SpinDoctorDiffusion MRI simulations

The Bloch-Torrey equation on finite element meshes of cells and tissue, in Julia

Cells and tissue

Recipes for plates, disks, cylinders, spheres and dense samples of periodic tissue, with layers, an extracellular space and permeable membranes, and realistic neurons.

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Signals and ADCs

Solve the Bloch-Torrey equation for any gradient sequence, or compute the ADC with the homogenized model, the matrix formalism, the Kärger model and short-time approximations.

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Periodic boundaries

Samples of densely packed tissue with periodic boundary conditions, free of the walls of a finite sample.

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Fast

Multithreaded assembly, built-in time stepping with sparse direct solvers, and NVIDIA GPUs through CUDA and cuDSS.

What is SpinDoctor?

SpinDoctor simulates diffusion magnetic resonance imaging (dMRI) in biological tissue [1]. The water in the tissue diffuses in compartments (cells, their layers, and the extracellular space) separated by permeable membranes, and the magnetization of its spins follows the Bloch-Torrey partial differential equation. SpinDoctor solves this equation with P1 finite elements on meshes created by TetGen [2] and Triangle, and computes:

the dMRI signal for scalar (PGSE, double PGSE, OGSE) and arbitrary three-dimensional gradient sequences;
apparent diffusion coefficients (ADC): by fitting the signal, with the homogenized ADC model, with the matrix formalism (Laplace eigenfunctions), and with the short diffusion time approximation;
analytical solutions for layered plates, cylinders and spheres, for validation.

The compartments may have different initial spin densities, diffusion tensors, T2 relaxation and permeabilities [3].

This is the Julia version of the SpinDoctor MATLAB toolbox.

Citing

If you use SpinDoctor in your research, please cite [1], and [4] for the matrix formalism.