Matlab and SPM based code to extract features of network dynamics from neurophysiological recordings
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README.md

README.md

Network Dynamics Measures for EEG

Code accompanying Rosch et al (2017): Network dynamics in the healthy and epileptic developing brain. bioRxiv

This repository contains code that can be used to reproduce analyses to identify differences in network dynamics between different resting state EEG patterns. This code was used for the above manuscript to describe abnormalities in network dynamics that characterise two severe epilepsy syndromes of early infancy, Ohtahara syndrome and West syndrome / Infantile Spasms. When running the code, you will need to download and unzip the folder, and define the home-folder in the ee_housekeeping function

Network Dynamics

The code runs on Matlab (tested with 2016b) and requires a number of toolboxes to run:

  • The chaotic systems toolbox - to generate synthetic time series based on an existing fourier spectrum (included in this repo)
  • The k-Wave toolbox - to estimate the sharpness in a two-dimensional image (included in this repo)
  • cbrewer - to provide different colour palettes (included in this repo)
  • textprogressbar - to easily visualise progress during slow computational steps (included in this repo)
  • Statistic Parametric Mapping - For the filtering of EEG signals, this code relies on fieldtrip provided as part of the standard SPM distribution; this can be easily replaced by another filter method of your choice (SPM is not included here)

Custom routines included in this repository

The repository includes a number of different routines to be run manually to illustrate the different analysis steps performed for the manuscript above. Most of these will produce a visual output and are further explained below.

Plot an example EEG segment

ee_eegplot

For illustration purposes, we are providing a single 10s window of normal EEG from a 6 month-old infant, which can be visualised by running ee_eegplot, which will produce the figure below.

Example EEG

Estimate dynamics matrices using a sliding window approach

ee_estimate

Based on such 10s EEG windows, the ee_estimate function will use a sliding window approach to estimate network-correlation dynamics and scalp bandpower distribution dynamics. This example function will use the normal EEG segment provided, and plot the derived correlation-dynamics and power-dynamics matrices for each filter band, this produces the figure at the top of this page.

Visualise the dynamics measures used for analysis

ee_visualise_measures

In order to visualise the measures used for further analysis, running ee_visualise_measures will perform the same analysis on a simple selection of synthetically generated matrices that differe in the smoothness of transitions between different regions, and in the amplitude of the difference contained in the matrix. The code will produce the illustrative figure below that is the basis for Fig 3 in the manuscript.

Analyse synthetic EEG time series

ee_synthgen

As part of the statistical analysis, we generated surrogate time series with known frequency compositions based on the existing EEG windows. The routine ee_synthgen will generate a few such time series and illustrate the dynamics matrices that are derived from performing the equivalent analysis to that performed in ee_estimate. This will result in the figure shown below, showing example surrogate time series, as well as the dynamics matrices.

Surrogate time series

Reproduce dotplots from Manuscript

ee_dotplotfigures 

This function loads the dynamics measures estimated from our EEG segments and plots them using the ee_dotplot function to reproduce the figures shown in the manuscript as Fig 6.

Optimise thresholds for categorisation based on single measure

ee_simanneal

This routine will apply a simulated annealing approach (as implemented in Matlab) to optimise categorisation of disease groups (i.e. Ohtahara syndrome, West syndrome, and normal controls) based on single dynamics metrics. The routine will adjust two thresholds that separate groups according to whether the individual measurement lies above, below or between the thresholds. This optimisation is based on a purity measure for the resultant clustering (defined in ee_impurity).

The maximally achieved purity is then used to rank different measures in terms of how well they separate different groups. The routine will produce a 3D scatter plot of the three highest ranking measures, also shown in the manuscript in Fig 8 (although note that the annealing results may yield slightly different measures being included in the top three). The full ranklist from the publication is available as Allstats_cluster_purity.csv in the Analysis folder of this repository.

Perform k-means clustering to evaluate combinations of different measures

ee_kmeans

This routine will apply a k-means clustering approach to automatically identify clusters in combinations of network dynamics measures, drawn from the Allstats_cluster_purity.csv ranklist derived from the purity ranking above. The resultant clusters are then evaluated for purity, sensitivity (in terms of separating healthy from abnormal EEG patterns), and specificity (again healthy vs abnormal). This is repeated for different numbers of measures included in the clustering (ranging from 1 - 30) and the results are given as the following output figure.

To illustrate the clustering process, we also show a 2D clustering based on the 2 highest ranking variables from the ranklist above. This clustering is not very robust, so will likely appear different with different runs of the same code.

Other custom functions

  • ee_dotplot - custom dotplot function that will also indicate significant results from t-test
  • ee_housekeeping - function to define filepaths and modify path
  • ee_impurity - objective function optimised during the simulated annealing optimisation above

DOI