I'm working with patients affected by cortical focal dysplasia; images of these patients often show thickening in some areas of the cortex. 

In many cases the reconstruction of the pial boundary is not accurate. I have been trying to correct this boundary but I couldn't understand the procedure.

I have already checked accuracy and intensity of white matter and have found no issues.

I have attached a self explanatory picture.

I wonder if you can help me to fix grey matter boundary errors.