Hi Alexarae

it's pretty much impossible for us to diagnose the problem from a single slice of the wm.mgz. If you upload the subject and send us some voxel coords of where the problem is we will take a look.

cheers Bruce

p.s. in general you don't need nearly that many control points. You aren't drawing the WM as much as you are giving the algorithm an idea that that intensity value should be considered WM in that area

On Wed, 31 Jul 2013, lexi bryon wrote:

Dear Freesurfer experts,

I am running recon-all on child brains and I am have an issue with one brain. One entire temporal gyrus is being excluded from the white matter boundary line. I have entered control points and rerun recon-all using autorecon2-cp. This added the desired white matter to wm.mgz: see attached photo.

But as you can see it does not recognize it as white matter and/or create the correct white matter boundary/ pial surface.

Any ideas?

Sincerely, Alexarae