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Hi Falk, 

That is great to know -  I only let it sit a couple hours and thought that the lack of any screen output meant it was stuck. I will try it again and wait the full length of a recon-all command. 

My bad on the number of jobs discrepancy. I was messing around with number of CPUs allocated for FreeSurfer to see if that changed anything, but yes, I have kept the number of jobs consistent with the setting. 

Thank you for your help!

Best wishes,
Joanna 

--

Joanna Eckhardt

Neurosciences Graduate Program

University of California, San Diego

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of falk.luesebrink@med.ovgu.de <falk.luesebrink@med.ovgu.de>
Sent: Tuesday, May 10, 2022 6:42 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Recon-all Freezes on Parallel
 
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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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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


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