Bennett Allan Landman1, Jonathan A. Farrell2,3, Peter C. van Zijl2,3
1Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA; 2Radiology, Johns Hopkins University School of Medicine, Baltimore, MD, USA; 3F.M. Kirby Research Center for Functional Brain Imaging, Kennedy Krieger Institute, Baltimore, MD, USA
Diffusion-weighted MRI techniques provide contrasts sensitive to tissue micro-architecture, but current derived-contrasts are non-specific for white matter pathologies. Significant efforts are underway to enhance inference of micro-architecture, and computational models are essential. Previous simulations were largely limited to cylinders and spheres. We present an efficient and flexible framework for simulating diffusion in arbitrary, 3-D compartments and demonstrate our approach by comparing diffusion in healthy, broken, crimped, and bulging axons. This open-source framework enables quantitative comparison of diffusion in biologically relevant restriction geometries which are not analytically accessible and provides a basis for developing and testing higher order diffusion model methods.