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I’m not familiar with the gtmseg command, but I think you can revert to the old recon-all behavior by setting FS_V8_XOPTS=0 on the recon-all command line.  That is listed under recon-all behavior at, 
https://surfer.nmr.mgh.harvard.edu/fswiki/rel7downloads/rel8notes

- R.

On Mar 8, 2025, at 19:06, Miguel Ángel Rivas Fernández <miguelrivasfdez@gmail.com> wrote:

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Dear Freesurfer developers,

I have run the recon-all command with version 8.0.0 and now I would like to run the gtmseg command. However, I received the message below. It seems to be looking for the file talairach.m3z in the transforms folder, but that is not one of the outputs in the new version. In the latest version of Freesurfer, is it no longer possible to run gtmseg? Is there any way to enable the recon-all from previous versions in version 8, or should I download an older version?


setenv SUBJECTS_DIR /input/Freesurfer_outputs/
cd /home/matlab
/usr/local/freesurfer//bin/gtmseg --s sub-NDARINVEMZZZWB9

freesurfer-linux-ubuntu20_x86_64-8.0.0-20250204-0f2bd3a
gtmseg 8.0.0
Linux test-757bb4cd4-g5rv5 6.4.0-150600.23.30-default #1 SMP PREEMPT_DYNAMIC Sat Dec  7 08:37:53 UTC 2024 (8c25a0a) x86_64 x86_64 x86_64 GNU/Linux
xcerebralseg --s sub-NDARINVEMZZZWB9 --threads 1 --o apas+head.mgz
ERROR: cannot find /input/Freesurfer_outputs//sub-NDARINVEMZZZWB9/mri/transforms/talairach.m3z
ERROR: xcerebralseg --s sub-NDARINVEMZZZWB9 --threads 1 --o apas+head.mgz
gtmseg exited with errors



Thank you very much

Best

-- 
Miguel Ángel Rivas Fernández




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