swallowing-meg-connectivity

MATLAB / FieldTrip pipeline for source-level MEG connectivity analysis of swallowing

Source-level MEG Connectivity Analysis Pipeline

This repository contains MATLAB scripts implementing a complete source-level MEG connectivity analysis pipeline based on FieldTrip. The pipeline is designed for data recorded on CTF MEG systems and enables the estimation of frequency-specific functional and directed connectivity between cortical regions of interest (ROIs).

The code supports end-to-end processing starting from raw MEG datasets and culminates in group-level statistical analyses of large-scale cortical networks.

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Overview of the Pipeline

The pipeline implements the following main analysis steps:

1. Trial Definition and Preprocessing

   • Raw MEG data recorded on CTF systems (.ds format)
   • Trials defined based on manually marked event triggers
   • Analysis focuses on EMG2 (active swallowing condition) and EMG3 (control condition)
   • Optional band-pass filtering and line-noise removal

2. Source Reconstruction

   • Linearly Constrained Minimum Variance (LCMV) beamformer
   • Source reconstruction performed using FieldTrip
   • Fixed-orientation source estimates on a warped MNI grid

3. ROI-Level Signal Extraction

   • ROI-level time series are computed internally during beamforming
   • Source estimates are aggregated across predefined cortical ROIs
   • No standalone ROI time-series extraction module is provided

4. Connectivity Analysis

   • Weighted Phase Lag Index (wPLI) for undirected functional connectivity
   • Phase Slope Index (PSI) for directed connectivity
   • Frequency-specific analysis across standard bands:
     • theta, alpha, beta, low gamma, high gamma

5. Statistical Analysis

   • Group-level contrasts (EMG2 vs. EMG3)
   • Laterality indices
   • Cluster-based permutation testing (CBPT) at the ROI × ROI level

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Data Requirements

• MEG system: CTF
• Data format: Native CTF .ds datasets
• Event markers: Manually defined triggers (EMG2, EMG3)
• Pipeline entry point: Raw .ds files (no preprocessed input required)

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Software Requirements

• MATLAB
• FieldTrip (tested with version 2023-12-20)

FieldTrip must be installed and added to the MATLAB path prior to running the scripts.

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Repository Structure

• preprocessing/ Trial definition and preprocessing
• beamformer/ LCMV beamformer source reconstruction and ROI aggregation
• connectivity/ wPLI and PSI connectivity analysis
• statistics/ Statistical analysis and permutation testing

Each subfolder contains a dedicated README.md describing its role within the pipeline.

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Notes

• The code is provided for transparency and reproducibility of the analysis approach.
• Scripts are organized modularly and can be adapted to related MEG connectivity studies.
• Visualization scripts used for figure generation are intentionally not included as core pipeline components.

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Citation

If you use this code or parts of the analysis pipeline in your work, please cite:

Oostenveld, R., Fries, P., Maris, E., & Schoffelen, J.-M. (2011).
FieldTrip: Open Source Software for Advanced Analysis of MEG, EEG, and Invasive Electrophysiological Data.
Computational Intelligence and Neuroscience, 2011, Article ID 156869.

Additional methodological citations should follow the corresponding primary publications.