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.
[cid:image002.jpg@01D2D47E.75797E70]
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
