I am looking to mask out a small region of the GM when calculating the cortical thickness of ROIs across the brain. Essentially I have a couple of cases with small GM lesions where the cortical thickness is less likely to be meaningful for my analysis.

I have binary lesion masks and also full recon-all s for these cases. I was thinking I would need to mask the cortical thickness map somehow (potentially mapping the mask volume to a surface?) before using the mris_anatomical_stats to calculate cortical thickness.

Is this the best way to go about this?

Many thanks

James