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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@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
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