hmmm, I guess the only thing you can really do is edit the brain.finalsurfs.mgz and replace the hyperintense voxels with lower intensities (around 50 or so I would think). We don't usually see hyperintensitities in GM in T1-weighted images unless they are MR-distortions caused by low bandwidth sequences. Is that what's going on in your dataset?

On Mon, 26 Nov 2012, ?? ? wrote:

Hello FS experts,   I have a MRI volume where there is regional hyperintensity at cortex and thus the segmentation takes that regional cortex as white matter. In other words, the segmentation process is too aggressive toward the pial surface.   I modifed the WM by manual erase across several slices and run -autorecon2-wm and -autorecon3. However, when I checked the results, I found the "original surface" is right (green color in the appended file; the tesselation is compatible with my manural editing) but the "white matter surface" is not updated (yellor color in the appended file; the surface is not adjusted, just like the old one before my editing).   Could anybody guide me how to solve this issue? Thank you very much, JoJo