ROI Analyses in FreeSurfer

Note: This is a short post jotting down my thoughts on FreeSurfer ROI analysis. This will be developed into a longer post later; however, this is a topic I've been looking into for some time, and I want to keep track of my sources. 

Regions of interest (ROIs) are groups of voxels that parameter estimates (or other data) are extracted from. With volumetric data, you specify the x-, y-, and z-coordinates of the origin for your ROI, and then build a sphere around it. (Spheres aren't the only method, but they are common.) You can do this with, for example: AFNI's 3dUndump; SPM's Marsbar toolbox; FSL's fslmaths.

I haven't been able to find out how to do a similar procedure with FreeSurfer. FS is 2D, so the ROI would probably be a circle instead of a sphere. Once your ROI is defined, then you could extract thickness, volume, and other measurements from the ROI.

See this post by Doug Greve about using a vertex as the base for an ROI: