Hi Raquel
The log says:
Command terminated by signal 9
Which is a message from the Linux scheduler, and usually means you ran out of
ram. It looks like you have 5G on that machine and some of it was in use at the
time. Can you find a machine with more ram to try it on? Or free up the memory
before running recon-all?
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Gool, Raquel van (Stud.
FPN / Alumni FPN)
Sent: Monday, March 8, 2021 9:26 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] mris_sphere error: terminated by signal 9
External Email - Use Caution
Dear FreeSurfer experts,
I'm attempting to use recon-all on my subjects and I have one of my subjects
exit with errors after it is terminated by signal 9 during -sphere of
autorecon3.
I tried rerunning this particular step with command recon-all -autorecon3
-subjid subj07 -sphere. Unfortunately mris_sphere keeps being terminated. I
experience this exact same problem with another one of my other subjects,
whereas the rest of my subjects manage to finish recon-all.
I use freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b on a virtual
machine (VirtualBox) on my windows computer. Linux developer-VirtualBox
5.4.0-65-generic #73~18.04.1-Ubuntu SMP Tue Jan 19 09:02:24 UTC 2021 x86_64
x86_64 x86_64 GNU/Linux
Any thoughts on how to troubleshoot this? Thanks a lot.
Regards,
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