I think you could just load the cortex.label map onto the surface and 
edit those regions out. Then they will not contribute to smoothed maps, 
etc...  Doug: any reason this wouldn't work?

Bruce

On Tue, 13 Feb 2018, James Hobart wrote:

> 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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