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