Interhemispheric PLI Analysis Tool

Overview

MATLAB toolbox for computing Phase Lag Index (PLI) connectivity metrics between interhemispheric electrode pairs. Features automated batch processing, quality control, statistical validation, and publication-ready visualizations.

Key Features:

• Standard PLI and Weighted PLI (wPLI) calculation
• Surrogate-based statistical significance testing
• Automated quality control and bad channel detection
• Topographic map generation
• Configurable frequency bands and electrode pairs

Default Electrode Pairs (10-20 System): Fp1-Fp2, F7-F8, F3-F4, T3-T4, C3-C4, T5-T6, P3-P4, O1-O2

Prerequisites

• MATLAB R2016b or later
• EEGLAB toolbox (added to MATLAB path)
• Signal Processing Toolbox

Usage

1. Place EEG files in the data/ folder
2. In MATLAB, navigate to the toolbox folder
3. Run:

   PLI_Analysis

4. Results are saved to output/PLI_Results.xlsx

Supported File Formats:

Format	Extension	Notes
EDF	.edf	European Data Format
BDF	.bdf	BioSemi format
CNT	.cnt	Neuroscan format
SET	.set	EEGLAB native format
MAT	.mat	Must contain variable named EEG
BrainVision	.vhdr	Header file

Configuration

Edit config_pli.m to customize. All options explained below:

Analysis Options

Setting	Default	Description
computePLI	true	Compute standard Phase Lag Index
computeWPLI	true	Compute Weighted PLI (more robust)
computeSignificance	false	Statistical testing (slow, enable if needed)

Frequency Bands

Band	Range (Hz)	Associated With
Delta	0.5-4	Deep sleep, unconscious processes
Theta	4-8	Memory encoding, meditation
Alpha	8-13	Relaxed wakefulness, eyes closed
Beta	13-30	Active thinking, concentration
Gamma	30-45	High-level cognitive processing

Visualization

Setting	Default	Description
generateTopoplots	true	Create scalp maps (disable if not needed)
saveFigures	true	Save figures to disk
figureFormat	'png'	Format: 'png', 'jpg', 'fig'
figureResolution	300	DPI for saved figures

Quality Control

Setting	Default	Description
qc.enabled	false	Run automated data quality checks
minVarianceThreshold	0.1	Min channel variance (detect dead channels)
maxBadChannels	5	Max bad channels before QC fails
minDuration	5	Min recording length in seconds
saveReport	false	Save detailed QC reports to files

Statistics

Setting	Default	Description
numSurrogates	1000	Number of surrogates (more = slower but more accurate)
alphaLevel	0.05	Significance threshold (p < 0.05)

Output

Setting	Default	Description
folder	'output'	Output directory name
filename	'PLI_Results.xlsx'	Results file name

Output

Results are saved in long format (tidy data) - easy to filter, pivot, and analyze.

Excel Columns

Column	Description	Appears When
FileName	Source EEG file	Always
QC_Passed	Quality control status	qc.enabled = true
Band	Frequency band	Always
Pair	Electrode pair	Always
PLI	Phase Lag Index (0-1)	computePLI = true
wPLI	Weighted PLI (0-1)	computeWPLI = true
Significant	Statistical significance	computeSignificance = true
PValue	P-value from surrogate testing	computeSignificance = true

Columns only appear when their corresponding config option is enabled.

Example Output

FileName	QC_Passed	Band	Pair	PLI	wPLI	Significant	PValue
file1.edf	TRUE	Delta	Fp1-Fp2	0.32	0.28	TRUE	0.012
file1.edf	TRUE	Delta	F7-F8	0.18	0.15	FALSE	0.234
file1.edf	TRUE	Theta	Fp1-Fp2	0.41	0.38	TRUE	0.003

Interpreting PLI Values

• 0.0-0.2: Weak connectivity
• 0.2-0.4: Moderate connectivity
• 0.4-0.6: Strong connectivity
• 0.6-1.0: Very strong (verify data quality)

File Structure

PLI-Analysis/
├── PLI_Analysis.m              # Main script
├── config_pli.m                # Configuration
├── compute_wPLI.m              # wPLI function
├── compute_significance.m      # Statistical testing
├── compute_quality_metrics.m   # Quality control
├── generate_topoplots.m        # Visualization
├── README.md                   # Documentation
├── LICENSE                     # GPL-3.0 License
├── .gitignore                  # Git ignore rules
├── data/                       # Place EEG files here
└── output/                     # Created automatically
    ├── PLI_Results.xlsx
    ├── figures/
    └── quality_control/

Troubleshooting

No EEG files found: Place EEG files in the data/ folder.

Channel not found: Your EEG uses different channel names. Edit config.pairs in config_pli.m to match your labels (e.g., use T7 instead of T3).

Slow analysis: Disable significance testing (config.analysis.computeSignificance = false) or reduce config.stats.numSurrogates.

MAT file error: Ensure your .mat file contains a variable named EEG with standard EEGLAB structure.

Acknowledgment

If this toolbox helped your research, a brief acknowledgment is appreciated.