Working with Subcortical ROIs (Freesurfer)

In addition to surface-space ROIs, group-level analyses done in 2mm mni305 space can be used to produce ROIs for subcortical regions. We might use the GLM volumes as-is, as a binary mask, or we might wish to use significant clusters to isolate voxels from specific anatomical regions. This second case is what I will focus on for the time being.

Prerequisites

In addition to FreeSurfer, the steps described below make use of some of AFNI's command-line utilities. AFNI should be installed on all our lab workstations, but if you are working elsewhere, go ahead and find and install AFNI from here.

In particular, we will be making use of a utility called 3dcalc. FSL may have some similar utilities, but I've not learned about them if they exist, and I know that the method described below works.

Collect Your VOIS

Here I will document a scenario in which significant subcortical clusters have been identified using a group-level GLM in mni305 space. The goal will be to use those significant clusters to filter out subcortical regions.

The significant clusters will be found in your group-level glm directory. If you've generally followed directions elsewhere on this wiki, these files will probably be in a directory called $SUBJECTS_DIR/RFX/parfile.sm4.mni/contrast/glm.wls/osgm.