Analyze EEG Connectivity

Description

The Analyze EEG Connectivity module computes both functional and directional brain connectivity using two established EEG measures:

  • wPLI (Weighted Phase Lag Index): estimates non-zero-lag phase synchronization, minimizing volume conduction artifacts.

  • dPLI (Directed Phase Lag Index): estimates the direction of phase-lead/lag between pairs of EEG channels.

This tool automatically applies statistical correction using surrogate data testing and Wilcoxon signed-rank tests to retain only significant connections. It requires at least two clean brain channels and two valid epochs to run.

Note

For optimal results, it is strongly recommended to preprocess your data using the EEGInspector app in Snooz. This allows you to mark and exclude: - Non-brain channels (e.g., EOG, EMG, ECG) - Noisy/bad channels - Noisy epochs

Steps

1 - Input Files

Start by opening your PSG files (.edf, .eeg or .sts).

  • The .tsv file is also needed for the EDF format.

  • The .sig file is also needed for Stellate format.

  • The whole NATUS subject folder is also needed for the .eeg format.

2 - Events Exclusion

Use previously saved artifact annotations (e.g., from EEGInspector, Snooz artifact detection tool) to exclude noisy data from connectivity calculations.

Important

Connectivity cannot be performed on: - Fewer than 2 channels - Fewer than 2 valid epochs

3 - Filtering

  • Frequency Band Selection: Choose a predefined band (Delta, Theta, Alpha, Beta, Full) or define a custom band to match your research question.

  • Recording Scope Selection: Select Sleep Stages to analyze specific stages, Unscored to analyze the full recording or a chosen time segment, or Specific Annotations to base the analysis on event markers.

4 - Annotation Selection

Select specific annotations/events to perform connectivity analysis on. You can choose multiple annotations if needed.

5 - Connectivity Configuration

  • Connectivity Type: Choose between wPLI or dPLI.

  • Epoch Parameters: - Epoch length (seconds) - Epoch overlap (seconds) - Number of surrogates (for statistical testing) - P-value threshold (to retain only significant connections)

    Statistical testing ensures connections are not due to chance and provides more reliable connectivity estimates.

6 - Output Files

All files are saved in the selected Output folder, or next to the input file if “Save in the same folder” is checked.

Output files include:

  • Connectivity Matrix (TSV) - File: <Filename>_{wpli|dpli}_convalue.tsv

  • Connectivity Heatmap (PNG) - File: <Filename>_{wpli|dpli}_conheatmap.png - Visual matrix of the TSV data.

  • Head Connectivity Plot (PNG, optional) - File: <Filename>_{wpli|dpli}_contopomap.png - Saved only if a montage with ≥ 4 EEG channels is found.

Connectivity value ranges

Measure

Range and interpretation

wPLI

0 to 1 (0 = no phase coupling; 1 = strong coupling)

dPLI

0 to 1 (0.5 = neutral; > 0.5 = leads; < 0.5 = lags)

Head connectivity plot elements

Element

Description

Nodes

EEG channels (connected = filled black; unconnected = white)

Edges

wPLI: single color (darker means stronger); dPLI: gradient red -> purple -> blue (red = leader, blue = lagger)

Styling

Edge thickness and opacity scale with connection strength

Montage Handling

  • Montage is automatically selected from MNE built-ins.

  • For HydroCel 128/129, face/neck sensors are removed to clean up the layout.

Display Thresholds

Default thresholds for plotting:

wPLI:

  • neutral_min = 0.05 (ignore below)

  • moderate_min = 0.10 (thin & faint)

  • strong_min = 0.20 (thick & dark)

  • max_val = 0.40 (for opacity scaling)

dPLI (bias = dPLI − 0.5):

  • neutral_abs = 0.01 (ignore below)

  • moderate_abs = 0.02 (thin & faint)

  • strong_abs = 0.08 (thick & dark)

  • max_abs = 0.25 (for opacity scaling)

Note

An auto-density option (e.g., “keep top 15% of connections”) is implemented but currently disabled. It may be available in future versions.

References

[1] Stam, C. J., & van Straaten, E. C. W. (2012). Go with the flow: Use of a directed phase lag index (dPLI) to characterize patterns of phase relations in a large-scale model of brain dynamics. NeuroImage, 62(3), 1415–1428. https://doi.org/10.1016/j.neuroimage.2012.05.050

[2] Vinck, M., Oostenveld, R., van Wingerden, M., Battaglia, F., & Pennartz, C. M. (2011). An improved index of phase-synchronization for electrophysiological data in the presence of volume-conduction, noise and sample-size bias. NeuroImage, 55(4), 1548–1565. https://doi.org/10.1016/j.neuroimage.2011.01.055

[3] Duclos, C., Maschke, C., Mahdid, Y., Nadin, D., Rokos, A., Arbour, C., Badawy, M., Létourneau, J., Owen, A. M., Plourde, G., & Blain-Moraes, S. (2023). Brain responses to propofol in advance of recovery from coma and disorders of consciousness: A preliminary study. American Journal of Respiratory and Critical Care Medicine, 207(5), 602–613. https://doi.org/10.1164/rccm.202105-1223OC

Version History

  • v2.2.0Distributed with CEAMS package version 7.3.0 — Snooz beta 3.0.0

    • Initial release of the tool.