[Freesurfer] Pial surface not including parts of cortex

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Dear Freesurfer experts,

I was wondering if I could get some help with a problem that I keep experiencing. For some of the patients, their gray matter is not properly included in the pial surface. I have tried tkmregister and using control points but neither have been successful. I have read on a separate thread that editing the wm.mgz may be helpful but could I have some guidance on this please? Also, I know it can be difficult to tell the problem based on the description so please let me know if I can send something over to help. I'm still very much learning how to work freesurfer so I really appreciate your help. (Note: I am using version 5.3)

Thank you, Monica