Abstract
A user ready, portable, documented software package, NFTsim, is presented to facilitate numerical simulations of a wide range of brain systems using continuum neural field modeling. NFTsim enables users to simulate key aspects of brain activity at multiple scales. At the microscopic scale, it incorporates characteristics of local interactions between cells, neurotransmitter effects, synaptodendritic delays and feedbacks. At the mesoscopic scale, it incorporates information about medium to large scale axonal ranges of fibers, which are essential to model dissipative wave transmission and to produce synchronous oscillations and associated cross-correlation patterns as observed in local field potential recordings of active tissue. At the scale of the whole brain, NFTsim allows for the inclusion of long range pathways, such as thalamocortical projections, when generating macroscopic activity fields. The multiscale nature of the neural activity produced by NFTsim has the potential to enable the modeling of resulting quantities measurable via various neuroimaging techniques. In this work, we give a comprehensive description of the design and implementation of the software. Due to its modularity and flexibility, NFTsim enables the systematic study of an unlimited number of neural systems with multiple neural populations under a unified framework and allows for direct comparison with analytic and experimental predictions. The code is written in C++ and bundled with Matlab routines for a rapid quantitative analysis and visualization of the outputs. The output of NFTsim is stored in plain text file enabling users to select from a broad range of tools for offline analysis. This software enables a wide and convenient use of powerful physiologically-based neural field approaches to brain modeling. NFTsim is distributed under the Apache 2.0 license.
Highlights
The brain is a multiscale physical system, with structures ranging from the size of ion channels to the whole brain, and timescales running from sub-millisecond to multi-year durations
These range from microscale models of individual neurons and their substructures, through network-level models of discrete neurons, to population-level mesoscale and macroscale neural mass and neural field models that average over microstructure and apply from local brain areas up to the whole brain
Section Observables and diagnostics briefly discusses the main observables that can be currently computed in NFTsim and how these have been used to predict a range of brain phenomena and compare to experimental results
Summary
The brain is a multiscale physical system, with structures ranging from the size of ion channels to the whole brain, and timescales running from sub-millisecond to multi-year durations. To address the need for research-ready NFT simulation tools with direct application to the study of large-scale brain phenomena, this paper introduces and describes NFTsim, a software package that solves neural field equations expressed in differential form for simulating spatially extended systems containing arbitrary numbers of neural populations. The first phase involves writing a configuration file that specifies the neural field model as well as other parameters required to run a simulation.
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