[Loris-dev] Project customization and minc insertion

[David MacFarlane, Mr]

hi Michael,


Even if you're only working with MINCs, I would still recommend starting from the DICOMs for LORIS in order to have the raw data for provenance.


The dicomTar script puts it into a consistent format that the LORIS imaging scripts can process, and the LORIS imaging scripts will automatically convert it to MINC as well performing checks on the protocol, and mapping the scan type of the file to the LORIS mri_scan_types table.


The minc_insertion.pl script is what the LORIS tarchive pipeline uses under the hood and would probably be the best place to start if you need to start from the MINCs, but isn't generally intended to be directly run from users, so you'd most likely have to look up how the other scripts are calling it to see how it should be used.

________________________________
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: April 4, 2017 1:31:26 PM
To: loris-dev at bic.mni.mcgill.ca
Subject: [Loris-dev] Project customization and minc insertion


Hi LORIS dev community,


Our group is interested in using LORIS to store both raw and processed neuroimaging data (ie. image registration). We would also be working solely with minc files. I have a couple questions regarding the project customization steps and minc insertion scripts for this kind of setup.


Because we aren't working with dicoms, I'm assuming we'd skip the dicom archiving step (dicomTar.pl). The headers in the minc files are mapped differently compared to dicoms. Would I need to modify the mapDicomParameters function in the NeuroDB::MRI module to account for this? Also, to insert the raw scans, would I use registerFile.pl or minc_insertion.pl?


Some of the processed data we would be storing includes nonlinear registration images. In order to insert these into LORIS, would I use register_processed_data.pl?


Thanks,

Michael







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