It looks like mris_fix_topology for lh hemisphere core dumped. This is from your recon-all.log:
“ An extra large defect has been detected... This often happens because cerebellum or dura has not been removed from wm.mgz. This may cause recon-all to run very slowly or crash. if so, see https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect_freev... Large defect found - not a problem, but a curiousity *** stack smashing detected ***: terminated “
In the tutorial, it has instructions on how to correct topological defects.
Also, I noticed that the recon-all was run with ‘-parallel’ option. Use ‘-nthreads <num-of-threads>’ instead.
Best,
Yujing
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of William Graves Sent: Sunday, April 7, 2024 10:03 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] recon-all exits with errors
External Email - Use Caution Dear FreeSurfer Developers,
I’m trying to run recon-all as a pre-processing step in the AFNI resting-state analysis pipline, using the command: recon-all -subject $subj -i $anat_cm -all -parallel
So far it has successfully run on about 20 participants in my sample, but for the current participant it’s now suddenly throwing this error:
PIDs (691564 691567) completed and logs appended. Linux demeter 6.2.0-26-generic #26~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Thu Jul 13 16:27:29 UTC 2 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s R21-24 exited with ERRORS at Fri Apr 5 16:29:23 EDT 2024
I searched through the log file, tried Googling the error, and searched your email list archive, but couldn’t find anything to address this. The log file is attached, along with:
1) FreeSurfer version: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 2) Platform: Ubuntu 22.04.3 LTS
I’d appreciate any help or advice you could give!
Best, Will
--- William W. Graves, Ph.D. Associate Professor, Department of Psychology Rutgers, The State University of New Jersey Smith Hall, Room 337 101 Warren Street, Newark, NJ 07102 http://lbbil.rutgers.edu