Hi all,

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
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