Installation Guide

Prerequisites

Before installing AutoClean, ensure you have:

• Python ≥3.10
• pip (Python package installer)
• Git (for cloning the repository)

Installation Steps

1. Clone the repository:

   git clone https://github.com/cincibrainlab/autoclean_complete.git
   cd autoclean_complete
   

2. Create a virtual environment (recommended):

   python -m venv venv
   source venv/bin/activate  # On Windows, use: venv\Scripts\activate
   

3. Install dependencies:

   pip install -r requirements.txt
   

Required Dependencies

AutoClean requires several Python packages:

• mne: For EEG data processing
• rich: For console output formatting
• numpy: For numerical operations
• python-dotenv: For environment variable management
• mne-bids: For BIDS format support
• pyprep: For preprocessing utilities
• autoreject: For automated artifact rejection
• And more (see full list in requirements.txt)

Environment Setup

1. Create a .env file in your project root:

   touch .env
   

2. Add required environment variables:

   AUTOCLEAN_DIR=/path/to/output
   AUTOCLEAN_CONFIG=config.yml
   

Verification

To verify your installation:

1. Activate your virtual environment:

   source venv/bin/activate
   

2. Run a Python interpreter and try importing the package:

   import autoclean_preprocessing.autoclean_pipeline_v2 as autoclean
   

If no errors occur, the installation was successful!