We have been coming across several gray matter regions that are not included within the pial surface (red line) when it should be (e.g., very anterior parts of the temporal lobe). From my understanding of similar posts on the forum, it seems that there isn't a way to add this region to the pial surface so that the missing brain matter is included. We have tried using the clone tool to fill in this region, as per the tutorial and have experimented with this tool using the tutorial data. I followed the steps in the tutorial but could not observe any changes when the middle button was selected. Does anyone have any ideas on how to troubleshoot this issue? Can someone please explain to me why this is not possible? Also how does Freesurfer determine what regions to include within the pial surface? If there is a way that has been developed recently, please enlighten me. 

-Jing