Performing a region of interest analysis on MRI requires knowing where the regions are in your subject data. Typically, this has been done using hand-drawn masks in a 3d viewer. However, recent research has made the process mostly automatic and the open-source community has implemented everything you will need to automatically create labeled volumetric regions of interest [1-3]. With FreeSurfer 5.3, we have the option of performing cortical parcellation using 4 different atlases:

Destrieux atlas: aparc.a2009s
Desikan-Killiany atlas: aparc
Mindboggle: aparc.DKTatlas40
Brodman areas: BA and BA.thresh

We’ll first use freesurfer’s recon-all tool to perform a cortical reconstruction of our anatomical scans. Download freesurfer and register your copy. You’ll be sent an e-mail with a license. Follow the instructions and create the license file “.license” inside your freesurfer home directory (check the environment variable, FREESURFER_HOME, e.g., “$ echo $FREESURFER_HOME"). Then run the script, “$FREESURFER_HOME/FreeSurferEnv.sh” to setup necessary paths.

Next make sure you have set the environment variable for SUBJECTS_DIR to where you’d like your analysis to go (e.g., “$ export SUBJECTS_DIR=/some/directory“). For our example, we’ll keep this to a directory called “freesurfer” in our home directory, “~/”. Each subject we analyze will have its own folder insider … Continue reading...