When I see the images through freeview to edit, upper brainstem and optic chiasm were always included in wm or brainmask.mgz, as an attached picture below. Left side seems to be recognized as white matter, and right side as cortex. My concern is that this could affect the final value of e-TIV after recon-all process, so I need to edit these areas manually.

I'd appreciated your help. Thanks so much.