External Email - Use Caution

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

External Email - Use Caution

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

...............................................

[https://secure-web.cisco.com/1ZtGNQr8omS04_S_fS5DaL6JBWvyUltfp2W62yPm5Wy-vOl... ] Universitätsklinik für Neurologie

Otto-von-Guericke-Universität Magdeburg Medizinische Fakultät Leipziger Str. 44 39120 Magdeburg

Telefon: +49-391-6117-512

falk.luesebrink@med.ovgu.demailto:falk.luesebrink@med.ovgu.de https://secure-web.cisco.com/1JmCBS6iIyDld5dDxuNS-i3k6sSfCtIyjVrT3Pq3geQK2FW... ________________________________ 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

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 list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1pC88qYXSclzYSbGcnkhsynu6n74UatNtwiD9RjvQRaaBzr... The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://secure-web.cisco.com/18U7A3ek19GYc9vQa0qcyhnA_7tdGHopjk7Paf7nM5VtVQW... <https://secure-web.cisco.com/18U7A3ek19GYc9vQa0qcyhnA_7tdGHopjk7Paf7nM5VtVQW... > . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.