Try adding --samseg to the command line

On 3/8/2025 7:06 PM, Miguel Ángel Rivas Fernández 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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