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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
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
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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
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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.sohttp://secure-web.cisco.com/1dF9tLcnZOx0DHv3gocdjdhpbBkesdutxF2E9IX-HcmlwJEDpQmJLG_Jk3qpkjvl3-zBuJqfbWYd2SvRS4y3iuM3vtfPyjREOvowRIMvHQpjOzepzka7aIJQsLlssA1m0UkmOQyRlnhp8UatFg1_rGH-W_IZHtAgDtGIg5vqAfWUn4po-eaStXAuC4yaS2hpjcN3WmANETPnHg0vW9tLRoX8gGVihStHqP3xCNezgGqQIwpR2nbvDMf-i8iB0eQdxD4OCMuj9lzUHC97dFVZgtKBHGnRm1iEty5IMjD8aZUn_xbDJT7U3wEx4tJplS0ZmR9t8MZk3y27vyftNMXEHIA/http%3A%2F%2Fgemsbindings.cpython-312-x86_64-linux-gnu.so
Le lun. 23 mars 2026 à 17:22, Huang, Yujing <YHUANG43@mgh.harvard.edumailto:YHUANG43@mgh.harvard.edu> a écrit : Can you check if you have the binding library gemsbindings.cpython-38-x86_64-linux-gnu.sohttp://secure-web.cisco.com/1KH9t7i6r_kkTaev5XyitPQergfZ5TmqQVa0fi_1YI9PevXxm2WMYJfYUlQAPHwOQWbTLEM-R4q8WvUiuQ6IDeWLtIoF4YDoTZMgCu2x54-vPcF2GbNOedgQyuBza7eys3DIYjK2zsj3Mfz218HoWn52K1O-I05ogd2ghB1GU9VkhqjWQv2iKb_Q7NiuQjdNDrQcnDW82nu7PXeKop9eo8uzsNG_Lahm9zX34K4yfo3SgWOFNPEwoENUWFrOsgxszvlAq3tN-hluHZw6XjJ6_aJzuZ1LDj01oJ6tbHwI8E-8uOmJPG3Ic8r60KaaNjUw7YY7fz_djETLoYNgWX5SV8A/http%3A%2F%2Fgemsbindings.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.commailto:valentin.demeusy@gmail.com> Sent: Monday, March 23, 2026 8:34 AM To: freesurfer@nmr.mgh.harvard.edumailto: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.edumailto:freesurfer@nmr.mgh.harvard.edu To unsubscribe send an email to freesurfer-leave@nmr.mgh.harvard.edumailto:freesurfer-leave@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman3/lists/freesurfer@nmr.mgh.harvard.e...https://secure-web.cisco.com/1In-n88A-UUnnRKRJLJmo0BBG38rsvocRJj779QXtIPHVPMnyySEMYqol2QTBSS2b787t_lRf1tHAa0qOWGtHgf5NlHSPM8AW4Sp82bdECA83nNCLWVHHH7VWZbN2oj5p31vQncpbruHIBtaiYQ2VLbwEc1HCBlxvAdPU-pAmSvKiDJ0eGpvAyK3aZ3dNcwpjGJiQgJxi_z6mpUXBbTX5dR4LyyptULed6G1OUsW4AEYwVEDr4dj0Jyfq6qHQnYcXX94BQEycoK1STMZ0jbslqY51iv6Vr5PWG6Ier-MBdOT_QL582InlyitJgP2k-bUwcMYAiAfvKcGF7CF_fqvByA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman3%2Flists%2Ffreesurfer%40nmr.mgh.harvard.edu%2F 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/compliancelinehttps://secure-web.cisco.com/1cIi8SZG9v1Vi6ee9rWfhlqfIYF8XUemSKxPAOW4gwybp7KJMNetghsBoDNGHOBtMadG0miFicoTgTstiieBjtt9PSqzZR1UUywxm6sXB_se9-2yOQKQ5GX_SaaJV1MZYunDUo9Cg-2LpFyjatUC2dlFSih7UjDY9sYv7-Lf3PQH-4q2j_fhEkVHNPIw1qnPEgw_D98boWFNMPlviOqM-Rhv-_BgT4sv6Y7RGkRFUJGG8wXfCcg1unXmSnBIlUhHv74KIdw5gQ7ct2YYWy2ohxckiMaUMzTsBi4eEs8-5pbuC7KkBjHTwSMeVgwwOqZ4f32sbq3mnziUGckTGdxIuAg/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline <https://www.massgeneralbrigham.org/compliancelinehttps://secure-web.cisco.com/1cIi8SZG9v1Vi6ee9rWfhlqfIYF8XUemSKxPAOW4gwybp7KJMNetghsBoDNGHOBtMadG0miFicoTgTstiieBjtt9PSqzZR1UUywxm6sXB_se9-2yOQKQ5GX_SaaJV1MZYunDUo9Cg-2LpFyjatUC2dlFSih7UjDY9sYv7-Lf3PQH-4q2j_fhEkVHNPIw1qnPEgw_D98boWFNMPlviOqM-Rhv-_BgT4sv6Y7RGkRFUJGG8wXfCcg1unXmSnBIlUhHv74KIdw5gQ7ct2YYWy2ohxckiMaUMzTsBi4eEs8-5pbuC7KkBjHTwSMeVgwwOqZ4f32sbq3mnziUGckTGdxIuAg/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> .
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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 http://secure-web.cisco.com/1dF9tLcnZOx0DHv3gocdjdhpbBkesdutxF2E9IX-HcmlwJEDpQmJLG_Jk3qpkjvl3-zBuJqfbWYd2SvRS4y3iuM3vtfPyjREOvowRIMvHQpjOzepzka7aIJQsLlssA1m0UkmOQyRlnhp8UatFg1_rGH-W_IZHtAgDtGIg5vqAfWUn4po-eaStXAuC4yaS2hpjcN3WmANETPnHg0vW9tLRoX8gGVihStHqP3xCNezgGqQIwpR2nbvDMf-i8iB0eQdxD4OCMuj9lzUHC97dFVZgtKBHGnRm1iEty5IMjD8aZUn_xbDJT7U3wEx4tJplS0ZmR9t8MZk3y27vyftNMXEHIA/http%3A%2F%2Fgemsbindings.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 http://secure-web.cisco.com/1KH9t7i6r_kkTaev5XyitPQergfZ5TmqQVa0fi_1YI9PevXxm2WMYJfYUlQAPHwOQWbTLEM-R4q8WvUiuQ6IDeWLtIoF4YDoTZMgCu2x54-vPcF2GbNOedgQyuBza7eys3DIYjK2zsj3Mfz218HoWn52K1O-I05ogd2ghB1GU9VkhqjWQv2iKb_Q7NiuQjdNDrQcnDW82nu7PXeKop9eo8uzsNG_Lahm9zX34K4yfo3SgWOFNPEwoENUWFrOsgxszvlAq3tN-hluHZw6XjJ6_aJzuZ1LDj01oJ6tbHwI8E-8uOmJPG3Ic8r60KaaNjUw7YY7fz_djETLoYNgWX5SV8A/http%3A%2F%2Fgemsbindings.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
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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.edumailto: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.commailto:valentin.demeusy@gmail.com> Sent: Monday, March 23, 2026 12:30 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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.sohttp://secure-web.cisco.com/1dF9tLcnZOx0DHv3gocdjdhpbBkesdutxF2E9IX-HcmlwJEDpQmJLG_Jk3qpkjvl3-zBuJqfbWYd2SvRS4y3iuM3vtfPyjREOvowRIMvHQpjOzepzka7aIJQsLlssA1m0UkmOQyRlnhp8UatFg1_rGH-W_IZHtAgDtGIg5vqAfWUn4po-eaStXAuC4yaS2hpjcN3WmANETPnHg0vW9tLRoX8gGVihStHqP3xCNezgGqQIwpR2nbvDMf-i8iB0eQdxD4OCMuj9lzUHC97dFVZgtKBHGnRm1iEty5IMjD8aZUn_xbDJT7U3wEx4tJplS0ZmR9t8MZk3y27vyftNMXEHIA/http%3A%2F%2Fgemsbindings.cpython-312-x86_64-linux-gnu.so
Le lun. 23 mars 2026 à 17:22, Huang, Yujing <YHUANG43@mgh.harvard.edumailto:YHUANG43@mgh.harvard.edu> a écrit : Can you check if you have the binding library gemsbindings.cpython-38-x86_64-linux-gnu.sohttp://secure-web.cisco.com/1KH9t7i6r_kkTaev5XyitPQergfZ5TmqQVa0fi_1YI9PevXxm2WMYJfYUlQAPHwOQWbTLEM-R4q8WvUiuQ6IDeWLtIoF4YDoTZMgCu2x54-vPcF2GbNOedgQyuBza7eys3DIYjK2zsj3Mfz218HoWn52K1O-I05ogd2ghB1GU9VkhqjWQv2iKb_Q7NiuQjdNDrQcnDW82nu7PXeKop9eo8uzsNG_Lahm9zX34K4yfo3SgWOFNPEwoENUWFrOsgxszvlAq3tN-hluHZw6XjJ6_aJzuZ1LDj01oJ6tbHwI8E-8uOmJPG3Ic8r60KaaNjUw7YY7fz_djETLoYNgWX5SV8A/http%3A%2F%2Fgemsbindings.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.commailto:valentin.demeusy@gmail.com> Sent: Monday, March 23, 2026 8:34 AM To: freesurfer@nmr.mgh.harvard.edumailto: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
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The issue is addressed in the recent updates. See downloading instructions at, https://surfer.nmr.mgh.harvard.edu/fswiki/rel7downloads/rel8notes
External Email - Use Caution
Thanks, can you please also release a new version of the package ? ( https://secure-web.cisco.com/1pBrQ_g4ZBjox7cdALtSPxvlQ5cTFbaXA1DsmXaECrs9OH-... ) This would be easier for the people who wants to setup FreeSurfer 8.2.0 on Ubuntu 24 from scratch or for the docker images. Thank you.
Le jeu. 26 mars 2026 à 13:00, Huang, Yujing YHUANG43@mgh.harvard.edu a écrit :
The issue is addressed in the recent updates. See downloading instructions at, https://secure-web.cisco.com/1KLmDQyyV7L6HZAPsTcSfhYuhz_jGCRBZXBRPPVqCFRVnim...
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freesurfer@nmr.mgh.harvard.edu
-
Huang, Yujing -
Valentin Demeusy