Realistic head modeling of electromagnetic brain activity: an integrated Brainstorm-DUNEuro pipeline from MRI data to the FEM solutions

Takfarinas Medani; Juan Garcia-Prieto; Francois Tadel; Sophie Schrader; Marios Antonakakis; Anand Joshi; Christian Engwer; Carsten H. Wolters; John C. Mosher; Richard M. Leahy

doi:10.1117/12.2580935

15 February 2021 Realistic head modeling of electromagnetic brain activity: an integrated Brainstorm-DUNEuro pipeline from MRI data to the FEM solutions

Takfarinas Medani, Juan Garcia-Prieto, Francois Tadel, Sophie Schrader, Marios Antonakakis, Anand Joshi, Christian Engwer, Carsten H. Wolters, John C. Mosher, Richard M. Leahy

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Proceedings Volume 11595, Medical Imaging 2021: Physics of Medical Imaging; 1159554 (2021) https://doi.org/10.1117/12.2580935
Event: SPIE Medical Imaging, 2021, Online Only

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Abstract

Human brain activity generates scalp potentials (electroencephalography – EEG), intracranial potentials (iEEG), and external magnetic fields (magnetoencephalography – MEG), all capable of being recorded, often simultaneously, for use in research and clinical purposes. The so-called forward problem is modeling these fields at their sensors for a given putative neural source configuration. While early approaches modeled the head as a simple set of isotropic spheres, today’s ubiquitous magnetic resonance imaging (MRI) data allows detailed descriptions of head compartments with assigned isotropic and anisotropic conductivities. In this paper, we present a complete pipeline, integrated into the Brainstorm software, that allows users to generate an individual and accurate head model from the MRI and then calculate the electromagnetic forward solution using the finite element method (FEM). The head model generation is performed by the integration of the latest tools for MRI segmentation and FEM mesh generation. The final head model is divided into five main compartments: white matter, gray matter, cerebrospinal fluid (CSF), skull, and scalp. For the isotropic compartments, widely-used default conductivity values are assigned. For the brain tissues, we use the process of the effective medium approach (EMA) to estimate anisotropic conductivity tensors from diffusion weighted imaging (DWI) data. The FEM electromagnetic calculations are performed by the DUNEuro library, integrated into Brainstorm and accessible with a user-friendly graphical interface. This integrated pipeline, with full tutorials and example data sets freely available on the Brainstorm website, gives the neuroscience community easy access to advanced tools for electromagnetic modeling using FEM.

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Takfarinas Medani, Juan Garcia-Prieto, Francois Tadel, Sophie Schrader, Marios Antonakakis, Anand Joshi, Christian Engwer, Carsten H. Wolters, John C. Mosher, and Richard M. Leahy "Realistic head modeling of electromagnetic brain activity: an integrated Brainstorm-DUNEuro pipeline from MRI data to the FEM solutions", Proc. SPIE 11595, Medical Imaging 2021: Physics of Medical Imaging, 1159554 (15 February 2021); https://doi.org/10.1117/12.2580935

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