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I see. It seems then that the most appropriate path forward then is to not
specify -synthseg for any of the longitudinal processing.
You mentioned that the synth commands are currently experimental. I've also
been specifying -synthstrip (during CROSS),
I don't know if it is appropriate or not. The use of the synth commands
is experimental and I was not intending for anyone to use them yet.
That's why I put in the FS_ALLOW_DEEP hook to act as a barrier. You
obviously have the expertise to get past that barrier, but it put you
into a no-man's-l
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Thanks, Doug.
I've spent some time trying to troubleshoot this issue, and have realized
the following:
1). During the CROSS recon-all when I add -synthseg, no
mri/transforms/talairach.m3z file is created in the CROSS folder.
2). During the BASE recon-
Yes, that is the problem, not a lot of great options. One thing you
could try is to run synthmorph to create the m3z.
On 6/10/2024 2:36 PM, Dan Levitas wrote:
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Hello,
I am following the longitudinal freesurfer pipeline
(https://surfer.nmr.mgh.harvard.ed
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Hello,
I am following the longitudinal freesurfer pipeline (
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/LongitudinalTutorial)
and getting this error on the final (LONG) portion:
*ERROR: cannot find or read transforms/talairach.m3z*
I can c
