Martin, If you scroll up a few slices before and after where you are having the problem, do you see areas where the wm appears to disconnect even if it's only by one voxel?

I've attached a picture showing an example. Sometimes, even if the wm is disconnected nowhere near the surface problems you are seeing, it still might be causing that problem. You should look for disconnects outside the surface and add wm there. Let me know if this works otherwise it may be some other issue. Allison

On Mon, 24 Nov 2008, Martin Ystad wrote:

Hi, I have been trying to make freesurfer include all of my white matter in the wm-surface. It seems to run directly across some of the gyri in my brain volume (see attached picture). I first tried to add control points at the base of the gyri, and then along the gyri, but that did not seem to have much effect. Then I manually drew the white matter onto the wm.mgz-volume (see attached picture), but that did only help for some of my gyri. Do you have any tips on how to force freesurfer to include the remaining white matter in the wm surface?

Thanks, Martin Ystad