Hello FreeSurfer Community,

I am attempting to use mri_watershed to create BEM surfaces, but for some of my subjects part of the cerebellum is being cut off.  Adjusting the threshold was not sufficient, so I attempted to add a seed point in the cerebellum using the following command:

mri_watershed -atlas -useSRAS -surf ./surfout -s [105 182 81] ./T1.mgz ./brainvol

The coordinates for the seed point are from the T1.mgz image.  I reran mri_watershed and the seed point does not seem to be taken into consideration so I’m thinking that the input format I used may be wrong.  Could someone please tell me if I am not using the proper input format?  And what format to use if I wish to add multiple seed points?  Command output is attached.

Thanks in advance!

Kristen

Kristen Kanoff

Clinical Research Coordinator II
Department of Neurology

Massachusetts General Hospital

Boston, MA

Ph: 617-726-3958