps ensure your DICOMs are labelled consistently. >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Let us know if this works for you -- we can also walk >>>>>>>>>>>>>>>>>>>> you through an example of non-identified scans on >>>>>>>>>>>>>>>>>>>> Demo.loris.ca (MRI Violations module). >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>> Christine >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> The LORIS team >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> On Tue, Jul 30, 2019 at 10:47 AM Sotirios >>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos wrote: >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> I hope this is sufficient as the error for the visit >>>>>>>>>>>>>>>>>>>>> label disappeared. >>>>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> Please see the attached file. Also something i found. >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> lorisadmin at hbp:/data/loris/bin/mri$ cat >>>>>>>>>>>>>>>>>>>>> /data/loris/data//logs/TarLoad-17-39-xubBdv.log >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> ==> Loading file from disk >>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-17-39-UyQcG2/dcc0000_258024_v1_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> --> mapping DICOM parameter for >>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-17-39-UyQcG2/dcc0000_258024_v1_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> ==> computing md5 hash for MINC body. >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> --> md5: 6b1202fd63e29de4c9be1cd9925888a5 >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> ==> verifying acquisition protocol >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> Acquisition protocol is unknown >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> --> The minc file cannot be registered since the >>>>>>>>>>>>>>>>>>>>> AcquisitionProtocol is unknown >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> ???? ???, 30 ???? 2019 ???? 4:58 ?.?., ?/? Sotirios >>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos ??????: >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> Ok I fixed the login problem by using a known hash >>>>>>>>>>>>>>>>>>>>>> and by deleting the rows from the login_history i was able to login. >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> ???? ???, 30 ???? 2019 ???? 4:50 ?.?., ?/? Sotirios >>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos ??????: >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> there was no visit label 01 in the Visit_Windows >>>>>>>>>>>>>>>>>>>>>>> table and i don't know how to insert it because the record requires lots of >>>>>>>>>>>>>>>>>>>>>>> attributes. Also the system for a reason asked me to update my password and >>>>>>>>>>>>>>>>>>>>>>> now i don't remember it and my account got suspended. Is there a way to >>>>>>>>>>>>>>>>>>>>>>> reset it or set a simple password? I updated the password hash in the >>>>>>>>>>>>>>>>>>>>>>> users table by using the hash from another LORIS setup we had and i still >>>>>>>>>>>>>>>>>>>>>>> couldn't login ( also the attribute password is always NULL and the >>>>>>>>>>>>>>>>>>>>>>> expiration date is 1999-01-01 for some reason ). >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> Thanks >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> ???? ???, 29 ???? 2019 ???? 5:21 ?.?., ?/? Cecile >>>>>>>>>>>>>>>>>>>>>>> Madjar ??????: >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> Can you try adding the visit label v01 to the >>>>>>>>>>>>>>>>>>>>>>>> Visit_Windows table? >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> However, I noticed that in a previous dataset, the >>>>>>>>>>>>>>>>>>>>>>>> label was V1. Does that refer to the same visit? If so, you might want to >>>>>>>>>>>>>>>>>>>>>>>> harmonize the visit labels so they are all the same across datasets for a >>>>>>>>>>>>>>>>>>>>>>>> given timepoint, meaning you will need to relabel scans when the visit >>>>>>>>>>>>>>>>>>>>>>>> label is different but referring to the same visit label (v01 = V1 etc...). >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> Hope this helps, >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> On Mon, Jul 29, 2019 at 10:15 AM Sotirios >>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos wrote: >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> Could you help me with the "Visit label does not >>>>>>>>>>>>>>>>>>>>>>>>> exist"? I had changed $subjectID{'createVisitLabel'} to 1 as you had >>>>>>>>>>>>>>>>>>>>>>>>> suggested but it appears that this problem hasn't been resolved yet. >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> lorisadmin at hbp:/data/loris/bin/mri$ cat >>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data//logs/TarLoad-14-58-9Xog7H.log >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> ==> Loading file from disk >>>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> --> mapping DICOM parameter for >>>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> --> using user-defined filterParameters for >>>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> Candidate Mismatch Error is Visit label does not >>>>>>>>>>>>>>>>>>>>>>>>> exist >>>>>>>>>>>>>>>>>>>>>>>>> -> WARNING: This candidate was invalid. Logging to >>>>>>>>>>>>>>>>>>>>>>>>> MRICandidateErrors table with reason >>>>>>>>>>>>>>>>>>>>>>>>> Visit label does not exist >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 26 ???? 2019 ???? 3:02 ?.?., ?/? >>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos >>>>>>>>>>>>>>>>>>>>>>>>> ??????: >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> Hi Cecile, >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> The Center error was fixed. Still the insertion >>>>>>>>>>>>>>>>>>>>>>>>>> of mincs fails. Please see the output.txt file i attached. Also is there >>>>>>>>>>>>>>>>>>>>>>>>>> something else i need to change at the paths configuration? >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 25 ???? 2019 ???? 6:55 ?.?., ?/? Cecile >>>>>>>>>>>>>>>>>>>>>>>>>> Madjar ??????: >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> We are making progress! >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> I have a feeling this error comes from the fact >>>>>>>>>>>>>>>>>>>>>>>>>>> that your psc table does not have the MRI_alias populated for the DCC site. >>>>>>>>>>>>>>>>>>>>>>>>>>> Running the following query in the mysql database should fix this: >>>>>>>>>>>>>>>>>>>>>>>>>>> UPDATE psc SET MRI_alias="DCC", Alias="DCC" >>>>>>>>>>>>>>>>>>>>>>>>>>> WHERE Name="Data Coordinating Center"; >>>>>>>>>>>>>>>>>>>>>>>>>>> Repeat the same with all your sites (make sure >>>>>>>>>>>>>>>>>>>>>>>>>>> to change the Aliases between sites, they should all be unique). >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> Let me know how it goes! >>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> On Thu, Jul 25, 2019 at 11:43 AM Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos wrote: >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> Dear Cecile, >>>>>>>>>>>>>>>>>>>>>>>>>>>> You were right about your guesses. I did the >>>>>>>>>>>>>>>>>>>>>>>>>>>> modifications you suggested, i still get the "no mincs inserted" error, now >>>>>>>>>>>>>>>>>>>>>>>>>>>> i am getting the "No center found this candidate" error ( how do i fix >>>>>>>>>>>>>>>>>>>>>>>>>>>> that? from what i see the .dcm files contains a 'Institution Name', is that >>>>>>>>>>>>>>>>>>>>>>>>>>>> the center? ), so i guess that's why the validation fails, but i changed >>>>>>>>>>>>>>>>>>>>>>>>>>>> the force variable of tarchiveLoader to 1, shouldn't it have inserted the >>>>>>>>>>>>>>>>>>>>>>>>>>>> mincs then? Also it is optional to have a mail server, right? ( from what i >>>>>>>>>>>>>>>>>>>>>>>>>>>> see the mail error does not affect the $valid_study, so i assume we are >>>>>>>>>>>>>>>>>>>>>>>>>>>> okay with that ) >>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you a lot, >>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 25 ???? 2019 ???? 5:48 ?.?., ?/? >>>>>>>>>>>>>>>>>>>>>>>>>>>> Cecile Madjar ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> From what I understand, I believe you just >>>>>>>>>>>>>>>>>>>>>>>>>>>>> need to update a few config settings from the frontend in the Config module >>>>>>>>>>>>>>>>>>>>>>>>>>>>> (under the Admin menu). >>>>>>>>>>>>>>>>>>>>>>>>>>>>> [image: Screen Shot 2019-07-25 at 10.31.35 >>>>>>>>>>>>>>>>>>>>>>>>>>>>> AM.png] >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Then go to the Paths section of the config >>>>>>>>>>>>>>>>>>>>>>>>>>>>> module and update the "LORIS-MRI code" config setting to >>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri (my guess is that currently, it is set to >>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data) and click on the submit button. >>>>>>>>>>>>>>>>>>>>>>>>>>>>> [image: Screen Shot 2019-07-25 at 10.32.50 >>>>>>>>>>>>>>>>>>>>>>>>>>>>> AM.png] >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Then, go to Imaging Pipeline section of the >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Configuration module and update the "Loris-MRI Data Directory" to >>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/ (my guess is that it is empty at the moment in your >>>>>>>>>>>>>>>>>>>>>>>>>>>>> database which is why $data_dir is not defined when you run the >>>>>>>>>>>>>>>>>>>>>>>>>>>>> tarchiveLoader step of the insertion pipeline). >>>>>>>>>>>>>>>>>>>>>>>>>>>>> [image: Screen Shot 2019-07-25 at 10.40.52 >>>>>>>>>>>>>>>>>>>>>>>>>>>>> AM.png] >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Finally, I took a look at your environment >>>>>>>>>>>>>>>>>>>>>>>>>>>>> file and it might be a good idea to update your PERL5LIB variable to the >>>>>>>>>>>>>>>>>>>>>>>>>>>>> following (it has been added to the code a few releases ago as we realized >>>>>>>>>>>>>>>>>>>>>>>>>>>>> this was needed for the libraries. Not sure which version of LORIS-MRI you >>>>>>>>>>>>>>>>>>>>>>>>>>>>> are using but it does not hurt to update this variable to what I suggest >>>>>>>>>>>>>>>>>>>>>>>>>>>>> below): >>>>>>>>>>>>>>>>>>>>>>>>>>>>> export >>>>>>>>>>>>>>>>>>>>>>>>>>>>> PERL5LIB=/data/loris/bin/mri/uploadNeuroDB:/data/loris/bin/mri/dicom-archive:$PERL5LIB >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helps. Sorry you are experiencing so >>>>>>>>>>>>>>>>>>>>>>>>>>>>> much trouble setting things up. We probably need to update our WIKI. >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> On Thu, Jul 25, 2019 at 9:48 AM Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos wrote: >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The "Loris-MRI Data Directory" should be in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the environment file? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 25 ???? 2019 ???? 12:59 ?.?., ?/? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The scripts are located in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/. Somewhere I might have messed something up but i >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> remember following the instructions in the wiki.For example when i tried to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> execute the batch_uploads_imageuploader perl script the line >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> my $command = "$bin_dir/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl " >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> was pointing to an invalid path, for >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> example: it was repeating a pattern and had LORIS instead of loris ( i >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> think the mistake was that in the wiki it suggested to use $PROJECT for >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the name of the folder and i choosed 'loris' >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris/wiki/Imaging-Database >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ). See also the in image for the modification i did. Also i didn't find the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> section to config the $data_dir variable. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 24 ???? 2019 ???? 6:05 ?.?., ?/? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Cecile Madjar >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> It looks like you have one Config setting >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> not set (based on the first error message you got when running it the first >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> time). You need to set a value for "Loris-MRI Data Directory" in the Config >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> module under the Imaging pipeline section (from what I can see, it would be >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/ for your setup). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The reason you got that error message the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> second time is that the pipeline checks if the DICOM study was already >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> inserted in the tarchive table. Since you ran the study once already, the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> study is inserted into the tarchive, hence the message. However, the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> pipeline did not complete as the MINC files were not created and inserted >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> into the files/parameter_file table. In order to continue the insertion, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> you will then need to run the tarchiveLoader command suggested in the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> terminal during the second run: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -globLocation -profile prod >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive//2012/DCM_2012-12-05_ImagingUpload-17-43-ZUEFjb.tar >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -verbose >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Finally, I am a bit confused by your setup. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Where are the scripts located? In /data/loris/bin/mri or /data/loris/data? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> It feels like the Config setting "LORIS-MRI code" in the Paths section was >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> set to "/data/LORIS/data" but it should have been set to the directory >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> where the scripts are located (most probably /data/loris/bin/mri). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helps, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> On Wed, Jul 24, 2019 at 10:55 AM Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> wrote: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Ok first i execute this command: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> "lorisadmin at hbp:/data/loris/bin/mri$ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ./batch_uploads_imageuploader -profile prod < ~/Desktop/input.txt > log.txt >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at ./batch_uploads_imageuploader line 143. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at ./batch_uploads_imageuploader line 143. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $_ in pattern >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> match (m//) at ./batch_uploads_imageuploader line 147. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> base is DCC0000_258024_V01 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> path is /data/incoming/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> type is .tar.gz >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> fullpath is >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/incoming/DCC0000_258024_V01.tar.gz >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> source /tmp/ImagingUpload-17-43-ZUEFjb >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> targetlocation /data/loris/data/tarchive >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 256. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 284. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at /data/loris/bin/mri/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> tarchive_validation.pl line 219. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at /data/loris/bin/mri/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl line 270. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 711. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Can't exec "mail": No such file or >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> directory at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 721. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 722. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 723. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 724. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 724. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 725. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 735. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> No Mincs inserted >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The tarchiveLoader insertion script has >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> failed. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Running now the following command: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl -profile prod >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -upload_id 3 /data/incoming/DCC0000_258024_V01.tar.gz -verbose" >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I inserted the VisitLabel, but still the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Mincs are not inserted and i am getting this error >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> "lorisadmin at hbp:/data/loris/bin/mri$ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl -profile prod >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -upload_id 3 /data/incoming/DCC0000_258024_V01.tar.gz -verbose >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> find -path >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> \/tmp\/ImagingUpload\-17\-45\-5MsWEd -name '__MACOSX' -delete >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Spool message is: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The Scan for the uploadID 3 has already >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> been run with tarchiveID: 7. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> To continue with the rest of the insertion >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> pipeline, please run tarchiveLoader from a terminal as follows: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader -globLocation -profile prod >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive//2012/DCM_2012-12-05_ImagingUpload-17-43-ZUEFjb.tar >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -verbose" >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Which files should i delete? I thought >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> that deleting the files from the tarchive was enough. And i executed the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> last proposed command to continue to rest of the insertion pipeline ( check >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the image ). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 24 ???? 2019 ???? 5:05 ?.?., ?/? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Cecile Madjar >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sorry I was not clear before. Every >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visits of candidates are created in the session table with one entry per >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID/VisitLabel. So if the imaging pipeline created visits in the session >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> table (that are not attached to instruments) and you want to clean your >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> database completely, you can delete entries in that table as well. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Regarding your point 2, the imaging >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> pipeline can create the visit in the session table as long as the visit >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> label is present in the Visit_Windows table (which means the visit label >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> stored in the PatientName is a valid visit label). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> However, in your prod file, if the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> variable $subjectID{'createVisitLabel'} is set to 1 for candidates, the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit label should be created in the Visit_Windows table I believe. Here >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> is the line of the prod file you would need to change >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> . >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> In general, we prefer populating the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Visit_Windows table and set the $subjectID{'createVisitLabel'} to 0 for >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> candidate data to avoid insertion of badly labelled MRI data that are >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> complex to relabel. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Finally, regarding the candidate >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> creation, if you execute the following steps, the pipeline should be able >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> to create candidates: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - set in the Imaging Pipeline section of >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the config module the config setting "Upload creation of candidates" to Yes >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - manually transfer the scans to the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> LORIS server instead of uploading it via the imaging browser >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - run batch_imaging_upload.pl as you did >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> until now. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helps! >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> On Wed, Jul 24, 2019 at 8:47 AM Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> wrote: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> About my second question i replaced the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> name of the patient in the .dcm files and now i am getting an error that >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the visit label does not exist. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I thought it was supposed to be >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> automatically created. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> "Done adding archive info into database >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -globLocation -profile prod >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive//DCM_2012-12-05_ImagingUpload-15-42-yUwQQV.tar >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -verbose >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> md5sum >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive/DCM_2012-12-05_ImagingUpload-15-42-yUwQQV.tar >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> candidate id 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> => No Visit labelVisit label does not >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> exist >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Set centerID = 1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Number of MINC files that will be >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> considered for inserting into the database: 1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> log dir is /logs and log file is >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /logs/TarLoad-15-42-L6pocU.log >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> candidate id 258024 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> => No Visit label >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Cleaning up temp files: rm -rf >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-15-42-J2rQms/ImagingUpload-15-42-yUwQQV*" >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 24 ???? 2019 ???? 3:38 ?.?., >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ?/? Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 1) What are the records in the session >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> table? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 2) I tried to upload a non-phantom file >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> like this >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> input_file.txt: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/incoming/DCC0000_258024_V1.tar.gz >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> N DCC0000_258024_V1 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Terminal: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ./batch_uploads_imageuploader -profile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> prod < ~/Desktop/input.txt > log.txt >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and i get the following error in the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> log.txt file >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> "Running now the following command: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl -profile prod >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -upload_id 7 /data/incoming/DCC0000_258024_V1.tar.gz -verbose >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> find -path >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> \/tmp\/ImagingUpload\-14\-56\-FeLCB4 -name '__MACOSX' -delete >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Spool message is: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The PatientName read from the DICOM >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> header does not start with DCC0000_258024_V1 from the mri_upload table >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> " >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and the spool message is repeated for >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> each .dcm file. Should i preprocess every .dcm file and change the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PatientName to "DCC0000_258024_V1"? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 3) As far as it concerns the candidate >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> profile i have to create a new one each time before i try to upload a file? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Is there already a way to create a candidate profile and get the DCCID and >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID without the user interface? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 18 ???? 2019 ???? 5:00 ?.?., >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ?/? Cecile Madjar < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> cecile.madjar at mcin.ca> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> See answers to your questions below. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> About the 1st case we had a dicom with >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> a blank studyUID, maybe someone accidentally removed it. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> That is strange. Something must have >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> been done to the DICOM files. I have never seen a study with no StudyUID >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> out of the scanner. Usually, you need to manually erase it with some tool. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> However, DICOMs never cease to surprise me... >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Some other questions: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 1) What are the steps to remove all >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> of my patients and uploads?: because i want to try to reupload all the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> testing dicoms we had with a clean database. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Release 21.0 of LORIS-MRI will offer a >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> script to remove all the entries and files specific to an upload. However, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> this release is not yet out. Hopefully in the next few weeks. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> In the meantime, since your case is >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> particular and that you just want to start with a clean database, the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> following deletes should work (hopefully I won't forget any tables): >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from mri_violations_log; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> mri_protocol_violated_scans; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from MRICandidateErrors; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from parameter_file; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from files_qcstatus; # (if you >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> played with the QC part of the imaging browser for testing) >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from feedback_mri_comments; # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> (if you played with the QC part of the imaging browser for testing) >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from tarchive_series; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from tarchive_files; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from mri_upload; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from tarchive; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from mri_scanner; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from candidate where >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID="scanner"; >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I don't know if you want to also >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete entries in the session and candidate table too? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 2) We do not need to create the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> profile of a patient ( are the patients stored in the candidate table? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> because i can't see the ghosts ), because will it automatically be created >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> when importing a dicom? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I am not sure I understand fully this >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> question. All candidates are stored in the candidate table. The phantom >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> scans however are attached to a scanner candidate depending on where the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> scan happened. It is a bit of a weird concept that we have to redesign >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> eventually but never got a chance to get to it. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hopefully this answered your question, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> otherwise, don't hesitate to let me know. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 3) What is the difference between >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> uploading a dicom as phantom instead of importing as >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCCID_DCCID_VisitLabel? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> When you upload the scan as >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID_DCCID_VisitLabel, there is a check that makes sure the candidate IDs >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and visit label are valid at the time of upload. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> When you upload a scan as phantom, it >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> expects that the DICOM field PatientName and uploaded filename contains the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> string "phantom". We enforced this behaviour on the imaging uploader side >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in recent releases but I can't remember which one. Probably the upcoming >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 21.0 release. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> All those verifications might seem >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> cumbersome but they are here to ensure that the files inserted are all >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> valid and labelled properly as it is a bit messy to have to delete files >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> that were wrongly labelled. At least, the delete script present in release >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 21.0 will make this process easier but it is still good practice to verify >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> those things. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> With pleasure. Hopefully the answers >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> to your questions will be helpful. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PS: loris-dev mailing list: you will >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> find the initial answer I gave Sotirios below. I forgot to cc the loris-dev >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in my earlier reply... >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 16 ???? 2019 ???? 12:02 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ?.?., ?/? Cecile Madjar < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> cecile.madjar at mcin.ca> ??????: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Dear Sotirios, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you for reaching out. Since >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> your email was already organized in points, I will reply directly below >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> your questions below. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> C?cile >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 1) What do we do when the StudyUID >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> is blank on the header? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/minor/docs/AppendixA-Troubleshooting_guideline.md >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> There solution provided at the table 3 does not guide us how to find the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> information ( is possible ). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The StudyUID is the field used in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> our pipeline at the moment to check whether a DICOM study was already >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> inserted into LORIS with that same StudyUID since it is supposed to be >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> unique for every single study. Currently, we do not support insertion of >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DICOM studies if they do not have a StudyUID associated with them. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Is there a specific reason why the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> StudyUID is blank in the DICOM headers in your DICOM files? Did they go >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> through some processes before upload to LORIS? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 2) When i am about to upload a >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> non-phanton case i need a 'Visit Label'. Is there already a script that can >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> create a new visit label for a specific Candidate, so i can provide it as >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> input afterwards to the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> batch_uploads_imageuploader ( See option 5.1.3 https://github.com/aces/Loris-MRI/blob/minor/docs/05-PipelineLaunchOptions.md ) >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I am not sure if the front-end >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> allows for it but if you use batch_uploads_imageuploader, the insertion >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> scripts could create the visit label for you. However, it does need to be >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> included in the patient name in order for the script to know which label it >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> should use. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> For example: you upload V02 for >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> MTL0123 (DCCID: 456789) but V02 was not yet created for MTL0123; the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> insertion scripts will create a V02 visit for MTL0123 if the PatientName >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> field for the dataset is MTL0123_456789_V02 with Stage marked as "Not >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Started". >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> However, *note that for the script >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> to create the visit for the candidate, you have to make sure that all the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit label of your projects were inserted in the Visit_Windows table* >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> (otherwise, the visit will never be created as they were not specified as >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> being part of the list of visit label to expect). So in the example above, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> you should have one row in Visit_Windows with Visit_label="V02" set. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 3) Section 4.3 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/minor/docs/04-Scripts.md >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> What do we do when the folder contains multiple mnc files? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> This is a case by case. Most of the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> time, the MINC files that failed insertion into the imaging browser end up >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in the MRI violation module where you can see what went wrong with the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> acquisitions not inserted. If you notice that the MINC file should be >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> inserted as a specific protocol, you can force the insertion as explained >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in section 4.3. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> In your case, I have a feeling that >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> you want to be able to insert MINC files that did not go through the whole >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> pipeline insertion (DICOM archival, then dcm2mnc, then protocol >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> identification, then insertion...). In theory, you could call >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl on any MINC file, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> provided you have at least the following information: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - path to the MINC file >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - uploadID associated with the MINC >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> files or DICOM archive path from which those MINC files were created from >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Then the minc_insertion.pl script >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> will do the subject information and protocol validation etc... >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> If all the MINC files come from the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> same uploadID or TarchiveID, then you could run a loop in bash calling the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl script like this >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> for files deriving from uploadID=1: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ls /path/to/mnc/folder/* | while >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> read f; do minc_insertion.pl >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -profile prod -uploadID 1 -mincPath $f; done >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helped! >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>>>>>> >>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> -- >>>>>>>>>>>>> >>>>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> -- >>>>>>>>>>>> >>>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>>> >>>>>>>>>>> _______________________________________________ >>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> -- >>>>>>>>>> Shen Wang >>>>>>>>>> Loris Developer >>>>>>>>>> Montreal Neurological Institute >>>>>>>>>> McGill University >>>>>>>>>> >>>>>>>>>> >>>>>>>>> >>>>>>>>> -- >>>>>>>>> Shen Wang >>>>>>>>> Loris Developer >>>>>>>>> Montreal Neurological Institute >>>>>>>>> McGill University >>>>>>>>> >>>>>>>>> _______________________________________________ >>>>>> Loris-dev mailing list >>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>> >>>>> >>>>> >>>>> -- >>>>> >>>>> christine.rogers at mcgill.ca >>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>> Montreal Neurological Institute >>>>> McGill University | Montreal | Canada >>>>> >>>> >>> >>> -- >>> Shen Wang >>> Loris Developer >>> Montreal Neurological Institute >>> McGill University >>> >>> > > -- > Shen Wang > Loris Developer > Montreal Neurological Institute > McGill University > > -------------- next part -------------- An HTML attachment was scrubbed... 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