[Freesurfer] Making Anatomical Mass for optical data

Dear FreeSurfer Developers,

Currently we are trying to analyze our functional data (optical imaging) using ROI’s that are defined on the basis of FreeSurfer Segmentation. In order to do this, we need a 3 dimensional mask in which a particular region as identified by FreeSurfer is used as a mask for analyzing our functional data. How can we output from FreeSurfer what each voxel is classified as (hippocampus, etc.), or a mask having a value of 1 for each region, and a 0 for every other voxel. Also, what coordinate space would this be in? We would prefer either MNI or TAI (or a way to get into either space).

Thanks you so much for your help.

Sincerely,

Mark Fletcher

CNL Lab UIUC