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-land that we do not support./
On 6/17/2024 10:33 AM, Dan Levitas wrote:
External Email - Use Caution
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-all when no -synthseg is specified, a
mri/transforms/talairach.m3z file is created in the BASE folder.
3). During the LONG recon-all (no -synthseg) specified, I'm able to
successfully complete the process.
Is this approach (specify -synthseg only for the CROSS recon-all)
appropriate for longitudinal processing?
On Mon, Jun 17, 2024 at 10:21 AM Douglas N. Greve
<dgr...@mgh.harvard.edu> wrote:
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:
External Email - Use Caution
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 confirm that recon-all ran successfully during the CROSS
and BASE portions; it is only when I attempt to perform recon-all
-long that things fail.
My suspicion is that CA registration was not performed during
CROSS, as I used -synthseg (and -synthstrip) in that recon-all
command. I'm unsure if I need to go back and specify -careg in
the CROSS recon-all command (e.g. /recon-all -autorecon2
-careg/), or if there is some way to bypass this error. I tried
appending -nocareg to the end of my LONG recon-all command, but
this errored out with the following output:
/mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta
/N/project/Kawata_TBI_1/R01_HighSchool_BIDS/derivatives/freesurfer/sub-1000_ses-2pre.long.sub-1000/mri/transforms/cc_up.lta
sub-1000_ses-2pre.long.sub-1000
will read input aseg from aseg.auto_noCCseg.mgz
writing aseg with cc labels to aseg.auto.mgz
will write lta as
/N/project/Kawata_TBI_1/R01_HighSchool_BIDS/derivatives/freesurfer/sub-1000_ses-2pre.long.sub-1000/mri/transforms/cc_up.lta
reading aseg from
/N/project/Kawata_TBI_1/R01_HighSchool_BIDS/derivatives/freesurfer/sub-1000_ses-2pre.long.sub-1000/mri/aseg.auto_noCCseg.mgz
error:
mghRead(/N/project/Kawata_TBI_1/R01_HighSchool_BIDS/derivatives/freesurfer/sub-1000_ses-2pre.long.sub-1000/mri/aseg.auto_noCCseg.mgz,
-1): could not open file/
Thanks for the assistance.
Dan
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