Hi Claudia

it really depends on the individual case and what's causing the exclusion. Does the wm.mgz look accurate? If so, you may have a topological defect that is being fixed incorrectly. Usually we focus on fixing the white boundary and that will also correct the pial. You can set the expected gray matter intensities in the xopts file, but that is rarely necessary and only if your gray matter looks very different than the sequences we are used to.

If you can't sort it out feel free to upload you data.

cheers Bruce

On Mon, 29 Apr 2013, Claudia Dacquino wrote:

Hi Freesurfers,I have a question about pial editing. I have some reconructions in which there's a lot of grey matter excluded, and consequently white metter too. I did correct these images manually by control points editing, and then autorecon2-cp autorecon3, but some cortical grey matter continues to not be included in the pial surface, and I have white matter areas that are still not included in either the pial or white matter boundaries.  Is there anyother ethods for adding grey matter in the pial surfeces other than editing control points (such as by editing voxels to add grey matter), or something like that? Thanks for your help. Claudia