[Loris-dev] Import mri - scripts
Sotirios Nikoloutsopoulos
sotirisnik at gmail.com
Thu Jul 25 11:42:58 EDT 2019
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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Running now the following command: /data/loris/data/uploadNeuroDB/imaging_upload_file.pl -profile prod -upload_id 4 /data/incoming/DCC0000_258024_V01.tar.gz -verbose
find -path \/tmp\/ImagingUpload\-18\-24\-Tn9fQY -name '__MACOSX' -delete
/data/loris/bin/mri/dicom-archive/dicomTar.pl /tmp/ImagingUpload-18-24-Tn9fQY /data/loris/data/tarchive/ -clobber -database -profile prod -verbose
Source: /tmp/ImagingUpload-18-24-Tn9fQY
Target: /data/loris/data/tarchive
Testing for database connectivity.
Database is available.
You will archive the dir : ImagingUpload-18-24-Tn9fQY
You are creating a tar with the following command:
tar -cf /data/loris/data/tarchive/ImagingUpload-18-24-Tn9fQY.tar ImagingUpload-18-24-Tn9fQY
getting md5sums and gzipping!!
* Taken from dir : /tmp/ImagingUpload-18-24-Tn9fQY
* Archive target location : /data/loris/data/tarchive/DCM_2012-12-05_ImagingUpload-18-24-Tn9fQY.tar
* Name of creating host : 127.0.1.1
* Name of host OS : Linux
* Created by user : lorisadmin
* Archived on : 2019-07-25 18:24:43
* dicomSummary version : 1
* dicomTar version : 1
* md5sum for DICOM tarball : d5d7701c95f54efbdb745b358ce7c133 ImagingUpload-18-24-Tn9fQY.tar
* md5sum for DICOM tarball gzipped : 757a3d2ba29f885ea5dc0902e2a5cc62 ImagingUpload-18-24-Tn9fQY.tar.gz
* md5sum for complete archive : f7940af43992811324440d8153942654 DCM_2012-12-05_ImagingUpload-18-24-Tn9fQY.tar
Adding archive info into database
Removing temporary files from target location
Done adding archive info into database
/data/loris/bin/mri/uploadNeuroDB/tarchiveLoader -globLocation -profile prod /data/loris/data/tarchive//DCM_2012-12-05_ImagingUpload-18-24-Tn9fQY.tar -verbose
md5sum /data/loris/data/tarchive/DCM_2012-12-05_ImagingUpload-18-24-Tn9fQY.tar
PSCID is: DCC0000
CandID id: 258024
visit_label is: V01
Spool message is:
ERROR: No center found for this candidate
PSCID is: DCC0000
CandID id: 258024
visit_label is: V01
PSCID is: DCC0000
CandID id: 258024
visit_label is: V01
Number of MINC files that will be considered for inserting into the database: 1
log dir is /data/loris/data//logs and log file is /data/loris/data//logs/TarLoad-18-24-9_GgGT.log
PSCID is: DCC0000
CandID id: 258024
visit_label is: V01
PSCID is: DCC0000
CandID id: 258024
visit_label is: V01
candidate id 258024
=> No Visit label
Cleaning up temp files: rm -rf /tmp/TarLoad-18-24-hzcram/ImagingUpload-18-24-Tn9fQY*
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