Fmriprep doesn't create correct directory structure

Dear community,

I ran command fmriprep-docker -u $UID <in_dir> <out_dir> participant --participant-label <sub_id> --fs-license-file license.txt and everything looked normal with no BIDS validation error or anything else as far as I can tell. The problem is that there is no directory “<out_dir>/fmriprep/” being created. Instead, I am getting “<out_dir>/logs”, “<out_dir>/sourcedata/”, “<out_dir>/<sub_id>” and “<out_dir>/<sub_id>.html” which I thought should be created under “fmriprep/”. The “<out_dir>/<sub_id>.html” report only contains methods without any result figures. No errors reported. What could be the cause of this behaviour?

Thank you for your help in advance!

As of fmriprep v 21.0, the output directory structure changed:

See here:

and explanation of the philosophy here:

Additionally the --output-layout bids flag will now output fMRIPrep derivatives directly into the output directory, nesting FreeSurfer derivatives by default in <output>/sourcedata/freesurfer . This layout allows the output root to be a valid BIDS Derivatives dataset, simplifying data management and provenance tracking with content tracking tools, such as DataLad. This layout will likely become the default in future release series.


Thank you @jsein for this prompt and helpful answer.