you might need to place the control points a little more carefully, at least one of them looks like it is in gray matter (but hard to say on a single slice).

doug

Bruce Fischl wrote:

what image are you displaying in this png? If it is one of the brain*.mgz then your control points aren't working as the wm is still very dark where you place them. Did you run autorecon2-wm after putting the control points in?

On Tue, 10 May 2011, Moiyadi, Ammar wrote:

...

Dear Freesurfers,

Freesurfer's autorecon is having trouble tracing both gray and white matter boundaries in the temporal region of one of my subjects (even after I added control points for the white matter). I have attached a png screen shot of this abnormality and was wondering if anyone has any ideas to correct this since I have never seen such a large tracing error before.

Your input is much appreciated!

Ammar

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