Neurotheque Resources

Neurotheque Resources is a comprehensive, modular toolkit for EEG data processing and analysis. Built on state‐of‐the‐art libraries such as MNE-Python, autoreject it enables:

• Preprocessing & Channel Setup: Automatic bad channel detection and re-referencing with standardized electrode montages.
• Artifact Rejection: Advanced methods like ICA and auto-rejection for high-quality EEG data.
• Task & Trigger Parsing: Flexible logic to merge triggers for tasks like Go/No-Go, finger tapping, or mental imagery.
• Epoching & Analysis: Efficient epoch slicing, ROI averaging, time–frequency transforms, and ERP analyses.
• Report Generation: Automated HTML reporting (via MNE's Report) for visual inspection and documentation of analysis results.

This repository is designed for both single-subject and multi-subject pipelines, ensuring reproducibility and scalability.

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Table of Contents

1. Repository Structure
2. Installation & Quick Start
3. Usage Examples
4. Contributors & Acknowledgments
5. Contributing
6. License
7. Contact

Repository Structure

• notebooks/

  • tutorials/ – Step-by-step Jupyter notebooks illustrating basic usage and pipeline demos.
  • preprocessing/ – Notebooks focusing on data cleaning (filtering, ICA, etc.).
  • analysis/ – Notebooks showing advanced analysis tasks (ERP, ROI-based metrics, time–frequency transforms).

• src/

  • pipeline.py – The main pipeline driver, reading YAML configs or Python dicts to run each pipeline step in sequence.
  • steps/ – A suite of modular processing steps (e.g., LoadData, FilterStep, AutoRejectStep, ICAStep, SplitTasksStep, TriggerParsingStep) that can be combined in various orders.
  • strategies/ – Specialized scripts/pipelines for different paradigms (e.g., finger tapping, mental imagery).
  • utilities/ – Helper scripts like combine_py_files.py (for merging .py files) or export_repo_structure.py (for generating directory trees).

• doc/ – Additional documentation, user guides, or methodology reports.

• configs/ – YAML files detailing pipeline configurations (e.g., pilot_preprocessing_strategy.yml, gonogo_analysis.yml, etc.).

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Getting Started

Installation & Quick Start

1. Clone the repository:

   git clone https://github.com/UNFmontreal/neurotheque_resources.git
   cd neurotheque_resources

2. Install dependencies:

   pip install -r requirements.txt

Usage Examples

1. Run a Pipeline with a YAML Configuration

   python src/pipeline.py --config configs/pilot_preprocessing_strategy.yml

   This loads the steps specified in the config (e.g. LoadData, FilterStep, AutoRejectStep, etc.) and applies them to your EEG data.

2. Use a Strategy Script

   # Example: Using the finger tapping strategy
   from src.strategies.finger_tapping_strategy import run_finger_tapping_pipeline
   
   input_path = "data/raw/sub-01_ses-001_eeg.edf"
   output_path = "data/processed/sub-01_ses-001_preprocessed.fif"
   
   run_finger_tapping_pipeline(input_path, output_path)

3. Explore the Jupyter Notebooks

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