Hi Akram,
In that case, you will need to manually edit the WM volume to separate cerebellum from WM.
You can load both WM and filled volume to tkmedit, and go through the slices to see where in "filled" volume cerebellum is connected to WM, and then edit the WM to cut off the connections. Then, save the edited WM to replace the old one.
After the editing of WM, rerun mri_fill (or -stage2 of recon-all).
Hope that helps.
Xiao Han
On Tue, 12 Jul 2005, Bakkour, Akram wrote:
Dear all, I am working on a recent MPRAGE image obtained at MGH. First, we had trouble converting the files, but Dr. Ress converted it to analyze manually, I then used that analyze file in freesurfer. The image has a lot of inhomogeneity and the intensity is variable from the back and front of the brain and also between hemispheres. wmfill includes the cerebellum as RH even if I set the coordinates for the cutting planes in expert preferences. Any suggestions as to what I should try next? Thanks for the help! Regards, Akram.
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