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