I tried running the mounting command… when doing so, it seems Docker does not recognize parts for the nipreps/fmriprep container.
It flags --participant-label as unknown and lists the Docker commands.
Maybe try using --mount instead of -v, also put the mount flag after “Docker run”
So sudo docker run --mount /home/afton ……..
Hi @aftonnelson,
In your original fmriprep command, you specifiy --participant-label PIPS_01; however, I think it can simply be --participant-label 01
Assuming that your subject ID is just 01
This solution worked for me in the end!
sudo docker run -ti --rm -v /path/to/bids/dataset:/input -v
/path/to/output/folder:/output -v /path/to/freesurfer/license/license.txt:/license poldracklab/fmriprep:latest /input /output participant --participant-label 01 02 03 --fs-license-file /license --skip-bids-validation --n-cpus 4 --fs-no-reconall