Failure during --anat-only fmriprep preprocessing despite completed freesurfer recon

Hi all,

I’m running the --anat-only version of fmriprep using a singularity container on a high-performance computing cluster (no func due to space limitations on the cluster). In a recent batch job, 2 of 3 subjects completed successfully, but the third throws an error while generating its report. The relevant output is:

171226-16:35:38,54 workflow ERROR:
could not run node: fmriprep_wf.single_subject_06_wf.anat_preproc_wf.surface_recon_wf.autorecon_resume_wf.autorecon_surfs
171226-16:35:38,234 cli WARNING:
Errors occurred while generating reports for participants: 06 (1).

Any ideas for a solution on this?


Was there a freesurfer folder already present in the output folder? Could you share the full log and any crash files that might have been generated?

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:

rm /home/nb80a/bids/face_tuning/derivatives/freesurfer/sub-06/scripts/IsRunning.rh

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.



all good here! thanks Chris.