SpinDoctor

This is the documentation for SpinDoctor, and is based on the SpinDoctor User Guide.

SpinDoctor is a software package that performs numerical simulations of diffusion magnetic resonance imaging (dMRI) for prototyping purposes Jing-Rebecca Li, Van-Dang Nguyen, Try Nguyen Tran, Jan Valdman, Cong-Bang Trang, Khieu Van Nguyen, Duc Thach Son Vu, Hoang An Tran, Hoang Trong An Tran, Thi Minh Phuong Nguyen (2019).

SpinDoctor can be used

1. to solve the Bloch-Torrey partial differential equation (BTDPE) to obtain the dMRI signal (the toolbox provides a way of robustly fitting the dMRI signal to obtain the fitted Apparent Diffusion Coefficient (ADC));
2. to solve the diffusion equation for the homogenized ADC (HADC) model to obtain the ADC;
3. a short-time approximation formula for the ADC is also included in the toolbox for comparison with the simulated ADC;
4. Compute the dMRI signal using a matrix formalism (MF) analytical solution based Laplace eigenfunctions.

The PDEs and Laplace eigenvalue decompositions are solved by P1 finite elements. The geometry recipes create surface triangulations that are passed to TetGen to perform the finite element mesh generation (see Hang Si (2015)).

SpinDoctor has support for the following features:

1. multiple compartments connected through permeable membranes Dang Van Nguyen, Jing-Rebecca Li, Denis Grebenkov, Denis Le Bihan (2014), with different
   • initial spin densities,
   • diffusion tensors,
   • T2-relaxation, and
   • permeability coefficients for the BTPDE and MF (the HADC assumes negligible permeability);
2. diffusion-encoding gradient pulse sequences, including
   • the pulsed gradient spin echo sequence (PGSE),
   • the double-PGSE,
   • the oscillating gradient spin echo (OGSE), and
   • custom three-dimensional pulse sequences $\vec{g}(t) = (g_x(t), g_y(t), g_z(t))^\mathsf{T}$;
3. uniformly distributed gradient directions in 2D and 3D for high angular resolution diffusion imaging (HARDI).

SpinDoctor also comes with a geometry generation module, allowing for

1. spherical cells with a nucleus;
2. cylindrical cells with a myelin layer;
3. an extra-cellular space (ECS) enclosed in either a box, a convex hull, or a tight wrapping around the cells;
4. deformation of canonical cells by bending and twisting.

In addition, a variety of neuron meshes is available, whose surface geometries were extracted from NeuroMopho.org. The neurons may also be enclosed in an extracellular space as described above.