Hi Guang,

hard to say from just images, but it looks like those voxels are a lot darker than the rest of the gray matter. Did you visualize the surfaces? They may be voxels that contain a bunch of csf - if you look at them in another plane you could tell.

cheers, Bruce

On Wed, 31 Mar 2010, Guang Zeng wrote:

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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