I am running into issues with mri_watershed, which I am using the create the BEM surfaces. In testing different preflooding height threshold (recommended for accurate skull-stripping), I am running into the issues that an -h 56 produces results where the cerebellum is stripped away, but -h 57 leaves far too much non-brain material in the image. As a result, my BEM surfaces are unrepresentative of the brain (either shrunken in or enlarged). 

I do, however, already have a satisfying brain-mask. Is there a way to pass the brain mask to mri_watershed to create new BEM surfaces without it creating a new brain mask?

Clinical Research Coordinator
Division of Neurotherapeutics
Department of Psychiatry: Neurosciences
Massachusetts General Hospital
149 13th Street, Rm 2620e
Charlestown, MA 02129