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Hi Joanna,
if I remember correctly, you won't see any screen output until the process is finished using parallel. So, I suppose it doesn't freeze. Have you kept the process running for some time?
Also you state that you want to use only 2 jobs at a time. However, in the command line you specify 3 jobs.
Best,
Falk
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[http://secure-web.cisco.com/1Xg2HcdvF9dRzTa2ZFIhf3Kl-wpULX1tKJmpGmfMvcbKrMbd...] Universitätsklinik für Neurologie
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falk.luesebrink@med.ovgu.demailto:falk.luesebrink@med.ovgu.de http://secure-web.cisco.com/1grYGf0PQcjazx2N4roUOAW2_0PA5oVwsmBNBZj2LsRbmuKh... ________________________________ Von: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu im Auftrag von Joanna L Eckhardt jeckhardt@health.ucsd.edu Gesendet: Montag, 9. Mai 2022 23:27:02 An: freesurfer@nmr.mgh.harvard.edu Betreff: [Freesurfer] Recon-all Freezes on Parallel
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Dear FreeSurfer Team,
I have been trying to use the parallel command (following FreeSurfer tutorial) to run multiple subjects (Windows os running Ubuntu VM).
I only have 2 cores, so I have it set to 2 jobs instead of 8 as in the tutorial. When I use the code from the tutorial, there is an error with the .nii, and I assume it is because my files are .nii.gz.
developer@developer-VirtualBox:~/FreeSurfer/Cannabis_Reduced$ ls *.nii | parallel --jobs 3 recon-all -s {.} -i {} -all -qcache ls: cannot access '*.nii': No such file or directory
So I changed the code to .gz with everything else the same, and FreeSurfer does nothing (it stalls/freezes). Is this just because my computer cannot handle the job? Is there anything else I can do to run parallel? If not, I can always just run 1 subject at a time, but I want to check and see if there is another way to get this to work.
Thank you for your time! Joanna