FLIRT: A flexible image registration toolbox

Image registration is central to many challenges in medical imaging today and has a vast range of applications. The purpose of this note is to provide a toolbox for intensity based non-rigid registration problems. To do so, we review some of the most promising non-linear registration strategies currently used in medical imaging and show that all these techniques may be phrased in terms of a variational problem and allow for a unified treatment. Depending on the application at hand, it is often desirable to constrain the wanted deformation. The idea is to incorporate higher level information about the expected deformation. We examine the most common constraints and show again that they may be conveniently phrased in a variational setting. As a consequence, all of discussed modules allow for fast implementations and may be combined in any favorable order. We discuss individual methods for various applications, including the registration of histological serial sections of a human brain.