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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