The attached recon-all log is empty. What is your recon-all command line?

It sounds like you have both FS 7.1.1 and FS 7.4.1 installed on your system. The correct Freesurfer environment needs to be sourced before running recon-all - https://surfer.nmr.mgh.harvard.edu/fswiki/SetupConfiguration_Linux

Set ‘SUBJECTS_DIR’ to point to directory outside the Freesurfer installation tree, and make sure you have write permission. I’m attaching recon-all wiki page for your reference -  https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all.

Yujing

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Jeffrey Neal
Sent: Wednesday, November 6, 2024 3:17 PM
To: freesurfer@nmr.mgh.harvard.edu
Cc: Noah Reardon <nreardon@umich.edu>
Subject: [Freesurfer] [WARNING: ATTACHMENT UNSCANNED]Re: mri_convert: Command terminated by signal 9

Hello Freesurfer Developers,

I am working with a lab who is trying to use freesurfer command:
 Make recon-all -k 
which fails with: command terminated by signal 9. If we try re-running it, we have to remove the folder created by it before we can re-run the command again, which will then report missing files such as mri_convert along with a few others that magically disappear from the bin folder.

Everything works on version 7.1.1 as it should but they want to use 7.4.1 to make use of some more functions and version 7.4.1 is the version we are having the issue with.

OS: Ubuntu 22.04 LTS

Freesurfer :freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460

FREESURFER_HOME: /usr/local/freesurfer (points to 7.4.1)

uname -a: Linux linux-tpolk04 5.15.0-124-generic #134-Ubuntu SMP Fri Sep 27 20:20:17 UTC 2024 x86_64 x86_64 x86_64 GNU/Linux

See attached log for details.

I've CC'd a Grad member (Noah) of the lab who I've been working closely with to help resolve this who can answer some questions as well. I am the Desktop Support Specialist assisting with this issue so I can handle the technical side as needed. 

Best Regards,
Jeffrey Neal
jsneal@umich.edu
LSA EHTS Desktop Support Specialist Senior
University of Michigan

On Nov 6, 2024, at 10:43 AM, Jeffrey Neal <jsneal@umich.edu> wrote:

Hello Freesurfer Developers,

I am working with a lab who is trying to use freesurfer command:
 Make recon-all -k 
which fails with: command terminated by signal 9. If we try re-running it, we have to remove the folder created by it before we can re-run the command again, which will then report missing files such as mri_convert along with a few others that magically disappear from the bin folder.

Everything works on version 7.1.1 as it should but they want to use 7.4.1 to make use of some more functions and version 7.4.1 is the version we are having the issue with.

OS: Ubuntu 22.04 LTS

Freesurfer :freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460

FREESURFER_HOME: /usr/local/freesurfer (points to 7.4.1)

uname -a: Linux linux-tpolk04 5.15.0-124-generic #134-Ubuntu SMP Fri Sep 27 20:20:17 UTC 2024 x86_64 x86_64 x86_64 GNU/Linux

See attached log for details.

I've CC'd a Grad member (Noah) of the lab who I've been working closely with to help resolve this who can answer some questions as well. I am the Desktop Support Specialist assisting with this issue so I can handle the technical side as needed.