The ‘gtmseg’ issue is addressed in recent updates/fixes to FS 8.0. See this post for detail https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg77819.html

‘gtmseg’ is changed to use ‘samseg’ by default.

Yujing

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Simon Jones
Sent: Friday, May 16, 2025 1:19 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Freesurfer 8 + PetSurfer talairach.m3z

        External Email - Use Caution        

Dear FS

I tried to perform PetSurfer following recon-all pipeline using FreeSurfer 8. When I run

gtmseg –s $sub

I get error

ERROR: cannot find talairach.m3z

I was able to create the file talairach.m3z which is omitted from version 8 recon-all pipeline using mri_ca_register but I guess I should be converting the files in the subject/mri/transforms/synthmorph.1.0mm.1.0mm directory into talairach.m3z using mri_warp_convert. Is there an example of how to do that or are some other steps recommended?

Thanks,

Simon