NFTsim: Theory and Simulation of Multiscale Neural Field Dynamics

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 to define 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 enables 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.

Quantitative theory of deep brain stimulation of the subthalamic nucleus for the suppression of pathological rhythms in Parkinson’s disease

“…All numerical simulations of the CTBG neural field model in this work are performed using the NFTsim code package detailed by [ 79 ]. This package is used to solve Eqs (1) – (7) numerically for the spatially uniform case where the ∇ 2 in (4) is zero.…”

Biophysically based method to deconvolve spatiotemporal neurovascular signals from fMRI data

“…(v) The hemodynamic model could be extended to study laminar-specific fMRI data and fine-scale structures such as ocular dominance and orientation preference columns. (vi) A model of precise population synaptic activity, e.g., the neural field model described by Sanz-Leon et al (2018), in relation to hemodynamic effects could be incorporated in the method to better complement high-frequency neural measurements such as those by EEG.…”

Diffuse neural coupling mediates complex network dynamics through the formation of quasi-critical brain states

“…We simulated a 12 × 12 network of corticothalamic neural masses (Fig. 1a) using the neural field simulation software, nftSim 37 . The parameters for each neural mass were identically set to "eyes-closed" estimates 35 , which results in simulated activity with a characteristic 1/f spectrum and a peak in the alpha frequency band (8)(9)(10)(11)(12)(13).…”