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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