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Diffusion MRI simulation of realistic neurons with SpinDoctor and the Neuron Module
KTH, School of Electrical Engineering and Computer Science (EECS), Computer Science, Computational Science and Technology (CST).ORCID iD: 0000-0002-3213-0040
INRIA Saclay, Equipe DEFI, CMAP, Ecole Polytechnique, 91128 Palaiseau Cedex, France.
INRIA Saclay, Equipe Parietal, 1 Rue Honor ́e d’Estienne d’Orves, 91120 Palaiseau, France.
INRIA Saclay, Equipe DEFI, CMAP, Ecole Polytechnique, 91128 Palaiseau Cedex, France.
(English)Manuscript (preprint) (Other academic)
Abstract [en]

The diffusion MRI signal arising from neurons can be numerically simulated by solving the Bloch- Torrey partial differential equation. In this paper we present the Neuron Module that we imple- mented within the Matlab-based diffusion MRI simulation toolbox SpinDoctor. SpinDoctor uses finite element discretization and adaptive time integration to solve the Bloch-Torrey partial dif- ferential equation for general diffusion-encoding sequences, at multiple b-values and in multiple diffusion directions.

In order to facilitate the diffusion MRI simulation of realistic neurons by the research community, we constructed finite element meshes for a group of 36 pyramidal neurons and a group of 29 spindle neurons whose morphological descriptions were found in the publicly available neuron repositoryNeuroMorpho.Org. These finite elements meshes range from having 15163 nodes to 622553 nodes. We also broke the neurons into the soma and dendrite branches and created finite elements meshes for these cell components. Through the Neuron Module, these neuron and components finite element meshes can be seamlessly coupled with the functionalities of SpinDoctor to provide the diffusion MRI signal attributable to spins inside neurons. We make these meshes and the source code of the Neuron Module available to the public as an open-source package.

To illustrate some potential uses of the Neuron Module, we show numerical examples of the simu- lated dMRI signals in multiple diffusion directions from whole neurons as well as from the soma and dendrite branches, include a comparison of the high b-value behavior between dendrite branches and whole neurons.

Keywords [en]
Bloch-Torrey equation, diffusion magnetic resonance imaging, finite elements, simulation, neurons
National Category
Medical and Health Sciences
Research subject
Applied and Computational Mathematics; Computer Science; Biological Physics
Identifiers
URN: urn:nbn:se:kth:diva-263596OAI: oai:DiVA.org:kth-263596DiVA, id: diva2:1368361
Note

QC 20191111

Available from: 2019-11-06 Created: 2019-11-06 Last updated: 2019-11-11Bibliographically approved

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CiteExportLink to record
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