SpinDoctor: A MATLAB toolbox for diffusion MRI simulation

  title={SpinDoctor: A MATLAB toolbox for diffusion MRI simulation},
  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 Trong An Tran and Hoang Trong An Tran and Thi Minh Phuong Nguyen},

Practical computation of the diffusion MRI signal of realistic neurons based on Laplace eigenfunctions

A simulation framework is implemented inside the MATLAB-based diffusion MRI simulator SpinDoctor that efficiently computes the matrix formalism representation for realistic neurons using the finite element method, and it is shown that the matrix formallyism representation requires a few hundred eigenmodes to match the reference signal computed by solving the Bloch-Torrey equation when the cell geometry originates from realistic neurons.

Portable simulation framework for diffusion MRI

Practical computation of the diffusion MRI signal based on Laplace eigenfunctions: permeable interfaces

The simulation framework implemented inside the MATLAB-based diffusion MRI simulator SpinDoctor is extended to include geometries that contain permeable cell membranes and the effects of the magnitude of the permeability coefficient on the eigendecomposition of the diffusion and Bloch-Torrey operators are analyzed.

Disimpy: A massively parallel Monte Carlo simulator for generating diffusion-weighted MRI data in Python

Disimpy is a simulator for generating diffusion-weighted magnetic resonance imaging (dMRI) data that is useful in the development and validation of new methods for data acquisition and analysis and its source code is very approachable and easily extensible.

Three-dimensional micro-structurally informed in silico myocardium - towards virtual imaging trials in cardiac diffusion weighted MRI

Results confirm that the proposed method can generate richer numerical phantoms for the myocardium than previous studies and validate that the in-silico tissue is in the same class of disorderliness as the real tissue.

Contextual Fibre Growth to Generate Realistic Axonal Packing for Diffusion MRI Simulation

The potential of ConFiG is demonstrated by reaching the highest packing density and orientation dispersion ever, to the authors' knowledge, and the algorithm is compared with a ‘brute force’ growth approach showing that it is much more efficient, being O(n) compared to the O( n 2 ) brute-force method.

Virtual clinical trials in medical imaging: a review

This work summarizes the major developments and current status of the field of VCTs in medical imaging, and reviews the core components of a VCT: computational phantoms, simulators of different imaging modalities, and interpretation models.



A partition of unity finite element method for computational diffusion MRI

A Macroscopic Model for the Diffusion MRI Signal Accounting for Time-Dependent Diffusivity

A new asymptotic model is derived for the dMRI signal from the Bloch--Torrey equation governing the water proton magnetization under the influence of diffusion-encoding magnetic gradient pulses to aid in the understanding and interpretation of the apparent diffusion coefficient.

Numerical simulation of diffusion MRI signals using an adaptive time-stepping method

The effect on the MRI signal of water diffusion in biological tissues in the presence of applied magnetic field gradient pulses can be modelled by a multiple compartment Bloch–Torrey partial differential equation by coupling a standard Cartesian spatial discretization with an adaptive time discretizations.

A FEniCS-HPC framework for multi-compartment Bloch-Torrey models

A framework for the multi-compartment Bloch-Torrey models based on the FEniCSHPC platform is proposed, which is straightforward to implement and to parallelize and shows promise in validation against more realistic models.

Pulsed-gradient spin-echo monitoring of restricted diffusion in multilayered structures.

  • D. Grebenkov
  • Computer Science
    Journal of magnetic resonance
  • 2010

A simulation environment for diffusion weighted MR experiments in complex media

An approach is described that combines a Monte Carlo Brownian dynamics simulator capable of simulating diffusion in arbitrarily complex polygonal geometries with a signal integrator flexible enough to handle a variety of pulse sequences that provides a complete and general simulation environment for diffusion MRI experiments.

Microstructure Imaging Sequence Simulation Toolbox

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, 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.