I was wondering if Freesurfer has a standard way of cutting off the measurement of brain stem volume across subjects, or does the volume of the brain stem depend on the individual’s skull strip?  In the two examples below, you can see that the brain stem of the second individual extends beyond that of the first (visually and according to its aseg label).  Theoretically, could the reported volumes of these two individuals’ brain stems be different just because their skull strip was different?

Thank you,

Heather