Registration, atlases and cortical flattening

© Oxford University Press 2001. All rights reserved. This chapter discusses the details of structural analysis methods in functional magnetic resonance imaging (fMRI) to interpret, relate and compare spatial locations, beginning with a description of some preliminary and related processing methods. It proceeds with a discussion of registration including both manual and automatic registration, and gives a brief overview of the important concepts and various approaches involved in registration. The chapter also discusses the two basic tasks for which an atlas is helpful, and mentions that when analysing the functional response of the brain, it is the spatial relationships between different parts of the cortical surface which are of interest. Therefore, an understanding and analysis of these spatial relationships is critical for the knowledge of cognitive function. Analysing the spatial relations in three dimensions, however, is complicated. It is more natural to express the relations in a two-dimensional representation, since the cortical grey matter is in effect a folded two-dimensional surface. Cortical flattening provides a way of creating such a two-dimensional map from the three-dimensional images of the brain. Finally, the chapter discusses the three main applications of structural analysis in fMRI.