After looking through the archives my question still remains. I am wondering if the same rules apply for editing/correcting FLAIR images as it does for T1 images. For example, can I add control points to the WM.mgz then re-run recon-all using the command recon-all - s <subject> -autorecon2-cp -autorecon3. For visualization I have attached a screenshot of what I am attempting to correct.