scholarly journals Multiscale Modeling of EEG/MEG Response of a Compact Cluster of Tightly Spaced Pyramidal Neocortical Neurons

2020 ◽  
pp. 195-211
Author(s):  
Sergey N. Makarov ◽  
Jyrki Ahveninen ◽  
Matti Hämäläinen ◽  
Yoshio Okada ◽  
Gregory M. Noetscher ◽  
...  
Keyword(s):  
High Resolution ◽  
Boundary Element ◽  
Multiscale Modeling ◽  
Cluster Size ◽  
Fast Multipole Method ◽  
Head Model ◽  
Current Dipole ◽  
Neocortical Neurons ◽  
Dipole Sources ◽  
Compact Cluster

AbstractIn this study, the boundary element fast multipole method or BEM-FMM is applied to model compact clusters of tightly spaced pyramidal neocortical neurons firing simultaneously and coupled with a high-resolution macroscopic head model. The algorithm is capable of processing a very large number of surface-based unknowns along with a virtually unlimited number of elementary microscopic current dipole sources distributed within the neuronal arbor.The realistic cluster size may be as large as 10,000 individual neurons, while the overall computation times do not exceed several minutes on a standard server. Using this approach, we attempt to establish how well the conventional lumped-dipole model used in electroencephalography/magnetoencephalography (EEG/MEG) analysis approximates a compact cluster of realistic neurons situated either in a gyrus (EEG response dominance) or in a sulcus (MEG response dominance).

scholarly journals A Software Toolkit for TMS Electric-Field Modeling with Boundary Element Fast Multipole Method: An Efficient MATLAB Implementation

2020 ◽  
Author(s):  
Sergey N. Makarov ◽  
William A. Wartman ◽  
Mohammad Daneshzand ◽  
Kyoko Fujimoto ◽  
Tommi Raij ◽  
...  
Keyword(s):  
High Resolution ◽  
Boundary Element ◽  
Electric Fields ◽  
Fast Multipole Method ◽  
Human Head ◽  
Head Model ◽  
Fast Multipole ◽  
Software Toolkit ◽  
Model Repository ◽  
Multipole Method

AbstractBackgroundTranscranial magnetic stimulation (TMS) is currently the only non-invasive neurostimulation modality that enables painless and safe supra-threshold stimulation by employing electromagnetic induction to efficiently penetrate the skull. Accurate, fast, and high resolution modeling of the electric fields (E-fields) may significantly improve individualized targeting and dosing of TMS and therefore enhance the efficiency of existing clinical protocols as well as help establish new application domains.ObjectiveTo present and disseminate our TMS modeling software toolkit, including several new algorithmic developments, and to apply this software to realistic TMS modeling scenarios given a high-resolution model of the human head including cortical geometry and an accurate coil model.MethodThe recently developed charge-based boundary element fast multipole method (BEM-FMM) is employed as an alternative to the 1st order finite element method (FEM) most commonly used today. The BEM-FMM approach provides high accuracy and unconstrained field resolution close to and across cortical interfaces. Here, the previously proposed BEM-FMM algorithm has been improved in several novel ways.Results and ConclusionsThe improvements resulted in a threefold increase in computational speed while maintaining the same solution accuracy. The computational code based on the MATLAB® platform is made available to all interested researchers, along with a coil model repository and examples to create custom coils, head model repository, and supporting documentation. The presented software toolkit may be useful for post-hoc analyses of navigated TMS data using high-resolution subject-specific head models as well as accurate and fast modeling for the purposes of TMS coil/hardware development.

scholarly journals Solving High-Resolution Forward Problems for Extra- and Intracranial Neurophysiological Recordings Using Boundary Element Fast Multipole Method

2019 ◽  
Author(s):  
Sergey N Makarov ◽  
Matti Hämäläinen ◽  
Yoshio Okada ◽  
Gregory M Noetscher ◽  
Jyrki Ahveninen ◽  
...  
Keyword(s):  
High Resolution ◽  
Boundary Element ◽  
Fast Multipole Method ◽  
Field Potential ◽  
Head Model ◽  
Practical Case ◽  
Source Modeling ◽  
Fast Multipole ◽  
Forward Solution ◽  
Multipole Method

AbstractWe present a general numerical approach for solving the forward problem in high-resolution. This approach can be employed in the analysis of noninvasive electroencephalography (EEG) and magnetoencephalography (MEG) as well as invasive electrocorticography (ECoG), stereoencephalography (sEEG), and local field potential (LFP) recordings. The underlying algorithm is our recently developed boundary element fast multipole method (BEM-FMM) that simulates anatomically realistic head models with unprecedented numerical accuracy and speed. This is achieved by utilizing the adjoint double layer formulation and zeroth-order basis functions in conjunction with the FMM acceleration. We present the mathematical formalism in detail and validate the method by applying it to the canonical multilayer sphere problem. The numerical error of BEM-FMM is 2-10 times lower while the computational speed is 1.5–20 times faster than those of the standard first-order FEM. We present four practical case studies: (i) evaluation of the effect of a detailed head model on the accuracy of EEG/MEG forward solution; (ii) demonstration of the ability to accurately calculate the electric potential and the magnetic field in the immediate vicinity of the sources and conductivity boundaries; (iii) computation of the field of a spatially extended cortical equivalent dipole layer; and (iv) taking into account the effect a fontanel for infant EEG source modeling and comparison of the results with a commercially available FEM. In all cases, BEM-FMM provided versatile, fast, and accurate high-resolution modeling of the electromagnetic field and has the potential of becoming a standard tool for modeling both extracranial and intracranial electrophysiological signals.

scholarly journals Comparative Performance of the Finite Element Method and the Boundary Element Fast Multipole Method for Problems Mimicking Transcranial Magnetic Stimulation (TMS)

2018 ◽  
Author(s):  
Aung Thu Htet ◽  
Guilherme B. Saturnino ◽  
Edward H. Burnham ◽  
Gregory M. Noetscher ◽  
Aapo Nummenmaa ◽  
...  
Keyword(s):  
Finite Element Method ◽  
Finite Element ◽  
Transcranial Magnetic Stimulation ◽  
High Resolution ◽  
Boundary Element ◽  
Magnetic Stimulation ◽  
Performance Metrics ◽  
Fast Multipole Method ◽  
The Finite Element Method ◽  
First Case

AbstractA study pertinent to the numerical modeling of cortical neurostimulation is conducted in an effort to compare the performance of the finite element method (FEM) and an original formulation of the boundary element fast multipole method (BEM-FMM) at matched computational performance metrics. We consider two problems: (i) a canonic multi-sphere geometry and an external magnetic-dipole excitation where the analytical solution is available and; (ii) a problem with realistic head models excited by a realistic coil geometry. In the first case, the FEM algorithm tested is a fast open-source getDP solver running within the SimNIBS 2.1.1 environment. In the second case, a high-end commercial FEM software package ANSYS Maxwell 3D is used. The BEM-FMM method runs in the MATLAB® 2018a environment.In the first case, we observe that the BEM-FMM algorithm gives a smaller solution error for all mesh resolutions and runs significantly faster for high-resolution meshes when the number of triangular facets exceeds approximately 0.25 M. We present other relevant simulation results such as volumetric mesh generation times for the FEM, time necessary to compute the potential integrals for the BEM-FMM, and solution performance metrics for different hardware/operating system combinations. In the second case, we observe an excellent agreement for electric field distribution across different cranium compartments and, at the same time, a speed improvement of three orders of magnitude when the BEM-FMM algorithm used.This study may provide a justification for anticipated use of the BEM-FMM algorithm for high-resolution realistic transcranial magnetic stimulation scenarios.

scholarly journals Preprocessing General Head Models for BEM-FMM Modeling Pertinent to Brain Stimulation

2020 ◽  
pp. 325-343
Author(s):  
William A. Wartman
Keyword(s):  
High Resolution ◽  
Electric Fields ◽  
Fast Multipole Method ◽  
Head Model ◽  
Computation Method ◽  
Modeling Software ◽  
Meshing Scheme ◽  
Electric Fields And Currents ◽  
Tissue Models ◽  
The Brain

AbstractIntroduction: Transcranial magnetic stimulation (TMS) is a major noninvasive neurostimulation method in which a coil placed near the head employs electromagnetic induction to produce electric fields and currents within the brain. To predict the actual site of stimulation, numerical simulation of the electric fields within the head using high-resolution subject-specific head models is required. A TMS modeling software toolkit has been developed based on the boundary element fast multipole method (BEM-FMM), which has several advantages over conventional finite element method (FEM) solvers.Objective: To extend the applicability of the BEM-FMM TMS simulation toolkit to head models whose meshing scheme produces a single mesh for every unique tissue instead of producing a single mesh for every unique tissue/tissue boundary.Method: The MIDA model of the IT’IS Foundation, Switzerland, comprises 115 high-resolution tissue models in the form that the BEM-FMM toolkit is modified to accept. The updated BEM-FMM toolkit is tested using this head model.Results: The BEM-FMM toolkit has been successfully modified to accept head models consisting of one unique mesh per unique tissue while still supporting its initial model format of one unique mesh per boundary between two specific tissues. Performance impacts occur in the preprocessing phase only, meaning that the charge computation method performs equally well regardless of model format.

Fast Multipole Virtual Boundary Element - Least Square Method for Solving 2-D Elastic Problems

2011 ◽  
Vol 204-210 ◽  
pp. 2196-2201
Author(s):  
Yan Tao Jiang ◽  
Si Tian Chen ◽  
Cheng Hua Li
Keyword(s):  
Boundary Element ◽  
Large Scale ◽  
Fast Multipole Method ◽  
Main Idea ◽  
Least Square Method ◽  
Least Square ◽  
Fast Multipole ◽  
Large Scale Problems ◽  
Virtual Boundary ◽  
Virtual Boundary Element

In this paper, the fast multipole virtual boundary element - least square method (Fast Multipole VBE - LSM) is proposed and used to simulate 2-D elastic problems, which is based on the fast multipole method (FMM) and virtual boundary element - least square method (VBE - LSM).The main idea of the method is to change computational model by applying the FMM to conventional VBE - LSM. The memory and operations could be reduced to be of linear proportion to the degree of freedom (DOF) and large scale problems could be effectively solved on a common desktop with this method. Numerical results show that this method holds virtues of high feasibility, accuracy and efficiency. Moreover, the idea of this method can be generalized and extended in application.

scholarly journals Performance of diethylene glycol-based particle counters in the sub-3 nm size range

2013 ◽  
Vol 6 (7) ◽  
pp. 1793-1804 ◽  
Author(s):  
D. Wimmer ◽  
K. Lehtipalo ◽  
A. Franchin ◽  
J. Kangasluoma ◽  
F. Kreissl ◽  
...  
Keyword(s):  
High Resolution ◽  
Laminar Flow ◽  
Nucleation Rate ◽  
Diethylene Glycol ◽  
Cluster Size ◽  
Detection Efficiency ◽  
Working Fluid ◽  
Critical Cluster ◽  
Mixing Ratios ◽  
Critical Cluster Size

Abstract. When studying new particle formation, the uncertainty in determining the "true" nucleation rate is considerably reduced when using condensation particle counters (CPCs) capable of measuring concentrations of aerosol particles at sizes close to or even at the critical cluster size (1–2 nm). Recently, CPCs able to reliably detect particles below 2 nm in size and even close to 1 nm became available. Using these instruments, the corrections needed for calculating nucleation rates are substantially reduced compared to scaling the observed formation rate to the nucleation rate at the critical cluster size. However, this improved instrumentation requires a careful characterization of their cut-off size and the shape of the detection efficiency curve because relatively small shifts in the cut-off size can translate into larger relative errors when measuring particles close to the cut-off size. Here we describe the development of two continuous-flow CPCs using diethylene glycol (DEG) as the working fluid. The design is based on two TSI 3776 counters. Several sets of measurements to characterize their performance at different temperature settings were carried out. Furthermore, two mixing-type particle size magnifiers (PSM) A09 from Airmodus were characterized in parallel. One PSM was operated at the highest mixing ratio (1 L min−1 saturator flow), and the other was operated in a scanning mode, where the mixing ratios are changed periodically, resulting in a range of cut-off sizes. The mixing ratios are determined by varying the saturator flow, where the aerosol flow stays constant at 2.5 L min−1. Different test aerosols were generated using a nano-differential mobility analyser (nano-DMA) or a high-resolution DMA, to obtain detection efficiency curves for all four CPCs. One calibration setup included a high-resolution mass spectrometer (APi-TOF) for the determination of the chemical composition of the generated clusters. The lowest cut-off sizes were achieved with negatively charged ammonium sulfate clusters, resulting in cut-offs of 1.4 nm for the laminar flow CPCs and 1.2 and 1.1 nm for the PSMs. A comparison of one of the laminar-flow CPCs and one of the PSMs measuring ambient and laboratory air showed good agreement between the instruments.

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