Hi, there,

I have a scan which FreeSurfer skull-stripping gave me a bad brainmask (see fig. 1).
I created a brainmask by using SPM segmentation results, then converted it to FreeSurfer format with --conform flag on.
Finally, I masked T1.mgz using this brainmask, and I used it as my brainmask.mgz (see fig. 2) to run the rest part (-autorecon2  -autorecon3)

However,  when I loaded the new aseg.mgz,  I found that lots of boundary voxel were not labled (see fig. 3)

Anyone can give me some suggestions to fix this problem? Thanks a lot!

Guang

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