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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@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
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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,