Hi Mahinda
it depends on whether the frontal regions in the brainmask.mgz have intensities significantly lower than 110. Probably what you are seeing is incorrect topology fixing which is usually due to incorrect segmentation. The question is why is the segmentation incorrect.
cheers Bruce
On Sun, 4 Dec 2011, Mahinda Yogarajah wrote:
Dear Freesurfer Experts,
I am processing some coronally acquired 3T GE FSPGR T1 volumes. I have noticed that on occasion slices pial and white surfaces at the very front of the brain can go very wrong - either frontal slices are excluded all together (present in brainmask.mgz but no pial or wm surfaces derived) or white matter is mistakenly classified as grey matter.
In order to correct this am I correct in assuming that the best method would be to use control points to fix the intensity normalisation ? Alternatively, when is it better to edit the wm.mgz volume to include those voxels which are white matter ? - It is not entirely clear to me from the tutorial.
Thank you.
M