I’m trying to figure out what I’m doing wrong because I have run multiple tests but fmriprep seems to not finish and also doesn’t throw any errors. I am using the spartan hpc cluster (melbourne) with this script:
I also tried running it on a local machine (with 8CPUS and 16GB memory) and it didn’t finish for 48 hours. I tried with no reconall and it finished in ~1.5 hours.
it seems to me that this node is not the actuall problem.
The problem has the looks of a memory issue, however the fact that you were running with --nthreads 1 makes me doubtful.
Could you run this one subject exactly the same way but adding the -vvv flag, so we get extra verbose output? Please make sure you don’t reuse the work directory (otherwise the process will likely end up finishing).
Hi! So I tried several times and it didn’t finish, not even when I used the old working directory. I uploaded the verbose output files on github as well.
I ended up running freesurfer separately and then running fmriprep and it worked! So I’m running my entire dataset with pre-done freesurfer now.