[Loris-dev] Create DCCID and Organizing CIVET outputs

[Mouna Safi-Harab]

Hi Michael,


Here are my answers to your questions:


1) Setting createCandidates to 1 in the prod file does indeed allow for creation of the candidate from the MRI pipeline. You will need to make sure that 1) the PatientName header is anonymized properly in the DICOM files, and 2) getSubjectIDs() function in this prod file is a) splitting the PatientName header information in a way that is consistent with the anonymization and your project DCCID/PSCID/VisitLabel convention, and b) has the $subjectID{'createVisitLabel'} option set to 1 as you will also likely need the MRI pipeline to create the visit for that candidate as well.

However, projects using the Imaging Uploader GUI unfortunately does not allow for this option. If you want a way to make it work for now, you can disable the check on Lines 378-395  in NDB_Menu_Filter_imaging_uploader.class.inc (which sole purpose is to check if the CandID is registered in the database). We can look at this from our end, and make sure the option createCandidate is propagated to the Imaging Uploader GUI as well in a seamless manner to the user (will discuss this at our internal meeting).


2) Loris-MRI codebase provides an example of how to insert files from another processing pipeline into the database. Check the DTIPrep/ directory for an example you can follow. Essentially, inserting processed files into LORIS is a two-step process: you will need a 1) wrapper script that "understands" or "knows" how/where the processed files are stored (this step is processing pipeline dependent), and then 2) have that wrapper script call a generic file called uploadNeuroDB/register_processed_data.pl. The register_processed_data.pl file would take in many required arguments, some of which are the full path of the file you are going to register. Other parameters are the acquisition protocol ID. So yes, the"white_matter", "pve", "tal_mask" were initially created to allow for CIVET outputs to be registered with the correct acquisition protocol. Other required parameters are the sourceFileID which would be the ID of the initial file you sent to CIVET for processing. The second step should be processing pipeline independent.


I hope the above answers your questions, or at least, gives you a starting point.


- Mouna


________________________________
From: loris-dev-bounces at bic.mni.mcgill.ca <loris-dev-bounces at bic.mni.mcgill.ca> on behalf of Michael Joseph <michael.joseph at sickkids.ca>
Sent: Wednesday, April 19, 2017 4:03 PM
To: loris-dev at bic.mni.mcgill.ca
Subject: [Loris-dev] Create DCCID and Organizing CIVET outputs


Hi Loris dev community,


I have 2 questions:


1) Is there a way to register new candidates into Loris from the back-end without a DCCID? Essentially, I'd like to add candidates and sessions while running the tarchiveLoader script. I noticed that the prod file has a createCandidates variable. Is there anything else that needs to be modified?


2) How are CIVET outputs typically organized in Loris? I noticed that in the mri_scan_type table, there are labels like "white_matter", "pve", "tal_msk". I'm assuming the most of the files from CIVET would get registered using these labels. Also, is there a good way of linking to the htmls from the CIVET QC pipeline?


Thanks,

Michael

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