Alex Thalamo-Cortical Model — extended thalamo-cortical neural mass model for M/EEG / electrophysiology
- Overview
- Features
- Model Structure & Theory
- Getting Started
- Using ATCM
- Analyses & Outputs
- Customization
- Contributing
- Licence
- Citations
ATCM is a MATLAB toolbox implementing an extended thalamo-cortical neural mass model (TCM) suitable for M/EEG and related electrophysiological data. It builds on canonical thalamo-cortical motifs, using Morris-Lecar–like dynamics and neural mass populations to model cortical laminar structure, thalamic relay/reticular interactions, and modulatory effects.
It supports:
- time-series simulations under different inputs
- spectral / transfer function analyses
- modal decompositions and singular spectrum methods
- parameter estimation (via e.g. variational Laplace within DCM frameworks)
- Rich dynamic behavior (oscillations, spindles, gamma, etc.)
- Flexible input types (deterministic pulses, continuous drives, noise etc.)
- Multiple integration algorithms & time-stepping options
- Tools for spectral / transfer function computation
- Support for prior specification, modal decomposition, and fitting/inverting the model to data
- Populations included: cortical (e.g. superficial, deep), inhibitory interneurons, thalamic relay and reticular nuclei.
- Neuronal dynamics via membrane potential / activation gating (Morris-Lecar-like) equations.
- Synaptic coupling between populations, with both excitatory and inhibitory connections.
- Optional modulation (e.g. neuromodulatory effects) in some versions / scripts.
- Modal decomposition & spectral analyses rely on linearization / transfer-function approximations in certain regimes.
- MATLAB (tested on version 2023a)
- Signal Processing Toolbox (for spectral analyses)
- Optional: toolboxes for optimization / variational inference (e.g. fitVariationalLaplaceThermo.m in https://github.com/alexandershaw4/aLogLikeFit)
- Clone this repository:
git clone https://github.com/alexandershaw4/atcm.git