MNE - Neurophysiology Analysis

When to Use

• Processing EEG/MEG recordings from clinical or research studies.
• Analyzing event-related potentials (ERPs).
• Source localization (finding where in the brain signals originate).
• Connectivity analysis between brain regions.
• Preprocessing neurophysiological data for machine learning.

Core Principles

Raw → Epochs → Evoked

Sensor Space vs. Source Space

Frequency Analysis

Quick Reference

Standard Imports

import mne
import numpy as np

Basic Patterns

# 1. Load data
raw = mne.io.read_raw_fif("sample_audvis_raw.fif")
# Or: raw = mne.io.read_raw_edf("eeg.edf")

# 2. Filter and cleaning
raw.filter(l_freq=1, h_freq=40)  # Bandpass filter
raw.notch_filter(freqs=[50, 100]) # Remove power line noise

# 3. Find events and create Epochs
events = mne.find_events(raw)
epochs = mne.Epochs(raw, events, event_id={'stimulus': 1}, tmin=-0.2, tmax=0.5)
epochs.average().plot() # Plot Evoked potential

# 4. Frequency analysis
epochs.compute_psd().plot()

Critical Rules

✅ DO

• Filter before epoching - Apply filters to continuous data, not epochs.
• Check data quality - Use

  raw.plot()

  to visually inspect for artifacts.
• Set montage - Assign electrode positions for proper visualization.
• Reject bad epochs - Remove epochs with artifacts before averaging.

❌ DON'T

• Don't filter too aggressively - Over-filtering removes signal along with noise.
• Don't ignore reference - EEG signals are relative. Know your reference electrode.
• Don't mix sampling rates - Ensure all channels have the same sampling rate.

Advanced Patterns

Source Localization

# Compute forward solution and inverse
fwd = mne.make_forward_solution(raw.info, trans, src, bem)
inv = mne.minimum_norm.make_inverse_operator(raw.info, fwd, cov)
stc = mne.minimum_norm.apply_inverse(evoked, inv)
stc.plot()

Connectivity Analysis

from mne.connectivity import spectral_connectivity

# Compute connectivity between channels
con, freqs, times, n_epochs, n_tapers = spectral_connectivity(
    epochs, method='coh', mode='multitaper')