Oh, actually, I just found some more output.
"ERROR: it appears that recon-all is already running
for sub-06 based on the presence of /home/nb80a/bids/face_tuning/derivatives/freesurfer/sub-06/scripts/IsRunning.rh. It could
also be that recon-all was running at one point but
died in an unexpected way. If it is the case that there
is a process running, you can kill it and start over or
just let it run. If the process has died, you should type:
and re-run. Or you can add -no-isrunning to the recon-all
I think fmriprep might have been interrupted towards the end of the recon (not enough allotted time in my initial 3-subject job), leaving an IsRunning.rh file. Following the output’s suggestion, I deleted the file and reran the fmriprep command.
will update when i know whether this works.