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?