Dear all,
I'm new in freesurfer. I ran "recon-all -all" on 8 subjects without error, and I loaded the wm.mgz and the surfs. White matter surface (yellow line) seems pretty good by visual inspection, but the wm.mgz seems not so good everywhere. There are certain white-matter areas, which are clearly inside the yellow line (WM surface) but they are not considered as white-matter on the wm.mgz image. So it seems for me that calculating white-matter volume is more accurate using the white-matter surface instead of wm.mgz. What does wm.mgz used for? Does it has any impact on the white-matter volume reported by freesurfer? Is it a problem, that wm.mgz doesn't fit well the white-matter surface everywhere? What is the reason that wm.mgz doesn't fit the WM surface everywhere?
Thanks a lot, Gabor