This open access book bridges common tools in medical imaging and neuroscience with the
numerical solution of brain modelling PDEs. The connection between these areas is established
through the use of two existing tools FreeSurfer and FEniCS and one novel tool the SVM-Tk
developed for this book. The reader will learn the basics of magnetic resonance imaging and
quickly proceed to generating their first FEniCS brain meshes from T1-weighted images. The
book's presentation concludes with the reader solving a simplified PDE model of gadobutrol
diffusion in the brain that incorporates diffusion tensor images of various resolution and
complex multi-domain variable-resolution FEniCS meshes with detailed markings of anatomical
brain regions. After completing this book the reader will have a solid foundation for
performing patient-specific finite element simulations of biomechanical models of the human
brain.
