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SpinDoctor: a Matlab toolbox for diffusion MRI simulation
INRIA Saclay, Equipe DEFI, CMAP, Ecole Polytechnique, Route de Saclay, 91128 Palaiseau Cedex, France.
KTH, School of Electrical Engineering and Computer Science (EECS), Computational Science and Technology (CST).ORCID iD: 0000-0002-3213-0040
INRIA Saclay, Equipe DEFI, CMAP, Ecole Polytechnique, Route de Saclay, 91128 Palaiseau Cedex, France.
Institute of Mathematics, Faculty of Science, University of South Bohemia, Ceske Budejovice and Institute of Information Theory and Automation of the ASCR, Prague, Czech Republic.
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2019 (English)In: NeuroImage, ISSN 1053-8119, E-ISSN 1095-9572, ISSN 1053-8119Article in journal (Refereed) In press
Abstract [en]

The complex transverse water proton magnetization subject to diffusion-encoding magnetic field gradient pulses in a heterogeneous medium can be modeled by the multiple compartment Bloch-Torrey partial differential equation (BTPDE). A mathematical model for the time-dependent apparent diffusion coefficient (ADC), called the H-ADC model, was obtained recently using homogenization techniques on the BTPDE. Under the assumption of negligible water exchange between compartments, the H-ADC model produces the ADC of a diffusion medium from the solution of a diffusion equation (DE) subject to a time-dependent Neumann boundary condition. This paper describes a publicly available Matlab toolbox called SpinDoctor that can be used 1) to solve the BTPDE to obtain the dMRI signal (the toolbox provides a way of robustly fitting the dMRI signal to obtain the fitted ADC); 2) to solve the DE of the H-ADC 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. The PDEs are solved by P 1 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 that is included in the toolbox. SpinDoctor provides built-in options of including 1) spherical cells with a nucleus; 2) cylindrical cells with a myelin layer; 3) an extra-cellular space (ECS) enclosed either a) in a box or b) in a tight wrapping around the cells; 4) deformation of canonical cells by bending and twisting. 5) permeable membranes for the BT-PDE (the H-ADC assumes negligible permeability). Built-in diffusion-encoding pulse sequences include the Pulsed Gradient Spin Echo and the Oscillating Gradient Spin Echo.

Place, publisher, year, edition, pages
2019.
Keywords [en]
Bloch-Torrey equation, diffusion magnetic resonance imaging, finite elements, simulation, apparent diffusion coefficient.
National Category
Natural Sciences Engineering and Technology
Research subject
Applied and Computational Mathematics; Applied Medical Technology; Computer Science
Identifiers
URN: urn:nbn:se:kth:diva-243290DOI: 10.1016/j.neuroimage.2019.116120Scopus ID: 2-s2.0-85071780835OAI: oai:DiVA.org:kth-243290DiVA, id: diva2:1285723
Note

QC 20190304

Available from: 2019-02-05 Created: 2019-02-05 Last updated: 2019-10-04Bibliographically approved

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Nguyen, Van Dang

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