Hi Satra,

yes, the aseg is used in the surface recon, but the thickness won't be identically zero there. We let the surface settle wherever it wants, but mask those regions out of group studies. I should probably write something one of these days to automatically generate a mask. It would be easy enough.

Bruce On Wed, 5 Jul 2006, Satrajit Ghosh wrote:

Dear Bruce,

Does the autoseg information get used for surface extraction? For example, when autoseg classfies the ventricles and basalganglia, are the surface extraction routines supposed to treat these voxels as part of white matter and continue? Ideally at the end of the day any place where the surface runs through a non-cortical patch, the thickness would be zero?

Thanks,

Satra

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer