You may want to take a look at this paper for how to deal with large lesions:

http://www.ncbi.nlm.nih.gov/pubmed/21175010

On 8/2/12 5:55 PM, Jesse Bledsoe wrote:
Hello FS experts,

I am wondering if anyone has experience using FreeSurfer or other program to analyze cortical thickness and subcortical volumes in children with pediatric brain tumors? Will adding control points in tumor regions be an adequate intervention for the topological defects? Thought I'd ask for advice before taking the plunge.

Best regards,
Jesse 

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