MATLAB scripts for detecting and validating phase amplitude coupling (PAC) in electrophysiological data.
Written and maintained by Robert Seymour, June 2017.
Seymour, R. A., Rippon, G., & Kessler, K. (2017). The Detection of Phase Amplitude Coupling During Sensory Processing. Frontiers in Neuroscience 11, 487. https://doi.org/10.3389/fnins.2017.00487
The pre-print of the manuscript is available to download on Biorxiv, and the published manuscript is available to download on the Frontiers website.
Please download the MEG and anatomical data from Figshare.
Scripts can be easily adapted for your computer by modifying the sensory_PAC.m script:
data_dir = 'path_to_data';
scripts_dir = 'path_to_scripts';
fieldtrip_dir = 'path_to_fieldtrip';
subject = {'sub-01','sub-02','sub-03','sub-04','sub-05','sub-06','sub-07',...
'sub-08','sub-09','sub-10','sub-11','sub-12','sub-13','sub-14',...
'sub-15','sub-16'};Fieldtrip version 20161024 was used during data analysis, and can be found from the /fieldtrip folder.
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1_preprocessing_elektra_frontiers_PAC.m = this script performs simple preprocessing steps and removes bad trials
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2_get_source_power.m = this script performs source analysis in the gamma (40-60Hz) and alpha (8-13Hz) bands.
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3_get_VE_frontiers_PAC.m = this script computes a V1 virtual electrode, using the HCP-MMP-1.0 atlas. Other atlases could easy be used (e.g. the AAL atlas).
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4_calc_pow_change.m = this script calculates the change in oscillatory power (1-100Hz) using the V1 virtual electrode.
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5_visual_PAC_four_methods.m = this script uses 4 different methods to quantify alpha-gamma PAC. Non-parametric statistics are then applied to determine changes in PAC between baseline and grating periods.
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6_check_non_sinusoidal.m = this script checks the low-frequency phase for differences in non-sinusoidal oscillations.
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7_simulated_PAC_analysis.m = this script simulates PAC, checks for the detection of this coupling using three approaches, and investigates how much data is needed for reliable PAC estimates.
The calc_MI function can be used in isolation, for data arranged in a Fieldtrip structure:
Please note: This function is still under-development, but will be back-compatible with data presented within the manuscript.
function [MI_matrix_raw,MI_matrix_surr] = calc_MI(virtsens,toi,phase,amp,diag,surrogates,approach)
% Inputs:
% - virtsens = MEG data (1 channel)
% - toi = times of interest in seconds e.g. [0.3 1.5]
% - phases of interest e.g. [4 22] currently increasing in 1Hz steps
% - amplitudes of interest e.g. [30 80] currently increasing in 2Hz steps
% - diag = 'yes' or 'no' to turn on or off diagrams during computation
% - surrogates = 'yes' or 'no' to turn on or off surrogates during computation
% - approach = 'tort','ozkurt','canolty','PLV'
% Optional Inputs:
% - Number of phase bins used in KL-MI-Tort approach (default = 18)
%
% Outputs:
% - MI_matrix_raw = phase amplitude comodulogram (no surrogates)
% - MI_matrix_surr = = phase amplitude comodulogram (with surrogates)
%Currently the function only accepts data from a single channel which could be obtained using an atlas-based approach (e.g. AAL atlas or HCP-MMP 1.0).
The PAC algorithms from Tort et al., (2010), Ozkurt & Schnitzler (2011), Canolty et al., (2006) and Cohen (2008) are implemented, and more will be added soon.
Example use:
% To produce a PAC comodulogram on a single channel using the
% Tort et al., (2010) approach, 0.3-1.5s post-stimulus onset between
% 7-13Hz phase and 34-100Hz amplitude, normalised by surrogate data:
[MI_matrix] = calc_MI(VE_V1,[0.3 1.5],[7 13],[34 100],'no','yes','tort')
Please be aware of the various methodological pitfalls in PAC analysis before applying the scripts to your own data (see Seymour, Kessler & Rippon manuscript).
For more information/queries please raise an ISSUE within Github or email me: robbyseymour [at] gmail.com . I am also very keen for collaborations to help improve and expand this code.