Image registration is central to many of the challenges in brain imaging today.
Initially developed as an image processing subspecialty to geometrically transform one image to match another, registration now has a vast range of applications. In this chapter, we review the registration strategies currently used in medical imaging , with a particular focus on their ability to detect and measure differences. These include methods developed for automated image labeling and for pathology detection in individuals or groups. We show that these algorithms can serve as powerful tools to investigate how regional anatomy is altered in disease, and with age, gender, handedness and other clinical or genetic factors. They may also fuse information from multiple imaging devices to correlate different measures of brain structure and function.