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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.
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