From sotirisnik at gmail.com Tue Oct 1 06:55:31 2019 From: sotirisnik at gmail.com (Sotirios Nikoloutsopoulos) Date: Tue, 1 Oct 2019 13:55:31 +0300 Subject: [Loris-dev] Import mri - scripts In-Reply-To: References: Message-ID: Hi, i would like whenever a dicom is imported to mark all their coressponding qc_status to "pass". I was thinking of creating a trigger for that, but which tables do i need to add entries to? So far from what i see i need to add entres at the table "files" whenever an insertion happens to files_qcstatus. Thanks ???? ???, 30 ??? 2019 ???? 4:04 ?.?., ?/? Sotirios Nikoloutsopoulos < sotirisnik at gmail.com> ??????: > Oh, sorry i should have asked for StudyID, at the beginning of my email i > sent 3 hours ago (not StudyUID). > > ???? ???, 30 ??? 2019 ???? 3:55 ?.?., ?/? Sotirios Nikoloutsopoulos < > sotirisnik at gmail.com> ??????: > >> Hi, >> >> that's the Study Instance UID, not the StudyID. So the StudyID i am >> looking for is not stored in the database? >> >> [image: image.png] >> >> Thanks. >> >> ???? ???, 30 ??? 2019 ???? 3:38 ?.?., ?/? Cecile Madjar < >> cecile.madjar at mcin.ca> ??????: >> >>> Hi Sotirios, >>> >>> The StudyUID is stored in the DicomArchiveID field of the >>> tarchive table. It can also be found in the metadata field but it is mixed >>> with many other information. >>> >>> Hope this helps, >>> >>> C?cile >>> >>> On Mon, Sep 30, 2019 at 6:00 AM Sotirios Nikoloutsopoulos < >>> sotirisnik at gmail.com> wrote: >>> >>>> Hi, >>>> >>>> Is StudyUID stored somewhere at the tables? At the tarchive table, >>>> specifically at the AcquisitonMetadata column i found something called >>>> 'Unique Study ID" in its context, but that must be the Study Instance UID. >>>> >>>> Thanks >>>> >>>> ???? ???, 27 ??? 2019 ???? 4:22 ?.?., ?/? Cecile Madjar < >>>> cecile.madjar at mcin.ca> ??????: >>>> >>>>> Hi Sotirios, >>>>> >>>>> Your observation is correct. A little explanation below. >>>>> >>>>> MINC files get inserted into the MRI violation tables if: >>>>> >>>>> - the scan type could not be identified (not matching an entry in >>>>> the mri_protocol table) >>>>> - one parameter of the scan type is out of the expected range >>>>> present in the mri_protocol_checks (extra filtering in case you need to be >>>>> stricker on some parameters not present in the mri_protocol table) >>>>> - if the CandID and PSCID do not match >>>>> >>>>> The following cases do not get in the MRI violation tables as it >>>>> happens before the conversion of the DICOM to MINC files and only MINC >>>>> files violations are logged there: >>>>> >>>>> - "No single DICOM" (since no valid DICOM could be found to >>>>> convert to MINC) >>>>> - "Study already inserted" (duplicate StudyUID) since this error >>>>> happens at the dicomTar.pl level (way before conversion into MINC files) >>>>> >>>>> Glad everything is working out!! >>>>> Best, >>>>> >>>>> C?cile >>>>> >>>>> On Fri, Sep 27, 2019 at 6:17 AM Sotirios Nikoloutsopoulos < >>>>> sotirisnik at gmail.com> wrote: >>>>> >>>>>> Hi, >>>>>> >>>>>> the mri passed, for some reason it consumed 5.12GB of ram. Now about >>>>>> the mri_violations, dicoms are triggered to be inserted there only if there >>>>>> is a violation for Tr_min, Tr_max, in general for its header parameter? >>>>>> Because i don't see the cases of 'No single dicom" or with the 2 studyiuid >>>>>> to be there. >>>>>> >>>>>> Thanks >>>>>> >>>>>> ???? ???, 26 ??? 2019 ???? 5:07 ?.?., ?/? Cecile Madjar < >>>>>> cecile.madjar at mcin.ca> ??????: >>>>>> >>>>>>> Hi Sotirios, >>>>>>> >>>>>>> Sorry to hear you are having issues with the memory. I think most of >>>>>>> our VMs are set up with 4GB of RAM so with 4GB you should be fine. >>>>>>> >>>>>>> Hope this helps! >>>>>>> >>>>>>> C?cile >>>>>>> >>>>>>> On Thu, Sep 26, 2019 at 9:48 AM Sotirios Nikoloutsopoulos < >>>>>>> sotirisnik at gmail.com> wrote: >>>>>>> >>>>>>>> Hi, >>>>>>>> >>>>>>>> about that dicom that had that insertion error it's about 30mb and >>>>>>>> when it is being processed the ram is being drastically increased from 2gb >>>>>>>> to 3.28 and then the whole virtual machine is frozen. What is the >>>>>>>> recommended size of ram for using Loris? >>>>>>>> >>>>>>>> Thanks >>>>>>>> >>>>>>>> [image: image.png] >>>>>>>> >>>>>>>> >>>>>>>> ???? ???, 24 ??? 2019 ???? 11:24 ?.?., ?/? Cecile Madjar < >>>>>>>> cecile.madjar at mcin.ca> ??????: >>>>>>>> >>>>>>>>> Hi Sotirios, >>>>>>>>> >>>>>>>>> Glad to see that the StudyUID problem was fixed! >>>>>>>>> >>>>>>>>> For the delete script issue, if you are absolutely certain that no >>>>>>>>> processes are run for that uploadID, you can update the mri_upload table >>>>>>>>> and set the column Inserting to 0 instead of 1 for that uploadID. >>>>>>>>> It looks like for some reason the scripts did not update this field when it >>>>>>>>> stopped the insertion. Not sure why that would be the case though. >>>>>>>>> Note: only do that update if you are certain that there is no >>>>>>>>> processing happening. >>>>>>>>> >>>>>>>>> Hope this helps! >>>>>>>>> >>>>>>>>> >>>>>>>>> On Tue, Sep 24, 2019 at 11:57 AM Sotirios Nikoloutsopoulos < >>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>> >>>>>>>>>> Hi, >>>>>>>>>> >>>>>>>>>> about the Dicoms i reported that didn't have a StudyID they >>>>>>>>>> actually do >>>>>>>>>> >>>>>>>>>> [image: image.png] >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> [image: image.png] >>>>>>>>>> >>>>>>>>>> I thought that this might be a permission because "w" was missing >>>>>>>>>> at the group. After using chmod -R 775 only 102809579 passed, but with no >>>>>>>>>> mnic files. Also now i have this error >>>>>>>>>> >>>>>>>>>> (loris-mri-python) lorisadmin at loris-VirtualBox:/data/loris/bin/mri/tools$ >>>>>>>>>> ./delete_imaging_upload.pl -uploadID 34 -ignore >>>>>>>>>> Cannot delete upload 34: the MRI pipeline is currently processing >>>>>>>>>> it. >>>>>>>>>> >>>>>>>>>> How can solve this? >>>>>>>>>> >>>>>>>>>> Thanks >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> ???? ???, 24 ??? 2019 ???? 2:30 ?.?., ?/? Sotirios >>>>>>>>>> Nikoloutsopoulos ??????: >>>>>>>>>> >>>>>>>>>>> Hi, >>>>>>>>>>> >>>>>>>>>>> Here is our auto dicom uploading python script: >>>>>>>>>>> https://github.com/aueb-wim/DataQualityControlTool/blob/loris1/mipqctool/dicom_uploader.py >>>>>>>>>>> >>>>>>>>>>> To give you a brief idea: >>>>>>>>>>> Per folder it will: >>>>>>>>>>> 1) Delete all the .bak files >>>>>>>>>>> 2) Locate .dcm files and update the Patient header >>>>>>>>>>> 3) Furthermore we are interesting in finding TR_min, TR_max, >>>>>>>>>>> TE_min, TE_max parameters of T1 protocol and do an update at the >>>>>>>>>>> mri_protocol table >>>>>>>>>>> https://github.com/aueb-wim/DataQualityControlTool/blob/loris1/mipqctool/dicom_uploader.py#L205 >>>>>>>>>>> For some reason some files are missing >>>>>>>>>>> SeriesDescription/ProtocolName >>>>>>>>>>> >>>>>>>>>>> In total i have 7 folders >>>>>>>>>>> >>>>>>>>>>> [image: image.png] >>>>>>>>>>> >>>>>>>>>>> 3/7 passed >>>>>>>>>>> >>>>>>>>>>> [image: image.png] >>>>>>>>>>> >>>>>>>>>>> Also about the first patient with DC0000 had a violation "T1 >>>>>>>>>>> AXIAL SE GADO", but my script didn't output a TE of 17 nowhere and i find >>>>>>>>>>> that weird since Loris detects the SeriesDescription. >>>>>>>>>>> [image: image.png] >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> Now about the 4/7 that didn't passed >>>>>>>>>>> >>>>>>>>>>> 102327840 and 102809579 outputs "The target directory does not >>>>>>>>>>> contain a single DICOM file.", therefore they are missing their StudyUID >>>>>>>>>>> >>>>>>>>>>> 102506134 has 2 studyuid "You can't use it with data from >>>>>>>>>>> multiple studies." >>>>>>>>>>> >>>>>>>>>>> and 102761034 "No data could be converted into valid MINC files. >>>>>>>>>>> localizer, scout will not be considered!" What is this? >>>>>>>>>>> >>>>>>>>>>> If i wanted to force the insertion of 102327840, 102809579 and >>>>>>>>>>> 102506134 can i just pass a flag parameter to >>>>>>>>>>> batch_uploads_imageuploader.pl? or modify imaging_upload_file.pl >>>>>>>>>>> ? >>>>>>>>>>> >>>>>>>>>>> Thank you, >>>>>>>>>>> >>>>>>>>>>> Sotirios >>>>>>>>>>> >>>>>>>>>>> PS >>>>>>>>>>> >>>>>>>>>>> To diagnose a folder search the name of the folder at >>>>>>>>>>> dicom_output.txt. >>>>>>>>>>> >>>>>>>>>>> ???? ???, 20 ??? 2019 ???? 4:54 ?.?., ?/? Christine Rogers, Ms. < >>>>>>>>>>> christine.rogers at mcgill.ca> ??????: >>>>>>>>>>> >>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>> Glad to hear about your progress. >>>>>>>>>>>> >>>>>>>>>>>> Yes, the script you used to delete imaging data is fully >>>>>>>>>>>> documented here >>>>>>>>>>>> >>>>>>>>>>>> -- let us know if you didn't find the answers you were looking for there. >>>>>>>>>>>> (Is it possible the null row in *mri_scanner* seen in your >>>>>>>>>>>> database management software is a visual placeholder for you as the user? >>>>>>>>>>>> I'm not sure why a scanner would ever be registered with ID='0' as your >>>>>>>>>>>> screenshot showed.) >>>>>>>>>>>> >>>>>>>>>>>> Best, >>>>>>>>>>>> Christine >>>>>>>>>>>> >>>>>>>>>>>> On Fri, Sep 20, 2019 at 9:45 AM Sotirios Nikoloutsopoulos < >>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>> >>>>>>>>>>>>> I fixed it with this >>>>>>>>>>>>> >>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>> >>>>>>>>>>>>> ???? ???, 20 ??? 2019 ???? 4:37 ?.?., ?/? Sotirios >>>>>>>>>>>>> Nikoloutsopoulos ??????: >>>>>>>>>>>>> >>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>> >>>>>>>>>>>>>> I tried to create a new candidate using the API, is there >>>>>>>>>>>>>> something wrong with the structure? why did i receive a 500 internal error? >>>>>>>>>>>>>> In the loris-error log it state that there is something wrong with token, >>>>>>>>>>>>>> but i verfied that the type of the token is a string. >>>>>>>>>>>>>> >>>>>>>>>>>>>> [Fri Sep 20 16:35:26.874732 2019] [php7:error] [pid 4535] >>>>>>>>>>>>>> [client 127.0.0.1:59674] PHP Fatal error: Uncaught >>>>>>>>>>>>>> TypeError: Argument 1 passed to SinglePointLogin::JWTAuthenticate() must be >>>>>>>>>>>>>> of the type string, null given, called in >>>>>>>>>>>>>> /var/www/loris/php/libraries/SinglePointLogin.class.inc on line 169 and >>>>>>>>>>>>>> defined in >>>>>>>>>>>>>> /var/www/loris/php/libraries/SinglePointLogin.class.inc:192\nStack >>>>>>>>>>>>>> trace:\n#0 /var/www/loris/php/libraries/SinglePointLogin.class.inc(169): >>>>>>>>>>>>>> SinglePointLogin->JWTAuthenticate(NULL)\n#1 >>>>>>>>>>>>>> /var/www/loris/php/libraries/NDB_Client.class.inc(171): >>>>>>>>>>>>>> SinglePointLogin->authenticate()\n#2 >>>>>>>>>>>>>> /var/www/loris/htdocs/api/v0.0.2/APIBase.php(73): >>>>>>>>>>>>>> NDB_Client->initialize('/var/www/loris/...')\n#3 >>>>>>>>>>>>>> /var/www/loris/htdocs/api/v0.0.2/Candidates.php(44): >>>>>>>>>>>>>> Loris\\API\\APIBase->__construct('POST')\n#4 >>>>>>>>>>>>>> /var/www/loris/htdocs/api/v0.0.2/Candidates.php(244): >>>>>>>>>>>>>> Loris\\API\\Candidates->__construct('POST', Array)\n#5 {main}\n thrown in >>>>>>>>>>>>>> /var/www/loris/php/libraries/SinglePointLogin.class.inc on line 192 >>>>>>>>>>>>>> >>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>> >>>>>>>>>>>>>> ???? ???, 20 ??? 2019 ???? 2:39 ?.?., ?/? Sotirios >>>>>>>>>>>>>> Nikoloutsopoulos ??????: >>>>>>>>>>>>>> >>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> Is there a way also to delete candidates? Just to let you >>>>>>>>>>>>>>> know what i did to clear candidates, because maybe i may have missed >>>>>>>>>>>>>>> dependencies. >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> First i deleted all their uploads >>>>>>>>>>>>>>> ./delete_imaging_upload.pl -uploadID 13 etc ( is there a >>>>>>>>>>>>>>> way to omit the backup file ? ) >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> Afterwards i had some scanner candidates, so i deleted all >>>>>>>>>>>>>>> the entries from mri_scanner except that i couldn't delete this entry with >>>>>>>>>>>>>>> the 0 ID. >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> Lastly i deleted the session and then the candidate table. >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> Thanks >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> ???? ???, 19 ??? 2019 ???? 7:57 ?.?., ?/? Christine Rogers, >>>>>>>>>>>>>>> Ms. ??????: >>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> We recommend that you use our existing tools for creating >>>>>>>>>>>>>>>> new candidates - either the LORIS API or if you are using a PHP script, by >>>>>>>>>>>>>>>> calling the Candidate class's createNew() >>>>>>>>>>>>>>>> function. >>>>>>>>>>>>>>>> These will create the necessary records for you. (It's not recommended to >>>>>>>>>>>>>>>> make direct modifications to mysql database tables in your script, if I >>>>>>>>>>>>>>>> understand you.) >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> The CandID should be a randomized 6 digit randomized ID, >>>>>>>>>>>>>>>> and there are multiple reasons for this. >>>>>>>>>>>>>>>> You can use the PSCID for project-specific IDs and the >>>>>>>>>>>>>>>> External ID field in the candidate table can also be used for any values >>>>>>>>>>>>>>>> you like. >>>>>>>>>>>>>>>> Additionally, any number of custom IDs can be added in >>>>>>>>>>>>>>>> parallel - these are entered/visible in the Candidate Information module >>>>>>>>>>>>>>>> and added in the back-end as candidate parameters. >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>> Christine >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> On Tue, Sep 17, 2019 at 7:31 PM Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> We are building a script that will auto insert the >>>>>>>>>>>>>>>>> candidates based on their ExternalID. We would like to know whethere when >>>>>>>>>>>>>>>>> we are creating a new profile in the candidate table, if we also have to >>>>>>>>>>>>>>>>> insert a new record at another table? Furthermore is there a problem that >>>>>>>>>>>>>>>>> in our case CandID won't be a 6digit? ( should we start it from 100000?) >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Thanks >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> ???? ???, 13 ??? 2019 ???? 5:38 ?.?., ?/? Melanie Legault, >>>>>>>>>>>>>>>>> Mrs ??????: >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> That would normally be the case but the numeric part of >>>>>>>>>>>>>>>>>> the PSCID get paded with 0 on the left. >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Ex. for sequential ID made of center ID of `ABC` plus 4 >>>>>>>>>>>>>>>>>> numerical char with a min value of 1, the sequence would be: >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> ABC0001 >>>>>>>>>>>>>>>>>> ABC0002 >>>>>>>>>>>>>>>>>> ... >>>>>>>>>>>>>>>>>> ABC0010 >>>>>>>>>>>>>>>>>> ... >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> thus sorting them ascending will always get the latest >>>>>>>>>>>>>>>>>> value generated as the max value. >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> M?lanie >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> ------------------------------ >>>>>>>>>>>>>>>>>> *From:* Sotirios Nikoloutsopoulos >>>>>>>>>>>>>>>>>> *Sent:* September 13, 2019 10:15 >>>>>>>>>>>>>>>>>> *To:* Melanie Legault, Mrs >>>>>>>>>>>>>>>>>> *Cc:* Christine Rogers, Ms. ; >>>>>>>>>>>>>>>>>> loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>>>>>> *Subject:* Re: [Loris-dev] Import mri - scripts >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> I see, although the PSCID value is varchar(255), it must >>>>>>>>>>>>>>>>>> be stored within a specific length of characters. Otherwise if we were to >>>>>>>>>>>>>>>>>> sort strings with different lengths the result would not be sorted >>>>>>>>>>>>>>>>>> correctly ( e.x. 1,2,10,11 as strings would result to 1, 10, 11, 2 ). >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Thanks >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> ???? ???, 13 ??? 2019 ???? 4:52 ?.?., ?/? Melanie >>>>>>>>>>>>>>>>>> Legault, Mrs ??????: >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Hello Sotirios, >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> There is no `last value` stored anywhere. >>>>>>>>>>>>>>>>>> The code simply look for the PSCID with the max value and >>>>>>>>>>>>>>>>>> increase that value by 1 in order to generate the next PSCID. >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Hope this info help. >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> M?lanie Legault | Software developer | Faculty of >>>>>>>>>>>>>>>>>> Medicine | McGill University >>>>>>>>>>>>>>>>>> 3801 University, Montr?al, QC H3A 2B4 >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> ------------------------------ >>>>>>>>>>>>>>>>>> *From:* loris-dev-bounces at bic.mni.mcgill.ca < >>>>>>>>>>>>>>>>>> loris-dev-bounces at bic.mni.mcgill.ca> on behalf of >>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos >>>>>>>>>>>>>>>>>> *Sent:* September 13, 2019 9:43 >>>>>>>>>>>>>>>>>> *To:* Christine Rogers, Ms. >>>>>>>>>>>>>>>>>> *Cc:* loris-dev at bic.mni.mcgill.ca < >>>>>>>>>>>>>>>>>> loris-dev at bic.mni.mcgill.ca> >>>>>>>>>>>>>>>>>> *Subject:* Re: [Loris-dev] Import mri - scripts >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> how does Loris determine the next available PSCID value >>>>>>>>>>>>>>>>>> for a new candidate? >>>>>>>>>>>>>>>>>> https://github.com/aces/Loris/wiki/Project-Customization >>>>>>>>>>>>>>>>>> e.x in the default case the PSCID is sequential, but where do we store the >>>>>>>>>>>>>>>>>> last value for the sequential sequence? >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Thanks >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> ???? ???, 10 ??? 2019 ???? 4:00 ?.?., ?/? Sotirios >>>>>>>>>>>>>>>>>> Nikoloutsopoulos ??????: >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> the parameters in the mri_protocol you have assigned are >>>>>>>>>>>>>>>>>> global standard? or were assigned after trial and error? >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Thanks >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> ???? ???, 8 ??? 2019 ???? 10:11 ?.?., ?/? Christine >>>>>>>>>>>>>>>>>> Rogers, Ms. ??????: >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Given you have done the initial setup of your tables to >>>>>>>>>>>>>>>>>> match your intended protocol/parameters according to instructions -- >>>>>>>>>>>>>>>>>> the Troubleshooting guide documentation recommends >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> re-running the pipeline (and first deleting prior uploads). >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>> Christine >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> On Sun, Sep 8, 2019 at 10:22 AM Sotirios Nikoloutsopoulos >>>>>>>>>>>>>>>>>> wrote: >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> *if i were to change their status to resolve what would >>>>>>>>>>>>>>>>>> happen? >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> ???? ???, 8 ??? 2019 ???? 5:12 ?.?., ?/? Sotirios >>>>>>>>>>>>>>>>>> Nikoloutsopoulos ??????: >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> I noticed that i can view the mnics at the brainbrowser >>>>>>>>>>>>>>>>>> from the mri_violations page ( those mnics are stored at >>>>>>>>>>>>>>>>>> /data/loris/data/trashbin/ if i were to click their issue to resolve what >>>>>>>>>>>>>>>>>> would happend? would they appear in the dicom_archive view too? ). >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> ???? ???, 8 ??? 2019 ???? 4:17 ?.?., ?/? Sotirios >>>>>>>>>>>>>>>>>> Nikoloutsopoulos ??????: >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> The defaut values of the schema exists in my local >>>>>>>>>>>>>>>>>> database. If i adjust the default values of TR_min and TE_min the mincs >>>>>>>>>>>>>>>>>> will be uploaded? >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Thanks >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> ???? ???, 7 ??? 2019 ???? 5:48 ?.?., ?/? Christine >>>>>>>>>>>>>>>>>> Rogers, Ms. ??????: >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Is it possible that you haven't set up your mri_protocol >>>>>>>>>>>>>>>>>> table ? (and mri_scan_type table too, for additional types of scans) >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Like the psc table, this is a pre-requisite for the >>>>>>>>>>>>>>>>>> Imaging insertion setup : See the install/setup documentation : >>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/master/docs/02-Install.md >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> To add new rows, just use MySQL insert statements. You >>>>>>>>>>>>>>>>>> can adapt the insert statements which load the default table values --> >>>>>>>>>>>>>>>>>> e.g. Here on GitHub : >>>>>>>>>>>>>>>>>> https://github.com/aces/Loris/blob/master/SQL/0000-00-00-schema.sql#L718 >>>>>>>>>>>>>>>>>> (see also the mri_scan_type table) >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>> Christine >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> On Fri, Sep 6, 2019 at 8:32 PM Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> I see that i can edit the values but not how to insert >>>>>>>>>>>>>>>>>> new rows. >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> If i choose Inserted with flag then will the minc be >>>>>>>>>>>>>>>>>> inserted? >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> ???? ???, 7 ??? 2019 ???? 3:21 ?.?., ?/? Christine >>>>>>>>>>>>>>>>>> Rogers, Ms. ??????: >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Glad to hear that *dcmodify* worked correctly. >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> For the MRI Violations module, the screenshot is enough. >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> It says "could not identify scan type", which we knew >>>>>>>>>>>>>>>>>> already. Did you click on the link on those words? >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> It will take you to the next page of the module, showing >>>>>>>>>>>>>>>>>> for each scan what the scan parameters were, and will also show for >>>>>>>>>>>>>>>>>> comparison what's stored in your *mri_protocol* table. >>>>>>>>>>>>>>>>>> Compare these values to find which parameter was not >>>>>>>>>>>>>>>>>> correct according to your *mri_protocol* table scan type >>>>>>>>>>>>>>>>>> definitions. >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> You may end up broadening your mri_protocol value ranges >>>>>>>>>>>>>>>>>> (e.g. TR, TE) for scans. >>>>>>>>>>>>>>>>>> This can be done in the front-end, by editing the >>>>>>>>>>>>>>>>>> database table directly in the same subpage of the MRI Violations module. >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> The MRI Violations module features are explained in more >>>>>>>>>>>>>>>>>> detail in the Help text for this module inside LORIS (click the ["?"] icon >>>>>>>>>>>>>>>>>> in the menu bar.) >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> See also: Loris-MRI troubleshooting guide >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> : no MINCs inserted- violated scans >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>> Christine >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> On Fri, Sep 6, 2019 at 8:11 PM Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> looks like my previous email's attachment wasn't >>>>>>>>>>>>>>>>>> delivered due to security reasons, i uploaded my file at google drive >>>>>>>>>>>>>>>>>> https://drive.google.com/file/d/1U_TRbo_qGgfpQfs-SqeG9J3bMMqNfUU4/view?usp=sharing >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> ???? ???, 7 ??? 2019 ???? 3:02 ?.?., ?/? Sotirios >>>>>>>>>>>>>>>>>> Nikoloutsopoulos ??????: >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> From Dicat's view seems that dcmodify worked in both cases >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> For the mri_violations i attached the .html output from >>>>>>>>>>>>>>>>>> webbrowser, so that you can check the filelds easier. >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Thanks >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> ???? ???, 6 ??? 2019 ???? 7:49 ?.?., ?/? Christine >>>>>>>>>>>>>>>>>> Rogers, Ms. ??????: >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Hi Sotirios -- >>>>>>>>>>>>>>>>>> Great, sounds like more progress. >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> About the dcmodify command -- I'm not sure why you're >>>>>>>>>>>>>>>>>> getting an Endian warning. (it's a warning not an error, correct?) >>>>>>>>>>>>>>>>>> To clarify -- Were the DICOM headers (PatientName) all >>>>>>>>>>>>>>>>>> successfully relabelled, after the command ran? >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> You can use also our DICAT tool ( >>>>>>>>>>>>>>>>>> https://github.com/aces/DICAT) to verify and/or update >>>>>>>>>>>>>>>>>> local DICOM headers -- though your dcmodify command is a great and fast >>>>>>>>>>>>>>>>>> solution for bulk header updates. >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> If you're concerned about fields being changed (e.g. >>>>>>>>>>>>>>>>>> "(2001,105f)" from the warning message) - you can also dcmdump a DICOM >>>>>>>>>>>>>>>>>> slice before and look at these fields specifically. >>>>>>>>>>>>>>>>>> It's also not a bad "sanity check" to backup your DICOMS >>>>>>>>>>>>>>>>>> before/after running dcmodify, and use dcmdump on each version to diff the >>>>>>>>>>>>>>>>>> outputs -- this will pinpoint what changed. >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Re the protocol violation -- AcquisitionProtocol not >>>>>>>>>>>>>>>>>> recognized or unknown : this means your scans did not match what is >>>>>>>>>>>>>>>>>> stored in your mri_protocol table. >>>>>>>>>>>>>>>>>> Check the MRI Violations front-end module -- can you see >>>>>>>>>>>>>>>>>> why they didn't match? >>>>>>>>>>>>>>>>>> Send us an example, in addition to the contents of the >>>>>>>>>>>>>>>>>> mri_protocol table, if you can't find the source of the mismatch. >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>> Christine >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> On Fri, Sep 6, 2019 at 12:04 PM Sotirios Nikoloutsopoulos >>>>>>>>>>>>>>>>>> wrote: >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Here is the psc table >>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> I created 2 candidates profiles through the interface >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> then runned dcmodify command to a dicom file >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> dcmodify -ma PatientName="DCC0000_258024_V1" >>>>>>>>>>>>>>>>>> /home/lorisadmin/DICOMS/000535670/501/*.dcm >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> and got those warning: is this okay? >>>>>>>>>>>>>>>>>> W: Found element (2001,105f) with VR UN and undefined >>>>>>>>>>>>>>>>>> length, reading a sequence with transfer syntax LittleEndianImplicit >>>>>>>>>>>>>>>>>> (CP-246) >>>>>>>>>>>>>>>>>> W: Found element (2005,1083) with VR UN and undefined >>>>>>>>>>>>>>>>>> length, reading a sequence with transfer syntax LittleEndianImplicit >>>>>>>>>>>>>>>>>> (CP-246) >>>>>>>>>>>>>>>>>> W: Found element (2005,1402) with VR UN and undefined >>>>>>>>>>>>>>>>>> length, reading a sequence with transfer syntax LittleEndianImplicit >>>>>>>>>>>>>>>>>> (CP-246) >>>>>>>>>>>>>>>>>> W: Found element (2005,140f) with VR UN and undefined >>>>>>>>>>>>>>>>>> length, reading a sequence with transfer syntax LittleEndianImplicit >>>>>>>>>>>>>>>>>> (CP-246) >>>>>>>>>>>>>>>>>> W: Found element (2001,105f) with VR UN and undefined >>>>>>>>>>>>>>>>>> length, reading a sequence with transfer syntax LittleEndianImplicit >>>>>>>>>>>>>>>>>> (CP-246) >>>>>>>>>>>>>>>>>> W: Found element (2005,1083) with VR UN and undefined >>>>>>>>>>>>>>>>>> length, reading a sequence with transfer syntax LittleEndianImplicit >>>>>>>>>>>>>>>>>> (CP-246) >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> dcmodify at another Dicom didn't show warnings. Below you >>>>>>>>>>>>>>>>>> can see the execution for the second dicom. Mnics could not be inserted due >>>>>>>>>>>>>>>>>> to AcquisitionProtocol being unknown. >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Running now the following command: >>>>>>>>>>>>>>>>>> /data/loris/bin/mri//uploadNeuroDB/imaging_upload_file.pl >>>>>>>>>>>>>>>>>> -profile prod -upload_id 12 /data/incoming/DCC0001_602102_V1.tar.gz -verbose >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> find -path \/tmp\/ImagingUpload\-18\-36\-mTrxXs -name >>>>>>>>>>>>>>>>>> '__MACOSX' -delete >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> dicomTar.pl \/tmp\/ImagingUpload\-18\-36\-mTrxXs >>>>>>>>>>>>>>>>>> \/data\/loris\/data\/tarchive\/ -database -profile prod -verbose >>>>>>>>>>>>>>>>>> Source: /tmp/ImagingUpload-18-36-mTrxXs >>>>>>>>>>>>>>>>>> Target: /data/loris/data/tarchive >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Testing for database connectivity. >>>>>>>>>>>>>>>>>> Database is available. >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> You will archive the dir : ImagingUpload-18-36-mTrxXs >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> You are creating a tar with the following command: >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> tar -cf >>>>>>>>>>>>>>>>>> /data/loris/data/tarchive/ImagingUpload-18-36-mTrxXs.tar >>>>>>>>>>>>>>>>>> ImagingUpload-18-36-mTrxXs >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> getting md5sums and gzipping!! >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> * Taken from dir : >>>>>>>>>>>>>>>>>> /tmp/ImagingUpload-18-36-mTrxXs >>>>>>>>>>>>>>>>>> * Archive target location : >>>>>>>>>>>>>>>>>> /data/loris/data/tarchive/DCM_2016-08-22_ImagingUpload-18-36-mTrxXs.tar >>>>>>>>>>>>>>>>>> * Name of creating host : 127.0.1.1 >>>>>>>>>>>>>>>>>> * Name of host OS : Linux >>>>>>>>>>>>>>>>>> * Created by user : lorisadmin >>>>>>>>>>>>>>>>>> * Archived on : 2019-09-06 >>>>>>>>>>>>>>>>>> 18:36:50 >>>>>>>>>>>>>>>>>> * dicomSummary version : 1 >>>>>>>>>>>>>>>>>> * dicomTar version : 1 >>>>>>>>>>>>>>>>>> * md5sum for DICOM tarball : >>>>>>>>>>>>>>>>>> b1dcdc8903dd2d9a5443227db2aa2814 ImagingUpload-18-36-mTrxXs.tar >>>>>>>>>>>>>>>>>> * md5sum for DICOM tarball gzipped : >>>>>>>>>>>>>>>>>> aeae87f20155a6805f7e0cfe5212ea5f ImagingUpload-18-36-mTrxXs.tar.gz >>>>>>>>>>>>>>>>>> * md5sum for complete archive : >>>>>>>>>>>>>>>>>> 1d9258d1f077ebc49111ab7ba22a8d6e >>>>>>>>>>>>>>>>>> DCM_2016-08-22_ImagingUpload-18-36-mTrxXs.tar >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Adding archive info into database >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Removing temporary files from target location >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Done adding archive info into database >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> \/data\/loris\/bin\/mri\//uploadNeuroDB/tarchiveLoader.pl >>>>>>>>>>>>>>>>>> -globLocation -profile prod >>>>>>>>>>>>>>>>>> \/data\/loris\/data\/tarchive\/\/DCM_2016\-08\-22_ImagingUpload\-18\-36\-mTrxXs\.tar >>>>>>>>>>>>>>>>>> -uploadID 12 -verbose >>>>>>>>>>>>>>>>>> md5sum >>>>>>>>>>>>>>>>>> /data/loris/data/tarchive/DCM_2016-08-22_ImagingUpload-18-36-mTrxXs.tar >>>>>>>>>>>>>>>>>> PSCID is: DCC0001 >>>>>>>>>>>>>>>>>> CandID id: 602102 >>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>> PSCID is: DCC0001 >>>>>>>>>>>>>>>>>> CandID id: 602102 >>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>> candidate id 602102 >>>>>>>>>>>>>>>>>> Set centerID = 1 >>>>>>>>>>>>>>>>>> PSCID is: DCC0001 >>>>>>>>>>>>>>>>>> CandID id: 602102 >>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>> PSCID is: DCC0001 >>>>>>>>>>>>>>>>>> CandID id: 602102 >>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Number of MINC files that will be considered for >>>>>>>>>>>>>>>>>> inserting into the database: 2 >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> log dir is /data/loris/data//logs and log file is >>>>>>>>>>>>>>>>>> /data/loris/data//logs/TarLoad-18-37-31ajWx.log >>>>>>>>>>>>>>>>>> PSCID is: DCC0001 >>>>>>>>>>>>>>>>>> CandID id: 602102 >>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>> PSCID is: DCC0001 >>>>>>>>>>>>>>>>>> CandID id: 602102 >>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>> candidate id 602102 >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> log dir is /data/loris/data//logs and log file is >>>>>>>>>>>>>>>>>> /data/loris/data//logs/TarLoad-18-37-fanZFj.log >>>>>>>>>>>>>>>>>> PSCID is: DCC0001 >>>>>>>>>>>>>>>>>> CandID id: 602102 >>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>> PSCID is: DCC0001 >>>>>>>>>>>>>>>>>> CandID id: 602102 >>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>> candidate id 602102 >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Cleaning up temp files: rm -rf >>>>>>>>>>>>>>>>>> /tmp/TarLoad-18-37-to5pYZ/ImagingUpload-18-36-mTrxXs* >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> (loris-mri-python) lorisadmin at loris-VirtualBox:/data/loris/bin/mri$ >>>>>>>>>>>>>>>>>> cat /data/loris/data/logs/TarLoad-18-37-fanZFj.log >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> ==> Loading file from disk >>>>>>>>>>>>>>>>>> /tmp/TarLoad-18-37-to5pYZ/dcc0001_602102_v1_20160822_072406_205e1d1_mri.mnc >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> --> mapping DICOM parameter for >>>>>>>>>>>>>>>>>> /tmp/TarLoad-18-37-to5pYZ/dcc0001_602102_v1_20160822_072406_205e1d1_mri.mnc >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> ==> computing md5 hash for MINC body. >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> --> md5: 02022dda60d9de429340fec838f50cfe >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> ==> verifying acquisition protocol >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Acquisition protocol is unknown >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> --> The minc file cannot be registered since the >>>>>>>>>>>>>>>>>> AcquisitionProtocol is unknown >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> ???? ???, 4 ??? 2019 ???? 10:46 ?.?., ?/? Christine >>>>>>>>>>>>>>>>>> Rogers, Ms. ??????: >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Hi Sotirios: >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Sure -- you can delete imaging datasets with the >>>>>>>>>>>>>>>>>> *delete_imaging_upload* script -- >>>>>>>>>>>>>>>>>> details here: >>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/21.0-dev/docs/scripts_md/delete_imaging_upload.md >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> What's in your *psc* table? (Is it properly populated? This >>>>>>>>>>>>>>>>>> is a pre-requisite to loading imaging data. >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> ) >>>>>>>>>>>>>>>>>> The foreign key constraint error on the candidate record >>>>>>>>>>>>>>>>>> is curious. >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> There are also a few options for creating candidates when >>>>>>>>>>>>>>>>>> inserting imaging data: >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> -- Method 1 : in 2 steps with the API then DICOM >>>>>>>>>>>>>>>>>> insertion pipeline >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> a. via the LORIS API -- Create the candidates (and >>>>>>>>>>>>>>>>>> visits, optionally I think) >>>>>>>>>>>>>>>>>> How to: >>>>>>>>>>>>>>>>>> https://github.com/aces/Loris/blob/master/docs/API/LorisRESTAPI.md#30-candidate-api >>>>>>>>>>>>>>>>>> Ensure you get the DCCID/CandID assigned by LORIS. >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Then as a second step: >>>>>>>>>>>>>>>>>> b. Use the imaging insertion pipeline >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> to load your DICOMs. >>>>>>>>>>>>>>>>>> You will want to first ensure that the PatientName header >>>>>>>>>>>>>>>>>> in the DICOMs as well as tar package are correctly labelled with >>>>>>>>>>>>>>>>>> PSCID_DCCID_VisitLabel >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> -- Method 2: for BIDS-format datasets: >>>>>>>>>>>>>>>>>> How to : >>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/master/docs/05-PipelineLaunchOptions.md#52---pipeline-launch-for-bids-datasets >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Be sure to use the *-c* and *-s* options when running >>>>>>>>>>>>>>>>>> the bids_import script, to automatically create your >>>>>>>>>>>>>>>>>> candidates and sessions. >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>> Christine >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> On Wed, Sep 4, 2019 at 11:43 AM Sotirios Nikoloutsopoulos >>>>>>>>>>>>>>>>>> wrote: >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> How do i delete a Study? And everytime do i have to >>>>>>>>>>>>>>>>>> create a new candidate to get DCCID and a PSCID? >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> *First execution:* >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> (loris-mri-python) lorisadmin at loris-VirtualBox:/data/loris/bin/mri$ >>>>>>>>>>>>>>>>>> ./batch_uploads_imageuploader.pl -profile prod < >>>>>>>>>>>>>>>>>> ~/Desktop/input.txt > log.txt >>>>>>>>>>>>>>>>>> Use of uninitialized value $_ in pattern match (m//) at ./ >>>>>>>>>>>>>>>>>> batch_uploads_imageuploader.pl line 144. >>>>>>>>>>>>>>>>>> DBD::mysql::db do failed: Cannot add or update a child >>>>>>>>>>>>>>>>>> row: a foreign key constraint fails (`LORIS`.`candidate`, CONSTRAINT >>>>>>>>>>>>>>>>>> `FK_candidate_1` FOREIGN KEY (`RegistrationCenterID`) REFERENCES `psc` >>>>>>>>>>>>>>>>>> (`CenterID`)) at /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 1060. >>>>>>>>>>>>>>>>>> ERROR: Failed to insert record in table mri_scanner: >>>>>>>>>>>>>>>>>> The following database commands failed: >>>>>>>>>>>>>>>>>> PREPARE s FROM 'INSERT INTO mri_scanner >>>>>>>>>>>>>>>>>> (CandID,Model,Software,Serial_number,Manufacturer) VALUES (?,?,?,?,?)'; >>>>>>>>>>>>>>>>>> SET >>>>>>>>>>>>>>>>>> @x1='242126', at x2='Achieva', at x3='3.2.2\3.2.2.0', at x4='34037', at x5='Philips >>>>>>>>>>>>>>>>>> Medical Systems'; >>>>>>>>>>>>>>>>>> EXECUTE s USING @x1, at x2, at x3, at x4, at x5; >>>>>>>>>>>>>>>>>> Error obtained:Cannot add or update a child row: a >>>>>>>>>>>>>>>>>> foreign key constraint fails (`LORIS`.`mri_scanner`, CONSTRAINT >>>>>>>>>>>>>>>>>> `FK_mri_scanner_1` FOREIGN KEY (`CandID`) REFERENCES `candidate` >>>>>>>>>>>>>>>>>> (`CandID`)) (error code 1452) >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> ERROR: The validation has failed. Either re-run the >>>>>>>>>>>>>>>>>> validation again and fix the problem. Or re-run tarchiveLoader.pl using >>>>>>>>>>>>>>>>>> -force to force the execution. >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> The tarchiveLoader.pl insertion script has failed. >>>>>>>>>>>>>>>>>> Can't exec "mail": No such file or directory at ./ >>>>>>>>>>>>>>>>>> batch_uploads_imageuploader.pl line 249. >>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at ./ >>>>>>>>>>>>>>>>>> batch_uploads_imageuploader.pl line 250. >>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at ./ >>>>>>>>>>>>>>>>>> batch_uploads_imageuploader.pl line 251. >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> *And second execution: * >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> (loris-mri-python) lorisadmin at loris-VirtualBox:/data/loris/bin/mri$ >>>>>>>>>>>>>>>>>> ./batch_uploads_imageuploader.pl -profile prod < >>>>>>>>>>>>>>>>>> ~/Desktop/input.txt > log.txt >>>>>>>>>>>>>>>>>> Use of uninitialized value $_ in pattern match (m//) at ./ >>>>>>>>>>>>>>>>>> batch_uploads_imageuploader.pl line 144. >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> PROBLEM: >>>>>>>>>>>>>>>>>> The user 'lorisadmin' has already inserted this study. >>>>>>>>>>>>>>>>>> The unique study ID is >>>>>>>>>>>>>>>>>> '1.3.51.0.1.1.10.49.10.222.1422753.1420953'. >>>>>>>>>>>>>>>>>> This is the information retained from the first time the >>>>>>>>>>>>>>>>>> study was inserted: >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> * Taken from dir : >>>>>>>>>>>>>>>>>> /tmp/ImagingUpload-18-33-Qq7HGy >>>>>>>>>>>>>>>>>> * Archive target location : >>>>>>>>>>>>>>>>>> /data/loris/data/tarchive/DCM_2012-12-05_ImagingUpload-18-33-Qq7HGy.tar >>>>>>>>>>>>>>>>>> * Name of creating host : 127.0.1.1 >>>>>>>>>>>>>>>>>> * Name of host OS : Linux >>>>>>>>>>>>>>>>>> * Created by user : lorisadmin >>>>>>>>>>>>>>>>>> * Archived on : 2019-09-04 >>>>>>>>>>>>>>>>>> 18:33:05 >>>>>>>>>>>>>>>>>> * dicomSummary version : 1 >>>>>>>>>>>>>>>>>> * dicomTar version : 1 >>>>>>>>>>>>>>>>>> * md5sum for DICOM tarball : >>>>>>>>>>>>>>>>>> 4a301b0318178b09b91e63544282364d ImagingUpload-18-33-Qq7HGy.tar >>>>>>>>>>>>>>>>>> * md5sum for DICOM tarball gzipped : >>>>>>>>>>>>>>>>>> 9d95ea2b9111be236808bfd65d7e65ec ImagingUpload-18-33-Qq7HGy.tar.gz >>>>>>>>>>>>>>>>>> * md5sum for complete archive : >>>>>>>>>>>>>>>>>> ab19a86357f1d4053aa3b81c8a071053 >>>>>>>>>>>>>>>>>> DCM_2012-12-05_ImagingUpload-18-33-Qq7HGy.tar >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Last update of record: >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> The dicomTar.pl execution has failed. >>>>>>>>>>>>>>>>>> Can't exec "mail": No such file or directory at ./ >>>>>>>>>>>>>>>>>> batch_uploads_imageuploader.pl line 249. >>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at ./ >>>>>>>>>>>>>>>>>> batch_uploads_imageuploader.pl line 250. >>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at ./ >>>>>>>>>>>>>>>>>> batch_uploads_imageuploader.pl line 251. >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> ???? ???, 4 ??? 2019 ???? 5:35 ?.?., ?/? Christine >>>>>>>>>>>>>>>>>> Rogers, Ms. ??????: >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Ok, this sounds like good progress. Let us know when you >>>>>>>>>>>>>>>>>> next encounter issues as you progress through the Imaging >>>>>>>>>>>>>>>>>> Install/Setup docs >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> . >>>>>>>>>>>>>>>>>> I'll look into how we can better handle the incoming/ >>>>>>>>>>>>>>>>>> directory next time. >>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>> Christine >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> On Wed, Sep 4, 2019 at 10:23 AM Sotirios Nikoloutsopoulos >>>>>>>>>>>>>>>>>> wrote: >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> /data/loris/bin/mri/dicom-archive/.loris_mri/database_config.py >>>>>>>>>>>>>>>>>> is populated correctly except its port is 'port' : ''. Also i have >>>>>>>>>>>>>>>>>> tested that i can connect to MySQL with lorisuser. >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> I executed the script again, because the only error i had >>>>>>>>>>>>>>>>>> previously was that the /data/incoming folder didn't exist and there are no >>>>>>>>>>>>>>>>>> errors reported back except of warnings <>>>>>>>>>>>>>>>>> on the command line interface can be insecure>>. >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> ???? ???, 4 ??? 2019 ???? 4:53 ?.?., ?/? Christine >>>>>>>>>>>>>>>>>> Rogers, Ms. ??????: >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> It's possible -- if the script was unable to connect to >>>>>>>>>>>>>>>>>> the database during its execution (e.g. typo in the password), that would >>>>>>>>>>>>>>>>>> explain the underpopulated Image path and Loris-MRI code path you saw in >>>>>>>>>>>>>>>>>> the Config module. >>>>>>>>>>>>>>>>>> It's hard to tell without seeing the output from your >>>>>>>>>>>>>>>>>> script run -- Did you see a sign of any such error? >>>>>>>>>>>>>>>>>> The Config fields are populated by the imaging_install.sh >>>>>>>>>>>>>>>>>> script (starting at line 222 >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> ) >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> For example, check if the database connection information >>>>>>>>>>>>>>>>>> was populated accurately in $mridir >>>>>>>>>>>>>>>>>> /dicom-archive/.loris_mri/database_config.py >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>> Christine >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> On Wed, Sep 4, 2019 at 9:34 AM Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Hi Christine, >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> If you are referring to the imaging_install.sh here is an >>>>>>>>>>>>>>>>>> image with the configurations i typed. Maybe the problem is somewhere at >>>>>>>>>>>>>>>>>> the last part which asks to configure as much as possible automatically? >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Thanks >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> ???? ???, 4 ??? 2019 ???? 4:16 ?.?., ?/? Christine >>>>>>>>>>>>>>>>>> Rogers, Ms. ??????: >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Glad to hear your LORIS core install is up and working >>>>>>>>>>>>>>>>>> and all the front-end pages are loading. >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> > lorisadmin at loris-VirtualBox:/var/www/loris$ chmod 775 >>>>>>>>>>>>>>>>>> project >>>>>>>>>>>>>>>>>> > and the web interface worked. >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Yes, it's important that project/ have 775 permissions >>>>>>>>>>>>>>>>>> and that lorisadmin be part of the sudoers group, per step >>>>>>>>>>>>>>>>>> 1 in the install Readme >>>>>>>>>>>>>>>>>> . >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> > As for the Paths, LORIS-MRI code and Image should >>>>>>>>>>>>>>>>>> change LORIS to loris, right? >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> These imaging paths will be updated during your imaging >>>>>>>>>>>>>>>>>> installation by >>>>>>>>>>>>>>>>>> an automated script -- you do not need to set them manually via the Config >>>>>>>>>>>>>>>>>> module. >>>>>>>>>>>>>>>>>> Please continue to follow the Setup Guide >>>>>>>>>>>>>>>>>> for detailed >>>>>>>>>>>>>>>>>> steps to follow. >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>> Christine >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> On Wed, Sep 4, 2019 at 8:05 AM Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> As for the Paths, LORIS-MRI code and Image should change >>>>>>>>>>>>>>>>>> LORIS to loris, right? >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> ???? ???, 4 ??? 2019 ???? 2:28 ?.?., ?/? Sotirios >>>>>>>>>>>>>>>>>> Nikoloutsopoulos ??????: >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> i used >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> curl -sL https://deb.nodesource.com/setup_8.x | sudo -E bash - >>>>>>>>>>>>>>>>>> sudo apt-get install -y nodejs >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> you had suggested in the past, make worked and now i can >>>>>>>>>>>>>>>>>> see all the contents in the web-interface, but i don't need make install? >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Thanks >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.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 >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> 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 >>>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> -- >>>>>>>>>>>> >>>>>>>>>>>> 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... 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Name: image.png Type: image/png Size: 175139 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 42208 bytes Desc: not available URL: From cecile.madjar at mcin.ca Tue Oct 1 09:21:16 2019 From: cecile.madjar at mcin.ca (Cecile Madjar) Date: Tue, 1 Oct 2019 09:21:16 -0400 Subject: [Loris-dev] Import mri - scripts In-Reply-To: References: Message-ID: Hi Sotirios, In the mri_upload table, there is a TarchiveID column associated with the MRI upload you inserted. When this value is NULL, it means no DICOMs were inserted into the tarchive tables. At the end of the insertion of the DICOMs in the tarchive tables, this value is updated with the correct TarchiveID associated with the upload. Could this correspond to what you want to do? Regarding the files_qcstatus, this table is only linked to the files table (hence, the MINC files). You could always create a new table for dicom_qcstatus and link it to the tarchive table? C?cile On Tue, Oct 1, 2019 at 6:56 AM Sotirios Nikoloutsopoulos < sotirisnik at gmail.com> wrote: > Hi, > > i would like whenever a dicom is imported to mark all their coressponding > qc_status to "pass". I was thinking of creating a trigger for that, but > which tables do i need to add entries to? So far from what i see i need to > add entres at the table "files" whenever an insertion happens to > files_qcstatus. > > Thanks > > ???? ???, 30 ??? 2019 ???? 4:04 ?.?., ?/? Sotirios Nikoloutsopoulos < > sotirisnik at gmail.com> ??????: > >> Oh, sorry i should have asked for StudyID, at the beginning of my email i >> sent 3 hours ago (not StudyUID). >> >> ???? ???, 30 ??? 2019 ???? 3:55 ?.?., ?/? Sotirios Nikoloutsopoulos < >> sotirisnik at gmail.com> ??????: >> >>> Hi, >>> >>> that's the Study Instance UID, not the StudyID. So the StudyID i am >>> looking for is not stored in the database? >>> >>> [image: image.png] >>> >>> Thanks. >>> >>> ???? ???, 30 ??? 2019 ???? 3:38 ?.?., ?/? Cecile Madjar < >>> cecile.madjar at mcin.ca> ??????: >>> >>>> Hi Sotirios, >>>> >>>> The StudyUID is stored in the DicomArchiveID field of the >>>> tarchive table. It can also be found in the metadata field but it is mixed >>>> with many other information. >>>> >>>> Hope this helps, >>>> >>>> C?cile >>>> >>>> On Mon, Sep 30, 2019 at 6:00 AM Sotirios Nikoloutsopoulos < >>>> sotirisnik at gmail.com> wrote: >>>> >>>>> Hi, >>>>> >>>>> Is StudyUID stored somewhere at the tables? At the tarchive table, >>>>> specifically at the AcquisitonMetadata column i found something called >>>>> 'Unique Study ID" in its context, but that must be the Study Instance UID. >>>>> >>>>> Thanks >>>>> >>>>> ???? ???, 27 ??? 2019 ???? 4:22 ?.?., ?/? Cecile Madjar < >>>>> cecile.madjar at mcin.ca> ??????: >>>>> >>>>>> Hi Sotirios, >>>>>> >>>>>> Your observation is correct. A little explanation below. >>>>>> >>>>>> MINC files get inserted into the MRI violation tables if: >>>>>> >>>>>> - the scan type could not be identified (not matching an entry in >>>>>> the mri_protocol table) >>>>>> - one parameter of the scan type is out of the expected range >>>>>> present in the mri_protocol_checks (extra filtering in case you need to be >>>>>> stricker on some parameters not present in the mri_protocol table) >>>>>> - if the CandID and PSCID do not match >>>>>> >>>>>> The following cases do not get in the MRI violation tables as it >>>>>> happens before the conversion of the DICOM to MINC files and only MINC >>>>>> files violations are logged there: >>>>>> >>>>>> - "No single DICOM" (since no valid DICOM could be found to >>>>>> convert to MINC) >>>>>> - "Study already inserted" (duplicate StudyUID) since this error >>>>>> happens at the dicomTar.pl level (way before conversion into MINC files) >>>>>> >>>>>> Glad everything is working out!! >>>>>> Best, >>>>>> >>>>>> C?cile >>>>>> >>>>>> On Fri, Sep 27, 2019 at 6:17 AM Sotirios Nikoloutsopoulos < >>>>>> sotirisnik at gmail.com> wrote: >>>>>> >>>>>>> Hi, >>>>>>> >>>>>>> the mri passed, for some reason it consumed 5.12GB of ram. Now about >>>>>>> the mri_violations, dicoms are triggered to be inserted there only if there >>>>>>> is a violation for Tr_min, Tr_max, in general for its header parameter? >>>>>>> Because i don't see the cases of 'No single dicom" or with the 2 studyiuid >>>>>>> to be there. >>>>>>> >>>>>>> Thanks >>>>>>> >>>>>>> ???? ???, 26 ??? 2019 ???? 5:07 ?.?., ?/? Cecile Madjar < >>>>>>> cecile.madjar at mcin.ca> ??????: >>>>>>> >>>>>>>> Hi Sotirios, >>>>>>>> >>>>>>>> Sorry to hear you are having issues with the memory. I think most >>>>>>>> of our VMs are set up with 4GB of RAM so with 4GB you should be fine. >>>>>>>> >>>>>>>> Hope this helps! >>>>>>>> >>>>>>>> C?cile >>>>>>>> >>>>>>>> On Thu, Sep 26, 2019 at 9:48 AM Sotirios Nikoloutsopoulos < >>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>> >>>>>>>>> Hi, >>>>>>>>> >>>>>>>>> about that dicom that had that insertion error it's about 30mb and >>>>>>>>> when it is being processed the ram is being drastically increased from 2gb >>>>>>>>> to 3.28 and then the whole virtual machine is frozen. What is the >>>>>>>>> recommended size of ram for using Loris? >>>>>>>>> >>>>>>>>> Thanks >>>>>>>>> >>>>>>>>> [image: image.png] >>>>>>>>> >>>>>>>>> >>>>>>>>> ???? ???, 24 ??? 2019 ???? 11:24 ?.?., ?/? Cecile Madjar < >>>>>>>>> cecile.madjar at mcin.ca> ??????: >>>>>>>>> >>>>>>>>>> Hi Sotirios, >>>>>>>>>> >>>>>>>>>> Glad to see that the StudyUID problem was fixed! >>>>>>>>>> >>>>>>>>>> For the delete script issue, if you are absolutely certain that >>>>>>>>>> no processes are run for that uploadID, you can update the mri_upload table >>>>>>>>>> and set the column Inserting to 0 instead of 1 for that >>>>>>>>>> uploadID. It looks like for some reason the scripts did not update this >>>>>>>>>> field when it stopped the insertion. Not sure why that would be the case >>>>>>>>>> though. >>>>>>>>>> Note: only do that update if you are certain that there is no >>>>>>>>>> processing happening. >>>>>>>>>> >>>>>>>>>> Hope this helps! >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> On Tue, Sep 24, 2019 at 11:57 AM Sotirios Nikoloutsopoulos < >>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>> >>>>>>>>>>> Hi, >>>>>>>>>>> >>>>>>>>>>> about the Dicoms i reported that didn't have a StudyID they >>>>>>>>>>> actually do >>>>>>>>>>> >>>>>>>>>>> [image: image.png] >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> [image: image.png] >>>>>>>>>>> >>>>>>>>>>> I thought that this might be a permission because "w" was >>>>>>>>>>> missing at the group. After using chmod -R 775 only 102809579 passed, but >>>>>>>>>>> with no mnic files. Also now i have this error >>>>>>>>>>> >>>>>>>>>>> (loris-mri-python) lorisadmin at loris-VirtualBox:/data/loris/bin/mri/tools$ >>>>>>>>>>> ./delete_imaging_upload.pl -uploadID 34 -ignore >>>>>>>>>>> Cannot delete upload 34: the MRI pipeline is currently >>>>>>>>>>> processing it. >>>>>>>>>>> >>>>>>>>>>> How can solve this? >>>>>>>>>>> >>>>>>>>>>> Thanks >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> ???? ???, 24 ??? 2019 ???? 2:30 ?.?., ?/? Sotirios >>>>>>>>>>> Nikoloutsopoulos ??????: >>>>>>>>>>> >>>>>>>>>>>> Hi, >>>>>>>>>>>> >>>>>>>>>>>> Here is our auto dicom uploading python script: >>>>>>>>>>>> https://github.com/aueb-wim/DataQualityControlTool/blob/loris1/mipqctool/dicom_uploader.py >>>>>>>>>>>> >>>>>>>>>>>> To give you a brief idea: >>>>>>>>>>>> Per folder it will: >>>>>>>>>>>> 1) Delete all the .bak files >>>>>>>>>>>> 2) Locate .dcm files and update the Patient header >>>>>>>>>>>> 3) Furthermore we are interesting in finding TR_min, TR_max, >>>>>>>>>>>> TE_min, TE_max parameters of T1 protocol and do an update at the >>>>>>>>>>>> mri_protocol table >>>>>>>>>>>> https://github.com/aueb-wim/DataQualityControlTool/blob/loris1/mipqctool/dicom_uploader.py#L205 >>>>>>>>>>>> For some reason some files are missing >>>>>>>>>>>> SeriesDescription/ProtocolName >>>>>>>>>>>> >>>>>>>>>>>> In total i have 7 folders >>>>>>>>>>>> >>>>>>>>>>>> [image: image.png] >>>>>>>>>>>> >>>>>>>>>>>> 3/7 passed >>>>>>>>>>>> >>>>>>>>>>>> [image: image.png] >>>>>>>>>>>> >>>>>>>>>>>> Also about the first patient with DC0000 had a violation "T1 >>>>>>>>>>>> AXIAL SE GADO", but my script didn't output a TE of 17 nowhere and i find >>>>>>>>>>>> that weird since Loris detects the SeriesDescription. >>>>>>>>>>>> [image: image.png] >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> Now about the 4/7 that didn't passed >>>>>>>>>>>> >>>>>>>>>>>> 102327840 and 102809579 outputs "The target directory does not >>>>>>>>>>>> contain a single DICOM file.", therefore they are missing their StudyUID >>>>>>>>>>>> >>>>>>>>>>>> 102506134 has 2 studyuid "You can't use it with data from >>>>>>>>>>>> multiple studies." >>>>>>>>>>>> >>>>>>>>>>>> and 102761034 "No data could be converted into valid MINC >>>>>>>>>>>> files. localizer, scout will not be considered!" What is this? >>>>>>>>>>>> >>>>>>>>>>>> If i wanted to force the insertion of 102327840, 102809579 and >>>>>>>>>>>> 102506134 can i just pass a flag parameter to >>>>>>>>>>>> batch_uploads_imageuploader.pl? or modify >>>>>>>>>>>> imaging_upload_file.pl? >>>>>>>>>>>> >>>>>>>>>>>> Thank you, >>>>>>>>>>>> >>>>>>>>>>>> Sotirios >>>>>>>>>>>> >>>>>>>>>>>> PS >>>>>>>>>>>> >>>>>>>>>>>> To diagnose a folder search the name of the folder at >>>>>>>>>>>> dicom_output.txt. >>>>>>>>>>>> >>>>>>>>>>>> ???? ???, 20 ??? 2019 ???? 4:54 ?.?., ?/? Christine Rogers, Ms. >>>>>>>>>>>> ??????: >>>>>>>>>>>> >>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>> Glad to hear about your progress. >>>>>>>>>>>>> >>>>>>>>>>>>> Yes, the script you used to delete imaging data is fully >>>>>>>>>>>>> documented here >>>>>>>>>>>>> >>>>>>>>>>>>> -- let us know if you didn't find the answers you were looking for there. >>>>>>>>>>>>> (Is it possible the null row in *mri_scanner* seen in your >>>>>>>>>>>>> database management software is a visual placeholder for you as the user? >>>>>>>>>>>>> I'm not sure why a scanner would ever be registered with ID='0' as your >>>>>>>>>>>>> screenshot showed.) >>>>>>>>>>>>> >>>>>>>>>>>>> Best, >>>>>>>>>>>>> Christine >>>>>>>>>>>>> >>>>>>>>>>>>> On Fri, Sep 20, 2019 at 9:45 AM Sotirios Nikoloutsopoulos < >>>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>> >>>>>>>>>>>>>> I fixed it with this >>>>>>>>>>>>>> >>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>> >>>>>>>>>>>>>> ???? ???, 20 ??? 2019 ???? 4:37 ?.?., ?/? Sotirios >>>>>>>>>>>>>> Nikoloutsopoulos ??????: >>>>>>>>>>>>>> >>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> I tried to create a new candidate using the API, is there >>>>>>>>>>>>>>> something wrong with the structure? why did i receive a 500 internal error? >>>>>>>>>>>>>>> In the loris-error log it state that there is something wrong with token, >>>>>>>>>>>>>>> but i verfied that the type of the token is a string. >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> [Fri Sep 20 16:35:26.874732 2019] [php7:error] [pid 4535] >>>>>>>>>>>>>>> [client 127.0.0.1:59674] PHP Fatal error: Uncaught >>>>>>>>>>>>>>> TypeError: Argument 1 passed to SinglePointLogin::JWTAuthenticate() must be >>>>>>>>>>>>>>> of the type string, null given, called in >>>>>>>>>>>>>>> /var/www/loris/php/libraries/SinglePointLogin.class.inc on line 169 and >>>>>>>>>>>>>>> defined in >>>>>>>>>>>>>>> /var/www/loris/php/libraries/SinglePointLogin.class.inc:192\nStack >>>>>>>>>>>>>>> trace:\n#0 /var/www/loris/php/libraries/SinglePointLogin.class.inc(169): >>>>>>>>>>>>>>> SinglePointLogin->JWTAuthenticate(NULL)\n#1 >>>>>>>>>>>>>>> /var/www/loris/php/libraries/NDB_Client.class.inc(171): >>>>>>>>>>>>>>> SinglePointLogin->authenticate()\n#2 >>>>>>>>>>>>>>> /var/www/loris/htdocs/api/v0.0.2/APIBase.php(73): >>>>>>>>>>>>>>> NDB_Client->initialize('/var/www/loris/...')\n#3 >>>>>>>>>>>>>>> /var/www/loris/htdocs/api/v0.0.2/Candidates.php(44): >>>>>>>>>>>>>>> Loris\\API\\APIBase->__construct('POST')\n#4 >>>>>>>>>>>>>>> /var/www/loris/htdocs/api/v0.0.2/Candidates.php(244): >>>>>>>>>>>>>>> Loris\\API\\Candidates->__construct('POST', Array)\n#5 {main}\n thrown in >>>>>>>>>>>>>>> /var/www/loris/php/libraries/SinglePointLogin.class.inc on line 192 >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> ???? ???, 20 ??? 2019 ???? 2:39 ?.?., ?/? Sotirios >>>>>>>>>>>>>>> Nikoloutsopoulos ??????: >>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Is there a way also to delete candidates? Just to let you >>>>>>>>>>>>>>>> know what i did to clear candidates, because maybe i may have missed >>>>>>>>>>>>>>>> dependencies. >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> First i deleted all their uploads >>>>>>>>>>>>>>>> ./delete_imaging_upload.pl -uploadID 13 etc ( is there a >>>>>>>>>>>>>>>> way to omit the backup file ? ) >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Afterwards i had some scanner candidates, so i deleted all >>>>>>>>>>>>>>>> the entries from mri_scanner except that i couldn't delete this entry with >>>>>>>>>>>>>>>> the 0 ID. >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Lastly i deleted the session and then the candidate table. >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Thanks >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> ???? ???, 19 ??? 2019 ???? 7:57 ?.?., ?/? Christine Rogers, >>>>>>>>>>>>>>>> Ms. ??????: >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> We recommend that you use our existing tools for creating >>>>>>>>>>>>>>>>> new candidates - either the LORIS API or if you are using a PHP script, by >>>>>>>>>>>>>>>>> calling the Candidate class's createNew() >>>>>>>>>>>>>>>>> function. >>>>>>>>>>>>>>>>> These will create the necessary records for you. (It's not recommended to >>>>>>>>>>>>>>>>> make direct modifications to mysql database tables in your script, if I >>>>>>>>>>>>>>>>> understand you.) >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> The CandID should be a randomized 6 digit randomized ID, >>>>>>>>>>>>>>>>> and there are multiple reasons for this. >>>>>>>>>>>>>>>>> You can use the PSCID for project-specific IDs and the >>>>>>>>>>>>>>>>> External ID field in the candidate table can also be used for any values >>>>>>>>>>>>>>>>> you like. >>>>>>>>>>>>>>>>> Additionally, any number of custom IDs can be added in >>>>>>>>>>>>>>>>> parallel - these are entered/visible in the Candidate Information module >>>>>>>>>>>>>>>>> and added in the back-end as candidate parameters. >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>> Christine >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> On Tue, Sep 17, 2019 at 7:31 PM Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> We are building a script that will auto insert the >>>>>>>>>>>>>>>>>> candidates based on their ExternalID. We would like to know whethere when >>>>>>>>>>>>>>>>>> we are creating a new profile in the candidate table, if we also have to >>>>>>>>>>>>>>>>>> insert a new record at another table? Furthermore is there a problem that >>>>>>>>>>>>>>>>>> in our case CandID won't be a 6digit? ( should we start it from 100000?) >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Thanks >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> ???? ???, 13 ??? 2019 ???? 5:38 ?.?., ?/? Melanie >>>>>>>>>>>>>>>>>> Legault, Mrs ??????: >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> That would normally be the case but the numeric part of >>>>>>>>>>>>>>>>>>> the PSCID get paded with 0 on the left. >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Ex. for sequential ID made of center ID of `ABC` plus 4 >>>>>>>>>>>>>>>>>>> numerical char with a min value of 1, the sequence would be: >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> ABC0001 >>>>>>>>>>>>>>>>>>> ABC0002 >>>>>>>>>>>>>>>>>>> ... >>>>>>>>>>>>>>>>>>> ABC0010 >>>>>>>>>>>>>>>>>>> ... >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> thus sorting them ascending will always get the latest >>>>>>>>>>>>>>>>>>> value generated as the max value. >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> M?lanie >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> ------------------------------ >>>>>>>>>>>>>>>>>>> *From:* Sotirios Nikoloutsopoulos >>>>>>>>>>>>>>>>>>> *Sent:* September 13, 2019 10:15 >>>>>>>>>>>>>>>>>>> *To:* Melanie Legault, Mrs >>>>>>>>>>>>>>>>>>> *Cc:* Christine Rogers, Ms. ; >>>>>>>>>>>>>>>>>>> loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>>>>>> > >>>>>>>>>>>>>>>>>>> *Subject:* Re: [Loris-dev] Import mri - scripts >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> I see, although the PSCID value is varchar(255), it must >>>>>>>>>>>>>>>>>>> be stored within a specific length of characters. Otherwise if we were to >>>>>>>>>>>>>>>>>>> sort strings with different lengths the result would not be sorted >>>>>>>>>>>>>>>>>>> correctly ( e.x. 1,2,10,11 as strings would result to 1, 10, 11, 2 ). >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Thanks >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> ???? ???, 13 ??? 2019 ???? 4:52 ?.?., ?/? Melanie >>>>>>>>>>>>>>>>>>> Legault, Mrs ??????: >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Hello Sotirios, >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> There is no `last value` stored anywhere. >>>>>>>>>>>>>>>>>>> The code simply look for the PSCID with the max value >>>>>>>>>>>>>>>>>>> and increase that value by 1 in order to generate the next PSCID. >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Hope this info help. >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> M?lanie Legault | Software developer | Faculty of >>>>>>>>>>>>>>>>>>> Medicine | McGill University >>>>>>>>>>>>>>>>>>> 3801 University, Montr?al, QC H3A 2B4 >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> ------------------------------ >>>>>>>>>>>>>>>>>>> *From:* loris-dev-bounces at bic.mni.mcgill.ca < >>>>>>>>>>>>>>>>>>> loris-dev-bounces at bic.mni.mcgill.ca> on behalf of >>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos >>>>>>>>>>>>>>>>>>> *Sent:* September 13, 2019 9:43 >>>>>>>>>>>>>>>>>>> *To:* Christine Rogers, Ms. >>>>>>>>>>>>>>>>>>> *Cc:* loris-dev at bic.mni.mcgill.ca < >>>>>>>>>>>>>>>>>>> loris-dev at bic.mni.mcgill.ca> >>>>>>>>>>>>>>>>>>> *Subject:* Re: [Loris-dev] Import mri - scripts >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> how does Loris determine the next available PSCID value >>>>>>>>>>>>>>>>>>> for a new candidate? >>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris/wiki/Project-Customization >>>>>>>>>>>>>>>>>>> e.x in the default case the PSCID is sequential, but where do we store the >>>>>>>>>>>>>>>>>>> last value for the sequential sequence? >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Thanks >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> ???? ???, 10 ??? 2019 ???? 4:00 ?.?., ?/? Sotirios >>>>>>>>>>>>>>>>>>> Nikoloutsopoulos ??????: >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> the parameters in the mri_protocol you have assigned are >>>>>>>>>>>>>>>>>>> global standard? or were assigned after trial and error? >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Thanks >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> ???? ???, 8 ??? 2019 ???? 10:11 ?.?., ?/? Christine >>>>>>>>>>>>>>>>>>> Rogers, Ms. ??????: >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Given you have done the initial setup of your tables to >>>>>>>>>>>>>>>>>>> match your intended protocol/parameters according to instructions -- >>>>>>>>>>>>>>>>>>> the Troubleshooting guide documentation recommends >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> re-running the pipeline (and first deleting prior uploads). >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>> Christine >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> On Sun, Sep 8, 2019 at 10:22 AM Sotirios >>>>>>>>>>>>>>>>>>> Nikoloutsopoulos wrote: >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> *if i were to change their status to resolve what would >>>>>>>>>>>>>>>>>>> happen? >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> ???? ???, 8 ??? 2019 ???? 5:12 ?.?., ?/? Sotirios >>>>>>>>>>>>>>>>>>> Nikoloutsopoulos ??????: >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> I noticed that i can view the mnics at the brainbrowser >>>>>>>>>>>>>>>>>>> from the mri_violations page ( those mnics are stored at >>>>>>>>>>>>>>>>>>> /data/loris/data/trashbin/ if i were to click their issue to resolve what >>>>>>>>>>>>>>>>>>> would happend? would they appear in the dicom_archive view too? ). >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> ???? ???, 8 ??? 2019 ???? 4:17 ?.?., ?/? Sotirios >>>>>>>>>>>>>>>>>>> Nikoloutsopoulos ??????: >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> The defaut values of the schema exists in my local >>>>>>>>>>>>>>>>>>> database. If i adjust the default values of TR_min and TE_min the mincs >>>>>>>>>>>>>>>>>>> will be uploaded? >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Thanks >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> ???? ???, 7 ??? 2019 ???? 5:48 ?.?., ?/? Christine >>>>>>>>>>>>>>>>>>> Rogers, Ms. ??????: >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Is it possible that you haven't set up your mri_protocol >>>>>>>>>>>>>>>>>>> table ? (and mri_scan_type table too, for additional types of scans) >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Like the psc table, this is a pre-requisite for the >>>>>>>>>>>>>>>>>>> Imaging insertion setup : See the install/setup documentation : >>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/master/docs/02-Install.md >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> To add new rows, just use MySQL insert statements. You >>>>>>>>>>>>>>>>>>> can adapt the insert statements which load the default table values --> >>>>>>>>>>>>>>>>>>> e.g. Here on GitHub : >>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris/blob/master/SQL/0000-00-00-schema.sql#L718 >>>>>>>>>>>>>>>>>>> (see also the mri_scan_type table) >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>> Christine >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> On Fri, Sep 6, 2019 at 8:32 PM Sotirios Nikoloutsopoulos >>>>>>>>>>>>>>>>>>> wrote: >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> I see that i can edit the values but not how to insert >>>>>>>>>>>>>>>>>>> new rows. >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> If i choose Inserted with flag then will the minc be >>>>>>>>>>>>>>>>>>> inserted? >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> ???? ???, 7 ??? 2019 ???? 3:21 ?.?., ?/? Christine >>>>>>>>>>>>>>>>>>> Rogers, Ms. ??????: >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Glad to hear that *dcmodify* worked correctly. >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> For the MRI Violations module, the screenshot is >>>>>>>>>>>>>>>>>>> enough. >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> It says "could not identify scan type", which we knew >>>>>>>>>>>>>>>>>>> already. Did you click on the link on those words? >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> It will take you to the next page of the module, showing >>>>>>>>>>>>>>>>>>> for each scan what the scan parameters were, and will also show for >>>>>>>>>>>>>>>>>>> comparison what's stored in your *mri_protocol* table. >>>>>>>>>>>>>>>>>>> Compare these values to find which parameter was not >>>>>>>>>>>>>>>>>>> correct according to your *mri_protocol* table scan >>>>>>>>>>>>>>>>>>> type definitions. >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> You may end up broadening your mri_protocol value ranges >>>>>>>>>>>>>>>>>>> (e.g. TR, TE) for scans. >>>>>>>>>>>>>>>>>>> This can be done in the front-end, by editing the >>>>>>>>>>>>>>>>>>> database table directly in the same subpage of the MRI Violations module. >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> The MRI Violations module features are explained in more >>>>>>>>>>>>>>>>>>> detail in the Help text for this module inside LORIS (click the ["?"] icon >>>>>>>>>>>>>>>>>>> in the menu bar.) >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> See also: Loris-MRI troubleshooting guide >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> : no MINCs inserted- violated scans >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>> Christine >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> On Fri, Sep 6, 2019 at 8:11 PM Sotirios Nikoloutsopoulos >>>>>>>>>>>>>>>>>>> wrote: >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> looks like my previous email's attachment wasn't >>>>>>>>>>>>>>>>>>> delivered due to security reasons, i uploaded my file at google drive >>>>>>>>>>>>>>>>>>> https://drive.google.com/file/d/1U_TRbo_qGgfpQfs-SqeG9J3bMMqNfUU4/view?usp=sharing >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> ???? ???, 7 ??? 2019 ???? 3:02 ?.?., ?/? Sotirios >>>>>>>>>>>>>>>>>>> Nikoloutsopoulos ??????: >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> From Dicat's view seems that dcmodify worked in both >>>>>>>>>>>>>>>>>>> cases >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> For the mri_violations i attached the .html output from >>>>>>>>>>>>>>>>>>> webbrowser, so that you can check the filelds easier. >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Thanks >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> ???? ???, 6 ??? 2019 ???? 7:49 ?.?., ?/? Christine >>>>>>>>>>>>>>>>>>> Rogers, Ms. ??????: >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Hi Sotirios -- >>>>>>>>>>>>>>>>>>> Great, sounds like more progress. >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> About the dcmodify command -- I'm not sure why you're >>>>>>>>>>>>>>>>>>> getting an Endian warning. (it's a warning not an error, correct?) >>>>>>>>>>>>>>>>>>> To clarify -- Were the DICOM headers (PatientName) all >>>>>>>>>>>>>>>>>>> successfully relabelled, after the command ran? >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> You can use also our DICAT tool ( >>>>>>>>>>>>>>>>>>> https://github.com/aces/DICAT) to verify and/or update >>>>>>>>>>>>>>>>>>> local DICOM headers -- though your dcmodify command is a great and fast >>>>>>>>>>>>>>>>>>> solution for bulk header updates. >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> If you're concerned about fields being changed (e.g. >>>>>>>>>>>>>>>>>>> "(2001,105f)" from the warning message) - you can also dcmdump a DICOM >>>>>>>>>>>>>>>>>>> slice before and look at these fields specifically. >>>>>>>>>>>>>>>>>>> It's also not a bad "sanity check" to backup your DICOMS >>>>>>>>>>>>>>>>>>> before/after running dcmodify, and use dcmdump on each version to diff the >>>>>>>>>>>>>>>>>>> outputs -- this will pinpoint what changed. >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Re the protocol violation -- AcquisitionProtocol not >>>>>>>>>>>>>>>>>>> recognized or unknown : this means your scans did not match what is >>>>>>>>>>>>>>>>>>> stored in your mri_protocol table. >>>>>>>>>>>>>>>>>>> Check the MRI Violations front-end module -- can you see >>>>>>>>>>>>>>>>>>> why they didn't match? >>>>>>>>>>>>>>>>>>> Send us an example, in addition to the contents of the >>>>>>>>>>>>>>>>>>> mri_protocol table, if you can't find the source of the mismatch. >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>> Christine >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> On Fri, Sep 6, 2019 at 12:04 PM Sotirios >>>>>>>>>>>>>>>>>>> Nikoloutsopoulos wrote: >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Here is the psc table >>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> I created 2 candidates profiles through the interface >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> then runned dcmodify command to a dicom file >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> dcmodify -ma PatientName="DCC0000_258024_V1" >>>>>>>>>>>>>>>>>>> /home/lorisadmin/DICOMS/000535670/501/*.dcm >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> and got those warning: is this okay? >>>>>>>>>>>>>>>>>>> W: Found element (2001,105f) with VR UN and undefined >>>>>>>>>>>>>>>>>>> length, reading a sequence with transfer syntax LittleEndianImplicit >>>>>>>>>>>>>>>>>>> (CP-246) >>>>>>>>>>>>>>>>>>> W: Found element (2005,1083) with VR UN and undefined >>>>>>>>>>>>>>>>>>> length, reading a sequence with transfer syntax LittleEndianImplicit >>>>>>>>>>>>>>>>>>> (CP-246) >>>>>>>>>>>>>>>>>>> W: Found element (2005,1402) with VR UN and undefined >>>>>>>>>>>>>>>>>>> length, reading a sequence with transfer syntax LittleEndianImplicit >>>>>>>>>>>>>>>>>>> (CP-246) >>>>>>>>>>>>>>>>>>> W: Found element (2005,140f) with VR UN and undefined >>>>>>>>>>>>>>>>>>> length, reading a sequence with transfer syntax LittleEndianImplicit >>>>>>>>>>>>>>>>>>> (CP-246) >>>>>>>>>>>>>>>>>>> W: Found element (2001,105f) with VR UN and undefined >>>>>>>>>>>>>>>>>>> length, reading a sequence with transfer syntax LittleEndianImplicit >>>>>>>>>>>>>>>>>>> (CP-246) >>>>>>>>>>>>>>>>>>> W: Found element (2005,1083) with VR UN and undefined >>>>>>>>>>>>>>>>>>> length, reading a sequence with transfer syntax LittleEndianImplicit >>>>>>>>>>>>>>>>>>> (CP-246) >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> dcmodify at another Dicom didn't show warnings. Below >>>>>>>>>>>>>>>>>>> you can see the execution for the second dicom. Mnics could not be inserted >>>>>>>>>>>>>>>>>>> due to AcquisitionProtocol being unknown. >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Running now the following command: >>>>>>>>>>>>>>>>>>> /data/loris/bin/mri//uploadNeuroDB/ >>>>>>>>>>>>>>>>>>> imaging_upload_file.pl -profile prod -upload_id 12 >>>>>>>>>>>>>>>>>>> /data/incoming/DCC0001_602102_V1.tar.gz -verbose >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> find -path \/tmp\/ImagingUpload\-18\-36\-mTrxXs -name >>>>>>>>>>>>>>>>>>> '__MACOSX' -delete >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> dicomTar.pl \/tmp\/ImagingUpload\-18\-36\-mTrxXs >>>>>>>>>>>>>>>>>>> \/data\/loris\/data\/tarchive\/ -database -profile prod -verbose >>>>>>>>>>>>>>>>>>> Source: /tmp/ImagingUpload-18-36-mTrxXs >>>>>>>>>>>>>>>>>>> Target: /data/loris/data/tarchive >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Testing for database connectivity. >>>>>>>>>>>>>>>>>>> Database is available. >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> You will archive the dir : ImagingUpload-18-36-mTrxXs >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> You are creating a tar with the following command: >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> tar -cf >>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive/ImagingUpload-18-36-mTrxXs.tar >>>>>>>>>>>>>>>>>>> ImagingUpload-18-36-mTrxXs >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> getting md5sums and gzipping!! >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> * Taken from dir : >>>>>>>>>>>>>>>>>>> /tmp/ImagingUpload-18-36-mTrxXs >>>>>>>>>>>>>>>>>>> * Archive target location : >>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive/DCM_2016-08-22_ImagingUpload-18-36-mTrxXs.tar >>>>>>>>>>>>>>>>>>> * Name of creating host : 127.0.1.1 >>>>>>>>>>>>>>>>>>> * Name of host OS : Linux >>>>>>>>>>>>>>>>>>> * Created by user : lorisadmin >>>>>>>>>>>>>>>>>>> * Archived on : 2019-09-06 >>>>>>>>>>>>>>>>>>> 18:36:50 >>>>>>>>>>>>>>>>>>> * dicomSummary version : 1 >>>>>>>>>>>>>>>>>>> * dicomTar version : 1 >>>>>>>>>>>>>>>>>>> * md5sum for DICOM tarball : >>>>>>>>>>>>>>>>>>> b1dcdc8903dd2d9a5443227db2aa2814 ImagingUpload-18-36-mTrxXs.tar >>>>>>>>>>>>>>>>>>> * md5sum for DICOM tarball gzipped : >>>>>>>>>>>>>>>>>>> aeae87f20155a6805f7e0cfe5212ea5f ImagingUpload-18-36-mTrxXs.tar.gz >>>>>>>>>>>>>>>>>>> * md5sum for complete archive : >>>>>>>>>>>>>>>>>>> 1d9258d1f077ebc49111ab7ba22a8d6e >>>>>>>>>>>>>>>>>>> DCM_2016-08-22_ImagingUpload-18-36-mTrxXs.tar >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Adding archive info into database >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Removing temporary files from target location >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Done adding archive info into database >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> \/data\/loris\/bin\/mri\//uploadNeuroDB/tarchiveLoader.pl >>>>>>>>>>>>>>>>>>> -globLocation -profile prod >>>>>>>>>>>>>>>>>>> \/data\/loris\/data\/tarchive\/\/DCM_2016\-08\-22_ImagingUpload\-18\-36\-mTrxXs\.tar >>>>>>>>>>>>>>>>>>> -uploadID 12 -verbose >>>>>>>>>>>>>>>>>>> md5sum >>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive/DCM_2016-08-22_ImagingUpload-18-36-mTrxXs.tar >>>>>>>>>>>>>>>>>>> PSCID is: DCC0001 >>>>>>>>>>>>>>>>>>> CandID id: 602102 >>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>> PSCID is: DCC0001 >>>>>>>>>>>>>>>>>>> CandID id: 602102 >>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>> candidate id 602102 >>>>>>>>>>>>>>>>>>> Set centerID = 1 >>>>>>>>>>>>>>>>>>> PSCID is: DCC0001 >>>>>>>>>>>>>>>>>>> CandID id: 602102 >>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>> PSCID is: DCC0001 >>>>>>>>>>>>>>>>>>> CandID id: 602102 >>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Number of MINC files that will be considered for >>>>>>>>>>>>>>>>>>> inserting into the database: 2 >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> log dir is /data/loris/data//logs and log file is >>>>>>>>>>>>>>>>>>> /data/loris/data//logs/TarLoad-18-37-31ajWx.log >>>>>>>>>>>>>>>>>>> PSCID is: DCC0001 >>>>>>>>>>>>>>>>>>> CandID id: 602102 >>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>> PSCID is: DCC0001 >>>>>>>>>>>>>>>>>>> CandID id: 602102 >>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>> candidate id 602102 >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> log dir is /data/loris/data//logs and log file is >>>>>>>>>>>>>>>>>>> /data/loris/data//logs/TarLoad-18-37-fanZFj.log >>>>>>>>>>>>>>>>>>> PSCID is: DCC0001 >>>>>>>>>>>>>>>>>>> CandID id: 602102 >>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>> PSCID is: DCC0001 >>>>>>>>>>>>>>>>>>> CandID id: 602102 >>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>> candidate id 602102 >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Cleaning up temp files: rm -rf >>>>>>>>>>>>>>>>>>> /tmp/TarLoad-18-37-to5pYZ/ImagingUpload-18-36-mTrxXs* >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> (loris-mri-python) lorisadmin at loris-VirtualBox:/data/loris/bin/mri$ >>>>>>>>>>>>>>>>>>> cat /data/loris/data/logs/TarLoad-18-37-fanZFj.log >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> ==> Loading file from disk >>>>>>>>>>>>>>>>>>> /tmp/TarLoad-18-37-to5pYZ/dcc0001_602102_v1_20160822_072406_205e1d1_mri.mnc >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> --> mapping DICOM parameter for >>>>>>>>>>>>>>>>>>> /tmp/TarLoad-18-37-to5pYZ/dcc0001_602102_v1_20160822_072406_205e1d1_mri.mnc >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> ==> computing md5 hash for MINC body. >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> --> md5: 02022dda60d9de429340fec838f50cfe >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> ==> verifying acquisition protocol >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Acquisition protocol is unknown >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> --> The minc file cannot be registered since the >>>>>>>>>>>>>>>>>>> AcquisitionProtocol is unknown >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> ???? ???, 4 ??? 2019 ???? 10:46 ?.?., ?/? Christine >>>>>>>>>>>>>>>>>>> Rogers, Ms. ??????: >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Hi Sotirios: >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Sure -- you can delete imaging datasets with the >>>>>>>>>>>>>>>>>>> *delete_imaging_upload* script -- >>>>>>>>>>>>>>>>>>> details here: >>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/21.0-dev/docs/scripts_md/delete_imaging_upload.md >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> What's in your *psc* table? (Is it properly populated? This >>>>>>>>>>>>>>>>>>> is a pre-requisite to loading imaging data. >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> ) >>>>>>>>>>>>>>>>>>> The foreign key constraint error on the candidate record >>>>>>>>>>>>>>>>>>> is curious. >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> There are also a few options for creating candidates >>>>>>>>>>>>>>>>>>> when inserting imaging data: >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> -- Method 1 : in 2 steps with the API then DICOM >>>>>>>>>>>>>>>>>>> insertion pipeline >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> a. via the LORIS API -- Create the candidates (and >>>>>>>>>>>>>>>>>>> visits, optionally I think) >>>>>>>>>>>>>>>>>>> How to: >>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris/blob/master/docs/API/LorisRESTAPI.md#30-candidate-api >>>>>>>>>>>>>>>>>>> Ensure you get the DCCID/CandID assigned by LORIS. >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Then as a second step: >>>>>>>>>>>>>>>>>>> b. Use the imaging insertion pipeline >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> to load your DICOMs. >>>>>>>>>>>>>>>>>>> You will want to first ensure that the PatientName >>>>>>>>>>>>>>>>>>> header in the DICOMs as well as tar package are correctly labelled with >>>>>>>>>>>>>>>>>>> PSCID_DCCID_VisitLabel >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> -- Method 2: for BIDS-format datasets: >>>>>>>>>>>>>>>>>>> How to : >>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/master/docs/05-PipelineLaunchOptions.md#52---pipeline-launch-for-bids-datasets >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Be sure to use the *-c* and *-s* options when running >>>>>>>>>>>>>>>>>>> the bids_import script, to automatically create your >>>>>>>>>>>>>>>>>>> candidates and sessions. >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>> Christine >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> On Wed, Sep 4, 2019 at 11:43 AM Sotirios >>>>>>>>>>>>>>>>>>> Nikoloutsopoulos wrote: >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> How do i delete a Study? And everytime do i have to >>>>>>>>>>>>>>>>>>> create a new candidate to get DCCID and a PSCID? >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> *First execution:* >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> (loris-mri-python) lorisadmin at loris-VirtualBox:/data/loris/bin/mri$ >>>>>>>>>>>>>>>>>>> ./batch_uploads_imageuploader.pl -profile prod < >>>>>>>>>>>>>>>>>>> ~/Desktop/input.txt > log.txt >>>>>>>>>>>>>>>>>>> Use of uninitialized value $_ in pattern match (m//) at >>>>>>>>>>>>>>>>>>> ./batch_uploads_imageuploader.pl line 144. >>>>>>>>>>>>>>>>>>> DBD::mysql::db do failed: Cannot add or update a child >>>>>>>>>>>>>>>>>>> row: a foreign key constraint fails (`LORIS`.`candidate`, CONSTRAINT >>>>>>>>>>>>>>>>>>> `FK_candidate_1` FOREIGN KEY (`RegistrationCenterID`) REFERENCES `psc` >>>>>>>>>>>>>>>>>>> (`CenterID`)) at /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 1060. >>>>>>>>>>>>>>>>>>> ERROR: Failed to insert record in table mri_scanner: >>>>>>>>>>>>>>>>>>> The following database commands failed: >>>>>>>>>>>>>>>>>>> PREPARE s FROM 'INSERT INTO mri_scanner >>>>>>>>>>>>>>>>>>> (CandID,Model,Software,Serial_number,Manufacturer) VALUES (?,?,?,?,?)'; >>>>>>>>>>>>>>>>>>> SET >>>>>>>>>>>>>>>>>>> @x1='242126', at x2='Achieva', at x3='3.2.2\3.2.2.0', at x4='34037', at x5='Philips >>>>>>>>>>>>>>>>>>> Medical Systems'; >>>>>>>>>>>>>>>>>>> EXECUTE s USING @x1, at x2, at x3, at x4, at x5; >>>>>>>>>>>>>>>>>>> Error obtained:Cannot add or update a child row: a >>>>>>>>>>>>>>>>>>> foreign key constraint fails (`LORIS`.`mri_scanner`, CONSTRAINT >>>>>>>>>>>>>>>>>>> `FK_mri_scanner_1` FOREIGN KEY (`CandID`) REFERENCES `candidate` >>>>>>>>>>>>>>>>>>> (`CandID`)) (error code 1452) >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> ERROR: The validation has failed. Either re-run the >>>>>>>>>>>>>>>>>>> validation again and fix the problem. Or re-run tarchiveLoader.pl using >>>>>>>>>>>>>>>>>>> -force to force the execution. >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> The tarchiveLoader.pl insertion script has failed. >>>>>>>>>>>>>>>>>>> Can't exec "mail": No such file or directory at ./ >>>>>>>>>>>>>>>>>>> batch_uploads_imageuploader.pl line 249. >>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at ./ >>>>>>>>>>>>>>>>>>> batch_uploads_imageuploader.pl line 250. >>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at ./ >>>>>>>>>>>>>>>>>>> batch_uploads_imageuploader.pl line 251. >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> *And second execution: * >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> (loris-mri-python) lorisadmin at loris-VirtualBox:/data/loris/bin/mri$ >>>>>>>>>>>>>>>>>>> ./batch_uploads_imageuploader.pl -profile prod < >>>>>>>>>>>>>>>>>>> ~/Desktop/input.txt > log.txt >>>>>>>>>>>>>>>>>>> Use of uninitialized value $_ in pattern match (m//) at >>>>>>>>>>>>>>>>>>> ./batch_uploads_imageuploader.pl line 144. >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> PROBLEM: >>>>>>>>>>>>>>>>>>> The user 'lorisadmin' has already inserted this study. >>>>>>>>>>>>>>>>>>> The unique study ID is >>>>>>>>>>>>>>>>>>> '1.3.51.0.1.1.10.49.10.222.1422753.1420953'. >>>>>>>>>>>>>>>>>>> This is the information retained from the first time the >>>>>>>>>>>>>>>>>>> study was inserted: >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> * Taken from dir : >>>>>>>>>>>>>>>>>>> /tmp/ImagingUpload-18-33-Qq7HGy >>>>>>>>>>>>>>>>>>> * Archive target location : >>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive/DCM_2012-12-05_ImagingUpload-18-33-Qq7HGy.tar >>>>>>>>>>>>>>>>>>> * Name of creating host : 127.0.1.1 >>>>>>>>>>>>>>>>>>> * Name of host OS : Linux >>>>>>>>>>>>>>>>>>> * Created by user : lorisadmin >>>>>>>>>>>>>>>>>>> * Archived on : 2019-09-04 >>>>>>>>>>>>>>>>>>> 18:33:05 >>>>>>>>>>>>>>>>>>> * dicomSummary version : 1 >>>>>>>>>>>>>>>>>>> * dicomTar version : 1 >>>>>>>>>>>>>>>>>>> * md5sum for DICOM tarball : >>>>>>>>>>>>>>>>>>> 4a301b0318178b09b91e63544282364d ImagingUpload-18-33-Qq7HGy.tar >>>>>>>>>>>>>>>>>>> * md5sum for DICOM tarball gzipped : >>>>>>>>>>>>>>>>>>> 9d95ea2b9111be236808bfd65d7e65ec ImagingUpload-18-33-Qq7HGy.tar.gz >>>>>>>>>>>>>>>>>>> * md5sum for complete archive : >>>>>>>>>>>>>>>>>>> ab19a86357f1d4053aa3b81c8a071053 >>>>>>>>>>>>>>>>>>> DCM_2012-12-05_ImagingUpload-18-33-Qq7HGy.tar >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Last update of record: >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> The dicomTar.pl execution has failed. >>>>>>>>>>>>>>>>>>> Can't exec "mail": No such file or directory at ./ >>>>>>>>>>>>>>>>>>> batch_uploads_imageuploader.pl line 249. >>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at ./ >>>>>>>>>>>>>>>>>>> batch_uploads_imageuploader.pl line 250. >>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at ./ >>>>>>>>>>>>>>>>>>> batch_uploads_imageuploader.pl line 251. >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> ???? ???, 4 ??? 2019 ???? 5:35 ?.?., ?/? Christine >>>>>>>>>>>>>>>>>>> Rogers, Ms. ??????: >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Ok, this sounds like good progress. Let us know when >>>>>>>>>>>>>>>>>>> you next encounter issues as you progress through the Imaging >>>>>>>>>>>>>>>>>>> Install/Setup docs >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> . >>>>>>>>>>>>>>>>>>> I'll look into how we can better handle the incoming/ >>>>>>>>>>>>>>>>>>> directory next time. >>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>> Christine >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> On Wed, Sep 4, 2019 at 10:23 AM Sotirios >>>>>>>>>>>>>>>>>>> Nikoloutsopoulos wrote: >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/dicom-archive/.loris_mri/database_config.py >>>>>>>>>>>>>>>>>>> is populated correctly except its port is 'port' : ''. Also i have >>>>>>>>>>>>>>>>>>> tested that i can connect to MySQL with lorisuser. >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> I executed the script again, because the only error i >>>>>>>>>>>>>>>>>>> had previously was that the /data/incoming folder didn't exist and there >>>>>>>>>>>>>>>>>>> are no errors reported back except of warnings <>>>>>>>>>>>>>>>>>> password on the command line interface can be insecure>>. >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> ???? ???, 4 ??? 2019 ???? 4:53 ?.?., ?/? Christine >>>>>>>>>>>>>>>>>>> Rogers, Ms. ??????: >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> It's possible -- if the script was unable to connect to >>>>>>>>>>>>>>>>>>> the database during its execution (e.g. typo in the password), that would >>>>>>>>>>>>>>>>>>> explain the underpopulated Image path and Loris-MRI code path you saw in >>>>>>>>>>>>>>>>>>> the Config module. >>>>>>>>>>>>>>>>>>> It's hard to tell without seeing the output from your >>>>>>>>>>>>>>>>>>> script run -- Did you see a sign of any such error? >>>>>>>>>>>>>>>>>>> The Config fields are populated by the >>>>>>>>>>>>>>>>>>> imaging_install.sh script (starting at line 222 >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> ) >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> For example, check if the database connection >>>>>>>>>>>>>>>>>>> information was populated accurately in $mridir >>>>>>>>>>>>>>>>>>> /dicom-archive/.loris_mri/database_config.py >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>> Christine >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> On Wed, Sep 4, 2019 at 9:34 AM Sotirios Nikoloutsopoulos >>>>>>>>>>>>>>>>>>> wrote: >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Hi Christine, >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> If you are referring to the imaging_install.sh here is >>>>>>>>>>>>>>>>>>> an image with the configurations i typed. Maybe the problem is somewhere at >>>>>>>>>>>>>>>>>>> the last part which asks to configure as much as possible automatically? >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Thanks >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> ???? ???, 4 ??? 2019 ???? 4:16 ?.?., ?/? Christine >>>>>>>>>>>>>>>>>>> Rogers, Ms. ??????: >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Glad to hear your LORIS core install is up and working >>>>>>>>>>>>>>>>>>> and all the front-end pages are loading. >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> > lorisadmin at loris-VirtualBox:/var/www/loris$ chmod 775 >>>>>>>>>>>>>>>>>>> project >>>>>>>>>>>>>>>>>>> > and the web interface worked. >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Yes, it's important that project/ have 775 permissions >>>>>>>>>>>>>>>>>>> and that lorisadmin be part of the sudoers group, per step >>>>>>>>>>>>>>>>>>> 1 in the install Readme >>>>>>>>>>>>>>>>>>> . >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> > As for the Paths, LORIS-MRI code and Image should >>>>>>>>>>>>>>>>>>> change LORIS to loris, right? >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> These imaging paths will be updated during your imaging >>>>>>>>>>>>>>>>>>> installation by >>>>>>>>>>>>>>>>>>> an automated script -- you do not need to set them manually via the Config >>>>>>>>>>>>>>>>>>> module. >>>>>>>>>>>>>>>>>>> Please continue to follow the Setup Guide >>>>>>>>>>>>>>>>>>> for detailed >>>>>>>>>>>>>>>>>>> steps to follow. >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>> Christine >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> On Wed, Sep 4, 2019 at 8:05 AM Sotirios Nikoloutsopoulos >>>>>>>>>>>>>>>>>>> wrote: >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> As for the Paths, LORIS-MRI code and Image should change >>>>>>>>>>>>>>>>>>> LORIS to loris, right? >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> ???? ???, 4 ??? 2019 ???? 2:28 ?.?., ?/? Sotirios >>>>>>>>>>>>>>>>>>> Nikoloutsopoulos ??????: >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> i used >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> curl -sL https://deb.nodesource.com/setup_8.x | sudo -E bash - >>>>>>>>>>>>>>>>>>> sudo apt-get install -y nodejs >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> you had suggested in the past, make worked and now i can >>>>>>>>>>>>>>>>>>> see all the contents in the web-interface, but i don't need make install? >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Thanks >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.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 >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> 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 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Name: image.png Type: image/png Size: 42208 bytes Desc: not available URL: From sotirisnik at gmail.com Tue Oct 1 09:33:15 2019 From: sotirisnik at gmail.com (Sotirios Nikoloutsopoulos) Date: Tue, 1 Oct 2019 16:33:15 +0300 Subject: [Loris-dev] Import mri - scripts In-Reply-To: References: Message-ID: When mincs are inserted their corresponding rows at the file table are inserted too [image: image.png] i would like to insert their rows at file_qcstatus as well, because i don't want manually to label them as passed throught the interface [image: image.png] That is the trigger i wrote CREATE DEFINER = CURRENT_USER TRIGGER `LORIS`.`files_AFTER_INSERT` AFTER INSERT ON `files` FOR EACH ROW BEGIN INSERT INTO files_qcstatus SET FileID = NEW.FileID, SeriesUID = NEW.SeriesUID, EchoTime = NEW.EchoTime, QCStatus = "Pass", QCFirstChangeTime = NOW(), QCLastChangeTime = NOW(); END although it contains some errors DBD::mysql::db do failed: Out of range value for column 'QCFirstChangeTime' at row 1 at /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 823. DBD::mysql::db do failed: Cannot add or update a child row: a foreign key constraint fails (`LORIS`.`parameter_file`, CONSTRAINT `FK_parameter_file_1` FOREIGN KEY (`FileID`) REFERENCES `files` (`FileID`)) at /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 848. ???? ???, 1 ??? 2019 ???? 4:21 ?.?., ?/? Cecile Madjar < cecile.madjar at mcin.ca> ??????: > Hi Sotirios, > > In the mri_upload table, there is a TarchiveID column associated with the > MRI upload you inserted. When this value is NULL, it means no DICOMs were > inserted into the tarchive tables. At the end of the insertion of the > DICOMs in the tarchive tables, this value is updated with the correct > TarchiveID associated with the upload. > > Could this correspond to what you want to do? > > Regarding the files_qcstatus, this table is only linked to the files table > (hence, the MINC files). You could always create a new table for > dicom_qcstatus and link it to the tarchive table? > > C?cile > > On Tue, Oct 1, 2019 at 6:56 AM Sotirios Nikoloutsopoulos < > sotirisnik at gmail.com> wrote: > >> Hi, >> >> i would like whenever a dicom is imported to mark all their coressponding >> qc_status to "pass". I was thinking of creating a trigger for that, but >> which tables do i need to add entries to? So far from what i see i need to >> add entres at the table "files" whenever an insertion happens to >> files_qcstatus. >> >> Thanks >> >> ???? ???, 30 ??? 2019 ???? 4:04 ?.?., ?/? Sotirios Nikoloutsopoulos < >> sotirisnik at gmail.com> ??????: >> >>> Oh, sorry i should have asked for StudyID, at the beginning of my email >>> i sent 3 hours ago (not StudyUID). >>> >>> ???? ???, 30 ??? 2019 ???? 3:55 ?.?., ?/? Sotirios Nikoloutsopoulos < >>> sotirisnik at gmail.com> ??????: >>> >>>> Hi, >>>> >>>> that's the Study Instance UID, not the StudyID. So the StudyID i am >>>> looking for is not stored in the database? >>>> >>>> [image: image.png] >>>> >>>> Thanks. >>>> >>>> ???? ???, 30 ??? 2019 ???? 3:38 ?.?., ?/? Cecile Madjar < >>>> cecile.madjar at mcin.ca> ??????: >>>> >>>>> Hi Sotirios, >>>>> >>>>> The StudyUID is stored in the DicomArchiveID field of the >>>>> tarchive table. It can also be found in the metadata field but it is mixed >>>>> with many other information. >>>>> >>>>> Hope this helps, >>>>> >>>>> C?cile >>>>> >>>>> On Mon, Sep 30, 2019 at 6:00 AM Sotirios Nikoloutsopoulos < >>>>> sotirisnik at gmail.com> wrote: >>>>> >>>>>> Hi, >>>>>> >>>>>> Is StudyUID stored somewhere at the tables? At the tarchive table, >>>>>> specifically at the AcquisitonMetadata column i found something called >>>>>> 'Unique Study ID" in its context, but that must be the Study Instance UID. >>>>>> >>>>>> Thanks >>>>>> >>>>>> ???? ???, 27 ??? 2019 ???? 4:22 ?.?., ?/? Cecile Madjar < >>>>>> cecile.madjar at mcin.ca> ??????: >>>>>> >>>>>>> Hi Sotirios, >>>>>>> >>>>>>> Your observation is correct. A little explanation below. >>>>>>> >>>>>>> MINC files get inserted into the MRI violation tables if: >>>>>>> >>>>>>> - the scan type could not be identified (not matching an entry >>>>>>> in the mri_protocol table) >>>>>>> - one parameter of the scan type is out of the expected range >>>>>>> present in the mri_protocol_checks (extra filtering in case you need to be >>>>>>> stricker on some parameters not present in the mri_protocol table) >>>>>>> - if the CandID and PSCID do not match >>>>>>> >>>>>>> The following cases do not get in the MRI violation tables as it >>>>>>> happens before the conversion of the DICOM to MINC files and only MINC >>>>>>> files violations are logged there: >>>>>>> >>>>>>> - "No single DICOM" (since no valid DICOM could be found to >>>>>>> convert to MINC) >>>>>>> - "Study already inserted" (duplicate StudyUID) since this error >>>>>>> happens at the dicomTar.pl level (way before conversion into MINC files) >>>>>>> >>>>>>> Glad everything is working out!! >>>>>>> Best, >>>>>>> >>>>>>> C?cile >>>>>>> >>>>>>> On Fri, Sep 27, 2019 at 6:17 AM Sotirios Nikoloutsopoulos < >>>>>>> sotirisnik at gmail.com> wrote: >>>>>>> >>>>>>>> Hi, >>>>>>>> >>>>>>>> the mri passed, for some reason it consumed 5.12GB of ram. Now >>>>>>>> about the mri_violations, dicoms are triggered to be inserted there only if >>>>>>>> there is a violation for Tr_min, Tr_max, in general for its header >>>>>>>> parameter? Because i don't see the cases of 'No single dicom" or with the 2 >>>>>>>> studyiuid to be there. >>>>>>>> >>>>>>>> Thanks >>>>>>>> >>>>>>>> ???? ???, 26 ??? 2019 ???? 5:07 ?.?., ?/? Cecile Madjar < >>>>>>>> cecile.madjar at mcin.ca> ??????: >>>>>>>> >>>>>>>>> Hi Sotirios, >>>>>>>>> >>>>>>>>> Sorry to hear you are having issues with the memory. I think most >>>>>>>>> of our VMs are set up with 4GB of RAM so with 4GB you should be fine. >>>>>>>>> >>>>>>>>> Hope this helps! >>>>>>>>> >>>>>>>>> C?cile >>>>>>>>> >>>>>>>>> On Thu, Sep 26, 2019 at 9:48 AM Sotirios Nikoloutsopoulos < >>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>> >>>>>>>>>> Hi, >>>>>>>>>> >>>>>>>>>> about that dicom that had that insertion error it's about 30mb >>>>>>>>>> and when it is being processed the ram is being drastically increased from >>>>>>>>>> 2gb to 3.28 and then the whole virtual machine is frozen. What is the >>>>>>>>>> recommended size of ram for using Loris? >>>>>>>>>> >>>>>>>>>> Thanks >>>>>>>>>> >>>>>>>>>> [image: image.png] >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> ???? ???, 24 ??? 2019 ???? 11:24 ?.?., ?/? Cecile Madjar < >>>>>>>>>> cecile.madjar at mcin.ca> ??????: >>>>>>>>>> >>>>>>>>>>> Hi Sotirios, >>>>>>>>>>> >>>>>>>>>>> Glad to see that the StudyUID problem was fixed! >>>>>>>>>>> >>>>>>>>>>> For the delete script issue, if you are absolutely certain that >>>>>>>>>>> no processes are run for that uploadID, you can update the mri_upload table >>>>>>>>>>> and set the column Inserting to 0 instead of 1 for that >>>>>>>>>>> uploadID. It looks like for some reason the scripts did not update this >>>>>>>>>>> field when it stopped the insertion. Not sure why that would be the case >>>>>>>>>>> though. >>>>>>>>>>> Note: only do that update if you are certain that there is no >>>>>>>>>>> processing happening. >>>>>>>>>>> >>>>>>>>>>> Hope this helps! >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> On Tue, Sep 24, 2019 at 11:57 AM Sotirios Nikoloutsopoulos < >>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>> >>>>>>>>>>>> Hi, >>>>>>>>>>>> >>>>>>>>>>>> about the Dicoms i reported that didn't have a StudyID they >>>>>>>>>>>> actually do >>>>>>>>>>>> >>>>>>>>>>>> [image: image.png] >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> [image: image.png] >>>>>>>>>>>> >>>>>>>>>>>> I thought that this might be a permission because "w" was >>>>>>>>>>>> missing at the group. After using chmod -R 775 only 102809579 passed, but >>>>>>>>>>>> with no mnic files. Also now i have this error >>>>>>>>>>>> >>>>>>>>>>>> (loris-mri-python) lorisadmin at loris-VirtualBox:/data/loris/bin/mri/tools$ >>>>>>>>>>>> ./delete_imaging_upload.pl -uploadID 34 -ignore >>>>>>>>>>>> Cannot delete upload 34: the MRI pipeline is currently >>>>>>>>>>>> processing it. >>>>>>>>>>>> >>>>>>>>>>>> How can solve this? >>>>>>>>>>>> >>>>>>>>>>>> Thanks >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> ???? ???, 24 ??? 2019 ???? 2:30 ?.?., ?/? Sotirios >>>>>>>>>>>> Nikoloutsopoulos ??????: >>>>>>>>>>>> >>>>>>>>>>>>> Hi, >>>>>>>>>>>>> >>>>>>>>>>>>> Here is our auto dicom uploading python script: >>>>>>>>>>>>> https://github.com/aueb-wim/DataQualityControlTool/blob/loris1/mipqctool/dicom_uploader.py >>>>>>>>>>>>> >>>>>>>>>>>>> To give you a brief idea: >>>>>>>>>>>>> Per folder it will: >>>>>>>>>>>>> 1) Delete all the .bak files >>>>>>>>>>>>> 2) Locate .dcm files and update the Patient header >>>>>>>>>>>>> 3) Furthermore we are interesting in finding TR_min, TR_max, >>>>>>>>>>>>> TE_min, TE_max parameters of T1 protocol and do an update at the >>>>>>>>>>>>> mri_protocol table >>>>>>>>>>>>> https://github.com/aueb-wim/DataQualityControlTool/blob/loris1/mipqctool/dicom_uploader.py#L205 >>>>>>>>>>>>> For some reason some files are missing >>>>>>>>>>>>> SeriesDescription/ProtocolName >>>>>>>>>>>>> >>>>>>>>>>>>> In total i have 7 folders >>>>>>>>>>>>> >>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>> >>>>>>>>>>>>> 3/7 passed >>>>>>>>>>>>> >>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>> >>>>>>>>>>>>> Also about the first patient with DC0000 had a violation "T1 >>>>>>>>>>>>> AXIAL SE GADO", but my script didn't output a TE of 17 nowhere and i find >>>>>>>>>>>>> that weird since Loris detects the SeriesDescription. >>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> Now about the 4/7 that didn't passed >>>>>>>>>>>>> >>>>>>>>>>>>> 102327840 and 102809579 outputs "The target directory does not >>>>>>>>>>>>> contain a single DICOM file.", therefore they are missing their StudyUID >>>>>>>>>>>>> >>>>>>>>>>>>> 102506134 has 2 studyuid "You can't use it with data from >>>>>>>>>>>>> multiple studies." >>>>>>>>>>>>> >>>>>>>>>>>>> and 102761034 "No data could be converted into valid MINC >>>>>>>>>>>>> files. localizer, scout will not be considered!" What is this? >>>>>>>>>>>>> >>>>>>>>>>>>> If i wanted to force the insertion of 102327840, 102809579 and >>>>>>>>>>>>> 102506134 can i just pass a flag parameter to >>>>>>>>>>>>> batch_uploads_imageuploader.pl? or modify >>>>>>>>>>>>> imaging_upload_file.pl? >>>>>>>>>>>>> >>>>>>>>>>>>> Thank you, >>>>>>>>>>>>> >>>>>>>>>>>>> Sotirios >>>>>>>>>>>>> >>>>>>>>>>>>> PS >>>>>>>>>>>>> >>>>>>>>>>>>> To diagnose a folder search the name of the folder at >>>>>>>>>>>>> dicom_output.txt. >>>>>>>>>>>>> >>>>>>>>>>>>> ???? ???, 20 ??? 2019 ???? 4:54 ?.?., ?/? Christine Rogers, >>>>>>>>>>>>> Ms. ??????: >>>>>>>>>>>>> >>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>> Glad to hear about your progress. >>>>>>>>>>>>>> >>>>>>>>>>>>>> Yes, the script you used to delete imaging data is fully >>>>>>>>>>>>>> documented here >>>>>>>>>>>>>> >>>>>>>>>>>>>> -- let us know if you didn't find the answers you were looking for there. >>>>>>>>>>>>>> (Is it possible the null row in *mri_scanner* seen in your >>>>>>>>>>>>>> database management software is a visual placeholder for you as the user? >>>>>>>>>>>>>> I'm not sure why a scanner would ever be registered with ID='0' as your >>>>>>>>>>>>>> screenshot showed.) >>>>>>>>>>>>>> >>>>>>>>>>>>>> Best, >>>>>>>>>>>>>> Christine >>>>>>>>>>>>>> >>>>>>>>>>>>>> On Fri, Sep 20, 2019 at 9:45 AM Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>> >>>>>>>>>>>>>>> I fixed it with this >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> ???? ???, 20 ??? 2019 ???? 4:37 ?.?., ?/? Sotirios >>>>>>>>>>>>>>> Nikoloutsopoulos ??????: >>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> I tried to create a new candidate using the API, is there >>>>>>>>>>>>>>>> something wrong with the structure? why did i receive a 500 internal error? >>>>>>>>>>>>>>>> In the loris-error log it state that there is something wrong with token, >>>>>>>>>>>>>>>> but i verfied that the type of the token is a string. >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> [Fri Sep 20 16:35:26.874732 2019] [php7:error] [pid 4535] >>>>>>>>>>>>>>>> [client 127.0.0.1:59674] PHP Fatal error: Uncaught >>>>>>>>>>>>>>>> TypeError: Argument 1 passed to SinglePointLogin::JWTAuthenticate() must be >>>>>>>>>>>>>>>> of the type string, null given, called in >>>>>>>>>>>>>>>> /var/www/loris/php/libraries/SinglePointLogin.class.inc on line 169 and >>>>>>>>>>>>>>>> defined in >>>>>>>>>>>>>>>> /var/www/loris/php/libraries/SinglePointLogin.class.inc:192\nStack >>>>>>>>>>>>>>>> trace:\n#0 /var/www/loris/php/libraries/SinglePointLogin.class.inc(169): >>>>>>>>>>>>>>>> SinglePointLogin->JWTAuthenticate(NULL)\n#1 >>>>>>>>>>>>>>>> /var/www/loris/php/libraries/NDB_Client.class.inc(171): >>>>>>>>>>>>>>>> SinglePointLogin->authenticate()\n#2 >>>>>>>>>>>>>>>> /var/www/loris/htdocs/api/v0.0.2/APIBase.php(73): >>>>>>>>>>>>>>>> NDB_Client->initialize('/var/www/loris/...')\n#3 >>>>>>>>>>>>>>>> /var/www/loris/htdocs/api/v0.0.2/Candidates.php(44): >>>>>>>>>>>>>>>> Loris\\API\\APIBase->__construct('POST')\n#4 >>>>>>>>>>>>>>>> /var/www/loris/htdocs/api/v0.0.2/Candidates.php(244): >>>>>>>>>>>>>>>> Loris\\API\\Candidates->__construct('POST', Array)\n#5 {main}\n thrown in >>>>>>>>>>>>>>>> /var/www/loris/php/libraries/SinglePointLogin.class.inc on line 192 >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> ???? ???, 20 ??? 2019 ???? 2:39 ?.?., ?/? Sotirios >>>>>>>>>>>>>>>> Nikoloutsopoulos ??????: >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Is there a way also to delete candidates? Just to let you >>>>>>>>>>>>>>>>> know what i did to clear candidates, because maybe i may have missed >>>>>>>>>>>>>>>>> dependencies. >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> First i deleted all their uploads >>>>>>>>>>>>>>>>> ./delete_imaging_upload.pl -uploadID 13 etc ( is there a >>>>>>>>>>>>>>>>> way to omit the backup file ? ) >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Afterwards i had some scanner candidates, so i deleted all >>>>>>>>>>>>>>>>> the entries from mri_scanner except that i couldn't delete this entry with >>>>>>>>>>>>>>>>> the 0 ID. >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Lastly i deleted the session and then the candidate table. >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Thanks >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> ???? ???, 19 ??? 2019 ???? 7:57 ?.?., ?/? Christine >>>>>>>>>>>>>>>>> Rogers, Ms. ??????: >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> We recommend that you use our existing tools for creating >>>>>>>>>>>>>>>>>> new candidates - either the LORIS API or if you are using a PHP script, by >>>>>>>>>>>>>>>>>> calling the Candidate class's createNew() >>>>>>>>>>>>>>>>>> function. >>>>>>>>>>>>>>>>>> These will create the necessary records for you. (It's not recommended to >>>>>>>>>>>>>>>>>> make direct modifications to mysql database tables in your script, if I >>>>>>>>>>>>>>>>>> understand you.) >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> The CandID should be a randomized 6 digit randomized ID, >>>>>>>>>>>>>>>>>> and there are multiple reasons for this. >>>>>>>>>>>>>>>>>> You can use the PSCID for project-specific IDs and the >>>>>>>>>>>>>>>>>> External ID field in the candidate table can also be used for any values >>>>>>>>>>>>>>>>>> you like. >>>>>>>>>>>>>>>>>> Additionally, any number of custom IDs can be added in >>>>>>>>>>>>>>>>>> parallel - these are entered/visible in the Candidate Information module >>>>>>>>>>>>>>>>>> and added in the back-end as candidate parameters. >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>> Christine >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> On Tue, Sep 17, 2019 at 7:31 PM Sotirios Nikoloutsopoulos >>>>>>>>>>>>>>>>>> wrote: >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> We are building a script that will auto insert the >>>>>>>>>>>>>>>>>>> candidates based on their ExternalID. We would like to know whethere when >>>>>>>>>>>>>>>>>>> we are creating a new profile in the candidate table, if we also have to >>>>>>>>>>>>>>>>>>> insert a new record at another table? Furthermore is there a problem that >>>>>>>>>>>>>>>>>>> in our case CandID won't be a 6digit? ( should we start it from 100000?) >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Thanks >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> ???? ???, 13 ??? 2019 ???? 5:38 ?.?., ?/? Melanie >>>>>>>>>>>>>>>>>>> Legault, Mrs ??????: >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> That would normally be the case but the numeric part of >>>>>>>>>>>>>>>>>>>> the PSCID get paded with 0 on the left. >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Ex. for sequential ID made of center ID of `ABC` plus 4 >>>>>>>>>>>>>>>>>>>> numerical char with a min value of 1, the sequence would be: >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> ABC0001 >>>>>>>>>>>>>>>>>>>> ABC0002 >>>>>>>>>>>>>>>>>>>> ... >>>>>>>>>>>>>>>>>>>> ABC0010 >>>>>>>>>>>>>>>>>>>> ... >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> thus sorting them ascending will always get the latest >>>>>>>>>>>>>>>>>>>> value generated as the max value. >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> M?lanie >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> ------------------------------ >>>>>>>>>>>>>>>>>>>> *From:* Sotirios Nikoloutsopoulos >>>>>>>>>>>>>>>>>>> > >>>>>>>>>>>>>>>>>>>> *Sent:* September 13, 2019 10:15 >>>>>>>>>>>>>>>>>>>> *To:* Melanie Legault, Mrs >>>>>>>>>>>>>>>>>>>> *Cc:* Christine Rogers, Ms. ; >>>>>>>>>>>>>>>>>>>> loris-dev at bic.mni.mcgill.ca < >>>>>>>>>>>>>>>>>>>> loris-dev at bic.mni.mcgill.ca> >>>>>>>>>>>>>>>>>>>> *Subject:* Re: [Loris-dev] Import mri - scripts >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> I see, although the PSCID value is varchar(255), it >>>>>>>>>>>>>>>>>>>> must be stored within a specific length of characters. Otherwise if we were >>>>>>>>>>>>>>>>>>>> to sort strings with different lengths the result would not be sorted >>>>>>>>>>>>>>>>>>>> correctly ( e.x. 1,2,10,11 as strings would result to 1, 10, 11, 2 ). >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Thanks >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> ???? ???, 13 ??? 2019 ???? 4:52 ?.?., ?/? Melanie >>>>>>>>>>>>>>>>>>>> Legault, Mrs ??????: >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Hello Sotirios, >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> There is no `last value` stored anywhere. >>>>>>>>>>>>>>>>>>>> The code simply look for the PSCID with the max value >>>>>>>>>>>>>>>>>>>> and increase that value by 1 in order to generate the next PSCID. >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Hope this info help. >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> M?lanie Legault | Software developer | Faculty of >>>>>>>>>>>>>>>>>>>> Medicine | McGill University >>>>>>>>>>>>>>>>>>>> 3801 University, Montr?al, QC H3A 2B4 >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> ------------------------------ >>>>>>>>>>>>>>>>>>>> *From:* loris-dev-bounces at bic.mni.mcgill.ca < >>>>>>>>>>>>>>>>>>>> loris-dev-bounces at bic.mni.mcgill.ca> on behalf of >>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos >>>>>>>>>>>>>>>>>>>> *Sent:* September 13, 2019 9:43 >>>>>>>>>>>>>>>>>>>> *To:* Christine Rogers, Ms. >>>>>>>>>>>>>>>>>>> > >>>>>>>>>>>>>>>>>>>> *Cc:* loris-dev at bic.mni.mcgill.ca < >>>>>>>>>>>>>>>>>>>> loris-dev at bic.mni.mcgill.ca> >>>>>>>>>>>>>>>>>>>> *Subject:* Re: [Loris-dev] Import mri - scripts >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> how does Loris determine the next available PSCID value >>>>>>>>>>>>>>>>>>>> for a new candidate? >>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris/wiki/Project-Customization >>>>>>>>>>>>>>>>>>>> e.x in the default case the PSCID is sequential, but where do we store the >>>>>>>>>>>>>>>>>>>> last value for the sequential sequence? >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Thanks >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> ???? ???, 10 ??? 2019 ???? 4:00 ?.?., ?/? Sotirios >>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos ??????: >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> the parameters in the mri_protocol you have assigned >>>>>>>>>>>>>>>>>>>> are global standard? or were assigned after trial and error? >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Thanks >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> ???? ???, 8 ??? 2019 ???? 10:11 ?.?., ?/? Christine >>>>>>>>>>>>>>>>>>>> Rogers, Ms. ??????: >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Given you have done the initial setup of your tables to >>>>>>>>>>>>>>>>>>>> match your intended protocol/parameters according to instructions -- >>>>>>>>>>>>>>>>>>>> the Troubleshooting guide documentation recommends >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> re-running the pipeline (and first deleting prior uploads). >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>> Christine >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> On Sun, Sep 8, 2019 at 10:22 AM Sotirios >>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos wrote: >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> *if i were to change their status to resolve what would >>>>>>>>>>>>>>>>>>>> happen? >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> ???? ???, 8 ??? 2019 ???? 5:12 ?.?., ?/? Sotirios >>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos ??????: >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> I noticed that i can view the mnics at the brainbrowser >>>>>>>>>>>>>>>>>>>> from the mri_violations page ( those mnics are stored at >>>>>>>>>>>>>>>>>>>> /data/loris/data/trashbin/ if i were to click their issue to resolve what >>>>>>>>>>>>>>>>>>>> would happend? would they appear in the dicom_archive view too? ). >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> ???? ???, 8 ??? 2019 ???? 4:17 ?.?., ?/? Sotirios >>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos ??????: >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> The defaut values of the schema exists in my local >>>>>>>>>>>>>>>>>>>> database. If i adjust the default values of TR_min and TE_min the mincs >>>>>>>>>>>>>>>>>>>> will be uploaded? >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Thanks >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> ???? ???, 7 ??? 2019 ???? 5:48 ?.?., ?/? Christine >>>>>>>>>>>>>>>>>>>> Rogers, Ms. ??????: >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Is it possible that you haven't set up your >>>>>>>>>>>>>>>>>>>> mri_protocol table ? (and mri_scan_type table too, for additional types >>>>>>>>>>>>>>>>>>>> of scans) >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Like the psc table, this is a pre-requisite for the >>>>>>>>>>>>>>>>>>>> Imaging insertion setup : See the install/setup documentation : >>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/master/docs/02-Install.md >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> To add new rows, just use MySQL insert statements. You >>>>>>>>>>>>>>>>>>>> can adapt the insert statements which load the default table values --> >>>>>>>>>>>>>>>>>>>> e.g. Here on GitHub : >>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris/blob/master/SQL/0000-00-00-schema.sql#L718 >>>>>>>>>>>>>>>>>>>> (see also the mri_scan_type table) >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>> Christine >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> On Fri, Sep 6, 2019 at 8:32 PM Sotirios >>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos wrote: >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> I see that i can edit the values but not how to insert >>>>>>>>>>>>>>>>>>>> new rows. >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> If i choose Inserted with flag then will the minc be >>>>>>>>>>>>>>>>>>>> inserted? >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> ???? ???, 7 ??? 2019 ???? 3:21 ?.?., ?/? Christine >>>>>>>>>>>>>>>>>>>> Rogers, Ms. ??????: >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Glad to hear that *dcmodify* worked correctly. >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> For the MRI Violations module, the screenshot is >>>>>>>>>>>>>>>>>>>> enough. >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> It says "could not identify scan type", which we knew >>>>>>>>>>>>>>>>>>>> already. Did you click on the link on those words? >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> It will take you to the next page of the module, >>>>>>>>>>>>>>>>>>>> showing for each scan what the scan parameters were, and will also show for >>>>>>>>>>>>>>>>>>>> comparison what's stored in your *mri_protocol* >>>>>>>>>>>>>>>>>>>> table. >>>>>>>>>>>>>>>>>>>> Compare these values to find which parameter was not >>>>>>>>>>>>>>>>>>>> correct according to your *mri_protocol* table scan >>>>>>>>>>>>>>>>>>>> type definitions. >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> You may end up broadening your mri_protocol value >>>>>>>>>>>>>>>>>>>> ranges (e.g. TR, TE) for scans. >>>>>>>>>>>>>>>>>>>> This can be done in the front-end, by editing the >>>>>>>>>>>>>>>>>>>> database table directly in the same subpage of the MRI Violations module. >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> The MRI Violations module features are explained in >>>>>>>>>>>>>>>>>>>> more detail in the Help text for this module inside LORIS (click the >>>>>>>>>>>>>>>>>>>> ["?"] icon in the menu bar.) >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> See also: Loris-MRI troubleshooting guide >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> : no MINCs inserted- violated scans >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>> Christine >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> On Fri, Sep 6, 2019 at 8:11 PM Sotirios >>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos wrote: >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> looks like my previous email's attachment wasn't >>>>>>>>>>>>>>>>>>>> delivered due to security reasons, i uploaded my file at google drive >>>>>>>>>>>>>>>>>>>> https://drive.google.com/file/d/1U_TRbo_qGgfpQfs-SqeG9J3bMMqNfUU4/view?usp=sharing >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> ???? ???, 7 ??? 2019 ???? 3:02 ?.?., ?/? Sotirios >>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos ??????: >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> From Dicat's view seems that dcmodify worked in both >>>>>>>>>>>>>>>>>>>> cases >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> For the mri_violations i attached the .html output from >>>>>>>>>>>>>>>>>>>> webbrowser, so that you can check the filelds easier. >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Thanks >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> ???? ???, 6 ??? 2019 ???? 7:49 ?.?., ?/? Christine >>>>>>>>>>>>>>>>>>>> Rogers, Ms. ??????: >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Hi Sotirios -- >>>>>>>>>>>>>>>>>>>> Great, sounds like more progress. >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> About the dcmodify command -- I'm not sure why you're >>>>>>>>>>>>>>>>>>>> getting an Endian warning. (it's a warning not an error, correct?) >>>>>>>>>>>>>>>>>>>> To clarify -- Were the DICOM headers (PatientName) all >>>>>>>>>>>>>>>>>>>> successfully relabelled, after the command ran? >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> You can use also our DICAT tool ( >>>>>>>>>>>>>>>>>>>> https://github.com/aces/DICAT) to verify and/or update >>>>>>>>>>>>>>>>>>>> local DICOM headers -- though your dcmodify command is a great and fast >>>>>>>>>>>>>>>>>>>> solution for bulk header updates. >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> If you're concerned about fields being changed (e.g. >>>>>>>>>>>>>>>>>>>> "(2001,105f)" from the warning message) - you can also dcmdump a DICOM >>>>>>>>>>>>>>>>>>>> slice before and look at these fields specifically. >>>>>>>>>>>>>>>>>>>> It's also not a bad "sanity check" to backup your >>>>>>>>>>>>>>>>>>>> DICOMS before/after running dcmodify, and use dcmdump on each version to >>>>>>>>>>>>>>>>>>>> diff the outputs -- this will pinpoint what changed. >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Re the protocol violation -- AcquisitionProtocol not >>>>>>>>>>>>>>>>>>>> recognized or unknown : this means your scans did not match what is >>>>>>>>>>>>>>>>>>>> stored in your mri_protocol table. >>>>>>>>>>>>>>>>>>>> Check the MRI Violations front-end module -- can you >>>>>>>>>>>>>>>>>>>> see why they didn't match? >>>>>>>>>>>>>>>>>>>> Send us an example, in addition to the contents of the >>>>>>>>>>>>>>>>>>>> mri_protocol table, if you can't find the source of the mismatch. >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>> Christine >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> On Fri, Sep 6, 2019 at 12:04 PM Sotirios >>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos wrote: >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Here is the psc table >>>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> I created 2 candidates profiles through the interface >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> then runned dcmodify command to a dicom file >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> dcmodify -ma PatientName="DCC0000_258024_V1" >>>>>>>>>>>>>>>>>>>> /home/lorisadmin/DICOMS/000535670/501/*.dcm >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> and got those warning: is this okay? >>>>>>>>>>>>>>>>>>>> W: Found element (2001,105f) with VR UN and undefined >>>>>>>>>>>>>>>>>>>> length, reading a sequence with transfer syntax LittleEndianImplicit >>>>>>>>>>>>>>>>>>>> (CP-246) >>>>>>>>>>>>>>>>>>>> W: Found element (2005,1083) with VR UN and undefined >>>>>>>>>>>>>>>>>>>> length, reading a sequence with transfer syntax LittleEndianImplicit >>>>>>>>>>>>>>>>>>>> (CP-246) >>>>>>>>>>>>>>>>>>>> W: Found element (2005,1402) with VR UN and undefined >>>>>>>>>>>>>>>>>>>> length, reading a sequence with transfer syntax LittleEndianImplicit >>>>>>>>>>>>>>>>>>>> (CP-246) >>>>>>>>>>>>>>>>>>>> W: Found element (2005,140f) with VR UN and undefined >>>>>>>>>>>>>>>>>>>> length, reading a sequence with transfer syntax LittleEndianImplicit >>>>>>>>>>>>>>>>>>>> (CP-246) >>>>>>>>>>>>>>>>>>>> W: Found element (2001,105f) with VR UN and undefined >>>>>>>>>>>>>>>>>>>> length, reading a sequence with transfer syntax LittleEndianImplicit >>>>>>>>>>>>>>>>>>>> (CP-246) >>>>>>>>>>>>>>>>>>>> W: Found element (2005,1083) with VR UN and undefined >>>>>>>>>>>>>>>>>>>> length, reading a sequence with transfer syntax LittleEndianImplicit >>>>>>>>>>>>>>>>>>>> (CP-246) >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> dcmodify at another Dicom didn't show warnings. Below >>>>>>>>>>>>>>>>>>>> you can see the execution for the second dicom. Mnics could not be inserted >>>>>>>>>>>>>>>>>>>> due to AcquisitionProtocol being unknown. >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Running now the following command: >>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri//uploadNeuroDB/ >>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl -profile prod -upload_id 12 >>>>>>>>>>>>>>>>>>>> /data/incoming/DCC0001_602102_V1.tar.gz -verbose >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> find -path \/tmp\/ImagingUpload\-18\-36\-mTrxXs -name >>>>>>>>>>>>>>>>>>>> '__MACOSX' -delete >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> dicomTar.pl \/tmp\/ImagingUpload\-18\-36\-mTrxXs >>>>>>>>>>>>>>>>>>>> \/data\/loris\/data\/tarchive\/ -database -profile prod -verbose >>>>>>>>>>>>>>>>>>>> Source: /tmp/ImagingUpload-18-36-mTrxXs >>>>>>>>>>>>>>>>>>>> Target: /data/loris/data/tarchive >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Testing for database connectivity. >>>>>>>>>>>>>>>>>>>> Database is available. >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> You will archive the dir : ImagingUpload-18-36-mTrxXs >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> You are creating a tar with the following command: >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> tar -cf >>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive/ImagingUpload-18-36-mTrxXs.tar >>>>>>>>>>>>>>>>>>>> ImagingUpload-18-36-mTrxXs >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> getting md5sums and gzipping!! >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> * Taken from dir : >>>>>>>>>>>>>>>>>>>> /tmp/ImagingUpload-18-36-mTrxXs >>>>>>>>>>>>>>>>>>>> * Archive target location : >>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive/DCM_2016-08-22_ImagingUpload-18-36-mTrxXs.tar >>>>>>>>>>>>>>>>>>>> * Name of creating host : 127.0.1.1 >>>>>>>>>>>>>>>>>>>> * Name of host OS : Linux >>>>>>>>>>>>>>>>>>>> * Created by user : lorisadmin >>>>>>>>>>>>>>>>>>>> * Archived on : 2019-09-06 >>>>>>>>>>>>>>>>>>>> 18:36:50 >>>>>>>>>>>>>>>>>>>> * dicomSummary version : 1 >>>>>>>>>>>>>>>>>>>> * dicomTar version : 1 >>>>>>>>>>>>>>>>>>>> * md5sum for DICOM tarball : >>>>>>>>>>>>>>>>>>>> b1dcdc8903dd2d9a5443227db2aa2814 ImagingUpload-18-36-mTrxXs.tar >>>>>>>>>>>>>>>>>>>> * md5sum for DICOM tarball gzipped : >>>>>>>>>>>>>>>>>>>> aeae87f20155a6805f7e0cfe5212ea5f ImagingUpload-18-36-mTrxXs.tar.gz >>>>>>>>>>>>>>>>>>>> * md5sum for complete archive : >>>>>>>>>>>>>>>>>>>> 1d9258d1f077ebc49111ab7ba22a8d6e >>>>>>>>>>>>>>>>>>>> DCM_2016-08-22_ImagingUpload-18-36-mTrxXs.tar >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Adding archive info into database >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Removing temporary files from target location >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Done adding archive info into database >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> \/data\/loris\/bin\/mri\//uploadNeuroDB/tarchiveLoader.pl >>>>>>>>>>>>>>>>>>>> -globLocation -profile prod >>>>>>>>>>>>>>>>>>>> \/data\/loris\/data\/tarchive\/\/DCM_2016\-08\-22_ImagingUpload\-18\-36\-mTrxXs\.tar >>>>>>>>>>>>>>>>>>>> -uploadID 12 -verbose >>>>>>>>>>>>>>>>>>>> md5sum >>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive/DCM_2016-08-22_ImagingUpload-18-36-mTrxXs.tar >>>>>>>>>>>>>>>>>>>> PSCID is: DCC0001 >>>>>>>>>>>>>>>>>>>> CandID id: 602102 >>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>> PSCID is: DCC0001 >>>>>>>>>>>>>>>>>>>> CandID id: 602102 >>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>> candidate id 602102 >>>>>>>>>>>>>>>>>>>> Set centerID = 1 >>>>>>>>>>>>>>>>>>>> PSCID is: DCC0001 >>>>>>>>>>>>>>>>>>>> CandID id: 602102 >>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>> PSCID is: DCC0001 >>>>>>>>>>>>>>>>>>>> CandID id: 602102 >>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Number of MINC files that will be considered for >>>>>>>>>>>>>>>>>>>> inserting into the database: 2 >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> log dir is /data/loris/data//logs and log file is >>>>>>>>>>>>>>>>>>>> /data/loris/data//logs/TarLoad-18-37-31ajWx.log >>>>>>>>>>>>>>>>>>>> PSCID is: DCC0001 >>>>>>>>>>>>>>>>>>>> CandID id: 602102 >>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>> PSCID is: DCC0001 >>>>>>>>>>>>>>>>>>>> CandID id: 602102 >>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>> candidate id 602102 >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> log dir is /data/loris/data//logs and log file is >>>>>>>>>>>>>>>>>>>> /data/loris/data//logs/TarLoad-18-37-fanZFj.log >>>>>>>>>>>>>>>>>>>> PSCID is: DCC0001 >>>>>>>>>>>>>>>>>>>> CandID id: 602102 >>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>> PSCID is: DCC0001 >>>>>>>>>>>>>>>>>>>> CandID id: 602102 >>>>>>>>>>>>>>>>>>>> visit_label is: V1 >>>>>>>>>>>>>>>>>>>> candidate id 602102 >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Cleaning up temp files: rm -rf >>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-18-37-to5pYZ/ImagingUpload-18-36-mTrxXs* >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> (loris-mri-python) lorisadmin at loris-VirtualBox:/data/loris/bin/mri$ >>>>>>>>>>>>>>>>>>>> cat /data/loris/data/logs/TarLoad-18-37-fanZFj.log >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> ==> Loading file from disk >>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-18-37-to5pYZ/dcc0001_602102_v1_20160822_072406_205e1d1_mri.mnc >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> --> mapping DICOM parameter for >>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-18-37-to5pYZ/dcc0001_602102_v1_20160822_072406_205e1d1_mri.mnc >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> ==> computing md5 hash for MINC body. >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> --> md5: 02022dda60d9de429340fec838f50cfe >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> ==> verifying acquisition protocol >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Acquisition protocol is unknown >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> --> The minc file cannot be registered since the >>>>>>>>>>>>>>>>>>>> AcquisitionProtocol is unknown >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> ???? ???, 4 ??? 2019 ???? 10:46 ?.?., ?/? Christine >>>>>>>>>>>>>>>>>>>> Rogers, Ms. ??????: >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Hi Sotirios: >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Sure -- you can delete imaging datasets with the >>>>>>>>>>>>>>>>>>>> *delete_imaging_upload* script -- >>>>>>>>>>>>>>>>>>>> details here: >>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/21.0-dev/docs/scripts_md/delete_imaging_upload.md >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> What's in your *psc* table? (Is it properly >>>>>>>>>>>>>>>>>>>> populated? This is a pre-requisite to loading imaging >>>>>>>>>>>>>>>>>>>> data. >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> ) >>>>>>>>>>>>>>>>>>>> The foreign key constraint error on the candidate >>>>>>>>>>>>>>>>>>>> record is curious. >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> There are also a few options for creating candidates >>>>>>>>>>>>>>>>>>>> when inserting imaging data: >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> -- Method 1 : in 2 steps with the API then DICOM >>>>>>>>>>>>>>>>>>>> insertion pipeline >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> a. via the LORIS API -- Create the candidates (and >>>>>>>>>>>>>>>>>>>> visits, optionally I think) >>>>>>>>>>>>>>>>>>>> How to: >>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris/blob/master/docs/API/LorisRESTAPI.md#30-candidate-api >>>>>>>>>>>>>>>>>>>> Ensure you get the DCCID/CandID assigned by LORIS. >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Then as a second step: >>>>>>>>>>>>>>>>>>>> b. Use the imaging insertion pipeline >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> to load your DICOMs. >>>>>>>>>>>>>>>>>>>> You will want to first ensure that the PatientName >>>>>>>>>>>>>>>>>>>> header in the DICOMs as well as tar package are correctly labelled with >>>>>>>>>>>>>>>>>>>> PSCID_DCCID_VisitLabel >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> -- Method 2: for BIDS-format datasets: >>>>>>>>>>>>>>>>>>>> How to : >>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/master/docs/05-PipelineLaunchOptions.md#52---pipeline-launch-for-bids-datasets >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Be sure to use the *-c* and *-s* options when running >>>>>>>>>>>>>>>>>>>> the bids_import script, to automatically create your >>>>>>>>>>>>>>>>>>>> candidates and sessions. >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>> Christine >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> On Wed, Sep 4, 2019 at 11:43 AM Sotirios >>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos wrote: >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> How do i delete a Study? And everytime do i have to >>>>>>>>>>>>>>>>>>>> create a new candidate to get DCCID and a PSCID? >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> *First execution:* >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> (loris-mri-python) lorisadmin at loris-VirtualBox:/data/loris/bin/mri$ >>>>>>>>>>>>>>>>>>>> ./batch_uploads_imageuploader.pl -profile prod < >>>>>>>>>>>>>>>>>>>> ~/Desktop/input.txt > log.txt >>>>>>>>>>>>>>>>>>>> Use of uninitialized value $_ in pattern match (m//) at >>>>>>>>>>>>>>>>>>>> ./batch_uploads_imageuploader.pl line 144. >>>>>>>>>>>>>>>>>>>> DBD::mysql::db do failed: Cannot add or update a child >>>>>>>>>>>>>>>>>>>> row: a foreign key constraint fails (`LORIS`.`candidate`, CONSTRAINT >>>>>>>>>>>>>>>>>>>> `FK_candidate_1` FOREIGN KEY (`RegistrationCenterID`) REFERENCES `psc` >>>>>>>>>>>>>>>>>>>> (`CenterID`)) at /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 1060. >>>>>>>>>>>>>>>>>>>> ERROR: Failed to insert record in table mri_scanner: >>>>>>>>>>>>>>>>>>>> The following database commands failed: >>>>>>>>>>>>>>>>>>>> PREPARE s FROM 'INSERT INTO mri_scanner >>>>>>>>>>>>>>>>>>>> (CandID,Model,Software,Serial_number,Manufacturer) VALUES (?,?,?,?,?)'; >>>>>>>>>>>>>>>>>>>> SET >>>>>>>>>>>>>>>>>>>> @x1='242126', at x2='Achieva', at x3='3.2.2\3.2.2.0', at x4='34037', at x5='Philips >>>>>>>>>>>>>>>>>>>> Medical Systems'; >>>>>>>>>>>>>>>>>>>> EXECUTE s USING @x1, at x2, at x3, at x4, at x5; >>>>>>>>>>>>>>>>>>>> Error obtained:Cannot add or update a child row: a >>>>>>>>>>>>>>>>>>>> foreign key constraint fails (`LORIS`.`mri_scanner`, CONSTRAINT >>>>>>>>>>>>>>>>>>>> `FK_mri_scanner_1` FOREIGN KEY (`CandID`) REFERENCES `candidate` >>>>>>>>>>>>>>>>>>>> (`CandID`)) (error code 1452) >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> ERROR: The validation has failed. Either re-run the >>>>>>>>>>>>>>>>>>>> validation again and fix the problem. Or re-run tarchiveLoader.pl using >>>>>>>>>>>>>>>>>>>> -force to force the execution. >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> The tarchiveLoader.pl insertion script has failed. >>>>>>>>>>>>>>>>>>>> Can't exec "mail": No such file or directory at ./ >>>>>>>>>>>>>>>>>>>> batch_uploads_imageuploader.pl line 249. >>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at ./ >>>>>>>>>>>>>>>>>>>> batch_uploads_imageuploader.pl line 250. >>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at ./ >>>>>>>>>>>>>>>>>>>> batch_uploads_imageuploader.pl line 251. >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> *And second execution: * >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> (loris-mri-python) lorisadmin at loris-VirtualBox:/data/loris/bin/mri$ >>>>>>>>>>>>>>>>>>>> ./batch_uploads_imageuploader.pl -profile prod < >>>>>>>>>>>>>>>>>>>> ~/Desktop/input.txt > log.txt >>>>>>>>>>>>>>>>>>>> Use of uninitialized value $_ in pattern match (m//) at >>>>>>>>>>>>>>>>>>>> ./batch_uploads_imageuploader.pl line 144. >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> PROBLEM: >>>>>>>>>>>>>>>>>>>> The user 'lorisadmin' has already inserted this study. >>>>>>>>>>>>>>>>>>>> The unique study ID is >>>>>>>>>>>>>>>>>>>> '1.3.51.0.1.1.10.49.10.222.1422753.1420953'. >>>>>>>>>>>>>>>>>>>> This is the information retained from the first time >>>>>>>>>>>>>>>>>>>> the study was inserted: >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> * Taken from dir : >>>>>>>>>>>>>>>>>>>> /tmp/ImagingUpload-18-33-Qq7HGy >>>>>>>>>>>>>>>>>>>> * Archive target location : >>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive/DCM_2012-12-05_ImagingUpload-18-33-Qq7HGy.tar >>>>>>>>>>>>>>>>>>>> * Name of creating host : 127.0.1.1 >>>>>>>>>>>>>>>>>>>> * Name of host OS : Linux >>>>>>>>>>>>>>>>>>>> * Created by user : lorisadmin >>>>>>>>>>>>>>>>>>>> * Archived on : 2019-09-04 >>>>>>>>>>>>>>>>>>>> 18:33:05 >>>>>>>>>>>>>>>>>>>> * dicomSummary version : 1 >>>>>>>>>>>>>>>>>>>> * dicomTar version : 1 >>>>>>>>>>>>>>>>>>>> * md5sum for DICOM tarball : >>>>>>>>>>>>>>>>>>>> 4a301b0318178b09b91e63544282364d ImagingUpload-18-33-Qq7HGy.tar >>>>>>>>>>>>>>>>>>>> * md5sum for DICOM tarball gzipped : >>>>>>>>>>>>>>>>>>>> 9d95ea2b9111be236808bfd65d7e65ec ImagingUpload-18-33-Qq7HGy.tar.gz >>>>>>>>>>>>>>>>>>>> * md5sum for complete archive : >>>>>>>>>>>>>>>>>>>> ab19a86357f1d4053aa3b81c8a071053 >>>>>>>>>>>>>>>>>>>> DCM_2012-12-05_ImagingUpload-18-33-Qq7HGy.tar >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Last update of record: >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> The dicomTar.pl execution has failed. >>>>>>>>>>>>>>>>>>>> Can't exec "mail": No such file or directory at ./ >>>>>>>>>>>>>>>>>>>> batch_uploads_imageuploader.pl line 249. >>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at ./ >>>>>>>>>>>>>>>>>>>> batch_uploads_imageuploader.pl line 250. >>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at ./ >>>>>>>>>>>>>>>>>>>> batch_uploads_imageuploader.pl line 251. >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> ???? ???, 4 ??? 2019 ???? 5:35 ?.?., ?/? Christine >>>>>>>>>>>>>>>>>>>> Rogers, Ms. ??????: >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Ok, this sounds like good progress. Let us know when >>>>>>>>>>>>>>>>>>>> you next encounter issues as you progress through the Imaging >>>>>>>>>>>>>>>>>>>> Install/Setup docs >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> . >>>>>>>>>>>>>>>>>>>> I'll look into how we can better handle the incoming/ >>>>>>>>>>>>>>>>>>>> directory next time. >>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>> Christine >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> On Wed, Sep 4, 2019 at 10:23 AM Sotirios >>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos wrote: >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/dicom-archive/.loris_mri/database_config.py >>>>>>>>>>>>>>>>>>>> is populated correctly except its port is 'port' : ''. Also i have >>>>>>>>>>>>>>>>>>>> tested that i can connect to MySQL with lorisuser. >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> I executed the script again, because the only error i >>>>>>>>>>>>>>>>>>>> had previously was that the /data/incoming folder didn't exist and there >>>>>>>>>>>>>>>>>>>> are no errors reported back except of warnings <>>>>>>>>>>>>>>>>>>> password on the command line interface can be insecure>>. >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> ???? ???, 4 ??? 2019 ???? 4:53 ?.?., ?/? Christine >>>>>>>>>>>>>>>>>>>> Rogers, Ms. ??????: >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> It's possible -- if the script was unable to connect to >>>>>>>>>>>>>>>>>>>> the database during its execution (e.g. typo in the password), that would >>>>>>>>>>>>>>>>>>>> explain the underpopulated Image path and Loris-MRI code path you saw in >>>>>>>>>>>>>>>>>>>> the Config module. >>>>>>>>>>>>>>>>>>>> It's hard to tell without seeing the output from your >>>>>>>>>>>>>>>>>>>> script run -- Did you see a sign of any such error? >>>>>>>>>>>>>>>>>>>> The Config fields are populated by the >>>>>>>>>>>>>>>>>>>> imaging_install.sh script (starting at line 222 >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> ) >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> For example, check if the database connection >>>>>>>>>>>>>>>>>>>> information was populated accurately in $mridir >>>>>>>>>>>>>>>>>>>> /dicom-archive/.loris_mri/database_config.py >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>> Christine >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> On Wed, Sep 4, 2019 at 9:34 AM Sotirios >>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos wrote: >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Hi Christine, >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> If you are referring to the imaging_install.sh here is >>>>>>>>>>>>>>>>>>>> an image with the configurations i typed. Maybe the problem is somewhere at >>>>>>>>>>>>>>>>>>>> the last part which asks to configure as much as possible automatically? >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Thanks >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> ???? ???, 4 ??? 2019 ???? 4:16 ?.?., ?/? Christine >>>>>>>>>>>>>>>>>>>> Rogers, Ms. ??????: >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Glad to hear your LORIS core install is up and working >>>>>>>>>>>>>>>>>>>> and all the front-end pages are loading. >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> > lorisadmin at loris-VirtualBox:/var/www/loris$ chmod >>>>>>>>>>>>>>>>>>>> 775 project >>>>>>>>>>>>>>>>>>>> > and the web interface worked. >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Yes, it's important that project/ have 775 permissions >>>>>>>>>>>>>>>>>>>> and that lorisadmin be part of the sudoers group, per step >>>>>>>>>>>>>>>>>>>> 1 in the install Readme >>>>>>>>>>>>>>>>>>>> . >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> > As for the Paths, LORIS-MRI code and Image should >>>>>>>>>>>>>>>>>>>> change LORIS to loris, right? >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> These imaging paths will be updated during your >>>>>>>>>>>>>>>>>>>> imaging installation >>>>>>>>>>>>>>>>>>>> by an >>>>>>>>>>>>>>>>>>>> automated script -- you do not need to set them manually via the Config >>>>>>>>>>>>>>>>>>>> module. >>>>>>>>>>>>>>>>>>>> Please continue to follow the Setup Guide >>>>>>>>>>>>>>>>>>>> for >>>>>>>>>>>>>>>>>>>> detailed steps to follow. >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>>>>> Christine >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> On Wed, Sep 4, 2019 at 8:05 AM Sotirios >>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos wrote: >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> As for the Paths, LORIS-MRI code and Image should >>>>>>>>>>>>>>>>>>>> change LORIS to loris, right? >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> [image: image.png] >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> ???? ???, 4 ??? 2019 ???? 2:28 ?.?., ?/? Sotirios >>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos ??????: >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> i used >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> curl -sL https://deb.nodesource.com/setup_8.x | sudo -E bash - >>>>>>>>>>>>>>>>>>>> sudo apt-get install -y nodejs >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> you had suggested in the past, make worked and now i >>>>>>>>>>>>>>>>>>>> can see all the contents in the web-interface, but i don't need make >>>>>>>>>>>>>>>>>>>> install? >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Thanks >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.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 >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> 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 >>>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> -- >>>>>>>>>>>>>> >>>>>>>>>>>>>> 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... 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Name: image.png Type: image/png Size: 175139 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 42208 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 51987 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 42270 bytes Desc: not available URL: From xavier.lecoursboucher at mcgill.ca Tue Oct 1 11:36:17 2019 From: xavier.lecoursboucher at mcgill.ca (Xavier Lecours Boucher, Mr) Date: Tue, 1 Oct 2019 15:36:17 +0000 Subject: [Loris-dev] Import mri - scripts In-Reply-To: References: , Message-ID: Hi Sotirios, The first error occurs because the QCFirstChangeTime and columns are of type `unsigned integer` and not `datatime`. You should be using UNIX_TIMESTAMP() instead of NOW(). The second error occurs because the trigger triggers a rollback of the insert statement in the files table. See mysql documentation for trigger error handling. An error during either a BEFORE or AFTER trigger results in failure of the entire statement that caused trigger invocation. Thank you for sharing that. I hope it helps. -- Xavier ________________________________ From: loris-dev-bounces at bic.mni.mcgill.ca on behalf of Sotirios Nikoloutsopoulos Sent: October 1, 2019 8:33 AM To: Cecile Madjar Cc: loris-dev at bic.mni.mcgill.ca ; Christine Rogers, Ms. Subject: Re: [Loris-dev] Import mri - scripts When mincs are inserted their corresponding rows at the file table are inserted too [image.png] i would like to insert their rows at file_qcstatus as well, because i don't want manually to label them as passed throught the interface [image.png] That is the trigger i wrote CREATE DEFINER = CURRENT_USER TRIGGER `LORIS`.`files_AFTER_INSERT` AFTER INSERT ON `files` FOR EACH ROW BEGIN INSERT INTO files_qcstatus SET FileID = NEW.FileID, SeriesUID = NEW.SeriesUID, EchoTime = NEW.EchoTime, QCStatus = "Pass", QCFirstChangeTime = NOW(), QCLastChangeTime = NOW(); END although it contains some errors DBD::mysql::db do failed: Out of range value for column 'QCFirstChangeTime' at row 1 at /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 823. DBD::mysql::db do failed: Cannot add or update a child row: a foreign key constraint fails (`LORIS`.`parameter_file`, CONSTRAINT `FK_parameter_file_1` FOREIGN KEY (`FileID`) REFERENCES `files` (`FileID`)) at /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 848. ???? ???, 1 ??? 2019 ???? 4:21 ?.?., ?/? Cecile Madjar > ??????: Hi Sotirios, In the mri_upload table, there is a TarchiveID column associated with the MRI upload you inserted. When this value is NULL, it means no DICOMs were inserted into the tarchive tables. At the end of the insertion of the DICOMs in the tarchive tables, this value is updated with the correct TarchiveID associated with the upload. Could this correspond to what you want to do? Regarding the files_qcstatus, this table is only linked to the files table (hence, the MINC files). You could always create a new table for dicom_qcstatus and link it to the tarchive table? C?cile On Tue, Oct 1, 2019 at 6:56 AM Sotirios Nikoloutsopoulos > wrote: Hi, i would like whenever a dicom is imported to mark all their coressponding qc_status to "pass". I was thinking of creating a trigger for that, but which tables do i need to add entries to? So far from what i see i need to add entres at the table "files" whenever an insertion happens to files_qcstatus. Thanks ???? ???, 30 ??? 2019 ???? 4:04 ?.?., ?/? Sotirios Nikoloutsopoulos > ??????: Oh, sorry i should have asked for StudyID, at the beginning of my email i sent 3 hours ago (not StudyUID). ???? ???, 30 ??? 2019 ???? 3:55 ?.?., ?/? Sotirios Nikoloutsopoulos > ??????: Hi, that's the Study Instance UID, not the StudyID. So the StudyID i am looking for is not stored in the database? [image.png] Thanks. ???? ???, 30 ??? 2019 ???? 3:38 ?.?., ?/? Cecile Madjar > ??????: Hi Sotirios, The StudyUID is stored in the DicomArchiveID field of the tarchive table. It can also be found in the metadata field but it is mixed with many other information. Hope this helps, C?cile On Mon, Sep 30, 2019 at 6:00 AM Sotirios Nikoloutsopoulos > wrote: Hi, Is StudyUID stored somewhere at the tables? At the tarchive table, specifically at the AcquisitonMetadata column i found something called 'Unique Study ID" in its context, but that must be the Study Instance UID. Thanks ???? ???, 27 ??? 2019 ???? 4:22 ?.?., ?/? Cecile Madjar > ??????: Hi Sotirios, Your observation is correct. A little explanation below. MINC files get inserted into the MRI violation tables if: * the scan type could not be identified (not matching an entry in the mri_protocol table) * one parameter of the scan type is out of the expected range present in the mri_protocol_checks (extra filtering in case you need to be stricker on some parameters not present in the mri_protocol table) * if the CandID and PSCID do not match The following cases do not get in the MRI violation tables as it happens before the conversion of the DICOM to MINC files and only MINC files violations are logged there: * "No single DICOM" (since no valid DICOM could be found to convert to MINC) * "Study already inserted" (duplicate StudyUID) since this error happens at the dicomTar.pl level (way before conversion into MINC files) Glad everything is working out!! Best, C?cile On Fri, Sep 27, 2019 at 6:17 AM Sotirios Nikoloutsopoulos > wrote: Hi, the mri passed, for some reason it consumed 5.12GB of ram. Now about the mri_violations, dicoms are triggered to be inserted there only if there is a violation for Tr_min, Tr_max, in general for its header parameter? Because i don't see the cases of 'No single dicom" or with the 2 studyiuid to be there. Thanks ???? ???, 26 ??? 2019 ???? 5:07 ?.?., ?/? Cecile Madjar > ??????: Hi Sotirios, Sorry to hear you are having issues with the memory. I think most of our VMs are set up with 4GB of RAM so with 4GB you should be fine. Hope this helps! C?cile On Thu, Sep 26, 2019 at 9:48 AM Sotirios Nikoloutsopoulos > wrote: Hi, about that dicom that had that insertion error it's about 30mb and when it is being processed the ram is being drastically increased from 2gb to 3.28 and then the whole virtual machine is frozen. What is the recommended size of ram for using Loris? Thanks [image.png] ???? ???, 24 ??? 2019 ???? 11:24 ?.?., ?/? Cecile Madjar > ??????: Hi Sotirios, Glad to see that the StudyUID problem was fixed! For the delete script issue, if you are absolutely certain that no processes are run for that uploadID, you can update the mri_upload table and set the column Inserting to 0 instead of 1 for that uploadID. It looks like for some reason the scripts did not update this field when it stopped the insertion. Not sure why that would be the case though. Note: only do that update if you are certain that there is no processing happening. Hope this helps! On Tue, Sep 24, 2019 at 11:57 AM Sotirios Nikoloutsopoulos > wrote: Hi, about the Dicoms i reported that didn't have a StudyID they actually do [image.png] [image.png] I thought that this might be a permission because "w" was missing at the group. After using chmod -R 775 only 102809579 passed, but with no mnic files. Also now i have this error (loris-mri-python) lorisadmin at loris-VirtualBox:/data/loris/bin/mri/tools$ ./delete_imaging_upload.pl -uploadID 34 -ignore Cannot delete upload 34: the MRI pipeline is currently processing it. How can solve this? Thanks ???? ???, 24 ??? 2019 ???? 2:30 ?.?., ?/? Sotirios Nikoloutsopoulos > ??????: Hi, Here is our auto dicom uploading python script: https://github.com/aueb-wim/DataQualityControlTool/blob/loris1/mipqctool/dicom_uploader.py To give you a brief idea: Per folder it will: 1) Delete all the .bak files 2) Locate .dcm files and update the Patient header 3) Furthermore we are interesting in finding TR_min, TR_max, TE_min, TE_max parameters of T1 protocol and do an update at the mri_protocol table https://github.com/aueb-wim/DataQualityControlTool/blob/loris1/mipqctool/dicom_uploader.py#L205 For some reason some files are missing SeriesDescription/ProtocolName In total i have 7 folders [image.png] 3/7 passed [image.png] Also about the first patient with DC0000 had a violation "T1 AXIAL SE GADO", but my script didn't output a TE of 17 nowhere and i find that weird since Loris detects the SeriesDescription. [image.png] Now about the 4/7 that didn't passed 102327840 and 102809579 outputs "The target directory does not contain a single DICOM file.", therefore they are missing their StudyUID 102506134 has 2 studyuid "You can't use it with data from multiple studies." and 102761034 "No data could be converted into valid MINC files. localizer, scout will not be considered!" What is this? If i wanted to force the insertion of 102327840, 102809579 and 102506134 can i just pass a flag parameter to batch_uploads_imageuploader.pl? or modify imaging_upload_file.pl? Thank you, Sotirios PS To diagnose a folder search the name of the folder at dicom_output.txt. ???? ???, 20 ??? 2019 ???? 4:54 ?.?., ?/? Christine Rogers, Ms. > ??????: Hi Sotirios, Glad to hear about your progress. Yes, the script you used to delete imaging data is fully documented here -- let us know if you didn't find the answers you were looking for there. (Is it possible the null row in mri_scanner seen in your database management software is a visual placeholder for you as the user? I'm not sure why a scanner would ever be registered with ID='0' as your screenshot showed.) Best, Christine On Fri, Sep 20, 2019 at 9:45 AM Sotirios Nikoloutsopoulos > wrote: I fixed it with this [image.png] ???? ???, 20 ??? 2019 ???? 4:37 ?.?., ?/? Sotirios Nikoloutsopoulos > ??????: Hi, I tried to create a new candidate using the API, is there something wrong with the structure? why did i receive a 500 internal error? In the loris-error log it state that there is something wrong with token, but i verfied that the type of the token is a string. [Fri Sep 20 16:35:26.874732 2019] [php7:error] [pid 4535] [client 127.0.0.1:59674] PHP Fatal error: Uncaught TypeError: Argument 1 passed to SinglePointLogin::JWTAuthenticate() must be of the type string, null given, called in /var/www/loris/php/libraries/SinglePointLogin.class.inc on line 169 and defined in /var/www/loris/php/libraries/SinglePointLogin.class.inc:192\nStack trace:\n#0 /var/www/loris/php/libraries/SinglePointLogin.class.inc(169): SinglePointLogin->JWTAuthenticate(NULL)\n#1 /var/www/loris/php/libraries/NDB_Client.class.inc(171): SinglePointLogin->authenticate()\n#2 /var/www/loris/htdocs/api/v0.0.2/APIBase.php(73): NDB_Client->initialize('/var/www/loris/...')\n#3 /var/www/loris/htdocs/api/v0.0.2/Candidates.php(44): Loris\\API\\APIBase->__construct('POST')\n#4 /var/www/loris/htdocs/api/v0.0.2/Candidates.php(244): Loris\\API\\Candidates->__construct('POST', Array)\n#5 {main}\n thrown in /var/www/loris/php/libraries/SinglePointLogin.class.inc on line 192 [image.png] ???? ???, 20 ??? 2019 ???? 2:39 ?.?., ?/? Sotirios Nikoloutsopoulos > ??????: Hi, Is there a way also to delete candidates? Just to let you know what i did to clear candidates, because maybe i may have missed dependencies. First i deleted all their uploads ./delete_imaging_upload.pl -uploadID 13 etc ( is there a way to omit the backup file ? ) Afterwards i had some scanner candidates, so i deleted all the entries from mri_scanner except that i couldn't delete this entry with the 0 ID. [image.png] Lastly i deleted the session and then the candidate table. Thanks ???? ???, 19 ??? 2019 ???? 7:57 ?.?., ?/? Christine Rogers, Ms. > ??????: Hi Sotirios, We recommend that you use our existing tools for creating new candidates - either the LORIS API or if you are using a PHP script, by calling the Candidate class's createNew() function. These will create the necessary records for you. (It's not recommended to make direct modifications to mysql database tables in your script, if I understand you.) The CandID should be a randomized 6 digit randomized ID, and there are multiple reasons for this. You can use the PSCID for project-specific IDs and the External ID field in the candidate table can also be used for any values you like. Additionally, any number of custom IDs can be added in parallel - these are entered/visible in the Candidate Information module and added in the back-end as candidate parameters. Best, Christine On Tue, Sep 17, 2019 at 7:31 PM Sotirios Nikoloutsopoulos > wrote: Hi, We are building a script that will auto insert the candidates based on their ExternalID. We would like to know whethere when we are creating a new profile in the candidate table, if we also have to insert a new record at another table? Furthermore is there a problem that in our case CandID won't be a 6digit? ( should we start it from 100000?) Thanks [image.png] ???? ???, 13 ??? 2019 ???? 5:38 ?.?., ?/? Melanie Legault, Mrs > ??????: That would normally be the case but the numeric part of the PSCID get paded with 0 on the left. Ex. for sequential ID made of center ID of `ABC` plus 4 numerical char with a min value of 1, the sequence would be: ABC0001 ABC0002 ... ABC0010 ... thus sorting them ascending will always get the latest value generated as the max value. M?lanie ________________________________ From: Sotirios Nikoloutsopoulos > Sent: September 13, 2019 10:15 To: Melanie Legault, Mrs > Cc: Christine Rogers, Ms. >; loris-dev at bic.mni.mcgill.ca > Subject: Re: [Loris-dev] Import mri - scripts I see, although the PSCID value is varchar(255), it must be stored within a specific length of characters. Otherwise if we were to sort strings with different lengths the result would not be sorted correctly ( e.x. 1,2,10,11 as strings would result to 1, 10, 11, 2 ). Thanks ???? ???, 13 ??? 2019 ???? 4:52 ?.?., ?/? Melanie Legault, Mrs > ??????: Hello Sotirios, There is no `last value` stored anywhere. The code simply look for the PSCID with the max value and increase that value by 1 in order to generate the next PSCID. Hope this info help. M?lanie Legault | Software developer | Faculty of Medicine | McGill University 3801 University, Montr?al, QC H3A 2B4 ________________________________ From: loris-dev-bounces at bic.mni.mcgill.ca > on behalf of Sotirios Nikoloutsopoulos > Sent: September 13, 2019 9:43 To: Christine Rogers, Ms. > Cc: loris-dev at bic.mni.mcgill.ca > Subject: Re: [Loris-dev] Import mri - scripts Hi, how does Loris determine the next available PSCID value for a new candidate? https://github.com/aces/Loris/wiki/Project-Customization e.x in the default case the PSCID is sequential, but where do we store the last value for the sequential sequence? Thanks ???? ???, 10 ??? 2019 ???? 4:00 ?.?., ?/? Sotirios Nikoloutsopoulos > ??????: Hi, the parameters in the mri_protocol you have assigned are global standard? or were assigned after trial and error? Thanks ???? ???, 8 ??? 2019 ???? 10:11 ?.?., ?/? Christine Rogers, Ms. > ??????: Hi Sotirios, Given you have done the initial setup of your tables to match your intended protocol/parameters according to instructions -- the Troubleshooting guide documentation recommends re-running the pipeline (and first deleting prior uploads). Best, Christine On Sun, Sep 8, 2019 at 10:22 AM Sotirios Nikoloutsopoulos > wrote: *if i were to change their status to resolve what would happen? ???? ???, 8 ??? 2019 ???? 5:12 ?.?., ?/? Sotirios Nikoloutsopoulos > ??????: I noticed that i can view the mnics at the brainbrowser from the mri_violations page ( those mnics are stored at /data/loris/data/trashbin/ if i were to click their issue to resolve what would happend? would they appear in the dicom_archive view too? ). [https://lh5.googleusercontent.com/0G4f5Ms034ZaYEwHLLOzo4YBjQwcKxjSLRrE0XLZAR86JhsPocXi5tkAvgbELadS63HWgJ_A6eGF0BitFWhf4DCVx5EEFzThQm19QfKDpgrrIfGFZjdy4BanrmRjawJeo3kYt-5y] ???? ???, 8 ??? 2019 ???? 4:17 ?.?., ?/? Sotirios Nikoloutsopoulos > ??????: Hi, The defaut values of the schema exists in my local database. If i adjust the default values of TR_min and TE_min the mincs will be uploaded? [image.png] [image.png] Thanks ???? ???, 7 ??? 2019 ???? 5:48 ?.?., ?/? Christine Rogers, Ms. > ??????: Hi Sotirios, Is it possible that you haven't set up your mri_protocol table ? (and mri_scan_type table too, for additional types of scans) Like the psc table, this is a pre-requisite for the Imaging insertion setup : See the install/setup documentation : https://github.com/aces/Loris-MRI/blob/master/docs/02-Install.md To add new rows, just use MySQL insert statements. You can adapt the insert statements which load the default table values --> e.g. Here on GitHub : https://github.com/aces/Loris/blob/master/SQL/0000-00-00-schema.sql#L718 (see also the mri_scan_type table) Best, Christine On Fri, Sep 6, 2019 at 8:32 PM Sotirios Nikoloutsopoulos > wrote: I see that i can edit the values but not how to insert new rows. [image.png] If i choose Inserted with flag then will the minc be inserted? [image.png] ???? ???, 7 ??? 2019 ???? 3:21 ?.?., ?/? Christine Rogers, Ms. > ??????: Hi Sotirios, Glad to hear that dcmodify worked correctly. For the MRI Violations module, the screenshot is enough. It says "could not identify scan type", which we knew already. Did you click on the link on those words? It will take you to the next page of the module, showing for each scan what the scan parameters were, and will also show for comparison what's stored in your mri_protocol table. Compare these values to find which parameter was not correct according to your mri_protocol table scan type definitions. You may end up broadening your mri_protocol value ranges (e.g. TR, TE) for scans. This can be done in the front-end, by editing the database table directly in the same subpage of the MRI Violations module. The MRI Violations module features are explained in more detail in the Help text for this module inside LORIS (click the ["?"] icon in the menu bar.) See also: Loris-MRI troubleshooting guide: no MINCs inserted- violated scans Best, Christine On Fri, Sep 6, 2019 at 8:11 PM Sotirios Nikoloutsopoulos > wrote: Hi, looks like my previous email's attachment wasn't delivered due to security reasons, i uploaded my file at google drive https://drive.google.com/file/d/1U_TRbo_qGgfpQfs-SqeG9J3bMMqNfUU4/view?usp=sharing ???? ???, 7 ??? 2019 ???? 3:02 ?.?., ?/? Sotirios Nikoloutsopoulos > ??????: Hi, From Dicat's view seems that dcmodify worked in both cases [image.png] [image.png] For the mri_violations i attached the .html output from webbrowser, so that you can check the filelds easier. [image.png] Thanks ???? ???, 6 ??? 2019 ???? 7:49 ?.?., ?/? Christine Rogers, Ms. > ??????: Hi Sotirios -- Great, sounds like more progress. About the dcmodify command -- I'm not sure why you're getting an Endian warning. (it's a warning not an error, correct?) To clarify -- Were the DICOM headers (PatientName) all successfully relabelled, after the command ran? You can use also our DICAT tool (https://github.com/aces/DICAT) to verify and/or update local DICOM headers -- though your dcmodify command is a great and fast solution for bulk header updates. If you're concerned about fields being changed (e.g. "(2001,105f)" from the warning message) - you can also dcmdump a DICOM slice before and look at these fields specifically. It's also not a bad "sanity check" to backup your DICOMS before/after running dcmodify, and use dcmdump on each version to diff the outputs -- this will pinpoint what changed. Re the protocol violation -- AcquisitionProtocol not recognized or unknown : this means your scans did not match what is stored in your mri_protocol table. Check the MRI Violations front-end module -- can you see why they didn't match? Send us an example, in addition to the contents of the mri_protocol table, if you can't find the source of the mismatch. Best, Christine On Fri, Sep 6, 2019 at 12:04 PM Sotirios Nikoloutsopoulos > wrote: Here is the psc table [image.png] I created 2 candidates profiles through the interface [image.png] then runned dcmodify command to a dicom file dcmodify -ma PatientName="DCC0000_258024_V1" /home/lorisadmin/DICOMS/000535670/501/*.dcm and got those warning: is this okay? W: Found element (2001,105f) with VR UN and undefined length, reading a sequence with transfer syntax LittleEndianImplicit (CP-246) W: Found element (2005,1083) with VR UN and undefined length, reading a sequence with transfer syntax LittleEndianImplicit (CP-246) W: Found element (2005,1402) with VR UN and undefined length, reading a sequence with transfer syntax LittleEndianImplicit (CP-246) W: Found element (2005,140f) with VR UN and undefined length, reading a sequence with transfer syntax LittleEndianImplicit (CP-246) W: Found element (2001,105f) with VR UN and undefined length, reading a sequence with transfer syntax LittleEndianImplicit (CP-246) W: Found element (2005,1083) with VR UN and undefined length, reading a sequence with transfer syntax LittleEndianImplicit (CP-246) dcmodify at another Dicom didn't show warnings. Below you can see the execution for the second dicom. Mnics could not be inserted due to AcquisitionProtocol being unknown. Running now the following command: /data/loris/bin/mri//uploadNeuroDB/imaging_upload_file.pl -profile prod -upload_id 12 /data/incoming/DCC0001_602102_V1.tar.gz -verbose find -path \/tmp\/ImagingUpload\-18\-36\-mTrxXs -name '__MACOSX' -delete dicomTar.pl \/tmp\/ImagingUpload\-18\-36\-mTrxXs \/data\/loris\/data\/tarchive\/ -database -profile prod -verbose Source: /tmp/ImagingUpload-18-36-mTrxXs Target: /data/loris/data/tarchive Testing for database connectivity. Database is available. You will archive the dir : ImagingUpload-18-36-mTrxXs You are creating a tar with the following command: tar -cf /data/loris/data/tarchive/ImagingUpload-18-36-mTrxXs.tar ImagingUpload-18-36-mTrxXs getting md5sums and gzipping!! * Taken from dir : /tmp/ImagingUpload-18-36-mTrxXs * Archive target location : /data/loris/data/tarchive/DCM_2016-08-22_ImagingUpload-18-36-mTrxXs.tar * Name of creating host : 127.0.1.1 * Name of host OS : Linux * Created by user : lorisadmin * Archived on : 2019-09-06 18:36:50 * dicomSummary version : 1 * dicomTar version : 1 * md5sum for DICOM tarball : b1dcdc8903dd2d9a5443227db2aa2814 ImagingUpload-18-36-mTrxXs.tar * md5sum for DICOM tarball gzipped : aeae87f20155a6805f7e0cfe5212ea5f ImagingUpload-18-36-mTrxXs.tar.gz * md5sum for complete archive : 1d9258d1f077ebc49111ab7ba22a8d6e DCM_2016-08-22_ImagingUpload-18-36-mTrxXs.tar Adding archive info into database Removing temporary files from target location Done adding archive info into database \/data\/loris\/bin\/mri\//uploadNeuroDB/tarchiveLoader.pl -globLocation -profile prod \/data\/loris\/data\/tarchive\/\/DCM_2016\-08\-22_ImagingUpload\-18\-36\-mTrxXs\.tar -uploadID 12 -verbose md5sum /data/loris/data/tarchive/DCM_2016-08-22_ImagingUpload-18-36-mTrxXs.tar PSCID is: DCC0001 CandID id: 602102 visit_label is: V1 PSCID is: DCC0001 CandID id: 602102 visit_label is: V1 candidate id 602102 Set centerID = 1 PSCID is: DCC0001 CandID id: 602102 visit_label is: V1 PSCID is: DCC0001 CandID id: 602102 visit_label is: V1 Number of MINC files that will be considered for inserting into the database: 2 log dir is /data/loris/data//logs and log file is /data/loris/data//logs/TarLoad-18-37-31ajWx.log PSCID is: DCC0001 CandID id: 602102 visit_label is: V1 PSCID is: DCC0001 CandID id: 602102 visit_label is: V1 candidate id 602102 log dir is /data/loris/data//logs and log file is /data/loris/data//logs/TarLoad-18-37-fanZFj.log PSCID is: DCC0001 CandID id: 602102 visit_label is: V1 PSCID is: DCC0001 CandID id: 602102 visit_label is: V1 candidate id 602102 Cleaning up temp files: rm -rf /tmp/TarLoad-18-37-to5pYZ/ImagingUpload-18-36-mTrxXs* (loris-mri-python) lorisadmin at loris-VirtualBox:/data/loris/bin/mri$ cat /data/loris/data/logs/TarLoad-18-37-fanZFj.log ==> Loading file from disk /tmp/TarLoad-18-37-to5pYZ/dcc0001_602102_v1_20160822_072406_205e1d1_mri.mnc --> mapping DICOM parameter for /tmp/TarLoad-18-37-to5pYZ/dcc0001_602102_v1_20160822_072406_205e1d1_mri.mnc ==> computing md5 hash for MINC body. --> md5: 02022dda60d9de429340fec838f50cfe ==> verifying acquisition protocol Acquisition protocol is unknown --> The minc file cannot be registered since the AcquisitionProtocol is unknown ???? ???, 4 ??? 2019 ???? 10:46 ?.?., ?/? Christine Rogers, Ms. > ??????: Hi Sotirios: Sure -- you can delete imaging datasets with the delete_imaging_upload script -- details here: https://github.com/aces/Loris-MRI/blob/21.0-dev/docs/scripts_md/delete_imaging_upload.md What's in your psc table? (Is it properly populated? This is a pre-requisite to loading imaging data.) The foreign key constraint error on the candidate record is curious. There are also a few options for creating candidates when inserting imaging data: -- Method 1 : in 2 steps with the API then DICOM insertion pipeline a. via the LORIS API -- Create the candidates (and visits, optionally I think) How to: https://github.com/aces/Loris/blob/master/docs/API/LorisRESTAPI.md#30-candidate-api Ensure you get the DCCID/CandID assigned by LORIS. Then as a second step: b. Use the imaging insertion pipeline to load your DICOMs. You will want to first ensure that the PatientName header in the DICOMs as well as tar package are correctly labelled with PSCID_DCCID_VisitLabel -- Method 2: for BIDS-format datasets: How to : https://github.com/aces/Loris-MRI/blob/master/docs/05-PipelineLaunchOptions.md#52---pipeline-launch-for-bids-datasets Be sure to use the -c and -s options when running the bids_import script, to automatically create your candidates and sessions. Best, Christine On Wed, Sep 4, 2019 at 11:43 AM Sotirios Nikoloutsopoulos > wrote: How do i delete a Study? And everytime do i have to create a new candidate to get DCCID and a PSCID? First execution: (loris-mri-python) lorisadmin at loris-VirtualBox:/data/loris/bin/mri$ ./batch_uploads_imageuploader.pl -profile prod < ~/Desktop/input.txt > log.txt Use of uninitialized value $_ in pattern match (m//) at ./batch_uploads_imageuploader.pl line 144. DBD::mysql::db do failed: Cannot add or update a child row: a foreign key constraint fails (`LORIS`.`candidate`, CONSTRAINT `FK_candidate_1` FOREIGN KEY (`RegistrationCenterID`) REFERENCES `psc` (`CenterID`)) at /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 1060. ERROR: Failed to insert record in table mri_scanner: The following database commands failed: PREPARE s FROM 'INSERT INTO mri_scanner (CandID,Model,Software,Serial_number,Manufacturer) VALUES (?,?,?,?,?)'; SET @x1='242126', at x2='Achieva', at x3='3.2.2\3.2.2.0', at x4='34037', at x5='Philips Medical Systems'; EXECUTE s USING @x1, at x2, at x3, at x4, at x5; Error obtained:Cannot add or update a child row: a foreign key constraint fails (`LORIS`.`mri_scanner`, CONSTRAINT `FK_mri_scanner_1` FOREIGN KEY (`CandID`) REFERENCES `candidate` (`CandID`)) (error code 1452) ERROR: The validation has failed. Either re-run the validation again and fix the problem. Or re-run tarchiveLoader.pl using -force to force the execution. The tarchiveLoader.pl insertion script has failed. Can't exec "mail": No such file or directory at ./batch_uploads_imageuploader.pl line 249. print() on closed filehandle MAIL at ./batch_uploads_imageuploader.pl line 250. print() on closed filehandle MAIL at ./batch_uploads_imageuploader.pl line 251. And second execution: (loris-mri-python) lorisadmin at loris-VirtualBox:/data/loris/bin/mri$ ./batch_uploads_imageuploader.pl -profile prod < ~/Desktop/input.txt > log.txt Use of uninitialized value $_ in pattern match (m//) at ./batch_uploads_imageuploader.pl line 144. PROBLEM: The user 'lorisadmin' has already inserted this study. The unique study ID is '1.3.51.0.1.1.10.49.10.222.1422753.1420953'. This is the information retained from the first time the study was inserted: * Taken from dir : /tmp/ImagingUpload-18-33-Qq7HGy * Archive target location : /data/loris/data/tarchive/DCM_2012-12-05_ImagingUpload-18-33-Qq7HGy.tar * Name of creating host : 127.0.1.1 * Name of host OS : Linux * Created by user : lorisadmin * Archived on : 2019-09-04 18:33:05 * dicomSummary version : 1 * dicomTar version : 1 * md5sum for DICOM tarball : 4a301b0318178b09b91e63544282364d ImagingUpload-18-33-Qq7HGy.tar * md5sum for DICOM tarball gzipped : 9d95ea2b9111be236808bfd65d7e65ec ImagingUpload-18-33-Qq7HGy.tar.gz * md5sum for complete archive : ab19a86357f1d4053aa3b81c8a071053 DCM_2012-12-05_ImagingUpload-18-33-Qq7HGy.tar Last update of record: The dicomTar.pl execution has failed. Can't exec "mail": No such file or directory at ./batch_uploads_imageuploader.pl line 249. print() on closed filehandle MAIL at ./batch_uploads_imageuploader.pl line 250. print() on closed filehandle MAIL at ./batch_uploads_imageuploader.pl line 251. ???? ???, 4 ??? 2019 ???? 5:35 ?.?., ?/? Christine Rogers, Ms. > ??????: Hi Sotirios, Ok, this sounds like good progress. Let us know when you next encounter issues as you progress through the Imaging Install/Setup docs. I'll look into how we can better handle the incoming/ directory next time. Best, Christine On Wed, Sep 4, 2019 at 10:23 AM Sotirios Nikoloutsopoulos > wrote: /data/loris/bin/mri/dicom-archive/.loris_mri/database_config.py is populated correctly except its port is 'port' : ''. Also i have tested that i can connect to MySQL with lorisuser. I executed the script again, because the only error i had previously was that the /data/incoming folder didn't exist and there are no errors reported back except of warnings <>. ???? ???, 4 ??? 2019 ???? 4:53 ?.?., ?/? Christine Rogers, Ms. > ??????: Hi Sotirios, It's possible -- if the script was unable to connect to the database during its execution (e.g. typo in the password), that would explain the underpopulated Image path and Loris-MRI code path you saw in the Config module. It's hard to tell without seeing the output from your script run -- Did you see a sign of any such error? The Config fields are populated by the imaging_install.sh script (starting at line 222) For example, check if the database connection information was populated accurately in $mridir/dicom-archive/.loris_mri/database_config.py Best, Christine On Wed, Sep 4, 2019 at 9:34 AM Sotirios Nikoloutsopoulos > wrote: Hi Christine, If you are referring to the imaging_install.sh here is an image with the configurations i typed. Maybe the problem is somewhere at the last part which asks to configure as much as possible automatically? Thanks [https://lh5.googleusercontent.com/j0RRFnBHh5ePMY2WuojLIIsv8HZR46fvQUnNU9K0idwkhx_aEdCOMLKUnxI5lVupyRzSsP0weD2UNfywMc9VXykIOu0wJ1ao6cKNwlmJFrC3sJIXXAWT6aM7xHf-J134kCR0gbOs] ???? ???, 4 ??? 2019 ???? 4:16 ?.?., ?/? Christine Rogers, Ms. > ??????: Hi Sotirios, Glad to hear your LORIS core install is up and working and all the front-end pages are loading. > lorisadmin at loris-VirtualBox:/var/www/loris$ chmod 775 project > and the web interface worked. Yes, it's important that project/ have 775 permissions and that lorisadmin be part of the sudoers group, per step 1 in the install Readme. > As for the Paths, LORIS-MRI code and Image should change LORIS to loris, right? These imaging paths will be updated during your imaging installation by an automated script -- you do not need to set them manually via the Config module. Please continue to follow the Setup Guide for detailed steps to follow. Best, Christine On Wed, Sep 4, 2019 at 8:05 AM Sotirios Nikoloutsopoulos > wrote: As for the Paths, LORIS-MRI code and Image should change LORIS to loris, right? [image.png] ???? ???, 4 ??? 2019 ???? 2:28 ?.?., ?/? Sotirios Nikoloutsopoulos > ??????: Hi, i used curl -sL https://deb.nodesource.com/setup_8.x | sudo -E bash - sudo apt-get install -y nodejs you had suggested in the past, make worked and now i can see all the contents in the web-interface, but i don't need make install? Thanks _______________________________________________ Loris-dev mailing list Loris-dev at bic.mni.mcgill.ca https://mailman.bic.mni.mcgill.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 -- 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 -- 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... 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Name: Outlook-image.png.png Type: image/png Size: 10499 bytes Desc: Outlook-image.png.png URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Outlook-image.png.png Type: image/png Size: 14792 bytes Desc: Outlook-image.png.png URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Outlook-image.png.png Type: image/png Size: 96080 bytes Desc: Outlook-image.png.png URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Outlook-image.png.png Type: image/png Size: 69984 bytes Desc: Outlook-image.png.png URL: From sotirisnik at gmail.com Wed Oct 2 05:07:55 2019 From: sotirisnik at gmail.com (Sotirios Nikoloutsopoulos) Date: Wed, 2 Oct 2019 12:07:55 +0300 Subject: [Loris-dev] Import mri - scripts In-Reply-To: References: Message-ID: Hi, Yes, by parsing now() into unix_timestamp function it worked,but i thought that something else was causing the 2nd issue. Thanks On Tue, 1 Oct 2019, 18:36 Xavier Lecours Boucher, Mr, < xavier.lecoursboucher at mcgill.ca> wrote: > Hi Sotirios, > > The first error occurs because the QCFirstChangeTime and columns are of > type `unsigned integer` and not `datatime`. You should be using > UNIX_TIMESTAMP() instead of NOW(). > > The second error occurs because the trigger triggers a rollback of the > insert statement in the files table. > See mysql documentation for trigger error handling. > > An error during either a BEFORE or AFTER trigger results in failure of > the entire statement that caused trigger invocation. > > > Thank you for sharing that. I hope it helps. > -- Xavier > > ------------------------------ > *From:* loris-dev-bounces at bic.mni.mcgill.ca < > loris-dev-bounces at bic.mni.mcgill.ca> on behalf of Sotirios > Nikoloutsopoulos > *Sent:* October 1, 2019 8:33 AM > *To:* Cecile Madjar > *Cc:* loris-dev at bic.mni.mcgill.ca ; > Christine Rogers, Ms. > *Subject:* Re: [Loris-dev] Import mri - scripts > > When mincs are inserted their corresponding rows at the file table are > inserted too > [image: image.png] > > i would like to insert their rows at file_qcstatus as well, because i > don't want manually to label them as passed throught the interface > > [image: image.png] > > > That is the trigger i wrote > > CREATE DEFINER = CURRENT_USER TRIGGER `LORIS`.`files_AFTER_INSERT` AFTER > INSERT ON `files` FOR EACH ROW > BEGIN > INSERT INTO files_qcstatus > SET FileID = NEW.FileID, > SeriesUID = NEW.SeriesUID, > EchoTime = NEW.EchoTime, > QCStatus = "Pass", > QCFirstChangeTime = NOW(), > QCLastChangeTime = NOW(); > END > > although it contains some errors > > DBD::mysql::db do failed: Out of range value for column > 'QCFirstChangeTime' at row 1 at > /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 823. > DBD::mysql::db do failed: Cannot add or update a child row: a foreign key > constraint fails (`LORIS`.`parameter_file`, CONSTRAINT > `FK_parameter_file_1` FOREIGN KEY (`FileID`) REFERENCES `files` (`FileID`)) > at /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 848. > > > > > > > > > ???? ???, 1 ??? 2019 ???? 4:21 ?.?., ?/? Cecile Madjar < > cecile.madjar at mcin.ca> ??????: > > Hi Sotirios, > > In the mri_upload table, there is a TarchiveID column associated with the > MRI upload you inserted. When this value is NULL, it means no DICOMs were > inserted into the tarchive tables. At the end of the insertion of the > DICOMs in the tarchive tables, this value is updated with the correct > TarchiveID associated with the upload. > > Could this correspond to what you want to do? > > Regarding the files_qcstatus, this table is only linked to the files table > (hence, the MINC files). You could always create a new table for > dicom_qcstatus and link it to the tarchive table? > > C?cile > > On Tue, Oct 1, 2019 at 6:56 AM Sotirios Nikoloutsopoulos < > sotirisnik at gmail.com> wrote: > > Hi, > > i would like whenever a dicom is imported to mark all their coressponding > qc_status to "pass". I was thinking of creating a trigger for that, but > which tables do i need to add entries to? So far from what i see i need to > add entres at the table "files" whenever an insertion happens to > files_qcstatus. > > Thanks > > ???? ???, 30 ??? 2019 ???? 4:04 ?.?., ?/? Sotirios Nikoloutsopoulos < > sotirisnik at gmail.com> ??????: > > Oh, sorry i should have asked for StudyID, at the beginning of my email i > sent 3 hours ago (not StudyUID). > > ???? ???, 30 ??? 2019 ???? 3:55 ?.?., ?/? Sotirios Nikoloutsopoulos < > sotirisnik at gmail.com> ??????: > > Hi, > > that's the Study Instance UID, not the StudyID. So the StudyID i am > looking for is not stored in the database? > > [image: image.png] > > Thanks. > > ???? ???, 30 ??? 2019 ???? 3:38 ?.?., ?/? Cecile Madjar < > cecile.madjar at mcin.ca> ??????: > > Hi Sotirios, > > The StudyUID is stored in the DicomArchiveID field of the tarchive table. > It can also be found in the metadata field but it is mixed with many other > information. > > Hope this helps, > > C?cile > > On Mon, Sep 30, 2019 at 6:00 AM Sotirios Nikoloutsopoulos < > sotirisnik at gmail.com> wrote: > > Hi, > > Is StudyUID stored somewhere at the tables? At the tarchive table, > specifically at the AcquisitonMetadata column i found something called > 'Unique Study ID" in its context, but that must be the Study Instance UID. > > Thanks > > ???? ???, 27 ??? 2019 ???? 4:22 ?.?., ?/? Cecile Madjar < > cecile.madjar at mcin.ca> ??????: > > Hi Sotirios, > > Your observation is correct. A little explanation below. > > MINC files get inserted into the MRI violation tables if: > > - the scan type could not be identified (not matching an entry in the > mri_protocol table) > - one parameter of the scan type is out of the expected range present > in the mri_protocol_checks (extra filtering in case you need to be stricker > on some parameters not present in the mri_protocol table) > - if the CandID and PSCID do not match > > The following cases do not get in the MRI violation tables as it happens > before the conversion of the DICOM to MINC files and only MINC files > violations are logged there: > > - "No single DICOM" (since no valid DICOM could be found to convert to > MINC) > - "Study already inserted" (duplicate StudyUID) since this error > happens at the dicomTar.pl level (way before conversion into MINC files) > > Glad everything is working out!! > Best, > > C?cile > > On Fri, Sep 27, 2019 at 6:17 AM Sotirios Nikoloutsopoulos < > sotirisnik at gmail.com> wrote: > > Hi, > > the mri passed, for some reason it consumed 5.12GB of ram. Now about the > mri_violations, dicoms are triggered to be inserted there only if there is > a violation for Tr_min, Tr_max, in general for its header parameter? > Because i don't see the cases of 'No single dicom" or with the 2 studyiuid > to be there. > > Thanks > > ???? ???, 26 ??? 2019 ???? 5:07 ?.?., ?/? Cecile Madjar < > cecile.madjar at mcin.ca> ??????: > > Hi Sotirios, > > Sorry to hear you are having issues with the memory. I think most of our > VMs are set up with 4GB of RAM so with 4GB you should be fine. > > Hope this helps! > > C?cile > > On Thu, Sep 26, 2019 at 9:48 AM Sotirios Nikoloutsopoulos < > sotirisnik at gmail.com> wrote: > > Hi, > > about that dicom that had that insertion error it's about 30mb and when it > is being processed the ram is being drastically increased from 2gb to 3.28 > and then the whole virtual machine is frozen. What is the recommended size > of ram for using Loris? > > Thanks > > [image: image.png] > > > ???? ???, 24 ??? 2019 ???? 11:24 ?.?., ?/? Cecile Madjar < > cecile.madjar at mcin.ca> ??????: > > Hi Sotirios, > > Glad to see that the StudyUID problem was fixed! > > For the delete script issue, if you are absolutely certain that no > processes are run for that uploadID, you can update the mri_upload table > and set the column Inserting to 0 instead of 1 for that uploadID. It > looks like for some reason the scripts did not update this field when it > stopped the insertion. Not sure why that would be the case though. > Note: only do that update if you are certain that there is no processing > happening. > > Hope this helps! > > > On Tue, Sep 24, 2019 at 11:57 AM Sotirios Nikoloutsopoulos < > sotirisnik at gmail.com> wrote: > > Hi, > > about the Dicoms i reported that didn't have a StudyID they actually do > > [image: image.png] > > > [image: image.png] > > I thought that this might be a permission because "w" was missing at the > group. After using chmod -R 775 only 102809579 passed, but with no mnic > files. Also now i have this error > > (loris-mri-python) lorisadmin at loris-VirtualBox:/data/loris/bin/mri/tools$ > ./delete_imaging_upload.pl -uploadID 34 -ignore > Cannot delete upload 34: the MRI pipeline is currently processing it. > > How can solve this? > > Thanks > > > ???? ???, 24 ??? 2019 ???? 2:30 ?.?., ?/? Sotirios Nikoloutsopoulos < > sotirisnik at gmail.com> ??????: > > Hi, > > Here is our auto dicom uploading python script: > https://github.com/aueb-wim/DataQualityControlTool/blob/loris1/mipqctool/dicom_uploader.py > > To give you a brief idea: > Per folder it will: > 1) Delete all the .bak files > 2) Locate .dcm files and update the Patient header > 3) Furthermore we are interesting in finding TR_min, TR_max, TE_min, > TE_max parameters of T1 protocol and do an update at the mri_protocol table > https://github.com/aueb-wim/DataQualityControlTool/blob/loris1/mipqctool/dicom_uploader.py#L205 > For some reason some files are missing SeriesDescription/ProtocolName > > In total i have 7 folders > > [image: image.png] > > 3/7 passed > > [image: image.png] > > Also about the first patient with DC0000 had a violation "T1 AXIAL SE > GADO", but my script didn't output a TE of 17 nowhere and i find that weird > since Loris detects the SeriesDescription. > [image: image.png] > > > Now about the 4/7 that didn't passed > > 102327840 and 102809579 outputs "The target directory does not contain a > single DICOM file.", therefore they are missing their StudyUID > > 102506134 has 2 studyuid "You can't use it with data from multiple > studies." > > and 102761034 "No data could be converted into valid MINC files. > localizer, scout will not be considered!" What is this? > > If i wanted to force the insertion of 102327840, 102809579 and 102506134 > can i just pass a flag parameter to batch_uploads_imageuploader.pl? or > modify imaging_upload_file.pl? > > Thank you, > > Sotirios > > PS > > To diagnose a folder search the name of the folder at dicom_output.txt. > > ???? ???, 20 ??? 2019 ???? 4:54 ?.?., ?/? Christine Rogers, Ms. < > christine.rogers at mcgill.ca> ??????: > > Hi Sotirios, > Glad to hear about your progress. > > Yes, the script you used to delete imaging data is fully documented here > > -- let us know if you didn't find the answers you were looking for there. > (Is it possible the null row in *mri_scanner* seen in your database > management software is a visual placeholder for you as the user? I'm not > sure why a scanner would ever be registered with ID='0' as your screenshot > showed.) > > Best, > Christine > > On Fri, Sep 20, 2019 at 9:45 AM Sotirios Nikoloutsopoulos < > sotirisnik at gmail.com> wrote: > > I fixed it with this > > [image: image.png] > > ???? ???, 20 ??? 2019 ???? 4:37 ?.?., ?/? Sotirios Nikoloutsopoulos < > sotirisnik at gmail.com> ??????: > > Hi, > > I tried to create a new candidate using the API, is there something wrong > with the structure? why did i receive a 500 internal error? In the > loris-error log it state that there is something wrong with token, but i > verfied that the type of the token is a string. > > [Fri Sep 20 16:35:26.874732 2019] [php7:error] [pid 4535] [client > 127.0.0.1:59674] PHP Fatal error: Uncaught TypeError: Argument 1 passed > to SinglePointLogin::JWTAuthenticate() must be of the type string, null > given, called in /var/www/loris/php/libraries/SinglePointLogin.class.inc on > line 169 and defined in > /var/www/loris/php/libraries/SinglePointLogin.class.inc:192\nStack > trace:\n#0 /var/www/loris/php/libraries/SinglePointLogin.class.inc(169): > SinglePointLogin->JWTAuthenticate(NULL)\n#1 > /var/www/loris/php/libraries/NDB_Client.class.inc(171): > SinglePointLogin->authenticate()\n#2 > /var/www/loris/htdocs/api/v0.0.2/APIBase.php(73): > NDB_Client->initialize('/var/www/loris/...')\n#3 > /var/www/loris/htdocs/api/v0.0.2/Candidates.php(44): > Loris\\API\\APIBase->__construct('POST')\n#4 > /var/www/loris/htdocs/api/v0.0.2/Candidates.php(244): > Loris\\API\\Candidates->__construct('POST', Array)\n#5 {main}\n thrown in > /var/www/loris/php/libraries/SinglePointLogin.class.inc on line 192 > > [image: image.png] > > ???? ???, 20 ??? 2019 ???? 2:39 ?.?., ?/? Sotirios Nikoloutsopoulos < > sotirisnik at gmail.com> ??????: > > Hi, > > Is there a way also to delete candidates? Just to let you know what i did > to clear candidates, because maybe i may have missed dependencies. > > First i deleted all their uploads > ./delete_imaging_upload.pl -uploadID 13 etc ( is there a way to omit the > backup file ? ) > > Afterwards i had some scanner candidates, so i deleted all the entries > from mri_scanner except that i couldn't delete this entry with the 0 ID. > > [image: image.png] > > > Lastly i deleted the session and then the candidate table. > > Thanks > > ???? ???, 19 ??? 2019 ???? 7:57 ?.?., ?/? Christine Rogers, Ms. < > christine.rogers at mcgill.ca> ??????: > > Hi Sotirios, > > We recommend that you use our existing tools for creating new candidates - > either the LORIS API or if you are using a PHP script, by calling the Candidate > class's createNew() > function. > These will create the necessary records for you. (It's not recommended to > make direct modifications to mysql database tables in your script, if I > understand you.) > > The CandID should be a randomized 6 digit randomized ID, and there are > multiple reasons for this. > You can use the PSCID for project-specific IDs and the External ID field > in the candidate table can also be used for any values you like. > Additionally, any number of custom IDs can be added in parallel - these > are entered/visible in the Candidate Information module and added in the > back-end as candidate parameters. > > Best, > Christine > > > > On Tue, Sep 17, 2019 at 7:31 PM Sotirios Nikoloutsopoulos < > sotirisnik at gmail.com> wrote: > > Hi, > > We are building a script that will auto insert the candidates based on > their ExternalID. We would like to know whethere when we are creating a new > profile in the candidate table, if we also have to insert a new record at > another table? Furthermore is there a problem that in our case CandID won't > be a 6digit? ( should we start it from 100000?) > > Thanks > > [image: image.png] > > > ???? ???, 13 ??? 2019 ???? 5:38 ?.?., ?/? Melanie Legault, Mrs < > melanie.legault2 at mcgill.ca> ??????: > > That would normally be the case but the numeric part of the PSCID get > paded with 0 on the left. > > Ex. for sequential ID made of center ID of `ABC` plus 4 numerical char > with a min value of 1, the sequence would be: > > ABC0001 > ABC0002 > ... > ABC0010 > ... > > thus sorting them ascending will always get the latest value generated as > the max value. > > M?lanie > > ------------------------------ > *From:* Sotirios Nikoloutsopoulos > *Sent:* September 13, 2019 10:15 > *To:* Melanie Legault, Mrs > *Cc:* Christine Rogers, Ms. ; > loris-dev at bic.mni.mcgill.ca > *Subject:* Re: [Loris-dev] Import mri - scripts > > I see, although the PSCID value is varchar(255), it must be stored within > a specific length of characters. Otherwise if we were to sort strings with > different lengths the result would not be sorted correctly ( e.x. 1,2,10,11 > as strings would result to 1, 10, 11, 2 ). > > Thanks > > ???? ???, 13 ??? 2019 ???? 4:52 ?.?., ?/? Melanie Legault, Mrs < > melanie.legault2 at mcgill.ca> ??????: > > Hello Sotirios, > > There is no `last value` stored anywhere. > The code simply look for the PSCID with the max value and increase that > value by 1 in order to generate the next PSCID. > > Hope this info help. > > M?lanie Legault | Software developer | Faculty of Medicine | McGill > University > 3801 University, Montr?al, QC H3A 2B4 > > ------------------------------ > *From:* loris-dev-bounces at bic.mni.mcgill.ca < > loris-dev-bounces at bic.mni.mcgill.ca> on behalf of Sotirios > Nikoloutsopoulos > *Sent:* September 13, 2019 9:43 > *To:* Christine Rogers, Ms. > *Cc:* loris-dev at bic.mni.mcgill.ca > *Subject:* Re: [Loris-dev] Import mri - scripts > > Hi, > > how does Loris determine the next available PSCID value for a new > candidate? https://github.com/aces/Loris/wiki/Project-Customization e.x > in the default case the PSCID is sequential, but where do we store the last > value for the sequential sequence? > > Thanks > > ???? ???, 10 ??? 2019 ???? 4:00 ?.?., ?/? Sotirios Nikoloutsopoulos < > sotirisnik at gmail.com> ??????: > > Hi, > > the parameters in the mri_protocol you have assigned are global standard? > or were assigned after trial and error? > > Thanks > > ???? ???, 8 ??? 2019 ???? 10:11 ?.?., ?/? Christine Rogers, Ms. < > christine.rogers at mcgill.ca> ??????: > > Hi Sotirios, > > Given you have done the initial setup of your tables to match your > intended protocol/parameters according to instructions -- > the Troubleshooting guide documentation recommends > > re-running the pipeline (and first deleting prior uploads). > > Best, > Christine > > On Sun, Sep 8, 2019 at 10:22 AM Sotirios Nikoloutsopoulos < > sotirisnik at gmail.com> wrote: > > *if i were to change their status to resolve what would happen? > > ???? ???, 8 ??? 2019 ???? 5:12 ?.?., ?/? Sotirios Nikoloutsopoulos < > sotirisnik at gmail.com> ??????: > > I noticed that i can view the mnics at the brainbrowser from the > mri_violations page ( those mnics are stored at /data/loris/data/trashbin/ > if i were to click their issue to resolve what would happend? would they > appear in the dicom_archive view too? ). > > > > ???? ???, 8 ??? 2019 ???? 4:17 ?.?., ?/? Sotirios Nikoloutsopoulos < > sotirisnik at gmail.com> ??????: > > Hi, > > The defaut values of the schema exists in my local database. If i adjust > the default values of TR_min and TE_min the mincs will be uploaded? > > [image: image.png] > > > [image: image.png] > > Thanks > > ???? ???, 7 ??? 2019 ???? 5:48 ?.?., ?/? Christine Rogers, Ms. < > christine.rogers at mcgill.ca> ??????: > > Hi Sotirios, > > Is it possible that you haven't set up your mri_protocol table ? (and > mri_scan_type table too, for additional types of scans) > > Like the psc table, this is a pre-requisite for the Imaging insertion > setup : See the install/setup documentation : > https://github.com/aces/Loris-MRI/blob/master/docs/02-Install.md > > To add new rows, just use MySQL insert statements. You can adapt the > insert statements which load the default table values --> e.g. Here on > GitHub : > https://github.com/aces/Loris/blob/master/SQL/0000-00-00-schema.sql#L718 > (see also the mri_scan_type table) > > Best, > Christine > > On Fri, Sep 6, 2019 at 8:32 PM Sotirios Nikoloutsopoulos < > sotirisnik at gmail.com> wrote: > > I see that i can edit the values but not how to insert new rows. > > [image: image.png] > > If i choose Inserted with flag then will the minc be inserted? > > [image: image.png] > > ???? ???, 7 ??? 2019 ???? 3:21 ?.?., ?/? Christine Rogers, Ms. < > christine.rogers at mcgill.ca> ??????: > > Hi Sotirios, > > Glad to hear that *dcmodify* worked correctly. > > For the MRI Violations module, the screenshot is enough. > > It says "could not identify scan type", which we knew already. Did you > click on the link on those words? > > It will take you to the next page of the module, showing for each scan > what the scan parameters were, and will also show for comparison what's > stored in your *mri_protocol* table. > Compare these values to find which parameter was not correct according to > your *mri_protocol* table scan type definitions. > > You may end up broadening your mri_protocol value ranges (e.g. TR, TE) for > scans. > This can be done in the front-end, by editing the database table directly > in the same subpage of the MRI Violations module. > > The MRI Violations module features are explained in more detail in the > Help text for this module inside LORIS (click the ["?"] icon in the menu > bar.) > > See also: Loris-MRI troubleshooting guide > > : no MINCs inserted- violated scans > > Best, > Christine > > On Fri, Sep 6, 2019 at 8:11 PM Sotirios Nikoloutsopoulos < > sotirisnik at gmail.com> wrote: > > Hi, > > looks like my previous email's attachment wasn't delivered due to security > reasons, i uploaded my file at google drive > https://drive.google.com/file/d/1U_TRbo_qGgfpQfs-SqeG9J3bMMqNfUU4/view?usp=sharing > > ???? ???, 7 ??? 2019 ???? 3:02 ?.?., ?/? Sotirios Nikoloutsopoulos < > sotirisnik at gmail.com> ??????: > > Hi, > > From Dicat's view seems that dcmodify worked in both cases > > [image: image.png] > > [image: image.png] > > For the mri_violations i attached the .html output from webbrowser, so > that you can check the filelds easier. > > [image: image.png] > > Thanks > > > > ???? ???, 6 ??? 2019 ???? 7:49 ?.?., ?/? Christine Rogers, Ms. < > christine.rogers at mcgill.ca> ??????: > > Hi Sotirios -- > Great, sounds like more progress. > > About the dcmodify command -- I'm not sure why you're getting an Endian > warning. (it's a warning not an error, correct?) > To clarify -- Were the DICOM headers (PatientName) all successfully > relabelled, after the command ran? > > You can use also our DICAT tool (https://github.com/aces/DICAT) to verify > and/or update local DICOM headers -- though your dcmodify command is a > great and fast solution for bulk header updates. > > If you're concerned about fields being changed (e.g. "(2001,105f)" from > the warning message) - you can also dcmdump a DICOM slice before and look > at these fields specifically. > It's also not a bad "sanity check" to backup your DICOMS before/after > running dcmodify, and use dcmdump on each version to diff the outputs -- > this will pinpoint what changed. > > Re the protocol violation -- AcquisitionProtocol not recognized or unknown > : this means your scans did not match what is stored in your mri_protocol > table. > Check the MRI Violations front-end module -- can you see why they didn't > match? > Send us an example, in addition to the contents of the mri_protocol table, > if you can't find the source of the mismatch. > > Best, > Christine > > > On Fri, Sep 6, 2019 at 12:04 PM Sotirios Nikoloutsopoulos < > sotirisnik at gmail.com> wrote: > > Here is the psc table > [image: image.png] > > I created 2 candidates profiles through the interface > > [image: image.png] > > then runned dcmodify command to a dicom file > > dcmodify -ma PatientName="DCC0000_258024_V1" > /home/lorisadmin/DICOMS/000535670/501/*.dcm > > and got those warning: is this okay? > W: Found element (2001,105f) with VR UN and undefined length, reading a > sequence with transfer syntax LittleEndianImplicit (CP-246) > W: Found element (2005,1083) with VR UN and undefined length, reading a > sequence with transfer syntax LittleEndianImplicit (CP-246) > W: Found element (2005,1402) with VR UN and undefined length, reading a > sequence with transfer syntax LittleEndianImplicit (CP-246) > W: Found element (2005,140f) with VR UN and undefined length, reading a > sequence with transfer syntax LittleEndianImplicit (CP-246) > W: Found element (2001,105f) with VR UN and undefined length, reading a > sequence with transfer syntax LittleEndianImplicit (CP-246) > W: Found element (2005,1083) with VR UN and undefined length, reading a > sequence with transfer syntax LittleEndianImplicit (CP-246) > > dcmodify at another Dicom didn't show warnings. Below you can see the > execution for the second dicom. Mnics could not be inserted due to > AcquisitionProtocol being unknown. > > Running now the following command: /data/loris/bin/mri//uploadNeuroDB/ > imaging_upload_file.pl -profile prod -upload_id 12 > /data/incoming/DCC0001_602102_V1.tar.gz -verbose > > find -path \/tmp\/ImagingUpload\-18\-36\-mTrxXs -name '__MACOSX' -delete > > dicomTar.pl \/tmp\/ImagingUpload\-18\-36\-mTrxXs > \/data\/loris\/data\/tarchive\/ -database -profile prod -verbose > Source: /tmp/ImagingUpload-18-36-mTrxXs > Target: /data/loris/data/tarchive > > Testing for database connectivity. > Database is available. > > You will archive the dir : ImagingUpload-18-36-mTrxXs > > You are creating a tar with the following command: > > tar -cf /data/loris/data/tarchive/ImagingUpload-18-36-mTrxXs.tar > ImagingUpload-18-36-mTrxXs > > > getting md5sums and gzipping!! > > * Taken from dir : /tmp/ImagingUpload-18-36-mTrxXs > * Archive target location : > /data/loris/data/tarchive/DCM_2016-08-22_ImagingUpload-18-36-mTrxXs.tar > * Name of creating host : 127.0.1.1 > * Name of host OS : Linux > * Created by user : lorisadmin > * Archived on : 2019-09-06 18:36:50 > * dicomSummary version : 1 > * dicomTar version : 1 > * md5sum for DICOM tarball : b1dcdc8903dd2d9a5443227db2aa2814 > ImagingUpload-18-36-mTrxXs.tar > * md5sum for DICOM tarball gzipped : aeae87f20155a6805f7e0cfe5212ea5f > ImagingUpload-18-36-mTrxXs.tar.gz > * md5sum for complete archive : 1d9258d1f077ebc49111ab7ba22a8d6e > DCM_2016-08-22_ImagingUpload-18-36-mTrxXs.tar > > Adding archive info into database > > Removing temporary files from target location > > > Done adding archive info into database > > \/data\/loris\/bin\/mri\//uploadNeuroDB/tarchiveLoader.pl -globLocation > -profile prod > \/data\/loris\/data\/tarchive\/\/DCM_2016\-08\-22_ImagingUpload\-18\-36\-mTrxXs\.tar > -uploadID 12 -verbose > md5sum > /data/loris/data/tarchive/DCM_2016-08-22_ImagingUpload-18-36-mTrxXs.tar > PSCID is: DCC0001 > CandID id: 602102 > visit_label is: V1 > PSCID is: DCC0001 > CandID id: 602102 > visit_label is: V1 > candidate id 602102 > Set centerID = 1 > PSCID is: DCC0001 > CandID id: 602102 > visit_label is: V1 > PSCID is: DCC0001 > CandID id: 602102 > visit_label is: V1 > > Number of MINC files that will be considered for inserting into the > database: 2 > > log dir is /data/loris/data//logs and log file is > /data/loris/data//logs/TarLoad-18-37-31ajWx.log > PSCID is: DCC0001 > CandID id: 602102 > visit_label is: V1 > PSCID is: DCC0001 > CandID id: 602102 > visit_label is: V1 > candidate id 602102 > > log dir is /data/loris/data//logs and log file is > /data/loris/data//logs/TarLoad-18-37-fanZFj.log > PSCID is: DCC0001 > CandID id: 602102 > visit_label is: V1 > PSCID is: DCC0001 > CandID id: 602102 > visit_label is: V1 > candidate id 602102 > > Cleaning up temp files: rm -rf > /tmp/TarLoad-18-37-to5pYZ/ImagingUpload-18-36-mTrxXs* > > (loris-mri-python) lorisadmin at loris-VirtualBox:/data/loris/bin/mri$ cat > /data/loris/data/logs/TarLoad-18-37-fanZFj.log > > ==> Loading file from disk > /tmp/TarLoad-18-37-to5pYZ/dcc0001_602102_v1_20160822_072406_205e1d1_mri.mnc > > --> mapping DICOM parameter for > /tmp/TarLoad-18-37-to5pYZ/dcc0001_602102_v1_20160822_072406_205e1d1_mri.mnc > > ==> computing md5 hash for MINC body. > > --> md5: 02022dda60d9de429340fec838f50cfe > > ==> verifying acquisition protocol > > Acquisition protocol is unknown > > --> The minc file cannot be registered since the AcquisitionProtocol is > unknown > > ???? ???, 4 ??? 2019 ???? 10:46 ?.?., ?/? Christine Rogers, Ms. < > christine.rogers at mcgill.ca> ??????: > > Hi Sotirios: > > Sure -- you can delete imaging datasets with the *delete_imaging_upload* > script -- > details here: > https://github.com/aces/Loris-MRI/blob/21.0-dev/docs/scripts_md/delete_imaging_upload.md > > What's in your *psc* table? (Is it properly populated? This is a > pre-requisite to loading imaging data. > > ) > The foreign key constraint error on the candidate record is curious. > > There are also a few options for creating candidates when inserting > imaging data: > > -- Method 1 : in 2 steps with the API then DICOM insertion pipeline > > a. via the LORIS API -- Create the candidates (and visits, optionally I > think) > How to: > https://github.com/aces/Loris/blob/master/docs/API/LorisRESTAPI.md#30-candidate-api > Ensure you get the DCCID/CandID assigned by LORIS. > > Then as a second step: > b. Use the imaging insertion pipeline > > to load your DICOMs. > You will want to first ensure that the PatientName header in the DICOMs as > well as tar package are correctly labelled with PSCID_DCCID_VisitLabel > > -- Method 2: for BIDS-format datasets: > How to : > https://github.com/aces/Loris-MRI/blob/master/docs/05-PipelineLaunchOptions.md#52---pipeline-launch-for-bids-datasets > > Be sure to use the *-c* and *-s* options when running the bids_import script, > to automatically create your candidates and sessions. > > Best, > Christine > > On Wed, Sep 4, 2019 at 11:43 AM Sotirios Nikoloutsopoulos < > sotirisnik at gmail.com> wrote: > > How do i delete a Study? And everytime do i have to create a new candidate > to get DCCID and a PSCID? > > *First execution:* > > (loris-mri-python) lorisadmin at loris-VirtualBox:/data/loris/bin/mri$ ./ > batch_uploads_imageuploader.pl -profile prod < ~/Desktop/input.txt > > log.txt > Use of uninitialized value $_ in pattern match (m//) at ./ > batch_uploads_imageuploader.pl line 144. > DBD::mysql::db do failed: Cannot add or update a child row: a foreign key > constraint fails (`LORIS`.`candidate`, CONSTRAINT `FK_candidate_1` FOREIGN > KEY (`RegistrationCenterID`) REFERENCES `psc` (`CenterID`)) at > /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 1060. > ERROR: Failed to insert record in table mri_scanner: > The following database commands failed: > PREPARE s FROM 'INSERT INTO mri_scanner > (CandID,Model,Software,Serial_number,Manufacturer) VALUES (?,?,?,?,?)'; > SET > @x1='242126', at x2='Achieva', at x3='3.2.2\3.2.2.0', at x4='34037', at x5='Philips > Medical Systems'; > EXECUTE s USING @x1, at x2, at x3, at x4, at x5; > Error obtained:Cannot add or update a child row: a foreign key constraint > fails (`LORIS`.`mri_scanner`, CONSTRAINT `FK_mri_scanner_1` FOREIGN KEY > (`CandID`) REFERENCES `candidate` (`CandID`)) (error code 1452) > > ERROR: The validation has failed. Either re-run the validation again and > fix the problem. Or re-run tarchiveLoader.pl using -force to force the > execution. > > > The tarchiveLoader.pl insertion script has failed. > Can't exec "mail": No such file or directory at ./ > batch_uploads_imageuploader.pl line 249. > print() on closed filehandle MAIL at ./batch_uploads_imageuploader.pl > line 250. > print() on closed filehandle MAIL at ./batch_uploads_imageuploader.pl > line 251. > > > *And second execution: * > > (loris-mri-python) lorisadmin at loris-VirtualBox:/data/loris/bin/mri$ ./ > batch_uploads_imageuploader.pl -profile prod < ~/Desktop/input.txt > > log.txt > Use of uninitialized value $_ in pattern match (m//) at ./ > batch_uploads_imageuploader.pl line 144. > > PROBLEM: > The user 'lorisadmin' has already inserted this study. > The unique study ID is '1.3.51.0.1.1.10.49.10.222.1422753.1420953'. > This is the information retained from the first time the study was > inserted: > > * Taken from dir : /tmp/ImagingUpload-18-33-Qq7HGy > * Archive target location : > /data/loris/data/tarchive/DCM_2012-12-05_ImagingUpload-18-33-Qq7HGy.tar > * Name of creating host : 127.0.1.1 > * Name of host OS : Linux > * Created by user : lorisadmin > * Archived on : 2019-09-04 18:33:05 > * dicomSummary version : 1 > * dicomTar version : 1 > * md5sum for DICOM tarball : 4a301b0318178b09b91e63544282364d > ImagingUpload-18-33-Qq7HGy.tar > * md5sum for DICOM tarball gzipped : 9d95ea2b9111be236808bfd65d7e65ec > ImagingUpload-18-33-Qq7HGy.tar.gz > * md5sum for complete archive : ab19a86357f1d4053aa3b81c8a071053 > DCM_2012-12-05_ImagingUpload-18-33-Qq7HGy.tar > > > Last update of record: > > > > The dicomTar.pl execution has failed. > Can't exec "mail": No such file or directory at ./ > batch_uploads_imageuploader.pl line 249. > print() on closed filehandle MAIL at ./batch_uploads_imageuploader.pl > line 250. > print() on closed filehandle MAIL at ./batch_uploads_imageuploader.pl > line 251. > > ???? ???, 4 ??? 2019 ???? 5:35 ?.?., ?/? Christine Rogers, Ms. < > christine.rogers at mcgill.ca> ??????: > > Hi Sotirios, > > Ok, this sounds like good progress. Let us know when you next encounter > issues as you progress through the Imaging Install/Setup docs > . > I'll look into how we can better handle the incoming/ directory next time. > Best, > Christine > > On Wed, Sep 4, 2019 at 10:23 AM Sotirios Nikoloutsopoulos < > sotirisnik at gmail.com> wrote: > > /data/loris/bin/mri/dicom-archive/.loris_mri/database_config.py is > populated correctly except its port is 'port' : ''. Also i have tested > that i can connect to MySQL with lorisuser. > > I executed the script again, because the only error i had previously was > that the /data/incoming folder didn't exist and there are no errors > reported back except of warnings < command line interface can be insecure>>. > > > ???? ???, 4 ??? 2019 ???? 4:53 ?.?., ?/? Christine Rogers, Ms. < > christine.rogers at mcgill.ca> ??????: > > Hi Sotirios, > > It's possible -- if the script was unable to connect to the database > during its execution (e.g. typo in the password), that would explain the > underpopulated Image path and Loris-MRI code path you saw in the Config > module. > It's hard to tell without seeing the output from your script run -- Did > you see a sign of any such error? > The Config fields are populated by the imaging_install.sh script (starting > at line 222 > ) > > For example, check if the database connection information was populated > accurately in $mridir/dicom-archive/.loris_mri/database_config.py > > Best, > Christine > > > > On Wed, Sep 4, 2019 at 9:34 AM Sotirios Nikoloutsopoulos < > sotirisnik at gmail.com> wrote: > > Hi Christine, > > If you are referring to the imaging_install.sh here is an image with the > configurations i typed. Maybe the problem is somewhere at the last part > which asks to configure as much as possible automatically? > > Thanks > > > ???? ???, 4 ??? 2019 ???? 4:16 ?.?., ?/? Christine Rogers, Ms. < > christine.rogers at mcgill.ca> ??????: > > Hi Sotirios, > > Glad to hear your LORIS core install is up and working and all the > front-end pages are loading. > > > lorisadmin at loris-VirtualBox:/var/www/loris$ chmod 775 project > > and the web interface worked. > > Yes, it's important that project/ have 775 permissions and that lorisadmin > be part of the sudoers group, per step 1 in the install Readme > . > > > As for the Paths, LORIS-MRI code and Image should change LORIS to loris, > right? > > These imaging paths will be updated during your imaging installation > by an automated script -- you > do not need to set them manually via the Config module. > Please continue to follow the Setup Guide > for detailed steps to follow. > > Best, > Christine > > > > > On Wed, Sep 4, 2019 at 8:05 AM Sotirios Nikoloutsopoulos < > sotirisnik at gmail.com> wrote: > > As for the Paths, LORIS-MRI code and Image should change LORIS to loris, > right? > > [image: image.png] > > > ???? ???, 4 ??? 2019 ???? 2:28 ?.?., ?/? Sotirios Nikoloutsopoulos < > sotirisnik at gmail.com> ??????: > > Hi, > > i used > > curl -sL https://deb.nodesource.com/setup_8.x | sudo -E bash - > sudo apt-get install -y nodejs > > > you had suggested in the past, make worked and now i can see all the > contents in the web-interface, but i don't need make install? > > Thanks > > _______________________________________________ > Loris-dev mailing list > Loris-dev at bic.mni.mcgill.ca > https://mailman.bic.mni.mcgill.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 > > > > -- > > 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 > > > > -- > > 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: -------------- next part -------------- A non-text attachment was scrubbed... Name: Outlook-image.png.png Type: image/png Size: 23576 bytes Desc: not available URL: From sotirisnik at gmail.com Tue Oct 15 07:12:49 2019 From: sotirisnik at gmail.com (Sotirios Nikoloutsopoulos) Date: Tue, 15 Oct 2019 14:12:49 +0300 Subject: [Loris-dev] Modify GUI Message-ID: Hi, In which files can i modify the bar of the GUI? Specifically i would like to remove Clinical, Reports and Tools [image: image.png] and from the Admin tab i would like to remove the marked options. [image: image.png] Thanks, Sotirios -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 2916 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 6111 bytes Desc: not available URL: From christine.rogers at mcgill.ca Tue Oct 15 09:36:56 2019 From: christine.rogers at mcgill.ca (Christine Rogers, Ms.) Date: Tue, 15 Oct 2019 13:36:56 +0000 Subject: [Loris-dev] Modify GUI In-Reply-To: References: Message-ID: Hi Sotirios, To hide any Menu or menu item, in the database back-end set the Visible field to "false" in the LorisMenu table. Doing this for any parent menu records e.g. Clinical, Reports or Tools, should remove them from the top Menu Bar. best, Christine On Tue, Oct 15, 2019 at 7:13 AM Sotirios Nikoloutsopoulos > wrote: Hi, In which files can i modify the bar of the GUI? Specifically i would like to remove Clinical, Reports and Tools [image.png] and from the Admin tab i would like to remove the marked options. [image.png] Thanks, Sotirios _______________________________________________ Loris-dev mailing list Loris-dev at bic.mni.mcgill.ca https://mailman.bic.mni.mcgill.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: 2916 bytes Desc: image.png URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 6111 bytes Desc: image.png URL: From sotirisnik at gmail.com Tue Oct 15 10:05:35 2019 From: sotirisnik at gmail.com (Sotirios Nikoloutsopoulos) Date: Tue, 15 Oct 2019 17:05:35 +0300 Subject: [Loris-dev] Modify GUI In-Reply-To: References: Message-ID: Thank you Dave and Christine. ???? ???, 15 ??? 2019 ???? 4:36 ?.?., ?/? Christine Rogers, Ms. < christine.rogers at mcgill.ca> ??????: > Hi Sotirios, > To hide any Menu or menu item, in the database back-end set the *Visible* field > to "false" in the LorisMenu table > . > Doing this for any parent menu records e.g. Clinical, Reports or Tools, > should remove them from the top Menu Bar. > best, > Christine > > On Tue, Oct 15, 2019 at 7:13 AM Sotirios Nikoloutsopoulos < > sotirisnik at gmail.com> wrote: > >> Hi, >> >> In which files can i modify the bar of the GUI? Specifically i would like >> to remove Clinical, Reports and Tools >> >> >> [image: image.png] >> >> and from the Admin tab i would like to remove the marked options. >> >> [image: image.png] >> >> Thanks, >> >> Sotirios >> _______________________________________________ >> Loris-dev mailing list >> Loris-dev at bic.mni.mcgill.ca >> https://mailman.bic.mni.mcgill.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: 2916 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 6111 bytes Desc: not available URL: From sotirisnik at gmail.com Wed Oct 16 10:34:57 2019 From: sotirisnik at gmail.com (Sotirios Nikoloutsopoulos) Date: Wed, 16 Oct 2019 17:34:57 +0300 Subject: [Loris-dev] Quality Control form Message-ID: Hi, I can't load the page for quality_control. I get the following error in the loris-error.log, but in short the problem is "Table 'LORIS.mri_parameter_form doesn' exist" [image: image.png] [php7:error] [pid 6207] [client 127.0.0.1:41234] PHP Fatal error: Uncaught DatabaseException: Table 'LORIS.mri_parameter_form' doesn't exist in /var/www/loris/php/libraries/Database.class.inc:707\nStack trace:\n#0 /var/www/loris/php/libraries/Database.class.inc(739): Database->execute(Object(PDOStatement), Array)\n#1 /var/www/loris/php/libraries/NDB_Menu_Filter.class.inc(840): Database->pselect('SELECT PSCID, S...', Array)\n#2 /var/www/loris/php/libraries/NDB_Menu_Filter.class.inc(776): NDB_Menu_Filter->_getFullList()\n#3 /var/www/loris/php/libraries/NDB_Menu_Filter.class.inc(805): NDB_Menu_Filter->toArray()\n#4 /var/www/loris/php/libraries/NDB_Menu_Filter.class.inc(678): NDB_Menu_Filter->toJSON()\n#5 /var/www/loris/php/libraries/NDB_Page.class.inc(676): NDB_Menu_Filter->display()\n#6 /var/www/loris/php/libraries/NDB_Page.class.inc(655): NDB_Page->handle(Object(Zend\\Diactoros\\ServerRequest))\n#7 /var/www/loris/php/libraries/Module.class.inc(341): NDB_Page->process(Object(Zend\\Diactoros\\ServerRequest), Object(LORIS\\quality_control\\Quality_Control))\n#8 /var/www/loris/src/Middleware/Re in /var/www/loris/php/libraries/Database.class.inc on line 707, referer: http://localhost/quality_control/ Thank you, Sotirios -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 14637 bytes Desc: not available URL: From dave.macfarlane at mcin.ca Wed Oct 16 11:28:48 2019 From: dave.macfarlane at mcin.ca (Dave MacFarlane) Date: Wed, 16 Oct 2019 11:28:48 -0400 Subject: [Loris-dev] Quality Control form In-Reply-To: References: Message-ID: Hi Sotirios, The mri_parameter_form is an instrument that some LORIS modules assume exist, in the case of the quality control module to check whether there should be a scan inserted and compare it against whether or not there is a scan there. You should create an instrument named "mri_parameter_form" with questions such as "X_Scan_Done" for each scan type "X" (ie. T1, T2) that you have in your protocol (the "X" should match the mri_scan_types) and install it the same way as any other instrument. There are a few places (such as the quality control module, or some links in the imaging browser) that assume an instrument named that with questions of that form exist. - Dave On Wed, Oct 16, 2019 at 10:35 AM Sotirios Nikoloutsopoulos < sotirisnik at gmail.com> wrote: > Hi, > > I can't load the page for quality_control. I get the following error in > the loris-error.log, but in short the problem is "Table > 'LORIS.mri_parameter_form doesn' exist" > > [image: image.png] > > [php7:error] [pid 6207] [client 127.0.0.1:41234] PHP Fatal error: > Uncaught DatabaseException: Table 'LORIS.mri_parameter_form' doesn't exist > in /var/www/loris/php/libraries/Database.class.inc:707\nStack trace:\n#0 > /var/www/loris/php/libraries/Database.class.inc(739): > Database->execute(Object(PDOStatement), Array)\n#1 > /var/www/loris/php/libraries/NDB_Menu_Filter.class.inc(840): > Database->pselect('SELECT PSCID, S...', Array)\n#2 > /var/www/loris/php/libraries/NDB_Menu_Filter.class.inc(776): > NDB_Menu_Filter->_getFullList()\n#3 > /var/www/loris/php/libraries/NDB_Menu_Filter.class.inc(805): > NDB_Menu_Filter->toArray()\n#4 > /var/www/loris/php/libraries/NDB_Menu_Filter.class.inc(678): > NDB_Menu_Filter->toJSON()\n#5 > /var/www/loris/php/libraries/NDB_Page.class.inc(676): > NDB_Menu_Filter->display()\n#6 > /var/www/loris/php/libraries/NDB_Page.class.inc(655): > NDB_Page->handle(Object(Zend\\Diactoros\\ServerRequest))\n#7 > /var/www/loris/php/libraries/Module.class.inc(341): > NDB_Page->process(Object(Zend\\Diactoros\\ServerRequest), > Object(LORIS\\quality_control\\Quality_Control))\n#8 > /var/www/loris/src/Middleware/Re in > /var/www/loris/php/libraries/Database.class.inc on line 707, referer: > http://localhost/quality_control/ > > Thank you, > > Sotirios > _______________________________________________ > 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: image.png Type: image/png Size: 14637 bytes Desc: not available URL: From rida.abou-haidar at mcin.ca Wed Oct 30 13:47:43 2019 From: rida.abou-haidar at mcin.ca (Rida Abou-Haidar) Date: Wed, 30 Oct 2019 13:47:43 -0400 Subject: [Loris-dev] LORIS 22.0.0 testing round CANCELLED Message-ID: Hi everyone, Due to some unforeseen circumstances with branch maintenance. The testing round scheduled for this afternoon will be postponed to tomorrow afternoon. Sorry for the inconvenience. See y'all tomorrow, Rida Abou-Haidar CCNA Software Developer Montreal Neurological Institute McGill University rida.abou-haidar at mcin.ca -------------- next part -------------- An HTML attachment was scrubbed... URL: From rida.abou-haidar at mcin.ca Wed Oct 30 14:32:41 2019 From: rida.abou-haidar at mcin.ca (Rida Abou-Haidar) Date: Wed, 30 Oct 2019 14:32:41 -0400 Subject: [Loris-dev] LORIS 22.0.0 testing round CANCELLED In-Reply-To: References: Message-ID: Hi LORIS Dev users, Sorry this email was intended to be sent only to internal developers. please ignore it. Thank you, Rida Abou-Haidar CCNA Software Developer Montreal Neurological Institute McGill University rida.abou-haidar at mcin.ca On Wed, Oct 30, 2019 at 1:47 PM Rida Abou-Haidar wrote: > Hi everyone, > > Due to some unforeseen circumstances with branch maintenance. The testing > round scheduled for this afternoon will be postponed to tomorrow afternoon. > > Sorry for the inconvenience. > > See y'all tomorrow, > Rida Abou-Haidar > CCNA Software Developer > Montreal Neurological Institute > McGill University > rida.abou-haidar at mcin.ca > -------------- next part -------------- An HTML attachment was scrubbed... URL: