Hi Diana
the subcortical segmentation only uses the brainmask as a binary in brain/out of brain mask to remove non-brain tissue. The intensities are irrelevant - only the intensities in the norm.mgz matter for the aseg.
cheers Bruce On Tue, 21 Nov 2017, diana hobbs wrote:
Update to my first email:
Hello again FS Developers and anyone experiencing the same problems,
A colleague of mine has found what we think has already been addressed in the following link: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2016-November/048666....
From the sounds of it, this doesn't seem to be a real issue; however, I would love to better understand why this doesn't matter in the long run, i.e. why the brainmask does not later affect parcellation of subcortical regions(?).
Thank you for your time!
Diana