I am running fMRI-prep with version 20.2.3 using singularity. Although I am specifying my FS directory (which was already ran outside of fmri-prep), I think that FS is rerunning because all files and directories of FS get recreated during the fmri-prep run. I was wondering if you have any help with this? Also, fmri-prep never finishes (it has now been running for longer than 48h for one subject). It only created a couple of files in ‘anat’ (i.e., T1w_to-fsnative_mode-image_xfm.txt, fsnative_to-T1w_mode-image_xfm.txt, and desc-preproc_T1w.nii.gz and .json) and there is no ‘func’ output folder. Please find attached our complete log file here. According to the log-file, the pre-run FS directory is recognized, but then later on it says that it is executing recon-all…
Could someone help with this?
Thank you!
Best wishes
Julie
Can you provide a few pieces of info that might help us help you?
does your old FS directory contain recon-all outputs, or less complete FS outputs? If it doesn’t contain recon-all that would explain why recon-all is being run by fMRIprep.
please paste the command you are using to rub fMRIprep
how are you running it (python/docker/singularity), and what OS? How much memory/CPUs are you devoting to the job?
That’s certainly enough memory, and you can probably get away with using less memory (like 20 GB). Try raising n_procs to 8 or 16. That should drastically speed up performance.
Is it possible that the FS dir is not bound to singularity? That is, add -B /dir4. Then fmriprep can find the previous FS outputs.
Thank you! Thats a great suggestion regarding the memory, will def try that.
Sorry, completely my bad, I didn’t name my directories well when copying the command line to here. The freesurfer dir (dir3 in this case) is actually bound, if Im not mistaken: