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

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 implemented within the Matlab-based diffusion MRI simulation toolbox SpinDoctor. SpinDoctor uses finite element discretization and adaptive time integration to solve the Bloch-Torrey partial differential 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 repository NeuroMorpho.Org. These finite elements meshes range from having 15,163 nodes to 622,553 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 cell 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 simulated diffusion MRI signals in multiple diffusion directions from whole neurons as well as from the soma and dendrite branches, and include a comparison of the high b-value behavior between dendrite branches and whole neurons. In addition, we demonstrate that the neuron meshes can be used to perform Monte-Carlo diffusion MRI simulations as well. We show that at equivalent accuracy, if only one gradient direction needs to be simulated, SpinDoctor is faster than a GPU implementation of Monte-Carlo, but if many gradient directions need to be simulated, there is a break-even point when the GPU implementation of Monte-Carlo becomes faster than SpinDoctor. Furthermore, we numerically compute the eigenfunctions and the eigenvalues of the Bloch-Torrey and the Laplace operators on the neuron geometries using a finite elements discretization, in order to give guidance in the choice of the space and time discretization parameters for both finite elements and Monte-Carlo approaches. Finally, we perform a statistical study on the set of 65 neurons to test some candidate biomakers that can potentially indicate the soma size. This preliminary study exemplifies the possible research that can be conducted using the Neuron Module.