Brainlife.io MEG/EEG Apps Suite

A collection of Brainlife.io apps for MEG/EEG processing with MNE-Python. This meta-repository holds every app as a git submodule; each app is its own GitHub repository under BrainlifeMEEG, run on brainlife.io from its v1.0 branch.

Repository: https://github.com/BrainlifeMEEG/MEEG-apps-suite

Getting the code

git clone --recurse-submodules git@github.com:BrainlifeMEEG/MEEG-apps-suite.git
cd MEEG-apps-suite
git submodule update --init --recursive   # if cloned without --recurse-submodules

Each app also carries its own brainlife_utils/ submodule (shared helpers, from BrainlifeMEEG_utils).

Apps

Category	Apps
Format conversion to MNE .fif	bdf2mne, brainvision2mne, ctf2mne, edf2mne, eeglab2mne, egi2mne, fif2mne
MEG (FIF) specific	maxwell-filter, head-pos
Preparing raw data	add-flat-chan, add-montage, average-channels, concat, crop-raw, interpolate-raw, mark-bad-raw, resampling
Filtering	filter-raw, filter-epo
Artifact projectors (SSP / ICA)	SSP-projectors-ECG, SSP-projectors-EOG, emptyroom-proj, SSP-apply, plot_proj_topomaps-raw, ICA-fit, ICA-fit-epo, ICA-apply, ICA-apply-epo, ICA-plot, autoreject
Denoising	gedai, gedai-epo
Events and epochs	events, eventslog, epoch, drop-bad-epo, interpolate, rereference, apply-baseline, plot-epochs
Evoked responses	evoked-averaged, average-erp
Spectral features	psd, epoch-psd, peak-amplitude, peak-frequency
Data information	info-raw, info-epo, info-evoked
Source modelling	make-watershed-bem, make-bem, coreg, source-space, forward, noise-covariance, inverse-operator, source-estimate, label-timecourse
Full pipeline	meegflow-app

Each app's own README.md documents its inputs, outputs and configuration parameters.

Developing apps

• agent-instructions.md is the single source of conventions: app structure, brainlife_utils usage, output naming, product.json, Docker images, the App README policy, and how to work with the brainlife.io CLI and API.
• .claude/agents/ holds the Claude Code agents that apply those rules: auditing and fixing apps, syncing brainlife_utils, registering apps, switching the branch an app runs from, and setting up pipeline rules.
• docker-mne/, docker-mne-freesurfer/ and docker-mne-fsaverage/ hold the container images the apps run in.
• local_scripts/ holds project-level tooling (pipeline reproduction, rule setup).
• docs/archive/ holds superseded reports, kept for history.

Citation

If you use these apps in research, please cite:

@article{Hayashi2024,
  author  = {Hayashi, Soichi and Caron, Bradley A. and Heinsfeld, Anibal S. and others},
  title   = {brainlife.io: a decentralized and open-source cloud platform to support neuroscience research},
  journal = {Nature Methods},
  year    = {2024},
  volume  = {21},
  number  = {5},
  pages   = {809--813},
  doi     = {10.1038/s41592-024-02237-2}
}

@article{gramfort2013meg,
  title   = {MEG and EEG data analysis with MNE-Python},
  author  = {Gramfort, A. and Luessi, M. and Larson, E. and others},
  journal = {Frontiers in Neuroscience},
  volume  = {7},
  pages   = {267},
  year    = {2013},
  doi     = {10.3389/fnins.2013.00267}
}

Authors

• Maximilien Chaumon (https://github.com/dnacombo)
• Guiomar Niso (https://github.com/guiomar)
• Kami Salibayeva (https://github.com/KSalibay)
• Saeed Zahran (https://github.com/zahransa/)
• Aurore Bussalb (https://github.com/abussalb)
• Franco Pestilli (https://github.com/francopestilli)

See individual app repositories for detailed contributor lists.

License

All apps are licensed under AGPLv3 or later, as stated in license.txt and in each app repository, except where an app states otherwise (e.g. gedai, which wraps a PolyForm Noncommercial library).

MNE-Python is Copyright (c) 2011-2026 MNE-Python developers, licensed under the 3-Clause BSD License (https://mne.tools/stable/license.html).

Resources

• Brainlife.io documentation: https://brainlife.io/docs
• MNE-Python documentation: https://mne.tools/
• Bugs: open an issue in the individual app repository.