This work describes Microstructure Imaging Sequence Simulation Toolbox (MISST), a practical diffusion MRI simulator for development, testing, and optimisation of novel MR pulse sequences for microstructure imaging. Diffusion MRI measures molecular displacement at microscopic level and provides a non-invasive tool for probing tissue microstructure. The measured signal is determined by various cellular features such as size, shape, intracellular volume fraction, orientation, etc., as well as the acquisition parameters of the diffusion sequence. Numerical simulations are a key step in understanding the effect of various parameters on the measured signal, which is important when developing new techniques for characterizing tissue microstructure using diffusion MRI. Here we present MISST - a semi-analytical simulation software, which is based on a matrix method approach and computes diffusion signal for fully general, user specified pulse sequences and tissue models. Its key purpose is to provide a deep understanding of the restricted diffusion MRI signal for a wide range of realistic, fully flexible scanner acquisition protocols, in practical computational time.
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