Magnetic resonance brain image processing and arithmetic with FSL

Medical imaging has been transformed by a move from qualitative to quantitative approaches where image processing is used to enhance visual information and image analysis is used to derive structural and functional measurements. The ideal quantitative analysis methods are automatic and require no user intervention, and so-called image analysis pipelines exist for some applications. However, in the majority of cases automatic methods seldom live up to their name, may fail when prior assumptions are not met, and may not exist at all for new applications. The identification and careful use of well-known image processing and analysis techniques is a vital part of imaging and invaluable when problems arise with automatic methods. Here a number of key image analysis tasks in brain imaging are presented with particular reference to the freely available FMRIB Software Library.