SpinDoctor

This is a Julia implementation of the SpinDoctor toolbox. The original MATLAB toolbox can be found at https://github.com/jingrebeccali/SpinDoctor.

SpinDoctor is a software package that performs numerical simulations of diffusion magnetic resonance imaging (dMRI) for prototyping purposes.

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 combined with built-in MATLAB routines for solving ordinary differential equations. The finite element mesh generation is performed using an external package called TetGen.

SpinDoctor has support for the following features:

1. multiple compartments with compartment-wise constant
   • initial spin densities,
   • diffusion coefficients or diffusion tensors, and
   • T2-relaxation coefficients;
2. permeable membranes between compartments for the BTPDE and MF (the HADC assumes negligible permeability);
3. built-in diffusion-encoding pulse sequences, including
   • the Pulsed Gradient Spin Echo (PGSE) and double-PGSE,
   • the Ocsillating Gradient Spin Echo (OGSE), or
   • custom pulse sequences;
4. 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.

Spinning spindle spins in SpinDoctor

The above graphic visualizes the magnetization as a z-displacement for the spindle neuron geometry 03b_spindle4aACC (extracted from NeuroMorpho). The gradient is a PGSE sequence in the x-direction. The magnetization was computed for 200 time steps, and the exported vtk sequence was visualized using Paraview.

Getting started

1. The base folder contains a commented general purpose driver driver.jl.
2. The input files for the drivers are found in the folder setups, and define the structures needed for the simulations.
3. Multiple neuron meshes are found in the folder mesh_files. These can be loaded in the file setups/neuron.jl.
4. The user guide is found here.

How to cite us

The paper about SpinDoctor can be found at https://arxiv.org/abs/1902.01025.

If you use our software for research, please consider citing us:

@article{Li2019,
  author  = {Jing-Rebecca Li and Van-Dang Nguyen and Try Nguyen Tran and Jan Valdman and Cong-Bang Trang and Khieu Van Nguyen and Duc Thach Son Vu and Hoang An Tran and Hoang Trong An Tran and Thi Minh Phuong Nguyen},
  doi     = {https://doi.org/10.1016/j.neuroimage.2019.116120},
  issn    = {1053-8119},
  journal = {NeuroImage},
  pages   = {116120},
  title   = {{SpinDoctor: A MATLAB toolbox for diffusion MRI simulation}},
  url     = {http://www.sciencedirect.com/science/article/pii/S1053811919307116},
  volume  = {202},
  year    = {2019}
}