When using this function in any published study, please cite: Wolpert, N, Rebollo, I, Tallon‐Baudry, C. Electrogastrography for psychophysiological research: Practical considerations, analysis pipeline, and normative data in a large sample. Psychophysiology. 2020; 00:e13599.
Copyright (C) 2019, Laboratoire de Neurosciences Cognitives, Nicolai Wolpert, Ignacio Rebello & Catherine Tallon-Baudry Email: nicolaiwolpert@gmail.com
DISCLAIMER: This code is provided without explicit or implicit guarantee, and without any form of technical support. The code is not intended to be used for clinical purposes. The functions are free to use and can be redistributed, modified and adapted, under the terms of the CC BY-NC-SA version of creative commons license (see https://creativecommons.org/licenses/).
The aim of these scripts is to help the reader getting started with processing and analyzing the EGG signal. It provides some functions to filter and visualize the signal and detect artifacts. We also provide example EGG data that can be used in these scripts (Names: 'EGG_raw_example1.mat', 'EGG_raw_example2.mat' and 'EGG_raw_example3.mat'). EGG data that are loaded in this script have to be in fieldtrip format (e.g. the output of 'ft_preprocessing'), without any highpass-filter.
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The scripts are using the fieldtrip toolbox (Oostenveld et al., 2011). To install, go to http://www.fieldtriptoolbox.org/download/ and follow the instructions on http://www.fieldtriptoolbox.org/faq/should_i_add_fieldtrip_with_all_subdirectories _to_my_matlab_path/
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All the functions are called from 'Script_EGG_main'. Example data sets are provided. Download the data sets and specify the path and name in Script_EGG_main, as well as the path to the fieldtrip toolbox.
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Call 'compute_FFT_EGG'. Input: Raw EGG data in fieldtrip format This function computes a power spectrum for all the channels and outputs a fieldtrip structure containing the power spectrum. It plots the power spectrum, showing the channels in different colors and highlighting the normogastric range (0.033-0.067 Hz). The channel with the maximal power in normogastric range is highlighted with a star at the frequency of maximum power. Output: Fieldtrip data structure containing the power spectra, selcted channel and peak frequency.
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Call 'compute_filter_EGG'. Input: Raw EGG data, power spectrum (fieldtrip structure, output from 'compute_FFT_EGG') This function filters the EGG and computes the amplitude and phase of the EGG, on the channel with the highest peak in the power spectrum in the normogastric range. Output: Fieldtrip data structure with the filtered signal, amplitude and phase.
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Call ‘plot_EGG_visual_inspection'. Input: Filtered signal (output from 'compute_filter_EGG') This function creates a plot with the raw signal (first row), filtered signal (second row), phase time series (third row) and amplitude (fourth row). Output: plot
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Call 'compute_std_cycle_duration'. Input: Filtered signal (output from 'compute_filter_EGG') This function computes the standard deviation of cycle duration for the recording which is an estimate of the regularity of the phase. Output: Standard deviation of cycle duration
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Call 'show_prop_normogastria'. Input: Filtered signal (output from 'compute_filter_EGG') This function creates a plot with a histogram of cycle durations, with dotted red lines marking the mean +/- 3 standard deviations. Output: plot
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Call 'detect_EGG_artifacts'. Input: Filtered signal (output from 'compute_filter_EGG') This function looks for artifacted cycles in the phase time series. The two criteria for a cycle to be considered as artifact are: 1. A non-monotonous change in phase 2. a cycle duration below/above +/- 3 standard deviations. The function creates a plot with the raw signal (first row), the filtered signal (second row), the phase time series (third row) and the amplitude (fourth row). Artifacted cycles are shaded in red in the third row. Output: matrix with start and end samples of the artifacts