EEG Coherence Analysis

Computes magnitude-squared coherence (MSC) or imaginary part of coherency between all EEG channel pairs using Welch's method. The signal is segmented into overlapping windows, each windowed with a Hanning function, and the cross-spectral density is averaged across windows.

Usage

eegCoherence(
  x,
  method = c("coherence", "imaginary"),
  window_sec = 2,
  overlap = 0.5,
  band = c(8, 13),
  assay_name = NULL
)

Arguments

x: A PhysioExperiment object with EEG data (2D: time x channels).
method: Coherence method: "coherence" for magnitude-squared coherence or "imaginary" for imaginary part of coherency (default: "coherence").
window_sec: Window length in seconds for Welch's method (default: 2).
overlap: Overlap fraction between adjacent windows, from 0 to 1 exclusive (default: 0.5).
band: Numeric vector of length 2 specifying the frequency band in Hz over which to average coherence (default: c(8, 13) for alpha band).
assay_name: Name of the input assay. If NULL, the default assay is used.

Value

The input PhysioExperiment with connectivity results stored in metadata(x)$connectivity, a list containing:

matrix: Numeric n_channels x n_channels matrix of band-averaged coherence values.
method: Character string indicating the method used.
band: Numeric vector of the frequency band used.
freqs: Numeric vector of frequency bins.
spectra: 3D array (n_freqs x n_channels x n_channels) of frequency-resolved coherence values.

Details

Magnitude-squared coherence is defined as: $$MSC(f) = |S_{xy}(f)|^2 / (S_{xx}(f) \cdot S_{yy}(f))$$

Imaginary coherence uses the imaginary part of coherency to reduce volume conduction artifacts: $$ICoh(f) = |Im(S_{xy}(f) / \sqrt{S_{xx}(f) \cdot S_{yy}(f)})|$$

References

Lachaux, J. P., et al. (1999). Measuring phase synchrony in brain signals. Human Brain Mapping, 8(4), 194-208.

Examples

if (FALSE) { # \dontrun{
pe <- make_eeg(n_time = 5000, n_channels = 4, sr = 500)
pe <- eegCoherence(pe, method = "coherence", band = c(8, 13))
coh_matrix <- metadata(pe)$connectivity$matrix
} # }