[Freesurfer] question about effect of juxta-cortical lesion

Hi Folks,

We have a patient with a large juxta-cortical lesion (top right hand side in figure 1) Overall Freesurfer does a great job in defining the white and pial surfaces (figure 2 and 3) (It is actually amazing how well it does in this difficult case.)

However, I think that due to the lesion some of the cortical gray matter is not included. Could someone advice what is the recommended procedure in such cases. Should I add control points to correct for this issue ?

Also we have 3 MRI exams for this subject (each a year apart) and the lesion is present on every scan and I have the same issue on the other time-points.

Thanks Mehul