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Dear developers,

I am trying to clean up the extra dura left after skullstripping. Watershed parameter does not prove to be much helpful and when I try gcut I get the error below. In the archives I came across this exact problem before, https://secure-web.cisco.com/1JREA1RCtgfPRaolYsneD7S5EwcqlaqoCEQHN3rqgzcSwxB...

However, there was not an end solution available in the archived email exchange. I am not interested in cerebellum and am okay with cutting the cerebellum out of the brain mask as long as it does not interfere with being able to distinctly separate cortex from cerebellum in the following steps. From skullstripping tutorials, I have read that one should not start erasing cerebellum from the brainmask directly and was wondering if you could let me know why?

In sum, are there important reasons to keep the cerebellum despite only being interested in analyzing the cortex?

If not, could you please let me know what could be the reason for gcut's failure and if there is anyway to disable failure detection so I can see if the gcutted brain is usable?

...

" rm -f brainmask.gcuts.mgz mri_gcut -110 -mult brainmask.auto.mgz T1.mgz brainmask.auto.mgz brainmask.gcuts.mgz

INFO: Care must be taken to thoroughly inspect your data when using mri_gcut. In particular, inspect the edges of gm and cerebellum for over-aggressive cutting. Add -segmentation brainmask.gcuts.mgz to the tkmedit command string to view the voxels which gcut has removed.

reading mask... white mean: 107.529232 threshold set to: 107.529232*0.400000=43.011693 calculating weights... doing mincut... now doing maxflow, be patient... g-cut done! post-processing... post-processing done! masking... ** Gcutted brain is much smaller than the mask! ** Using the mask as the output instead!

cp brainmask.auto.mgz brainmask.mgz "

1) FreeSurfer version: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0. 2) Platform: Linux Mint 20.2

Thank you greatly for your time and efforts.

Kindest regards,

Begum Cerrahoglu