Glossary

A reference of key terms, abbreviations, and concepts used throughout the MNE-CPP documentation.

General Concepts

Term	Definition
BEM	Boundary-Element Model. A numerical method for computing the forward solution by discretizing the boundaries between tissue compartments of different electrical conductivity (scalp, skull, brain).
CMNE	Contextual Minimum-Norm Estimate. A deep-learning-based inverse method that uses an LSTM network to incorporate temporal context from preceding time samples. Training in Python (PyTorch), inference via ONNX Runtime in C++.
Coregistration	The process of aligning the MEG/EEG head coordinate system with the MRI coordinate system using fiducial landmarks. Stored in a `-trans.fif` file.
DICS	Dynamic Imaging of Coherent Sources. A frequency-domain beamformer that estimates source power and coherence using the cross-spectral density matrix.
dSPM	Dynamic Statistical Parametric Mapping. A noise-normalized variant of the minimum-norm estimate that produces statistical maps (F-statistic) rather than current amplitudes.
ECD	Equivalent Current Dipole. A point-source model used in dipole fitting to localize focal brain activity.
eLORETA	Exact Low-Resolution Electromagnetic Tomography. A distributed source localization method with exact zero localization error for single-dipole sources.
Evoked response	The averaged brain response time-locked to a stimulus event. Also called event-related field (ERF) for MEG and event-related potential (ERP) for EEG.
Forward solution	The theoretical prediction of the magnetic fields and electric potentials at the sensor locations given a set of source dipoles in the brain.
Gamma-MAP	Gamma Maximum a Posteriori. A sparse Bayesian inverse method using an EM algorithm with a Gamma hyperprior on source variances to promote focal source distributions.
Inverse operator	A matrix that maps measured sensor data to estimated source activity on the cortex or in a volume. Computed from the forward solution and noise-covariance matrix.
LCMV	Linearly Constrained Minimum Variance beamformer. A spatial filter that passes signals from a target location while minimizing output power from other sources.
MNA	MNE Node-graph for Analysis. A portable project file format (`.mna` JSON / `.mnx` CBOR) that bundles data references, processing parameters, and an executable computational graph into a single manifest. See MNA Format.
MNE	Minimum-Norm Estimate. A distributed source localization method that finds the source distribution with minimum overall power that explains the measured data.
Morphing	The process of mapping source estimates from one subject's cortical surface to another (e.g., `fsaverage`) for group analysis.
MxNE	Mixed-Norm Estimate. A sparse inverse method using L1/L2 mixed norms (group lasso) to find focal sources via iteratively reweighted least squares (IRLS).
Noise-covariance matrix	A matrix characterizing the spatial noise statistics of the sensor data. Used to weight channels appropriately in the inverse solution.
ONNX	Open Neural Network Exchange. An open format for machine learning models. MNE-CPP uses ONNX Runtime for CMNE inference, loading pre-trained LSTM models for source estimation.
RAP MUSIC	Recursively Applied and Projected Multiple Signal Classification. A subspace method for localizing multiple correlated sources by iteratively scanning, finding peaks, and projecting out found sources.
Regularization	A mathematical technique to stabilize the ill-posed inverse problem by trading off data fit against solution smoothness. Controlled by the regularization parameter (related to assumed SNR).
sLORETA	Standardized Low-Resolution Electromagnetic Tomography. A noise-normalized variant of the minimum-norm estimate with near-zero localization bias for point spread.
SNR	Signal-to-Noise Ratio. In MNE, the assumed SNR controls the regularization parameter $\lambda^2 = 1 / \text{SNR}^2$ .
SPHARA	Spatial Harmonic Analysis. Spatial basis functions computed from the sensor geometry for noise reduction, similar to spatial frequency filtering.
Source space	The set of candidate dipole locations (and orientations) on the cortical surface or in a volume where source currents are estimated.
SSP	Signal-Space Projection. A method for removing environmental noise and artifacts by projecting data away from known noise subspaces. See Signal-Space Projection.
SSS/tSSS	Signal Space Separation / temporal SSS. Methods for removing external interference from MEG data by decomposing the measured field into internal and external multipole components.
xDAWN	A supervised spatial filter designed to enhance event-related potentials by maximizing the signal-to-signal-plus-noise ratio. Used in BCI and ERP denoising.

MEG/EEG Systems and Sensors

Term	Definition
CTF	A MEG system manufacturer. CTF systems use axial gradiometers and software gradient compensation with reference channels. Uses a different head coordinate convention than Neuromag.
EEG	Electroencephalography. Measures electrical potentials on the scalp using electrode caps.
Gradiometer	A MEG sensor that measures the spatial gradient of the magnetic field. Planar gradiometers measure the gradient tangential to the helmet surface; axial gradiometers measure the radial gradient.
KIT	A 160-channel MEG system (also known as Yokogawa). Data can be imported with `mne_kit2fiff`.
Magnetometer	A MEG sensor that measures the absolute magnetic field strength at a single point. More sensitive to deep and distant sources than gradiometers, but also more sensitive to environmental noise.
MEG	Magnetoencephalography. Measures the magnetic fields produced by neuronal currents using superconducting sensors (SQUIDs) in a magnetically shielded room.
Neuromag / Vectorview	A 306-channel MEG system (Elekta / MEGIN) with 102 sensor triplets, each containing one magnetometer and two planar gradiometers. The MNE head coordinate convention originates from this system.
SQUID	Superconducting Quantum Interference Device. The ultra-sensitive magnetic sensor used in MEG systems, operating at liquid helium temperatures.

Channel Types

Type Abbreviation	Full Name	Unit	Description
MEG (mag)	Magnetometer	T (Tesla)	Measures absolute magnetic field
MEG (grad)	Planar gradiometer	T/m	Measures tangential field gradient
EEG	Electroencephalography	V (Volt)	Scalp electrical potential
EOG	Electrooculography	V	Eye movement channels
ECG	Electrocardiography	V	Heart activity channel
EMG	Electromyography	V	Muscle activity channels
STI	Stimulus / Trigger	—	Digital trigger channel (e.g., STI 014)
MISC	Miscellaneous	—	Unclassified or auxiliary channels
REF	Reference	T	Reference magnetometer channels (used in software gradient compensation)

Coordinate Systems

Coordinate System	Description
Head coordinates	Defined by three fiducial landmarks: nasion (N), left auricular point (LAP), and right auricular point (RAP). Origin midway between LAP and RAP; x-axis toward nasion; y-axis toward LAP; z-axis upward. See Forward Solution — Coordinate Systems.
Device coordinates	The MEG sensor coordinate system, defined by the MEG instrument. Relationship to head coordinates established via head position indicator (HPI) coils.
MRI (Surface RAS)	FreeSurfer surface coordinates. Origin at the center of the MRI volume; axes aligned with anatomical directions (Right, Anterior, Superior).
MNI Talairach	A standardized brain coordinate system based on the MNI152 template. Used for reporting source locations across subjects.
FreeSurfer Talairach	FreeSurfer's own Talairach transformation, which differs slightly from the MNI Talairach.

For details on coordinate transformations ( $T^-$ , $T^+$ , $T_1$ – $T_4$ ), see Forward Solution.

File Formats and Extensions

Extension	Format	Description
`.fif`	FIFF	Functional Imaging File Format. The native binary format for all MNE data. See FIFF Format.
`-raw.fif`	FIFF	Raw continuous MEG/EEG data
`-ave.fif`	FIFF	Averaged evoked response data
`-cov.fif`	FIFF	Noise-covariance matrix
`-fwd.fif`	FIFF	Forward solution
`-inv.fif`	FIFF	Inverse operator decomposition
`-src.fif`	FIFF	Source space description
`-bem.fif`	FIFF	BEM geometry
`-bem-sol.fif`	FIFF	BEM solution (precomputed geometry matrices)
`-trans.fif`	FIFF	Coordinate transformation (head-to-MRI)
`-sol.fif`	FIFF	BEM solution matrix
`.stc`	STC	Source Time Course. Binary file with source amplitudes over time for one hemisphere.
`.w`	W file	A single time-point snapshot of source amplitudes for one hemisphere.
`.label`	Label	FreeSurfer label file defining a region of interest (ROI) on the cortical surface.
`.annot`	Annotation	FreeSurfer cortical parcellation (atlas) file.
`.surf`	Surface	FreeSurfer binary surface file (vertices + triangles).
`.mgh` / `.mgz`	MRI volume	FreeSurfer MRI volume format (uncompressed / compressed).
`.hpts`	Head points	Text file with digitization point coordinates. See Data Conversion — hpts format.
`.mna`	MNA (JSON)	MNE analysis project file — data references, parameters, and executable graph. See MNA Format.
`.mnx`	MNA (CBOR)	Binary MNA project file in CBOR encoding. Same schema as `.mna` but more compact. Can also serve as a container file that encapsulates linked data files (raw, evoked, forward solutions, etc.) into a single self-contained archive.
`.onnx`	ONNX	Open Neural Network Exchange model file. Used for CMNE LSTM inference.

Environment Variables

Variable	Purpose
`SUBJECTS_DIR`	Directory containing FreeSurfer subject directories with anatomical MRI data.
`SUBJECT`	Name of the current subject's directory under `SUBJECTS_DIR`.
`FREESURFER_HOME`	Root directory of the FreeSurfer installation.
`MNE_ROOT`	Root directory of the MNE-C software installation.
`MNE_TRIGGER_CH_NAME`	Override the default trigger channel name (default: `STI 014`).
`MNE_TRIGGER_CH_MASK`	Bit mask applied to the trigger channel (useful for BDF files: `0xff`).

Rejection Thresholds

Default units for artifact rejection thresholds used in epoching:

Channel type	Unit	Typical threshold
Gradiometer	T/m	2000e-13 – 4000e-13
Magnetometer	T	4e-12 – 6e-12
EEG	V	100e-6 – 200e-6
EOG	V	150e-6 – 250e-6

General Concepts​

MEG/EEG Systems and Sensors​

Channel Types​

Coordinate Systems​

File Formats and Extensions​

Environment Variables​

Rejection Thresholds​

See Also​