MEEGFlow

A modular, configuration-driven MEEG preprocessing pipeline using MNE-Python.

MEEGFlow lets you run a full M/EEG preprocessing pipeline by writing a YAML config file — no boilerplate code required. Each step is a named, parameterisable function; you choose which steps to run, in what order, and with what parameters.

Features

• Flexible file discovery — supports BIDS datasets (BIDSReader) and custom glob patterns (GlobReader)
• Modular steps — filtering, ICA, bad-channel detection, epoching, interpolation, and more
• Configuration-driven — one YAML file controls the entire pipeline
• Custom steps — extend the pipeline with your own Python functions
• Rich progress bars — real-time feedback for batch processing
• Multiple outputs — clean .fif files, JSON reports, and interactive HTML reports

Quick start

pip install meegflow

meegflow --bids-root /path/to/bids \
         --config config.yaml \
         --subjects 01 02 \
         --tasks rest

See Installation and CLI usage for more detail.