MNE-Python is the standard open-source toolkit for EEG and MEG analysis: reading the vendor formats, filtering, artefact removal, epoching, time-frequency decomposition, source localization, and connectivity. If Brainstorm is the GUI-first option, MNE is the scripted one — which makes it the better fit when the analysis needs to be reproducible, batched over a cohort, or version-controlled.
Electrophysiology preprocessing differs from the MRI path documented elsewhere in this book in an important way: there is no equivalent of fMRIPrep. No widely agreed pipeline takes raw EEG and returns analysis-ready data, because the right choices depend heavily on the paradigm and the artefacts present. That places more decisions on you — filter cutoffs, referencing, ICA components to reject, epoch rejection thresholds — and makes recording those decisions unusually important.
MNE-BIDS connects it to the rest of the toolchain, reading and writing the EEG and MEG flavours of BIDS.
Related¶
Brainstorm — the GUI-first alternative
BIDS — via MNE-BIDS
Seizure disorders — where EEG concentrates here