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.

External Email - Use Caution
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.edumailto:jsneal@umich.edu LSA EHTS Desktop Support Specialist Senior University of Michigan
On Nov 6, 2024, at 10:43 AM, Jeffrey Neal <jsneal@umich.edumailto: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.
Hello,
Thanks for the helpful links. I did double check through everything and it all looks correct; Sorry about the log file I needed to change permissions on it. Here is the log file from the first email and here is an additional one from today as well as some screenshots: After running it once and getting the “terminated by signal 9” error when I try to run it again packages have disappeared out of the freesurfer/bin causing more issues. The command they are running is make recon-all -k. If you need to see the makefile or other things let me know and I will get them for you.
 Best Regards, Jeffrey Neal jsneal@umich.edu LSA EHTS Desktop Support Specialist Senior University of Michigan
On Nov 6, 2024, at 4:27 PM, Huang, Yujing YHUANG43@mgh.harvard.edu wrote:
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‘recon-all’ is a shell script that is ready to be run. I don’t understand why they need to have makefile to make recon-all.
Here are the steps to setup Freesurfer environment and run ‘recon-all’:
1. Source the correct Freesurfer environment needs to be sourced before running recon-all - https://surfer.nmr.mgh.harvard.edu/fswiki/SetupConfiguration_Linux 2. Set ‘SUBJECTS_DIR’ to point to directory outside the Freesurfer installation tree, and make sure you have write permission 3. Run recon-all https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all
(ex. recon-all -all -s <> -i <>)
Yujing
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Jeffrey Neal Sent: Monday, November 11, 2024 10:47 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Cc: Noah Reardon nreardon@umich.edu Subject: Re: [Freesurfer] [WARNING: ATTACHMENT UNSCANNED]Re: mri_convert: Command terminated by signal 9
Hello,
Thanks for the helpful links. I did double check through everything and it all looks correct; Sorry about the log file I needed to change permissions on it. Here is the log file from the first email and here is an additional one from today as well as some screenshots: After running it once and getting the “terminated by signal 9” error when I try to run it again packages have disappeared out of the freesurfer/bin causing more issues. The command they are running is make recon-all -k. If you need to see the makefile or other things let me know and I will get them for you.
[cid:image001.jpg@01DB3439.51793600] [cid:image002.png@01DB3439.51793600] Best Regards, Jeffrey Neal jsneal@umich.edumailto:jsneal@umich.edu LSA EHTS Desktop Support Specialist Senior University of Michigan
On Nov 6, 2024, at 4:27 PM, Huang, Yujing <YHUANG43@mgh.harvard.edumailto:YHUANG43@mgh.harvard.edu> wrote:
freesurfer@nmr.mgh.harvard.edu
-
Huang, Yujing -
Jeffrey Neal