Are you saying that synthseg itself is generating the wrong seg or that
something is going wrong further downstream? The recon-all stream with
synthseg is not a supported pipeline at the moment. For the standard
stream, can you send the full recon-all.log file?
On 1/29/2024 2:04 PM, Maya Yablonski wrote:
External Email - Use Caution
Hello,
I am running freesurfer v7.3.2 reconall with -synthseg on a pediatric
sample, and for one specific subject I keep getting a lot of gray
matter classified as white matter, which leads to the ?h.white
surfaces being too close to the pial surface. I have tried running
with and without the --robust option but the issue recurs. Are there
any expert options that I can play with before manually editing the
WM.mgz? The issue is pervasive throughout the brain so will require
heavily editing every single slice. The values for the misclassified
gray matter are 85-97 in the brainmask.mgz and 100-110 in the WM.mgz
and the T1 image looks ok by eye. When trying to run the same subject
with the default pipeline (no synthseg), it crashes with the following
error:
reading 1 input volumes...
logging results to talairach.log
reading
'/share/software/user/open/freesurfer/7.3.2/average/RB_all_2020-01-02.gca'...
GCAread took 0 minutes and 1 seconds.
average std = 7.2 using min determinant for regularization = 5.2
0 singular and 884 ill-conditioned covariance matrices regularized
reading 'nu.mgz'...
error: mghRead(/MYPATH/freesurfer/sub-2341/mri/brainmask.mgz, -1):
could not open file
error: mri_em_register: could not open mask volume brainmask.mgz.
I wonder if there's any parameter I can tweak in the expert.opts?
Thanks for any leads,
Maya
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