Dear Freesurfer community,

I am using the mri_watershed command to create BEM surfaces and have run into an issue with a large posterior chunk of skull being treated as brain. 

I have attempted the following to correct the issue:

1.  Removed the –atlas flag

2. Used –less to decrease the transition threshold used during the fine surface deformation

3. Used –man to set more/less stringent parameters for the intensity values

4. Adjusted the preflooding height

5. Used the –first_temp flag in combination with –man

Removing the –atlas flag and using –less to shrink the surface seemed to provide the best result (image shown above) but the issue is not entirely resolved.  Does anyone have any suggestions for a better approach?  I can manually adjust the brain mask created during the recon-all process but there doesn’t seem to be a way to do something similar when using mri_watershed alone.

I also attempted to use the –wat+temp flag (command:  mri_watershed -wat+temp -useSRAS -surf ./surfout ./T1.mgz ./brainvol) but I am getting the following error:

mri_watershed Error:

 Problem in find normal

The full command window output is attached.

Any help/suggestions would be very much appreciated!

Best,

Kristen