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Dear support
I'm running the following command in Freesurfer 7.4:
samseg --t1w ${SUBJECTS_DIR}/subjOPA${ss}/mri/orig/001.mgz --flair
${SUBJECTS_DIR}/subjOPA${ss}/mri/orig/oFL.mgz --t2w
${SUBJECTS_DIR}/subjOPA${ss}/mri/orig/oT2.mgz --s subjOPA${ss} --refmode
t1w --pallidum-separate --lesion --fill --threads 16 --save-posteriors
everything runs smoothly, but when I check the results I see some holes in
the midbrain, in particular the red nucleus is labeled as csf.
If I look at the T2.mgz file in the mri folder (I also run samseg2recon so
I'm not sure it is the name given by samseg) I see that the red nucleus is
set to zero, despite having non-zero values in the T2.norm.mgz volume.
Two questions:
1) how can I avoid low-intensity T2 regions to be set to CSF?
2) is it possible to provide a brain mask to samseg if I already have a
reliable one?
[image: Screenshot from 2025-04-02 15-20-51.png]
Simone Cauzzo
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