SpinDoctor Toolbox (developmental code, not documented)

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

Software requirements

The SpinDoctor Toolbox has been developed in the MATLAB R2020b and tested with MATLAB R2018a-R2021a.

SpinDoctor requires no additional MATLAB Toolboxes. However, if the MATLAB Parallel Computing Toolbox is available, the simulations can be run in parallel.

Getting started

1. The base folder contains a commented general purpose driver called driver_spindoctor.m. The other driver, driver_save_load.m, can save and load simulations.
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 setups/setup_neuron.m script.
4. The user guide is found here.

Updates July 2024

New features:

• Simulation of general gradient sequences is now supported. These sequences can be read directly from a Camino .scheme file. Simulations can be run for solve_btpde, solve_btpde_midpoint, and solve_mf.
• Segmenting a finite element mesh into soma and processes/dendrites when the mesh comes from a swc file.
• Code refactoring, to incorporate the new features.

Updates March 2021

All modules (master, T2, NeuronModule, MatrixFormalismModule) are now merged and found in the master branch. The previous versions of the modules are still found in their branches.

New features:

• Code refactoring, change of data structures
• New input file system, controlled by a structure setup
• Some speed and memory improvements (extensive vectorization, reduced memory usage in ODE solvers)
• Support for parallel outer loops (solve for multiple directions, amplitudes and sequences in parallel)
• Diffusion tensors as an alternative to scalar diffusion coefficients
• Matrix formalism with built in Matlab functions instead of PDE Toolbox
• Add convex hull ECS + tight wrap ECS for neurons (experimental feature)
• Simple interface for pulse sequences, the user can add custom sequences
  • by passing a function handle, for which the integral quantities are computed numerically,
  • or by manually defining a subclass of the Sequence class

Authors

Jing-Rebecca Li, Syver Døving Agdestein, Chengran Fang, Van-Dang Nguyen, Try Nguyen Tran.

How to cite us

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

If you use our software for research, please cite 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}
}

Citations for further developements such as the Neuron Module and the Matrix Formalism module can be found in the CITATION.bib file.

License

Copyright (C) 2019-2021 Jing-Rebecca Li

This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.

This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.

You should have received a copy of the GNU General Public License
along with this program.  If not, see <https://www.gnu.org/licenses/>.