External Email - Use Caution
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
