Introduction

The process of analysing brain imaging data is typically comprised of a series of stages. The study is designed with various choices made about the biology question that is to be addressed and the data necessary to answer the questions thus posed. Then the data is then acquired, and once that is completed, the images are processed in various automatic, semi-automatic, or manual ways and then analysed.

This book deals mainly with the final part, the data analysis, though there will be several side-tracks into the other topics. A single example will be used throughout: a mouse brain imaging study comparing two genotypes. The methods described herein should be easily transferable to any other structural imaging study which looks at brain shape, tissue classification, or signal intensities.