Portable simulation framework for diffusion MRI

•The specification of an intrinsic diffusion tensor and a T2-relaxation coefficient in each geometrical compartment.•The specification of a permeability coefficient on the interface between the geometrical compartments.•The periodic extension of the computational domain (assumed a box).•The specification of general diffusion-encoding gradient pulse sequences.•The simulation of thin-layer and thin-tube media using a discretization on manifolds.