MNE-style inverse operator. More...

#include <mne_inverse_operator.h>

Public Types
typedef QSharedPointer< MNEInverseOperator >	SPtr
typedef QSharedPointer< const MNEInverseOperator >	ConstSPtr

Public Member Functions
	MNEInverseOperator ()
	Constructs an empty inverse operator with invalid sentinel values.
	MNEInverseOperator (QIODevice &p_IODevice)
	Constructs an inverse operator by reading from a FIFF IO device.
	MNEInverseOperator (const FIFFLIB::FiffInfo &info, const MNEForwardSolution &forward, const FIFFLIB::FiffCov &noiseCov, float loose=0.2f, float depth=0.8f, bool fixed=false, bool limit_depth_chs=true)
	Constructs an inverse operator from measurement info, forward solution, and noise covariance.
	MNEInverseOperator (const MNEInverseOperator &other)
	Copy constructor.
	~MNEInverseOperator ()
	Destructor.
bool	assemble_kernel (const FSLIB::FsLabel &label, const QString &method, bool pick_normal, Eigen::MatrixXd &K, Eigen::SparseMatrix< double > &noise_norm, QList< Eigen::VectorXi > &vertno)
	Assemble the inverse kernel matrix.
bool	check_ch_names (const FIFFLIB::FiffInfo &info) const
	Verify that inverse-operator channels are present in the measurement info.
Eigen::MatrixXd	cluster_kernel (const FSLIB::FsAnnotationSet &annotationSet, qint32 clusterSize, Eigen::MatrixXd &D, const QString &method=QStringLiteral("cityblock")) const
	Cluster the inverse kernel by cortical parcellation.
Eigen::MatrixXd &	getKernel ()
	Access the most recently assembled kernel (mutable).
Eigen::MatrixXd	getKernel () const
	Access the most recently assembled kernel (const).
bool	isFixedOrient () const
	Check whether the inverse operator uses fixed source orientations.
MNEInverseOperator	prepare_inverse_operator (qint32 nave, float lambda2, bool dSPM, bool sLORETA=false) const
	Prepare the inverse operator for source estimation.
void	write (QIODevice &p_IODevice)
	Write the inverse operator to a FIFF file.
void	writeToStream (FIFFLIB::FiffStream *p_pStream)
	Write the inverse operator into an already-open FIFF stream.

Static Public Member Functions
static MNEInverseOperator	make_inverse_operator (const FIFFLIB::FiffInfo &info, MNEForwardSolution forward, const FIFFLIB::FiffCov &noiseCov, float loose=0.2f, float depth=0.8f, bool fixed=false, bool limit_depth_chs=true)
	Assemble an inverse operator from a forward solution and noise covariance.
static bool	read_inverse_operator (QIODevice &p_IODevice, MNEInverseOperator &inv)
	Read an inverse operator from a FIFF file.

Public Attributes
FIFFLIB::FiffInfoBase	info
FIFFLIB::fiff_int_t	methods
FIFFLIB::fiff_int_t	source_ori
FIFFLIB::fiff_int_t	nsource
FIFFLIB::fiff_int_t	nchan
FIFFLIB::fiff_int_t	coord_frame
Eigen::MatrixXf	source_nn
Eigen::VectorXd	sing
bool	eigen_leads_weighted
FIFFLIB::FiffNamedMatrix::SDPtr	eigen_leads
FIFFLIB::FiffNamedMatrix::SDPtr	eigen_fields
FIFFLIB::FiffCov::SDPtr	noise_cov
FIFFLIB::FiffCov::SDPtr	source_cov
FIFFLIB::FiffCov::SDPtr	orient_prior
FIFFLIB::FiffCov::SDPtr	depth_prior
FIFFLIB::FiffCov::SDPtr	fmri_prior
MNESourceSpaces	src
FIFFLIB::FiffCoordTrans	mri_head_t
FIFFLIB::fiff_int_t	nave
QList< FIFFLIB::FiffProj >	projs
Eigen::MatrixXd	proj
Eigen::MatrixXd	whitener
Eigen::VectorXd	reginv
Eigen::SparseMatrix< double >	noisenorm

Friends
std::ostream &	operator<< (std::ostream &out, const MNEInverseOperator &inv)
	Stream-output operator for diagnostic printing.

Detailed Description

MNE-style inverse operator.

Encapsulates the SVD decomposition of the whitened and weighted lead-field matrix together with noise and source covariance, priors, and the source space. Supports reading/writing FIFF files, preparation for application (regularisation, whitening, noise normalisation), and gain-matrix clustering.

Definition at line 137 of file mne_inverse_operator.h.

Member Typedef Documentation

◆ ConstSPtr

typedef QSharedPointer<const MNEInverseOperator> MNELIB::MNEInverseOperator::ConstSPtr

Const shared pointer type for MNEInverseOperator.

Definition at line 141 of file mne_inverse_operator.h.

◆ SPtr

typedef QSharedPointer<MNEInverseOperator> MNELIB::MNEInverseOperator::SPtr

Shared pointer type for MNEInverseOperator.

Definition at line 140 of file mne_inverse_operator.h.

Constructor & Destructor Documentation

◆ MNEInverseOperator() [1/4]

MNEInverseOperator::MNEInverseOperator ( )

Constructs an empty inverse operator with invalid sentinel values.

Definition at line 76 of file mne_inverse_operator.cpp.

◆ MNEInverseOperator() [2/4]

MNEInverseOperator::MNEInverseOperator ( QIODevice & p_IODevice )

explicit

Constructs an inverse operator by reading from a FIFF IO device.

Parameters

[in] p_IODevice IO device (e.g. QFile) containing the inverse operator.

Definition at line 98 of file mne_inverse_operator.cpp.

◆ MNEInverseOperator() [3/4]

MNEInverseOperator::MNEInverseOperator	(	const FIFFLIB::FiffInfo &	info,
		const MNEForwardSolution &	forward,
		const FIFFLIB::FiffCov &	noiseCov,
		float	loose = 0.2f,
		float	depth = 0.8f,
		bool	fixed = false,
		bool	limit_depth_chs = true )

Constructs an inverse operator from measurement info, forward solution, and noise covariance.

Parameters

[in]	info	Measurement info specifying channels; bad channels in info.bads are excluded.
[in]	forward	Forward operator.
[in]	noiseCov	Noise covariance matrix.
[in]	loose	Tangential-component weight in [0, 1] (ignored when `fixed` is true).
[in]	depth	Depth-weighting exponent in [0, 1]; 0 disables depth weighting.
[in]	fixed	If true, use fixed source orientations normal to the cortical mantle.
[in]	limit_depth_chs	If true, restrict depth weighting to gradiometers (or magnetometers/EEG as fallback).

Definition at line 107 of file mne_inverse_operator.cpp.

◆ MNEInverseOperator() [4/4]

MNEInverseOperator::MNEInverseOperator ( const MNEInverseOperator & other )

Copy constructor.

Parameters

[in] other Inverse operator to copy.

Definition at line 122 of file mne_inverse_operator.cpp.

◆ ~MNEInverseOperator()

MNEInverseOperator::~MNEInverseOperator ( )

default

Destructor.

Member Function Documentation

◆ assemble_kernel()

bool MNEInverseOperator::assemble_kernel	(	const FSLIB::FsLabel &	label,
		const QString &	method,
		bool	pick_normal,
		Eigen::MatrixXd &	K,
		Eigen::SparseMatrix< double > &	noise_norm,
		QList< Eigen::VectorXi > &	vertno )

Assemble the inverse kernel matrix.

Applies eigenfield/eigenlead decomposition, regularisation, whitening, projection, and optional noise normalisation to produce the kernel matrix that maps sensor data to source estimates.

Parameters

[in]	label	Cortical label restricting the source space (empty for all sources).
[in]	method	Inverse method: "MNE", "dSPM", or "sLORETA".
[in]	pick_normal	If true, keep only the surface-normal component (requires free orientation).
[out]	K	Assembled kernel matrix (nSources x nChannels).
[out]	noise_norm	Diagonal noise-normalisation matrix (empty for MNE).
[out]	vertno	Vertex numbers per hemisphere.

Returns: true on success.

Definition at line 158 of file mne_inverse_operator.cpp.

◆ check_ch_names()

bool MNEInverseOperator::check_ch_names ( const FIFFLIB::FiffInfo & info ) const

Verify that inverse-operator channels are present in the measurement info.

Parameters

[in] info Measurement info whose channel names are checked.

Returns: true if all channels match, false otherwise.

Definition at line 311 of file mne_inverse_operator.cpp.

◆ cluster_kernel()

MatrixXd MNEInverseOperator::cluster_kernel	(	const FSLIB::FsAnnotationSet &	annotationSet,
		qint32	clusterSize,
		Eigen::MatrixXd &	D,
		const QString &	method = QStringLiteral("cityblock") ) const

Cluster the inverse kernel by cortical parcellation.

Groups source-space points within each parcellation label using KMeans and returns a reduced kernel together with the cluster operator.

Parameters

[in]	annotationSet	Annotation set for left and right hemisphere.
[in]	clusterSize	Maximum number of sources per cluster.
[out]	D	Cluster operator matrix (nSources x nClusters).
[in]	method	Distance metric: "cityblock" or "sqeuclidean".

Returns: Clustered kernel matrix.

Definition at line 356 of file mne_inverse_operator.cpp.

◆ getKernel() [1/2]

Eigen::MatrixXd & MNELIB::MNEInverseOperator::getKernel ( )

inline

Access the most recently assembled kernel (mutable).

Returns: Reference to the kernel matrix.

Definition at line 382 of file mne_inverse_operator.h.

◆ getKernel() [2/2]

Eigen::MatrixXd MNELIB::MNEInverseOperator::getKernel ( ) const

inline

Access the most recently assembled kernel (const).

Returns: Copy of the kernel matrix.

Definition at line 389 of file mne_inverse_operator.h.

◆ isFixedOrient()

bool MNELIB::MNEInverseOperator::isFixedOrient ( ) const

inline

Check whether the inverse operator uses fixed source orientations.

Returns: true if orientation is fixed-normal.

Definition at line 396 of file mne_inverse_operator.h.

◆ make_inverse_operator()

MNEInverseOperator MNEInverseOperator::make_inverse_operator	(	const FIFFLIB::FiffInfo &	info,
		MNEForwardSolution	forward,
		const FIFFLIB::FiffCov &	noiseCov,
		float	loose = 0.2f,
		float	depth = 0.8f,
		bool	fixed = false,
		bool	limit_depth_chs = true )

static

Assemble an inverse operator from a forward solution and noise covariance.

Performs depth weighting, source-covariance construction, whitening, and SVD decomposition of the weighted lead-field matrix.

Parameters

[in]	info	Measurement info; bad channels in info.bads are excluded.
[in]	forward	Forward operator (modified internally for fixed orientation if needed).
[in]	noiseCov	Noise covariance matrix.
[in]	loose	Tangential-component weight in [0, 1].
[in]	depth	Depth-weighting exponent in [0, 1]; 0 disables.
[in]	fixed	Use fixed surface-normal orientations.
[in]	limit_depth_chs	Restrict depth weighting to gradiometers (or fallback).

Returns: Assembled inverse operator.

Definition at line 635 of file mne_inverse_operator.cpp.

◆ prepare_inverse_operator()

MNEInverseOperator MNEInverseOperator::prepare_inverse_operator	(	qint32	nave,
		float	lambda2,
		bool	dSPM,
		bool	sLORETA = false ) const

Prepare the inverse operator for source estimation.

Scales covariances by the number of averages, builds the regularised pseudo-inverse, the whitener, the SSP projector, and (optionally) the noise-normalisation factors for dSPM or sLORETA.

Parameters

[in]	nave	Number of averages (scales the noise covariance).
[in]	lambda2	Regularisation parameter (SNR^{-2}).
[in]	dSPM	Compute dSPM noise-normalisation factors.
[in]	sLORETA	Compute sLORETA noise-normalisation factors.

Returns: A prepared copy of the inverse operator ready for apply_inverse.

Definition at line 884 of file mne_inverse_operator.cpp.

◆ read_inverse_operator()

bool MNEInverseOperator::read_inverse_operator	(	QIODevice &	p_IODevice,
		MNEInverseOperator &	inv )

static

Read an inverse operator from a FIFF file.

Parameters

[in]	p_IODevice	FIFF IO device (e.g. QFile or QTcpSocket).
[in,out]	inv	Receives the loaded inverse operator.

Returns: true on success, false on failure.

Definition at line 1030 of file mne_inverse_operator.cpp.

◆ write()

void MNEInverseOperator::write ( QIODevice & p_IODevice )

Write the inverse operator to a FIFF file.

Parameters

[in] p_IODevice IO device to write to.

Definition at line 1263 of file mne_inverse_operator.cpp.

◆ writeToStream()

void MNEInverseOperator::writeToStream ( FIFFLIB::FiffStream * p_pStream )

Write the inverse operator into an already-open FIFF stream.

Parameters

[in] p_pStream Open FIFF stream.

Definition at line 1278 of file mne_inverse_operator.cpp.

◆ operator<<

std::ostream & operator<<	(	std::ostream &	out,
		const MNEInverseOperator &	inv )

friend

Stream-output operator for diagnostic printing.

Parameters

[in]	out	Output stream.
[in]	inv	Inverse operator to print.

Returns: The output stream.

Definition at line 403 of file mne_inverse_operator.h.

Member Data Documentation

◆ coord_frame

FIFFLIB::fiff_int_t MNELIB::MNEInverseOperator::coord_frame

Coordinate frame of the inverse (MRI or head).

Definition at line 354 of file mne_inverse_operator.h.

◆ depth_prior

FIFFLIB::FiffCov::SDPtr MNELIB::MNEInverseOperator::depth_prior

Depth prior (depth-weighting coefficients).

Definition at line 363 of file mne_inverse_operator.h.

◆ eigen_fields

FIFFLIB::FiffNamedMatrix::SDPtr MNELIB::MNEInverseOperator::eigen_fields

Left singular vectors (eigenfields), channels x components.

Definition at line 359 of file mne_inverse_operator.h.

◆ eigen_leads

FIFFLIB::FiffNamedMatrix::SDPtr MNELIB::MNEInverseOperator::eigen_leads

Right singular vectors (eigenleads), sources x components.

Definition at line 358 of file mne_inverse_operator.h.

◆ eigen_leads_weighted

bool MNELIB::MNEInverseOperator::eigen_leads_weighted

True if eigenleads already include R^{0.5} weighting.

Definition at line 357 of file mne_inverse_operator.h.

◆ fmri_prior

FIFFLIB::FiffCov::SDPtr MNELIB::MNEInverseOperator::fmri_prior

fMRI prior (if available).

Definition at line 364 of file mne_inverse_operator.h.

◆ info

FIFFLIB::FiffInfoBase MNELIB::MNEInverseOperator::info

Lightweight measurement info (channel names, types, etc.).

Definition at line 349 of file mne_inverse_operator.h.

◆ methods

FIFFLIB::fiff_int_t MNELIB::MNEInverseOperator::methods

Modality flag: FIFFV_MNE_MEG, _EEG, or _MEG_EEG.

Definition at line 350 of file mne_inverse_operator.h.

◆ mri_head_t

FIFFLIB::FiffCoordTrans MNELIB::MNEInverseOperator::mri_head_t

MRI-to-head coordinate transformation.

Definition at line 366 of file mne_inverse_operator.h.

◆ nave

FIFFLIB::fiff_int_t MNELIB::MNEInverseOperator::nave

Number of averages (default 1).

Definition at line 367 of file mne_inverse_operator.h.

◆ nchan

FIFFLIB::fiff_int_t MNELIB::MNEInverseOperator::nchan

Number of channels (= number of singular values).

Definition at line 353 of file mne_inverse_operator.h.

◆ noise_cov

FIFFLIB::FiffCov::SDPtr MNELIB::MNEInverseOperator::noise_cov

Noise covariance matrix.

Definition at line 360 of file mne_inverse_operator.h.

◆ noisenorm

Eigen::SparseMatrix<double> MNELIB::MNEInverseOperator::noisenorm

Diagonal noise-normalisation matrix (dSPM / sLORETA).

Definition at line 372 of file mne_inverse_operator.h.

◆ nsource

FIFFLIB::fiff_int_t MNELIB::MNEInverseOperator::nsource

Number of source-space points.

Definition at line 352 of file mne_inverse_operator.h.

◆ orient_prior

FIFFLIB::FiffCov::SDPtr MNELIB::MNEInverseOperator::orient_prior

Orientation prior (loose-constraint weighting).

Definition at line 362 of file mne_inverse_operator.h.

◆ proj

Eigen::MatrixXd MNELIB::MNEInverseOperator::proj

SSP projector matrix applied to data.

Definition at line 369 of file mne_inverse_operator.h.

◆ projs

QList<FIFFLIB::FiffProj> MNELIB::MNEInverseOperator::projs

SSP projectors read from the file.

Definition at line 368 of file mne_inverse_operator.h.

◆ reginv

Eigen::VectorXd MNELIB::MNEInverseOperator::reginv

Diagonal regularised inverse of the singular values.

Definition at line 371 of file mne_inverse_operator.h.

◆ sing

Eigen::VectorXd MNELIB::MNEInverseOperator::sing

Singular values of the whitened lead field.

Definition at line 356 of file mne_inverse_operator.h.

◆ source_cov

FIFFLIB::FiffCov::SDPtr MNELIB::MNEInverseOperator::source_cov

Source covariance matrix (depth + orientation weighting).

Definition at line 361 of file mne_inverse_operator.h.

◆ source_nn

Eigen::MatrixXf MNELIB::MNEInverseOperator::source_nn

Source-normal vectors (nsource x 3, or nsource*3 x 3 for free).

Definition at line 355 of file mne_inverse_operator.h.

◆ source_ori

FIFFLIB::fiff_int_t MNELIB::MNEInverseOperator::source_ori

Source orientation constraint (FIFFV_MNE_FREE_ORI / FIXED_ORI).

Definition at line 351 of file mne_inverse_operator.h.

◆ src

MNESourceSpaces MNELIB::MNEInverseOperator::src

Source space (surfaces and/or volume).

Definition at line 365 of file mne_inverse_operator.h.

◆ whitener

Eigen::MatrixXd MNELIB::MNEInverseOperator::whitener

Whitening matrix (derived from noise covariance).

Definition at line 370 of file mne_inverse_operator.h.

The documentation for this class was generated from the following files:

src/libraries/mne/mne_inverse_operator.h
src/libraries/mne/mne_inverse_operator.cpp

Public Types

Public Member Functions

Static Public Member Functions

Public Attributes

Friends

Detailed Description

Member Typedef Documentation

◆ ConstSPtr

◆ SPtr

Constructor & Destructor Documentation

◆ MNEInverseOperator() [1/4]

◆ MNEInverseOperator() [2/4]

◆ MNEInverseOperator() [3/4]

◆ MNEInverseOperator() [4/4]

◆ ~MNEInverseOperator()

Member Function Documentation

◆ assemble_kernel()

◆ check_ch_names()

◆ cluster_kernel()

◆ getKernel() [1/2]

◆ getKernel() [2/2]

◆ isFixedOrient()

◆ make_inverse_operator()

◆ prepare_inverse_operator()

◆ read_inverse_operator()

◆ write()

◆ writeToStream()

Friends And Related Symbol Documentation

◆ operator<<

Member Data Documentation

◆ coord_frame

◆ depth_prior

◆ eigen_fields

◆ eigen_leads

◆ eigen_leads_weighted

◆ fmri_prior

◆ info

◆ methods

◆ mri_head_t

◆ nave

◆ nchan

◆ noise_cov

◆ noisenorm

◆ nsource

◆ orient_prior

◆ proj

◆ projs

◆ reginv

◆ sing

◆ source_cov

◆ source_nn

◆ source_ori

◆ src

◆ whitener