Skip to content

Error on physio data in anat sub-directory #2164

Closed

Description

While conducting our multi-modal MRI study, also a physiological baseline (cardiac and respiratory) was acquired parallel to the anatomical measurements. According to the BIDS specifications on physiological recordings (https://bids-specification.readthedocs.io/en/latest/modality-specific-files/physiological-recordings.html), the physio data files (.tsv.gz and .json) may be stored in the subject's anatomical recordings sub-directory. We have T1w and PDw anatomical recordings and corresponding physio data only for the T1w recording. The subject directories currently look as follows:

...
./physio.json
./sub-01/
./sub-01/anat/
./sub-01/anat/sub-01_PDw.nii.gz
./sub-01/anat/sub-01_T1w.nii.gz
./sub-01/anat/sub-01_T1w.json
./sub-01/anat/sub-01_PDw.json
./sub-01/anat/sub-01_physio.tsv.gz
...

The specification's naming convention for physio data within modality sub-directories is:

<matches>[_recording-<label>]_physio.tsv.gz
<matches>[_recording-<label>]_physio.json

Therefore, in the example above, the part <matches> is sub-01, [_recording-<label>] is empty (we only have one physio recording), and the modality suffix is _physio. Hence, we have sub-01_physio.tsv.gz as the filename. Now, we are facing two problems.

  1. With this naming scheme we cannot relate the physio data to the T1w recording from the filename. Is there an alternative way to capture this relationship?
  2. The bids-validator (bids-validator@1.14.14 and also 1.14.15-dev) complains with an error about this naming scheme.
1: [ERR] Files with such naming scheme are not part of BIDS specification. ... (code: 1 - NOT_INCLUDED)
		./sub-01/anat/sub-01_physio.tsv.gz
			Evidence: sub-01_physio.tsv.gz

I had a look at the source code bids-validator/bids_validator/rules/file_level_rules.json. For EEG, *_physio.tsv.gz seems to be covered:

      "@@@_cont_ext_@@@": [
        "_physio\\.tsv\\.gz",
        "_stim\\.tsv\\.gz",
        "_physio\\.json",
        "_stim\\.json"
      ]

However, there is no such block for "anat_nonparametric" (where we have T1w and PDw suffixes) in this rules file. Is this the issue for why the bids-validator complains? I'm happy to provide a PR, if this is the correct place to fix it.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Metadata

Assignees

No one assigned

    Labels

    No labels
    No labels

    Type

    No type

    Projects

    No projects

    Milestone

    No milestone

    Relationships

    None yet

    Development

    No branches or pull requests

    Issue actions