[Loris-dev] Import mri - scripts

Wed Jul 24 08:38:45 EDT 2019

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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