Anatomy Pipeline

We collect a high resolution T1-weighted image on every subject, and use this image to define the coordinate space for all subsequent analyses. This section describes the processing steps for a subject's T1-weighted anatomy and should be performed before analyzing the rest of their MRI data.

AC-PC Alignment

Data can come off the scanner with arbitrary header information and the subject might not be properly position. So for each subject we start by defining a coordinate frame where 0,0,0 is at the anterior commissure, the anterior and posterior commissure are in the same X and Z planes, and the mid-line is centered in the image. Bob Dougherty wrote a nice tool to help with this. See mrAnatAverageAcpcNifti