We are working on editing the segmentation of a subject with severe atrophy due to a seizure event that occurred during infancy. In portions of the parietal and frontal lobe the atrophy is so severe that freesurfer can't find any WM or GM. Is there a way to manually fill in the GM so that it is captured within the surfs? Because we have other modalities that use the Desikan atlas, this is an important first step.

I have attached a few figures for examples.