[Loris-dev] Import mri - scripts
Sotirios Nikoloutsopoulos
sotirisnik at gmail.com
Tue Jul 30 09:50:57 EDT 2019
Hi,
there was no visit label 01 in the Visit_Windows table and i don't know how
to insert it because the record requires lots of attributes. Also the
system for a reason asked me to update my password and now i don't remember
it and my account got suspended. Is there a way to reset it or set a simple
password? I updated the password hash in the users table by using the hash
from another LORIS setup we had and i still couldn't login ( also the
attribute password is always NULL and the expiration date is 1999-01-01 for
some reason ).
Thanks
Στις Δευ, 29 Ιουλ 2019 στις 5:21 μ.μ., ο/η Cecile Madjar <
cecile.madjar at mcin.ca> έγραψε:
> Hi Sotirios,
>
> Can you try adding the visit label v01 to the Visit_Windows table?
>
> However, I noticed that in a previous dataset, the label was V1. Does that
> refer to the same visit? If so, you might want to harmonize the visit
> labels so they are all the same across datasets for a given timepoint,
> meaning you will need to relabel scans when the visit label is different
> but referring to the same visit label (v01 = V1 etc...).
>
> Hope this helps,
>
> Cécile
>
> On Mon, Jul 29, 2019 at 10:15 AM Sotirios Nikoloutsopoulos <
> sotirisnik at gmail.com> wrote:
>
>> Hi,
>>
>> Could you help me with the "Visit label does not exist"? I had changed
>> $subjectID{'createVisitLabel'} to 1 as you had suggested but it appears
>> that this problem hasn't been resolved yet.
>>
>> lorisadmin at hbp:/data/loris/bin/mri$ cat
>> /data/loris/data//logs/TarLoad-14-58-9Xog7H.log
>>
>> ==> Loading file from disk
>> /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc
>>
>> --> mapping DICOM parameter for
>> /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc
>>
>> --> using user-defined filterParameters for
>> /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc
>>
>> Candidate Mismatch Error is Visit label does not exist
>> -> WARNING: This candidate was invalid. Logging to
>> MRICandidateErrors table with reason Visit label does not
>> exist
>>
>> Thank you,
>>
>> Sotirios
>>
>> Στις Παρ, 26 Ιουλ 2019 στις 3:02 μ.μ., ο/η Sotirios Nikoloutsopoulos <
>> sotirisnik at gmail.com> έγραψε:
>>
>>> Hi Cecile,
>>>
>>> The Center error was fixed. Still the insertion of mincs fails. Please
>>> see the output.txt file i attached. Also is there something else i need to
>>> change at the paths configuration?
>>>
>>> Thank you,
>>>
>>> Sotirios
>>>
>>> Στις Πέμ, 25 Ιουλ 2019 στις 6:55 μ.μ., ο/η Cecile Madjar <
>>> cecile.madjar at mcin.ca> έγραψε:
>>>
>>>> Hi Sotirios,
>>>>
>>>> We are making progress!
>>>>
>>>> I have a feeling this error comes from the fact that your psc table
>>>> does not have the MRI_alias populated for the DCC site. Running the
>>>> following query in the mysql database should fix this:
>>>> UPDATE psc SET MRI_alias="DCC", Alias="DCC" WHERE Name="Data
>>>> Coordinating Center";
>>>> Repeat the same with all your sites (make sure to change the Aliases
>>>> between sites, they should all be unique).
>>>>
>>>> Let me know how it goes!
>>>> Best,
>>>>
>>>> Cécile
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> On Thu, Jul 25, 2019 at 11:43 AM Sotirios Nikoloutsopoulos <
>>>> sotirisnik at gmail.com> wrote:
>>>>
>>>>> Dear Cecile,
>>>>> You were right about your guesses. I did the modifications you
>>>>> suggested, i still get the "no mincs inserted" error, now i am getting the
>>>>> "No center found this candidate" error ( how do i fix that? from what i see
>>>>> the .dcm files contains a 'Institution Name', is that the center? ), so i
>>>>> guess that's why the validation fails, but i changed the force variable of
>>>>> tarchiveLoader to 1, shouldn't it have inserted the mincs then? Also it is
>>>>> optional to have a mail server, right? ( from what i see the mail error
>>>>> does not affect the $valid_study, so i assume we are okay with that )
>>>>> Thank you a lot,
>>>>> Sotirios
>>>>>
>>>>> Στις Πέμ, 25 Ιουλ 2019 στις 5:48 μ.μ., ο/η Cecile Madjar <
>>>>> cecile.madjar at mcin.ca> έγραψε:
>>>>>
>>>>>> Hi Sotirios,
>>>>>>
>>>>>> From what I understand, I believe you just need to update a few
>>>>>> config settings from the frontend in the Config module (under the Admin
>>>>>> menu).
>>>>>> [image: Screen Shot 2019-07-25 at 10.31.35 AM.png]
>>>>>>
>>>>>> Then go to the Paths section of the config module and update the
>>>>>> "LORIS-MRI code" config setting to /data/loris/bin/mri (my guess is that
>>>>>> currently, it is set to /data/LORIS/data) and click on the submit button.
>>>>>> [image: Screen Shot 2019-07-25 at 10.32.50 AM.png]
>>>>>>
>>>>>> Then, go to Imaging Pipeline section of the Configuration module and
>>>>>> update the "Loris-MRI Data Directory" to /data/loris/data/ (my guess is
>>>>>> that it is empty at the moment in your database which is why $data_dir is
>>>>>> not defined when you run the tarchiveLoader step of the insertion pipeline).
>>>>>> [image: Screen Shot 2019-07-25 at 10.40.52 AM.png]
>>>>>>
>>>>>> Finally, I took a look at your environment file and it might be a
>>>>>> good idea to update your PERL5LIB variable to the following (it has been
>>>>>> added to the code a few releases ago as we realized this was needed for the
>>>>>> libraries. Not sure which version of LORIS-MRI you are using but it does
>>>>>> not hurt to update this variable to what I suggest below):
>>>>>> export
>>>>>> PERL5LIB=/data/loris/bin/mri/uploadNeuroDB:/data/loris/bin/mri/dicom-archive:$PERL5LIB
>>>>>>
>>>>>> Hope this helps. Sorry you are experiencing so much trouble setting
>>>>>> things up. We probably need to update our WIKI.
>>>>>>
>>>>>> Best,
>>>>>>
>>>>>> Cécile
>>>>>>
>>>>>> On Thu, Jul 25, 2019 at 9:48 AM Sotirios Nikoloutsopoulos <
>>>>>> sotirisnik at gmail.com> wrote:
>>>>>>
>>>>>>> The "Loris-MRI Data Directory" should be in the environment file?
>>>>>>>
>>>>>>> Στις Πέμ, 25 Ιουλ 2019 στις 12:59 π.μ., ο/η Sotirios
>>>>>>> Nikoloutsopoulos <sotirisnik at gmail.com> έγραψε:
>>>>>>>
>>>>>>>> The scripts are located in /data/loris/bin/mri/. Somewhere I might
>>>>>>>> have messed something up but i remember following the instructions in the
>>>>>>>> wiki.For example when i tried to execute the batch_uploads_imageuploader
>>>>>>>> perl script the line
>>>>>>>>
>>>>>>>> my $command = "$bin_dir/uploadNeuroDB/imaging_upload_file.pl "
>>>>>>>>
>>>>>>>> was pointing to an invalid path, for example: it was repeating a
>>>>>>>> pattern and had LORIS instead of loris ( i think the mistake was that in
>>>>>>>> the wiki it suggested to use $PROJECT for the name of the folder and i
>>>>>>>> choosed 'loris'
>>>>>>>> https://github.com/aces/Loris/wiki/Imaging-Database ). See also
>>>>>>>> the in image for the modification i did. Also i didn't find the section to
>>>>>>>> config the $data_dir variable.
>>>>>>>>
>>>>>>>> Thank you,
>>>>>>>>
>>>>>>>> Sotirios
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> Στις Τετ, 24 Ιουλ 2019 στις 6:05 μ.μ., ο/η Cecile Madjar <
>>>>>>>> cecile.madjar at mcin.ca> έγραψε:
>>>>>>>>
>>>>>>>>> Hi Sotirios,
>>>>>>>>>
>>>>>>>>> It looks like you have one Config setting not set (based on the
>>>>>>>>> first error message you got when running it the first time). You need to
>>>>>>>>> set a value for "Loris-MRI Data Directory" in the Config module under the
>>>>>>>>> Imaging pipeline section (from what I can see, it would be
>>>>>>>>> /data/loris/data/ for your setup).
>>>>>>>>>
>>>>>>>>> The reason you got that error message the second time is that the
>>>>>>>>> pipeline checks if the DICOM study was already inserted in the tarchive
>>>>>>>>> table. Since you ran the study once already, the study is inserted into the
>>>>>>>>> tarchive, hence the message. However, the pipeline did not complete as the
>>>>>>>>> MINC files were not created and inserted into the files/parameter_file
>>>>>>>>> table. In order to continue the insertion, you will then need to run the
>>>>>>>>> tarchiveLoader command suggested in the terminal during the second run:
>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader -globLocation
>>>>>>>>> -profile prod
>>>>>>>>> /data/loris/data/tarchive//2012/DCM_2012-12-05_ImagingUpload-17-43-ZUEFjb.tar
>>>>>>>>> -verbose
>>>>>>>>>
>>>>>>>>> Finally, I am a bit confused by your setup. Where are the scripts
>>>>>>>>> located? In /data/loris/bin/mri or /data/loris/data? It feels like the
>>>>>>>>> Config setting "LORIS-MRI code" in the Paths section was set to
>>>>>>>>> "/data/LORIS/data" but it should have been set to the directory where the
>>>>>>>>> scripts are located (most probably /data/loris/bin/mri).
>>>>>>>>>
>>>>>>>>> Hope this helps,
>>>>>>>>>
>>>>>>>>> Cécile
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> On Wed, Jul 24, 2019 at 10:55 AM Sotirios Nikoloutsopoulos <
>>>>>>>>> sotirisnik at gmail.com> wrote:
>>>>>>>>>
>>>>>>>>>> Ok first i execute this command:
>>>>>>>>>>
>>>>>>>>>> "lorisadmin at hbp:/data/loris/bin/mri$
>>>>>>>>>> ./batch_uploads_imageuploader -profile prod < ~/Desktop/input.txt > log.txt
>>>>>>>>>> Use of uninitialized value $data_dir in concatenation (.) or
>>>>>>>>>> string at ./batch_uploads_imageuploader line 143.
>>>>>>>>>> Use of uninitialized value $data_dir in concatenation (.) or
>>>>>>>>>> string at ./batch_uploads_imageuploader line 143.
>>>>>>>>>> Use of uninitialized value $_ in pattern match (m//) at
>>>>>>>>>> ./batch_uploads_imageuploader line 147.
>>>>>>>>>> base is DCC0000_258024_V01
>>>>>>>>>> path is /data/incoming/
>>>>>>>>>> type is .tar.gz
>>>>>>>>>> fullpath is /data/incoming/DCC0000_258024_V01.tar.gz
>>>>>>>>>>
>>>>>>>>>> source /tmp/ImagingUpload-17-43-ZUEFjb
>>>>>>>>>> targetlocation /data/loris/data/tarchive
>>>>>>>>>>
>>>>>>>>>> Use of uninitialized value $data_dir in concatenation (.) or
>>>>>>>>>> string at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 256.
>>>>>>>>>> Use of uninitialized value $data_dir in concatenation (.) or
>>>>>>>>>> string at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 284.
>>>>>>>>>> Use of uninitialized value $data_dir in concatenation (.) or
>>>>>>>>>> string at /data/loris/bin/mri/uploadNeuroDB/
>>>>>>>>>> tarchive_validation.pl line 219.
>>>>>>>>>> Use of uninitialized value $data_dir in concatenation (.) or
>>>>>>>>>> string at /data/loris/bin/mri/uploadNeuroDB/minc_insertion.pl
>>>>>>>>>> line 270.
>>>>>>>>>> Use of uninitialized value $data_dir in concatenation (.) or
>>>>>>>>>> string at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 711.
>>>>>>>>>> Can't exec "mail": No such file or directory at
>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 721.
>>>>>>>>>> print() on closed filehandle MAIL at
>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 722.
>>>>>>>>>> print() on closed filehandle MAIL at
>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 723.
>>>>>>>>>> Use of uninitialized value $data_dir in concatenation (.) or
>>>>>>>>>> string at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 724.
>>>>>>>>>> print() on closed filehandle MAIL at
>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 724.
>>>>>>>>>> print() on closed filehandle MAIL at
>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 725.
>>>>>>>>>> Use of uninitialized value $data_dir in concatenation (.) or
>>>>>>>>>> string at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 735.
>>>>>>>>>>
>>>>>>>>>> No Mincs inserted
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> The tarchiveLoader insertion script has failed.
>>>>>>>>>> Running now the following command: /data/loris/data/uploadNeuroDB/
>>>>>>>>>> imaging_upload_file.pl -profile prod -upload_id 3
>>>>>>>>>> /data/incoming/DCC0000_258024_V01.tar.gz -verbose"
>>>>>>>>>>
>>>>>>>>>> I inserted the VisitLabel, but still the Mincs are not inserted
>>>>>>>>>> and i am getting this error
>>>>>>>>>>
>>>>>>>>>> "lorisadmin at hbp:/data/loris/bin/mri$
>>>>>>>>>> /data/loris/data/uploadNeuroDB/imaging_upload_file.pl -profile
>>>>>>>>>> prod -upload_id 3 /data/incoming/DCC0000_258024_V01.tar.gz -verbose
>>>>>>>>>>
>>>>>>>>>> find -path \/tmp\/ImagingUpload\-17\-45\-5MsWEd -name '__MACOSX'
>>>>>>>>>> -delete
>>>>>>>>>> Spool message is:
>>>>>>>>>> The Scan for the uploadID 3 has already been run with tarchiveID:
>>>>>>>>>> 7.
>>>>>>>>>> To continue with the rest of the insertion pipeline, please run
>>>>>>>>>> tarchiveLoader from a terminal as follows:
>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader -globLocation -profile prod
>>>>>>>>>> /data/loris/data/tarchive//2012/DCM_2012-12-05_ImagingUpload-17-43-ZUEFjb.tar
>>>>>>>>>> -verbose"
>>>>>>>>>>
>>>>>>>>>> Which files should i delete? I thought that deleting the files
>>>>>>>>>> from the tarchive was enough. And i executed the last proposed command to
>>>>>>>>>> continue to rest of the insertion pipeline ( check the image ).
>>>>>>>>>>
>>>>>>>>>> Thank you
>>>>>>>>>>
>>>>>>>>>> Στις Τετ, 24 Ιουλ 2019 στις 5:05 μ.μ., ο/η Cecile Madjar <
>>>>>>>>>> cecile.madjar at mcin.ca> έγραψε:
>>>>>>>>>>
>>>>>>>>>>> Hi Sotirios,
>>>>>>>>>>>
>>>>>>>>>>> Sorry I was not clear before. Every visits of candidates are
>>>>>>>>>>> created in the session table with one entry per CandID/VisitLabel. So if
>>>>>>>>>>> the imaging pipeline created visits in the session table (that are not
>>>>>>>>>>> attached to instruments) and you want to clean your database completely,
>>>>>>>>>>> you can delete entries in that table as well.
>>>>>>>>>>>
>>>>>>>>>>> Regarding your point 2, the imaging pipeline can create the
>>>>>>>>>>> visit in the session table as long as the visit label is present in the
>>>>>>>>>>> Visit_Windows table (which means the visit label stored in the PatientName
>>>>>>>>>>> is a valid visit label).
>>>>>>>>>>> However, in your prod file, if the
>>>>>>>>>>> variable $subjectID{'createVisitLabel'} is set to 1 for candidates, the
>>>>>>>>>>> visit label should be created in the Visit_Windows table I believe. Here
>>>>>>>>>>> is the line of the prod file you would need to change
>>>>>>>>>>> <https://github.com/aces/Loris-MRI/blob/81bae73ea6e86c9498519dadf574468ee1d992ca/dicom-archive/profileTemplate.pl#L59>
>>>>>>>>>>> .
>>>>>>>>>>> In general, we prefer populating the Visit_Windows table and set
>>>>>>>>>>> the $subjectID{'createVisitLabel'} to 0 for candidate data to avoid
>>>>>>>>>>> insertion of badly labelled MRI data that are complex to relabel.
>>>>>>>>>>>
>>>>>>>>>>> Finally, regarding the candidate creation, if you execute the
>>>>>>>>>>> following steps, the pipeline should be able to create candidates:
>>>>>>>>>>> - set in the Imaging Pipeline section of the config module the
>>>>>>>>>>> config setting "Upload creation of candidates" to Yes
>>>>>>>>>>> - manually transfer the scans to the LORIS server instead of
>>>>>>>>>>> uploading it via the imaging browser
>>>>>>>>>>> - run batch_imaging_upload.pl as you did until now.
>>>>>>>>>>>
>>>>>>>>>>> Hope this helps!
>>>>>>>>>>> Best,
>>>>>>>>>>>
>>>>>>>>>>> Cécile
>>>>>>>>>>>
>>>>>>>>>>> On Wed, Jul 24, 2019 at 8:47 AM Sotirios Nikoloutsopoulos <
>>>>>>>>>>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>
>>>>>>>>>>>> About my second question i replaced the name of the patient in
>>>>>>>>>>>> the .dcm files and now i am getting an error that the visit label does not
>>>>>>>>>>>> exist.
>>>>>>>>>>>> I thought it was supposed to be automatically created.
>>>>>>>>>>>>
>>>>>>>>>>>> "Done adding archive info into database
>>>>>>>>>>>>
>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader -globLocation
>>>>>>>>>>>> -profile prod
>>>>>>>>>>>> /data/loris/data/tarchive//DCM_2012-12-05_ImagingUpload-15-42-yUwQQV.tar
>>>>>>>>>>>> -verbose
>>>>>>>>>>>> md5sum
>>>>>>>>>>>> /data/loris/data/tarchive/DCM_2012-12-05_ImagingUpload-15-42-yUwQQV.tar
>>>>>>>>>>>> PSCID is: DCC0000
>>>>>>>>>>>> CandID id: 258024
>>>>>>>>>>>> visit_label is: V1
>>>>>>>>>>>> PSCID is: DCC0000
>>>>>>>>>>>> CandID id: 258024
>>>>>>>>>>>> visit_label is: V1
>>>>>>>>>>>> candidate id 258024
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> => No Visit labelVisit label does not exist
>>>>>>>>>>>> Set centerID = 1
>>>>>>>>>>>> PSCID is: DCC0000
>>>>>>>>>>>> CandID id: 258024
>>>>>>>>>>>> visit_label is: V1
>>>>>>>>>>>> PSCID is: DCC0000
>>>>>>>>>>>> CandID id: 258024
>>>>>>>>>>>> visit_label is: V1
>>>>>>>>>>>>
>>>>>>>>>>>> Number of MINC files that will be considered for inserting into
>>>>>>>>>>>> the database: 1
>>>>>>>>>>>>
>>>>>>>>>>>> log dir is /logs and log file is /logs/TarLoad-15-42-L6pocU.log
>>>>>>>>>>>> PSCID is: DCC0000
>>>>>>>>>>>> CandID id: 258024
>>>>>>>>>>>> visit_label is: V1
>>>>>>>>>>>> PSCID is: DCC0000
>>>>>>>>>>>> CandID id: 258024
>>>>>>>>>>>> visit_label is: V1
>>>>>>>>>>>> candidate id 258024
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> => No Visit label
>>>>>>>>>>>> Cleaning up temp files: rm -rf
>>>>>>>>>>>> /tmp/TarLoad-15-42-J2rQms/ImagingUpload-15-42-yUwQQV*"
>>>>>>>>>>>>
>>>>>>>>>>>> Στις Τετ, 24 Ιουλ 2019 στις 3:38 μ.μ., ο/η Sotirios
>>>>>>>>>>>> Nikoloutsopoulos <sotirisnik at gmail.com> έγραψε:
>>>>>>>>>>>>
>>>>>>>>>>>>> Hi,
>>>>>>>>>>>>>
>>>>>>>>>>>>> 1) What are the records in the session table?
>>>>>>>>>>>>>
>>>>>>>>>>>>> 2) I tried to upload a non-phantom file like this
>>>>>>>>>>>>>
>>>>>>>>>>>>> input_file.txt:
>>>>>>>>>>>>> /data/incoming/DCC0000_258024_V1.tar.gz N DCC0000_258024_V1
>>>>>>>>>>>>>
>>>>>>>>>>>>> Terminal:
>>>>>>>>>>>>> ./batch_uploads_imageuploader -profile prod <
>>>>>>>>>>>>> ~/Desktop/input.txt > log.txt
>>>>>>>>>>>>>
>>>>>>>>>>>>> and i get the following error in the log.txt file
>>>>>>>>>>>>>
>>>>>>>>>>>>> "Running now the following command:
>>>>>>>>>>>>> /data/loris/data/uploadNeuroDB/imaging_upload_file.pl
>>>>>>>>>>>>> -profile prod -upload_id 7 /data/incoming/DCC0000_258024_V1.tar.gz -verbose
>>>>>>>>>>>>>
>>>>>>>>>>>>> find -path \/tmp\/ImagingUpload\-14\-56\-FeLCB4 -name
>>>>>>>>>>>>> '__MACOSX' -delete
>>>>>>>>>>>>> Spool message is:
>>>>>>>>>>>>> The PatientName read from the DICOM header does not start with
>>>>>>>>>>>>> DCC0000_258024_V1 from the mri_upload table
>>>>>>>>>>>>> "
>>>>>>>>>>>>>
>>>>>>>>>>>>> and the spool message is repeated for each .dcm file. Should i
>>>>>>>>>>>>> preprocess every .dcm file and change the PatientName to
>>>>>>>>>>>>> "DCC0000_258024_V1"?
>>>>>>>>>>>>>
>>>>>>>>>>>>> 3) As far as it concerns the candidate profile i have to
>>>>>>>>>>>>> create a new one each time before i try to upload a file? Is there already
>>>>>>>>>>>>> a way to create a candidate profile and get the DCCID and PSCID without the
>>>>>>>>>>>>> user interface?
>>>>>>>>>>>>>
>>>>>>>>>>>>> Thank you,
>>>>>>>>>>>>>
>>>>>>>>>>>>> Sotirios
>>>>>>>>>>>>>
>>>>>>>>>>>>> Στις Πέμ, 18 Ιουλ 2019 στις 5:00 μ.μ., ο/η Cecile Madjar <
>>>>>>>>>>>>> cecile.madjar at mcin.ca> έγραψε:
>>>>>>>>>>>>>
>>>>>>>>>>>>>> Hi Sotirios,
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> See answers to your questions below.
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> About the 1st case we had a dicom with a blank studyUID,
>>>>>>>>>>>>>>> maybe someone accidentally removed it.
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>> That is strange. Something must have been done to the DICOM
>>>>>>>>>>>>>> files. I have never seen a study with no StudyUID out of the scanner.
>>>>>>>>>>>>>> Usually, you need to manually erase it with some tool. However, DICOMs
>>>>>>>>>>>>>> never cease to surprise me...
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Some other questions:
>>>>>>>>>>>>>>> 1) What are the steps to remove all of my patients and
>>>>>>>>>>>>>>> uploads?: because i want to try to reupload all the testing dicoms we had
>>>>>>>>>>>>>>> with a clean database.
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Release 21.0 of LORIS-MRI will offer a script to remove all
>>>>>>>>>>>>>> the entries and files specific to an upload. However, this release is not
>>>>>>>>>>>>>> yet out. Hopefully in the next few weeks.
>>>>>>>>>>>>>> In the meantime, since your case is particular and that you
>>>>>>>>>>>>>> just want to start with a clean database, the following deletes should work
>>>>>>>>>>>>>> (hopefully I won't forget any tables):
>>>>>>>>>>>>>> delete from mri_violations_log;
>>>>>>>>>>>>>> delete from mri_protocol_violated_scans;
>>>>>>>>>>>>>> delete from MRICandidateErrors;
>>>>>>>>>>>>>> delete from parameter_file;
>>>>>>>>>>>>>> delete from files_qcstatus; # (if you played with the QC part
>>>>>>>>>>>>>> of the imaging browser for testing)
>>>>>>>>>>>>>> delete from feedback_mri_comments; # (if you played with the
>>>>>>>>>>>>>> QC part of the imaging browser for testing)
>>>>>>>>>>>>>> delete from tarchive_series;
>>>>>>>>>>>>>> delete from tarchive_files;
>>>>>>>>>>>>>> delete from mri_upload;
>>>>>>>>>>>>>> delete from tarchive;
>>>>>>>>>>>>>> delete from mri_scanner;
>>>>>>>>>>>>>> delete from candidate where PSCID="scanner";
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> I don't know if you want to also delete entries in the
>>>>>>>>>>>>>> session and candidate table too?
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> 2) We do not need to create the profile of a patient ( are
>>>>>>>>>>>>>>> the patients stored in the candidate table? because i can't see the ghosts
>>>>>>>>>>>>>>> ), because will it automatically be created when importing a dicom?
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> I am not sure I understand fully this question. All
>>>>>>>>>>>>>> candidates are stored in the candidate table. The phantom scans however are
>>>>>>>>>>>>>> attached to a scanner candidate depending on where the scan happened. It is
>>>>>>>>>>>>>> a bit of a weird concept that we have to redesign eventually but never got
>>>>>>>>>>>>>> a chance to get to it.
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Hopefully this answered your question, otherwise, don't
>>>>>>>>>>>>>> hesitate to let me know.
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> 3) What is the difference between uploading a dicom as
>>>>>>>>>>>>>>> phantom instead of importing as PSCCID_DCCID_VisitLabel?
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> When you upload the scan as PSCID_DCCID_VisitLabel, there is
>>>>>>>>>>>>>> a check that makes sure the candidate IDs and visit label are valid at the
>>>>>>>>>>>>>> time of upload.
>>>>>>>>>>>>>> When you upload a scan as phantom, it expects that the DICOM
>>>>>>>>>>>>>> field PatientName and uploaded filename contains the string "phantom". We
>>>>>>>>>>>>>> enforced this behaviour on the imaging uploader side in recent releases but
>>>>>>>>>>>>>> I can't remember which one. Probably the upcoming 21.0 release.
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> All those verifications might seem cumbersome but they are
>>>>>>>>>>>>>> here to ensure that the files inserted are all valid and labelled properly
>>>>>>>>>>>>>> as it is a bit messy to have to delete files that were wrongly labelled. At
>>>>>>>>>>>>>> least, the delete script present in release 21.0 will make this process
>>>>>>>>>>>>>> easier but it is still good practice to verify those things.
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Thank you,
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> With pleasure. Hopefully the answers to your questions will
>>>>>>>>>>>>>> be helpful.
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Best,
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Cécile
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> PS: loris-dev mailing list: you will find the initial answer
>>>>>>>>>>>>>> I gave Sotirios below. I forgot to cc the loris-dev in my earlier reply...
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Στις Τρί, 16 Ιουλ 2019 στις 12:02 π.μ., ο/η Cecile Madjar <
>>>>>>>>>>>>>>> cecile.madjar at mcin.ca> έγραψε:
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> Dear Sotirios,
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> Thank you for reaching out. Since your email was already
>>>>>>>>>>>>>>>> organized in points, I will reply directly below your questions below.
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> Best,
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> Cécile
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> 1) What do we do when the StudyUID is blank on the header?
>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/minor/docs/AppendixA-Troubleshooting_guideline.md
>>>>>>>>>>>>>>>>> There solution provided at the table 3 does not guide us how to find the
>>>>>>>>>>>>>>>>> information ( is possible ).
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> The StudyUID is the field used in our pipeline at the
>>>>>>>>>>>>>>>> moment to check whether a DICOM study was already inserted into LORIS with
>>>>>>>>>>>>>>>> that same StudyUID since it is supposed to be unique for every single
>>>>>>>>>>>>>>>> study. Currently, we do not support insertion of DICOM studies if they do
>>>>>>>>>>>>>>>> not have a StudyUID associated with them.
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> Is there a specific reason why the StudyUID is blank in the
>>>>>>>>>>>>>>>> DICOM headers in your DICOM files? Did they go through some processes
>>>>>>>>>>>>>>>> before upload to LORIS?
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> 2) When i am about to upload a non-phanton case i need a
>>>>>>>>>>>>>>>>> 'Visit Label'. Is there already a script that can create a new visit label
>>>>>>>>>>>>>>>>> for a specific Candidate, so i can provide it as input afterwards to the
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> batch_uploads_imageuploader ( See option 5.1.3 https://github.com/aces/Loris-MRI/blob/minor/docs/05-PipelineLaunchOptions.md )
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> I am not sure if the front-end allows for it but if you use
>>>>>>>>>>>>>>>> batch_uploads_imageuploader, the insertion scripts could create the visit
>>>>>>>>>>>>>>>> label for you. However, it does need to be included in the patient name in
>>>>>>>>>>>>>>>> order for the script to know which label it should use.
>>>>>>>>>>>>>>>> For example: you upload V02 for MTL0123 (DCCID: 456789)
>>>>>>>>>>>>>>>> but V02 was not yet created for MTL0123; the insertion scripts will create
>>>>>>>>>>>>>>>> a V02 visit for MTL0123 if the PatientName field for the dataset is
>>>>>>>>>>>>>>>> MTL0123_456789_V02 with Stage marked as "Not Started".
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> However, *note that for the script to create the visit for
>>>>>>>>>>>>>>>> the candidate, you have to make sure that all the visit label of your
>>>>>>>>>>>>>>>> projects were inserted in the Visit_Windows table*
>>>>>>>>>>>>>>>> (otherwise, the visit will never be created as they were not specified as
>>>>>>>>>>>>>>>> being part of the list of visit label to expect). So in the example above,
>>>>>>>>>>>>>>>> you should have one row in Visit_Windows with Visit_label="V02" set.
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> 3) Section 4.3
>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/minor/docs/04-Scripts.md
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> What do we do when the folder contains multiple mnc files?
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> This is a case by case. Most of the time, the MINC files
>>>>>>>>>>>>>>>> that failed insertion into the imaging browser end up in the MRI violation
>>>>>>>>>>>>>>>> module where you can see what went wrong with the acquisitions not
>>>>>>>>>>>>>>>> inserted. If you notice that the MINC file should be inserted as a specific
>>>>>>>>>>>>>>>> protocol, you can force the insertion as explained in section 4.3.
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> In your case, I have a feeling that you want to be able to
>>>>>>>>>>>>>>>> insert MINC files that did not go through the whole pipeline insertion
>>>>>>>>>>>>>>>> (DICOM archival, then dcm2mnc, then protocol identification, then
>>>>>>>>>>>>>>>> insertion...). In theory, you could call minc_insertion.pl
>>>>>>>>>>>>>>>> on any MINC file, provided you have at least the following information:
>>>>>>>>>>>>>>>> - path to the MINC file
>>>>>>>>>>>>>>>> - uploadID associated with the MINC files or DICOM archive
>>>>>>>>>>>>>>>> path from which those MINC files were created from
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> Then the minc_insertion.pl script will do the subject
>>>>>>>>>>>>>>>> information and protocol validation etc...
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> If all the MINC files come from the same uploadID or
>>>>>>>>>>>>>>>> TarchiveID, then you could run a loop in bash calling the
>>>>>>>>>>>>>>>> minc_insertion.pl script like this for files deriving from
>>>>>>>>>>>>>>>> uploadID=1:
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> ls /path/to/mnc/folder/* | while read f; do
>>>>>>>>>>>>>>>> minc_insertion.pl -profile prod -uploadID 1 -mincPath $f;
>>>>>>>>>>>>>>>> done
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> Thank you,
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> Hope this helped!
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
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