MNE-BIDS-Pipeline

MNE-BIDS-Pipeline is a full-flegded processing pipeline for your MEG and EEG data.

• It operates on data stored according to the Brain Imaging Data Structure (BIDS).
• Under the hood, it uses MNE-Python.

💡 Basic concepts and features

• 🏆 Automated processing of MEG and EEG data from raw data to inverse solutions.
• 🛠️ Configuration via a simple text file.
• 📘 Extensive processing and analysis summary reports.
• 🧑‍🤝‍🧑 Process just a single participant, or as many as several hundreds of participants – in parallel.
• 💻 Execution via an easy-to-use command-line utility.
• 🆘 Helpful error messages in case something goes wrong.
• 👣 Data processing as a sequence of standard processing steps.
• ⏩ Steps are cached to avoid unnecessary recomputation.
• ⏏️ Data can be "ejected" from the pipeline at any stage. No lock-in!
• ☁️ Runs on your laptop, on a powerful server, or on a high-performance cluster via Dask.

📘 Installation and usage instructions

Please find the documentation at mne.tools/mne-bids-pipeline.

❤ Acknowledgments

The original pipeline for MEG/EEG data processing with MNE-Python was built jointly by the Cognition and Brain Dynamics Team and the MNE Python Team, based on scripts originally developed for this publication:

M. Jas, E. Larson, D. A. Engemann, J. Leppäkangas, S. Taulu, M. Hämäläinen, A. Gramfort (2018). A reproducible MEG/EEG group study with the MNE software: recommendations, quality assessments, and good practices. Frontiers in neuroscience, 12. https://doi.org/10.3389/fnins.2018.00530

The current iteration is based on BIDS and relies on the extensions to BIDS for EEG and MEG. See the following two references:

Pernet, C. R., Appelhoff, S., Gorgolewski, K. J., Flandin, G., Phillips, C., Delorme, A., Oostenveld, R. (2019). EEG-BIDS, an extension to the brain imaging data structure for electroencephalography. Scientific Data, 6, 103. https://doi.org/10.1038/s41597-019-0104-8

Niso, G., Gorgolewski, K. J., Bock, E., Brooks, T. L., Flandin, G., Gramfort, A., Henson, R. N., Jas, M., Litvak, V., Moreau, J., Oostenveld, R., Schoffelen, J., Tadel, F., Wexler, J., Baillet, S. (2018). MEG-BIDS, the brain imaging data structure extended to magnetoencephalography. Scientific Data, 5, 180110. https://doi.org/10.1038/sdata.2018.110

Contributing

see <./CONTRIBUTING.md>