Crash and resume problem about fmriprep calling freesurfer

My preprocessing is hung, So I turn off the terminal and rerun the preprocessing.

I have set a working directory using "-w " to speed the second preprocessing.

But I saw the warning in the terminal:

FreeSurfer cannot run if these are present, to avoid interfering with a running process. Please, make sure no other process is running recon-all on this subject and proceed to delete the files listed above.

It seems working directory file didn’t help the recon-all processing. Part of recon-all process did’nt finished in the first run.

Do I need delete the freesurfer files and rerun again? Or I just let it go?

The full warning should say that the files causing the problem are IsRunning scripts. These are in the FreeSurfer output directory, not the work directory. Easy solution, in your terminal you can just cd to the FreeSurfer output directory (that has all the individual subject folders in it), and then run rm */scripts/*Running*, which will delete all IsRunning files that are causing FreeSurfer to crash.


1 Like