This document describes how to perform a paired analysis in FreeSurfer. This includes a two time-point longitudinal analysis in which the same subject was scanned twice with each scan being run through FreeSurfer separately (using the longitudinal stream). It also includes a cross-over analysis in which each subject of a cohort has a matching subject in another cohort. In either, case this describes how to perform statistical tests on the difference between the pairs.
The overall strategy is to:
- Sample each individual's surface onto the average surface.
- Compute the difference between each of the pairs in the average surface space.
- Concatenate the differences into one file.
- Smooth on the surface (optional)
- Perform analysis with mri_glmfit on this file