On Apr 8, 2024, at 8:58 AM, Huang, Yujing <YHUANG43@mgh.harvard.edu> wrote:

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 MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect_freeview

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
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://lbbil.rutgers.edu

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