Running fMRI prep, but no output files appear

Hi, I’m currently running fMRIPrep using the following command

sudo docker run -ti --rm
-v /media/srd49/SD_Back/Grad_Projects/NSF_Auditory/source:/data:ro
-v /home/srd49/Documents/Vibrotactile_Speech_Learning_Project/derivatives:/out
-v /usr/local/freesurfer/license.txt:/opt/freesurfer/license.txt
poldracklab/fmriprep:20.0.2 /data /out/out participant\
–dummy-scans 3 --ignore slicetiming fieldmaps --medial-surface-nan --write-graph

It seems to be running just find when I look at the logs of the docker container. However, I find that there’s no output being written to my desktop. This seems to be the case even when I use the fmriprep-docker wrapper I was wondering if anybody had any insight why that is, or if I’m only supposed to see the files once the process is complete. Thank you for your time!

If it’s still running, I’d suggest waiting. From a glance your command looks reasonable, but derivatives can only be written when finally calculated.

You should see the directory /home/srd49/Documents/Vibrotactile_Speech_Learning_Project/derivatives/out/freesurfer written early, though.

Thanks for the quick reply! It hasn’t been too long, so I’ll wait and see what’s going on then!