Hello everyone,
In running the command:
docker run -ti --rm -v /scratch/tvanasse/BIDS_DIR_PILOT:/data:ro -v /scratch/tvanasse/BIDS_DIR_PILOT/derivatives:/out -v /scratch/tvanasse/tmp/workdir:/work nipreps/fmriprep:latest /data /out/fmriprep participant -w /work
I get the following error, from what I believe to be related to bids validation. However, my directory passes the BIDS validation program, so I’m not sure what is going on. I was able to run mriqc successfully.:
1: [ERR] Units in .tsv files must be valid SI units as described in the BIDS spec Appendix V (https://bids-specification.readthedocs.io/en/stable/99-appendices/05-units.html). (code: 124 - INVALID_TSV_UNITS)
./sub-06/ses-fmri1/eeg/sub-06_ses-fmri1_task-awak_channels.tsv
@ line: 4
Evidence: Subunit (μV) of unit μV is invalid.
./sub-06/ses-fmri1/eeg/sub-06_ses-fmri1_task-awak_channels.tsv
@ line: 5
Evidence: Subunit (μV) of unit μV is invalid.
./sub-06/ses-fmri1/eeg/sub-06_ses-fmri1_task-awak_channels.tsv
@ line: 6
Evidence: Subunit (μV) of unit μV is invalid.
./sub-06/ses-fmri1/eeg/sub-06_ses-fmri1_task-awak_channels.tsv
@ line: 7
Evidence: Subunit (μV) of unit μV is invalid.
./sub-06/ses-fmri1/eeg/sub-06_ses-fmri1_task-awak_channels.tsv
@ line: 8
Evidence: Subunit (μV) of unit μV is invalid.
./sub-06/ses-fmri1/eeg/sub-06_ses-fmri1_task-awak_channels.tsv
@ line: 9
Evidence: Subunit (μV) of unit μV is invalid.
./sub-06/ses-fmri1/eeg/sub-06_ses-fmri1_task-awak_channels.tsv
@ line: 10
Evidence: Subunit (μV) of unit μV is invalid.
./sub-06/ses-fmri1/eeg/sub-06_ses-fmri1_task-awak_channels.tsv
@ line: 11
Evidence: Subunit (μV) of unit μV is invalid.
./sub-06/ses-fmri1/eeg/sub-06_ses-fmri1_task-awak_channels.tsv
@ line: 12
Evidence: Subunit (μV) of unit μV is invalid.
./sub-06/ses-fmri1/eeg/sub-06_ses-fmri1_task-awak_channels.tsv
@ line: 13
Evidence: Subunit (μV) of unit μV is invalid.
... and 86 more files having this issue (Use --verbose to see them all).
The traceback is as follows:
Traceback (most recent call last):
File "/usr/local/miniconda/bin/fmriprep", line 10, in <module>
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 703, in parse_args
config.environment.exec_env, opts.bids_dir, opts.participant_label
File "/usr/local/miniconda/lib/python3.7/site-packages/fmriprep/utils/bids.py", line 155, in validate_input_dir
subprocess.check_call(['bids-validator', bids_dir, '-c', temp.name])
File "/usr/local/miniconda/lib/python3.7/subprocess.py", line 341, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['bids-validator', PosixPath('/data'), '-c', '/tmp/tmp896162zh']' returned non-zero exit status 1.
Edit: The first five lines of my ./sub-06/ses-fmri1/eeg/sub-06_ses-fmri1_task-awak_channels.tsv file are as follows:
name type units sampling_frequency
Fp1 EEG μV 5000
Fp2 EEG μV 5000
F3 EEG μV 5000
F4 EEG μV 5000
Any help would be appreciated.
Thanks,
Tom