Re: [Freesurfer] WM edit, remove GM bright rim

Hi Min

that looks like it might be a normalization problem. Can you post the orig.mgz and see what it looks like? Is there a bright rim in it also?

cheers Bruce On Wed, 16 Mar 2016, Min Liu wrote:

Dear Freesufer users, We have some T1 images having a rim of bright signal in the GM at some spots like the one showing in the attached Figure 1.  The WM surface goes out to include this bright signal and the cortex ends up artificially thin.  We followed the standard WM edit procedure, which is to erase the bright signal in wm.mgz. As shown in Figure 2, the bright rim is replaced with intensity 1 (red). However, that doesn't improve the situation.  Does anyone know a way to prevent the surface from going out?

Thanks,

-- Min