tools/minc_to_bids_converter.pl

[cmadjar]

Test Plan

• [ ] Set config options in 'MINC to BIDS Converter Tool Options' of the Configuration module

• [ ] Run following command:

  perl tools/minc_to_bids_converter.pl -profile prod -dataset_name BIDS_LORIS25_test -verbose

• [ ] Run bids-validator:

  sudo npm install -g bids-validator
  bids-validator /data/Loris-MRI/data/BIDS_export/BIDS_LORIS25_test/

• If validator gives errors with a code, enter into the 'BIDS Validation options to ignore' config under 'MINC to BIDS Converter Tool Options' the codes as values, and test that the warnings are silenced

Bugs previously found

• https://github.com/aces/Loris-MRI/issues/980
• https://github.com/aces/Loris-MRI/issues/981

[CamilleBeau]

I am getting this error from running the bids-validator:

(loris-mri-python) lorisadmin@cbeaudoin-test-26:/opt/Loris-MRI/bin/mri$ bids-validator /data/Loris-MRI/data/BIDS_export/BIDS_LORIS25_test/ /usr/lib/node_modules/bids-validator/dist/commonjs/cli.js:127308 var fd = FormData; ^

ReferenceError: FormData is not defined at node_modules/then-request/lib/browser.js (/usr/lib/node_modules/bids-validator/dist/commonjs/cli.js:127308:14) at __require2 (/usr/lib/node_modules/bids-validator/dist/commonjs/cli.js:111080:51) at Object. (/usr/lib/node_modules/bids-validator/dist/commonjs/cli.js:128964:36) at Module._compile (node:internal/modules/cjs/loader:1198:14) at Object.Module._extensions..js (node:internal/modules/cjs/loader:1252:10) at Module.load (node:internal/modules/cjs/loader:1076:32) at Function.Module._load (node:internal/modules/cjs/loader:911:12) at Module.require (node:internal/modules/cjs/loader:1100:19) at require (node:internal/modules/cjs/helpers:119:18) at Object. (/usr/lib/node_modules/bids-validator/bin/bids-validator:18:30)

[CamilleBeau]

Other than that, I got these warnings in the converter script, but everything else ran fine. Not sure all of these are expected or bugs:

WARNING: Cannot compute EffectiveEchoSpacing & TotalReadoutTime for demo_947103_V6_fMRI_001.mnc 'dicom_0x0019:el_0x1028' should be a number. Its value is 26.483 'dicom_0x0051:el_0x100b' should be a number. Its value is 64

WARNING: skipping demo_947103_V6_fieldmapDWI_002.mnc since fieldmapDWI is not listed in bids_mri_scan_type_rel. (also a few more like this) WARNING: skipping demo_300125_V1_fieldmapBOLD_003.mnc since fieldmapBOLD is not listed in bids_mri_scan_type_rel. WARNING: skipping demo_300125_V1_dwi25_001.mnc since dwi25 is not listed in bids_mri_scan_type_rel. WARNING: skipping demo_300170_V1_dwi65_001.mnc since dwi65 is not listed in bids_mri_scan_type_rel.

WARNING: SliceTiming is not supplied as the values read from the MINC header seem erroneous. This is most likely due to a dcm2mnc conversion problem

WARNING: Cannot compute EffectiveEchoSpacing & TotalReadoutTime for demo_300192_V1_fMRI_002.mnc 'dicom_0x0019:el_0x1028' should be a number. Its value is -49b, -9b, 83b, -29b, -91b, 123b, 58b, 64b 'dicom_0x0051:el_0x100b' should be a number. Its value is => This is unfortunately the result of a bad dcm2mnc conversion...

[CamilleBeau]

Note: Node.js >= 18 required for bids-validator to work

[CamilleBeau]

After #1127, the output from bids-validator looks like this:

Is this normal output or does it indicate an issue with the minc_to_bids_converter.pl?

[CamilleBeau]

Following discussion with Cecile, this script is passing tests with https://github.com/aces/Loris-MRI/pull/1127