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Repo that deals with datalad aspects for internal use
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bids-validator errors #299

Open mguaypaq opened 4 months ago

mguaypaq commented 4 months ago

While merging #294, I noticed a bunch of unrelated bids-validator errors, which we should probably fix:

bids-validator@1.14.0
(node:32074) Warning: Closing directory handle on garbage collection
(Use `node --trace-warnings ...` to show where the warning was created)
    1: [ERR] Files with such naming scheme are not part of BIDS specification. This error is most commonly caused by typos in file names that make them not BIDS compatible. Please consult the specification and make sure your files are named correctly. If this is not a file naming issue (for example when including files not yet covered by the BIDS specification) you should include a ".bidsignore" file in your dataset (see https://github.com/bids-standard/bids-validator#bidsignore for details). Please note that derived (processed) data should be placed in /derivatives folder and source data (such as DICOMS or behavioural logs in proprietary formats) should be placed in the /sourcedata folder. (code: 1 - NOT_INCLUDED)
        ./CHANGES.md
            Evidence: CHANGES.md
        ./sub-koreajisun001/dwi/sub-koreajisun001_acq-b0Mean.json
            Evidence: sub-koreajisun001_acq-b0Mean.json
        ./sub-koreajisun001/dwi/sub-koreajisun001_acq-b0Mean.nii.gz
            Evidence: sub-koreajisun001_acq-b0Mean.nii.gz
        ./sub-koreajisun002/anat/sub-koreajisun002_acq-MToff_MTR.json
            Evidence: sub-koreajisun002_acq-MToff_MTR.json
        ./sub-koreajisun002/anat/sub-koreajisun002_acq-MToff_MTR.nii.gz
            Evidence: sub-koreajisun002_acq-MToff_MTR.nii.gz
        ./sub-koreajisun002/anat/sub-koreajisun002_acq-MTon_MTR.json
            Evidence: sub-koreajisun002_acq-MTon_MTR.json
        ./sub-koreajisun002/anat/sub-koreajisun002_acq-MTon_MTR.nii.gz
            Evidence: sub-koreajisun002_acq-MTon_MTR.nii.gz
        ./sub-koreajisun002/dwi/sub-koreajisun002_acq-b0Mean.json
            Evidence: sub-koreajisun002_acq-b0Mean.json
        ./sub-koreajisun002/dwi/sub-koreajisun002_acq-b0Mean.nii.gz
            Evidence: sub-koreajisun002_acq-b0Mean.nii.gz
        ./sub-koreajisun003/anat/sub-koreajisun003_acq-MToff_MTR.json
            Evidence: sub-koreajisun003_acq-MToff_MTR.json
        ... and 783 more files having this issue (Use --verbose to see them all).

    Please visit https://neurostars.org/search?q=NOT_INCLUDED for existing conversations about this issue.

    2: [ERR] Empty cell in TSV file detected: The proper way of labeling missing values is "n/a". (code: 23 - TSV_EMPTY_CELL)
        ./participants.tsv
            @ line: 63
            Evidence: row 62: sub-bordeauxOfsep001  F   n/a unknown unknown n/a n/a     bordeaux_ofsep_0100004  bordeauxOfsep

    Please visit https://neurostars.org/search?q=TSV_EMPTY_CELL for existing conversations about this issue.

    3: [ERR] .bval and .bvec files must be single space delimited and contain only numerical values. (code: 47 - B_FILE)
        ./sub-unfErssm001/dwi/sub-unfErssm001_dwi.bval
        ./sub-unfErssm001/dwi/sub-unfErssm001_dwi.bvec
        ./sub-unfErssm002/dwi/sub-unfErssm002_dwi.bval
        ./sub-unfErssm002/dwi/sub-unfErssm002_dwi.bvec
        ./sub-unfErssm003/dwi/sub-unfErssm003_dwi.bval
        ./sub-unfErssm003/dwi/sub-unfErssm003_dwi.bvec
        ./sub-unfErssm004/dwi/sub-unfErssm004_dwi.bval
        ./sub-unfErssm004/dwi/sub-unfErssm004_dwi.bvec
        ./sub-unfErssm005/dwi/sub-unfErssm005_dwi.bval
        ./sub-unfErssm005/dwi/sub-unfErssm005_dwi.bvec
        ... and 82 more files having this issue (Use --verbose to see them all).

    Please visit https://neurostars.org/search?q=B_FILE for existing conversations about this issue.

    4: [ERR] Ses label contain an Illegal Character hyphen or underscore. Please edit the filename as per BIDS spec. (code: 63 - SESSION_VALUE_CONTAINS_ILLEGAL_CHARACTER)
        ./sub-zurichMPM01/ses-01/anat/sub-zurichMPM01_ses-01_RFSC_MT.json
            Evidence: ses name contains illegal character:/sub-zurichMPM01/ses-01/anat/sub-zurichMPM01_ses-01_RFSC_MT.json
        ./sub-zurichMPM01/ses-01/anat/sub-zurichMPM01_ses-01_RFSC_PD.json
            Evidence: ses name contains illegal character:/sub-zurichMPM01/ses-01/anat/sub-zurichMPM01_ses-01_RFSC_PD.json
        ./sub-zurichMPM01/ses-01/anat/sub-zurichMPM01_ses-01_RFSC_R1.json
            Evidence: ses name contains illegal character:/sub-zurichMPM01/ses-01/anat/sub-zurichMPM01_ses-01_RFSC_R1.json
        ./sub-zurichMPM01/ses-01/anat/sub-zurichMPM01_ses-01_RFSC_R2s_OLS.json
            Evidence: ses name contains illegal character:/sub-zurichMPM01/ses-01/anat/sub-zurichMPM01_ses-01_RFSC_R2s_OLS.json
        ./sub-zurichMPM01/ses-02/anat/sub-zurichMPM01_ses-02_RFSC_MT.json
            Evidence: ses name contains illegal character:/sub-zurichMPM01/ses-02/anat/sub-zurichMPM01_ses-02_RFSC_MT.json
        ./sub-zurichMPM01/ses-02/anat/sub-zurichMPM01_ses-02_RFSC_PD.json
            Evidence: ses name contains illegal character:/sub-zurichMPM01/ses-02/anat/sub-zurichMPM01_ses-02_RFSC_PD.json
        ./sub-zurichMPM01/ses-02/anat/sub-zurichMPM01_ses-02_RFSC_R1.json
            Evidence: ses name contains illegal character:/sub-zurichMPM01/ses-02/anat/sub-zurichMPM01_ses-02_RFSC_R1.json
        ./sub-zurichMPM01/ses-02/anat/sub-zurichMPM01_ses-02_RFSC_R2s_OLS.json
            Evidence: ses name contains illegal character:/sub-zurichMPM01/ses-02/anat/sub-zurichMPM01_ses-02_RFSC_R2s_OLS.json
        ./sub-zurichMPM02/ses-01/anat/sub-zurichMPM02_ses-01_RFSC_MT.json
            Evidence: ses name contains illegal character:/sub-zurichMPM02/ses-01/anat/sub-zurichMPM02_ses-01_RFSC_MT.json
        ./sub-zurichMPM02/ses-01/anat/sub-zurichMPM02_ses-01_RFSC_PD.json
            Evidence: ses name contains illegal character:/sub-zurichMPM02/ses-01/anat/sub-zurichMPM02_ses-01_RFSC_PD.json
        ... and 30 more files having this issue (Use --verbose to see them all).

    Please visit https://neurostars.org/search?q=SESSION_VALUE_CONTAINS_ILLEGAL_CHARACTER for existing conversations about this issue.

    5: [ERR] Empty files not allowed. (code: 99 - EMPTY_FILE)
        ./sub-calCadotte001/dwi/sub-calCadotte001_acq-b0Mean_dwi.json
        ./sub-koreajisun001/dwi/sub-koreajisun001_acq-b0Mean.json
        ./sub-koreajisun002/dwi/sub-koreajisun002_acq-b0Mean.json
        ./sub-koreajisun003/dwi/sub-koreajisun003_acq-b0Mean.json
        ./sub-koreajisun004/dwi/sub-koreajisun004_acq-b0Mean.json
        ./sub-koreajisun005/dwi/sub-koreajisun005_acq-b0Mean.json
        ./sub-koreajisun006/dwi/sub-koreajisun006_acq-b0Mean.json
        ./sub-koreajisun007/dwi/sub-koreajisun007_acq-b0Mean.json
        ./sub-koreajisun008/dwi/sub-koreajisun008_acq-b0Mean.json
        ./sub-koreajisun009/dwi/sub-koreajisun009_acq-b0Mean.json
        ... and 133 more files having this issue (Use --verbose to see them all).

    Please visit https://neurostars.org/search?q=EMPTY_FILE for existing conversations about this issue.

        Summary:                   Available Tasks:        Available Modalities: 
        7862 Files, 18.21GB                                MRI                   
        1559 - Subjects                                                          
        1 - Session                                                              

    If you have any questions, please post on https://neurostars.org/tags/bids.
mguaypaq commented 4 months ago

I fixed a few of the obvious problems found by bids-validator on sct-testing-large. I made a separate commit on the branch mgp/fix-bids for each thing I fixed. @kousu, could you have a quick look for sanity checking? There's still plenty of problems listed by bids-validator, but they look like they require more thinking.