Fmriprep 20.2.3: Validation error despite --skip_bids_validation

Hi everyone,

we just updated from fmriprep 20.1.1 to 20.2.3 and (using the same command as before with the same data) I suddenly get bids validation errors even though I called fmriprep with the --skip_bids_validation flag. Note that the root folder really does not have dataset_description.json, but it also did not have it before and 20.1.1 ran smoothly.

Command (running via docker from XNAT)

--skip_bids_validation --fs-license-file /input/config/freesurfer_license.txt --fs-no-reconall --output-spaces T1w --mem 24 /input /output participant

Error:

Traceback (most recent call last):

File “/usr/local/miniconda/bin/fmriprep”, line 10, in

sys.exit(main())

File “/usr/local/miniconda/lib/python3.7/site-packages/fmriprep/cli/run.py”, line 17, in main

parse_args()

File “/usr/local/miniconda/lib/python3.7/site-packages/fmriprep/cli/parser.py”, line 635, in parse_args

config.from_dict(vars(opts))

File “/usr/local/miniconda/lib/python3.7/site-packages/fmriprep/config.py”, line 648, in from_dict

execution.load(settings)

File “/usr/local/miniconda/lib/python3.7/site-packages/fmriprep/config.py”, line 218, in load

cls.init()

File “/usr/local/miniconda/lib/python3.7/site-packages/fmriprep/config.py”, line 469, in init

indexer=_indexer,

File “/usr/local/miniconda/lib/python3.7/site-packages/bids/layout/layout.py”, line 137, in init

root, description = validate_root(root, validate)

File “/usr/local/miniconda/lib/python3.7/site-packages/bids/layout/validation.py”, line 77, in validate_root

json.dumps(EXAMPLE_BIDS_DESCRIPTION)

bids.exceptions.BIDSValidationError: ‘dataset_description.json’ is missing from project root. Every valid BIDS dataset must have this file.

Example contents of ‘dataset_description.json’:

{“Name”: “Example dataset”, “BIDSVersion”: “1.0.2”}

Is this expected behavior? While adding the file is a possibility, I have limited control over the format of the data I get.

Best,

André

This has been answered on the github page. Sorry for the double post, after posting it here I assumed that this a “issue” so specific to fmriprep’s use that github issues is a better fit.

–skip-bids-validation` tells fMRIPrep not to try to run the external BIDS validator tool before running, itself. When we index datasets with PyBIDS, “validation” plays a different role, where it helps exclude files that are invalid.

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