External Email - Use Caution
The VirtualBox settings indicate you host machine has 4 real and 4 virtual
cores with 16G of RAM.
You could try shutting down the VM, and then change the VirtualBox settings to
give the VM 4 cores (instead of 2) and 12G of RAM (instead of 8G). Then
start the VM and try running your command again to see if performance improves
maybe first with 2 jobs and then 4. I would try not to run other
applications on your host machine at this time.
- R.
On May 9, 2022, at 17:47, Joanna L Eckhardt <jeckha...@health.ucsd.edu>
wrote: External Email - Use
Caution Oops, I meant to reply
all: Hi R ,See below, I gave 8 GB and 2 CPU in
settings.<image.png><image.png>--Joanna EckhardtNeurosciences
Graduate ProgramUniversity of California, San DiegoSent: Monday, May 9,
2022 2:41
PMTo: 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_______________________________________________Freesurfer mailing
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