SpinDoctor: A MATLAB toolbox for diffusion MRI simulation

@article{Li2019SpinDoctorAM,
  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},
  journal={NeuroImage},
  year={2019},
  volume={202}
}
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11 Citations
Background Citations
1
Methods Citations
4

11 Citations

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.

Diffusion MRI simulation of realistic neurons with SpinDoctor and the Neuron Module

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.

Challenges for biophysical modeling of microstructure

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.

ConFiG: Contextual Fibre Growth to generate realistic axonal packing for diffusion MRI simulation

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.

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