Sorry, I should not have suggested using ‘—no-samseg’. It will produce different results. We are working on fixing gemsbinding on Ubuntu 24.
From: Valentin Demeusy <valentin.demeusy@gmail.com>
Sent: Monday, March 23, 2026 1:41 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Re: [8.2.0] [Ubuntu 24] Issue with gtmseg with FreeSurfer 8.2.0 on Ubuntu 24
External Email - Use Caution
I tried the --no-samseg option but I get an error:
ERROR: cannot find /usr/local/freesurfer/8.2.0/subjects/fs/mri/transforms/talairach.m3z
Try using the --samseg flag
Le lun. 23 mars 2026 à 17:36, Huang, Yujing <YHUANG43@mgh.harvard.edu> a écrit :
The python version should be 3.8. We will investigate this further.
If you pass "--no-samseg" to gtmseg, it will not run samseg.
From: Valentin Demeusy <valentin.demeusy@gmail.com>
Sent: Monday, March 23, 2026 12:30 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Re: [8.2.0] [Ubuntu 24] Issue with gtmseg with FreeSurfer 8.2.0 on Ubuntu 24
External Email - Use Caution
No, I have this file instead: ${FREESURFER_HOME}/python/lib/python3.8/site-packages/samseg/gems/gemsbindings.cpython-312-x86_64-linux-gnu.so
Le lun. 23 mars 2026 à 17:22, Huang, Yujing <YHUANG43@mgh.harvard.edu> a écrit :
Can you check if you have the binding library gemsbindings.cpython-38-x86_64-linux-gnu.so in /usr/local/freesurfer/8.2.0/python/lib/python3.8/site-packages/samseg/gems/?
From: Valentin Demeusy <valentin.demeusy@gmail.com>
Sent: Monday, March 23, 2026 8:34 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] [8.2.0] [Ubuntu 24] Issue with gtmseg with FreeSurfer 8.2.0 on Ubuntu 24
External Email - Use Caution
Hello developpers,
I have an issue when I try to run `gtmseg` on Ubuntu 24 in a docker image.
I previously ran recon-all with the same FreeSurfer version and same OS flawlessly.
But when I run gtmseg (gtmseg --s $subjectName). I get the following error:
Traceback (most recent call last):
File "/usr/local/freesurfer/8.2.0/python/scripts/run_samseg", line 5, in <module>
from samseg.cli.run_samseg import main
File "/usr/local/freesurfer/8.2.0/python/lib/python3.8/site-packages/samseg/__init__.py", line 5, in <module>
from .SamsegUtility import *
File "/usr/local/freesurfer/8.2.0/python/lib/python3.8/site-packages/samseg/SamsegUtility.py", line 8, in <module>
from samseg import gems
File "/usr/local/freesurfer/8.2.0/python/lib/python3.8/site-packages/samseg/gems/__init__.py", line 1, in <module>
from .gemsbindings import *
ModuleNotFoundError: No module named 'samseg.gems.gemsbindings'
You will find the complete log at the end of this mail.
Thank you for your help
Valentin Demeusy
Here is the complete log of the command:
Mon Mar 23 02:43:20 UTC 2026
setenv SUBJECTS_DIR /mnt/subjectDir
cd /mnt/subjectDir/fs
/usr/local/freesurfer/8.2.0/bin/gtmseg --s fs
freesurfer-linux-ubuntu24_x86_64-8.2.0-20260314-d932c45
gtmseg 8.2.0
Linux 1587b43e469e 6.17.0-1008-azure #8~24.04.1-Ubuntu SMP Mon Jan 26 18:35:40 UTC 2026 x86_64 x86_64 x86_64 GNU/Linux
xcerebralseg --s fs --threads 1 --o apas+head.samseg.mgz
Mon Mar 23 02:43:20 UTC 2026
setenv SUBJECTS_DIR /mnt/subjectDir
cd /mnt/subjectDir/fs
/usr/local/freesurfer/8.2.0/bin/xcerebralseg --s fs --threads 1 --o apas+head.samseg.mgz
freesurfer-linux-ubuntu24_x86_64-8.2.0-20260314-d932c45
xcerebralseg 8.2.0
Linux 1587b43e469e 6.17.0-1008-azure #8~24.04.1-Ubuntu SMP Mon Jan 26 18:35:40 UTC 2026 x86_64 x86_64 x86_64 GNU/Linux
fs_time samseg --i /mnt/subjectDir/fs/mri/nu.mgz --o /mnt/subjectDir/fs/mri/xcerebral.samseg --threads 1 --cpvcw
/mnt/subjectDir/fs/mri/xcerebral.samseg /mnt/subjectDir/fs
/mnt/subjectDir/fs
Mon Mar 23 02:43:21 UTC 2026
setenv SUBJECTS_DIR /mnt/subjectDir
cd /mnt/subjectDir/fs
/usr/local/freesurfer/8.2.0/bin/samseg --i /mnt/subjectDir/fs/mri/nu.mgz --o /mnt/subjectDir/fs/mri/xcerebral.samseg --threads 1 --cpvcw
freesurfer-linux-ubuntu24_x86_64-8.2.0-20260314-d932c45
samseg 8.2.0
Linux 1587b43e469e 6.17.0-1008-azure #8~24.04.1-Ubuntu SMP Mon Jan 26 18:35:40 UTC 2026 x86_64 x86_64 x86_64 GNU/Linux
Using Block Coordinate Descent
NOT using Log Domain Cost And Gradient Calculator
run_samseg -o /mnt/subjectDir/fs/mri/xcerebral.samseg --threads 1 --atlas /usr/local/freesurfer/8.2.0/average/samseg/samseg+cc+pons+verm+charm+wmcrowns --save-warp -i /mnt/subjectDir/fs/mri/nu.mgz
Traceback (most recent call last):
File "/usr/local/freesurfer/8.2.0/python/scripts/run_samseg", line 5, in <module>
from samseg.cli.run_samseg import main
File "/usr/local/freesurfer/8.2.0/python/lib/python3.8/site-packages/samseg/__init__.py", line 5, in <module>
from .SamsegUtility import *
File "/usr/local/freesurfer/8.2.0/python/lib/python3.8/site-packages/samseg/SamsegUtility.py", line 8, in <module>
from samseg import gems
File "/usr/local/freesurfer/8.2.0/python/lib/python3.8/site-packages/samseg/gems/__init__.py", line 1, in <module>
from .gemsbindings import *
ModuleNotFoundError: No module named 'samseg.gems.gemsbindings'
run_samseg complete
Mon Mar 23 02:43:22 UTC 2026
lta_convert --inlta /mnt/subjectDir/fs/mri/xcerebral.samseg/samseg.talairach.lta --outmni /mnt/subjectDir/fs/mri/xcerebral.samseg/samseg.talairach.xfm
8.2.0
--inlta: /mnt/subjectDir/fs/mri/xcerebral.samseg/samseg.talairach.lta input LTA transform.
--outmni: /mnt/subjectDir/fs/mri/xcerebral.samseg/samseg.talairach.xfm output MNI/XFM matrix.
ERROR: lta_convert --inlta /mnt/subjectDir/fs/mri/xcerebral.samseg/samseg.talairach.lta --outmni /mnt/subjectDir/fs/mri/xcerebral.samseg/samseg.talairach.xfm
ERROR:
ERROR: xcerebralseg --s fs --threads 1 --o apas+head.samseg.mgz
gtmseg exited with errors_______________________________________________
Freesurfer mailing list -- freesurfer@nmr.mgh.harvard.edu
To unsubscribe send an email to freesurfer-leave@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman3/lists/freesurfer@nmr.mgh.harvard.edu/
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline <https://www.massgeneralbrigham.org/complianceline> ._______________________________________________
Freesurfer mailing list -- freesurfer@nmr.mgh.harvard.edu
To unsubscribe send an email to freesurfer-leave@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman3/lists/freesurfer@nmr.mgh.harvard.edu/
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline <https://www.massgeneralbrigham.org/complianceline> .