External Email - Use Caution
Oops, I meant to reply all:
Hi R ,
See below, I gave 8 GB and 2 CPU in settings.
[cid:f2395341-7e91-40b6-bc1c-d89bca3e4876]
[cid:32cfdb7f-40af-4c07-babd-c07a17f81269]
--
Joanna Eckhardt
Neurosciences Graduate Program
University of California, San Diego
________________________________
From: fsbu...@convergenceservice.com <fsbu...@convergenceservice.com>
Sent: Monday, May 9, 2022 2:41 PM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Cc: Joanna L Eckhardt <jeckha...@health.ucsd.edu>
Subject: Re: [Freesurfer] Recon-all Freezes on Parallel
In the VirtualBox settings, did you give the VM both cores to use?
It would also be good to know much memory your machine has, and how much of
that you gave to the VM in the VirtualBox settings.
- R.
On May 9, 2022, at 17:27, Joanna L Eckhardt <jeckha...@health.ucsd.edu> wrote:
External Email - Use Caution
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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