We run : fmriprep-docker sub-001 derivatives participant
And here are the errors:
1: [ERR] Files with such naming scheme are not part of BIDS specification.
2: [ERR] There are no subject folders (labeled “sub-*”) in the root of this dataset.
3: [ERR] Dataset does not contain any T1w scans
4: [ERR] Subject label in the filename doesn’t match with the path of the file.
And the result:
Summary: Available Tasks: Available Modalities:
5 Files, 112.29MB
0 - Subjects
1 - Session
I believe there are two possible ways to fix this. First is to encode the session information in the filenames, so sub-001_ses-1_T1w.json The other would be to move anat and func up a directory and remove the now empty ses-1 directory.
Having the session in the filename while being in the session directory may seem redundant but it ensures every filename is unique in the dataset.
1: [ERR] Files with such naming scheme are not part of BIDS specification.
2: [ERR] There are no subject folders
3: [ERR] Dataset does not contain any T1w scans.
4: [ERR] Subject label in the filename doesn’t match with the path of the file.
5: [ERR] Session label in the filename doesn’t match with the path of the file
One other thing while playing around with a test dataset I had to change sub-001_task-fluence_run-01_bold.tsv to sub-001_task-fluence_run-01_events.tsv
Thanks again.
I changed the three filenames inside “func” directory with “events” instead of “bold” but still the same error message:
1: [ERR] Quick validation failed - the general folder structure does not resemble a BIDS dataset.
the problem might also be in the call and not only in the file names (which were all pointed out by @rwblair).
Your dataset should look something like:
In your call, you’re missing the positional bids_dir argument or rather setting it in the wrong way, as you’re pointing to sub-001 which will in turn be mapped/treated as the input directory of your data in BIDS.
Hence, you need to specify the absolute path of your BIDS dataset and not that or the identifier of the participant you want to process: