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enhance dataset_description and sidecars to please the new bids_validator

Open bpinsard opened this issue 1 year ago • 1 comments

Summary

Running the new bids-validator I get more warnings than with the older one. eg

	[WARNING] JSON_KEY_RECOMMENDED A JSON file is missing a key listed as recommended.
		DatasetType
		/dataset_description.json

		GeneratedBy
		/dataset_description.json

		SourceDatasets
		/dataset_description.json

So we should maybe improve the currently generated dataset_description.json to include such tags.

It also get errors such as

	[ERROR] SIDECAR_KEY_REQUIRED A data file's JSON sidecar is missing a key listed as required.
		Units
		/sub-participant/ses-43/anat/sub-participant_ses-43_acq-stagefa5_echo-1_part-phase_MEGRE.nii.gz
		/sub-participant/ses-43/anat/sub-participant_ses-43_acq-stagefa5_echo-2_part-phase_MEGRE.nii.gz

So it seems that all part-phase should have Units defined in the json, in most cases this would be arbitrary. As heudiconv can set part-phase after dcm2niix in update_complex_name, it should be done in heudiconv.

Platform details:

Choose one:

  • [ ] Local environment
  • [x] Container
  • Heudiconv version:

1.3.2

bpinsard avatar Dec 10 '24 19:12 bpinsard

We would be also highly interested as the newest FMRIPREP is not working flawlessly with this current bids version (e.g. field maps are not recognised due to a different intendedFor field). Thanks a lot for your effort!

ChristianNSchmitz avatar Feb 07 '25 00:02 ChristianNSchmitz