Inverse operator. More...

#include <mne_inverse_operator.h>

Public Types
typedef QSharedPointer< MNEInverseOperator >	SPtr

typedef QSharedPointer< const MNEInverseOperator >	ConstSPtr

Public Member Functions
	MNEInverseOperator ()

	MNEInverseOperator (QIODevice &p_IODevice)

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

	MNEInverseOperator (const MNEInverseOperator &p_MNEInverseOperator)

	~MNEInverseOperator ()

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

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

Eigen::MatrixXd	cluster_kernel (const FSLIB::AnnotationSet &p_AnnotationSet, qint32 p_iClusterSize, Eigen::MatrixXd &p_D, QString p_sMethod="cityblock") const

Eigen::MatrixXd &	getKernel ()

Eigen::MatrixXd	getKernel () const

bool	isFixedOrient () const

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

void	write (QIODevice &p_IODevice)

void	writeToStream (FIFFLIB::FiffStream *p_pStream)

Static Public Member Functions
static MNEInverseOperator	make_inverse_operator (const FIFFLIB::FiffInfo &info, MNEForwardSolution forward, const FIFFLIB::FiffCov &p_noise_cov, float loose=0.2f, float depth=0.8f, bool fixed=false, bool limit_depth_chs=true)

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

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

MNESourceSpace	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 MNELIB::MNEInverseOperator &p_MNEInverseOperator)

Detailed Description

Inverse operator.

Inverse operator

Definition at line 141 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 145 of file mne_inverse_operator.h.

◆ SPtr

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

Shared pointer type for MNEInverseOperator.

Definition at line 144 of file mne_inverse_operator.h.

Constructor & Destructor Documentation

◆ MNEInverseOperator() [1/4]

MNEInverseOperator::MNEInverseOperator ( )

Default constructor

Definition at line 74 of file mne_inverse_operator.cpp.

◆ MNEInverseOperator() [2/4]

MNEInverseOperator::MNEInverseOperator ( QIODevice & p_IODevice )

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

Parameters

[in] p_IODevice IO device to read from the evoked data set.

Definition at line 96 of file mne_inverse_operator.cpp.

◆ MNEInverseOperator() [3/4]

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

Constructs an inverse operator by making one.

Parameters

[in]	info	The measurement info to specify the channels to include. Bad channels in info['bads'] are not used.
[in]	forward	Forward operator.
[in]	p_noise_cov	The noise covariance matrix.
[in]	loose	float in [0, 1]. Value that weights the source variances of the dipole components defining the tangent space of the cortical surfaces.
[in]	depth	float in [0, 1]. Depth weighting coefficients. If None, no depth weighting is performed.
[in]	fixed	Use fixed source orientations normal to the cortical mantle. If True, the loose parameter is ignored.
[in]	limit_depth_chs	If True, use only grad channels in depth weighting (equivalent to MNE C code). If grad chanels aren't present, only mag channels will be used (if no mag, then eeg). If False, use all channels.

Definition at line 105 of file mne_inverse_operator.cpp.

◆ MNEInverseOperator() [4/4]

MNEInverseOperator::MNEInverseOperator ( const MNEInverseOperator & p_MNEInverseOperator )

Copy constructor.

Parameters

[in] p_MNEInverseOperator MNE forward solution.

Definition at line 120 of file mne_inverse_operator.cpp.

◆ ~MNEInverseOperator()

MNEInverseOperator::~MNEInverseOperator ( )

Destroys the MNEInverseOperator.

Definition at line 152 of file mne_inverse_operator.cpp.

Member Function Documentation

◆ assemble_kernel()

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

Simple matrix multiplication followed by combination of the current components

This does all the data transformations to compute the weights for the eigenleads

Parameters

[in]	label	labels.
[in]	method	The applied normals. ("MNE" \| "dSPM" \| "sLORETA").
[in]	pick_normal	Pick normals.
[out]	K	Kernel.
[out]	noise_norm	Noise normals.
[out]	vertno	Vertices of the hemispheres.

Returns: the assembled kernel.

Definition at line 158 of file mne_inverse_operator.cpp.

◆ check_ch_names()

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

Check that channels in inverse operator are measurements.

Parameters

[in] info The measurement info.

Returns: true when successful, false otherwise.

Definition at line 307 of file mne_inverse_operator.cpp.

◆ cluster_kernel()

MatrixXd MNEInverseOperator::cluster_kernel	(	const FSLIB::AnnotationSet &	p_AnnotationSet,
		qint32	p_iClusterSize,
		Eigen::MatrixXd &	p_D,
		QString	p_sMethod = `"cityblock"`
	)		const

Clusters the current kernel

Parameters

[in]	p_AnnotationSet	Annotation set containing the annotation of left & right hemisphere.
[in]	p_iClusterSize	Maximal cluster size per roi.
[out]	p_D	The cluster operator.
[in]	p_sMethod	"cityblock" or "sqeuclidean".

Returns: the clustered kernel.

Definition at line 352 of file mne_inverse_operator.cpp.

◆ getKernel() [1/2]

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

inline

Returns the current kernel

Returns: the current kernel.

Definition at line 389 of file mne_inverse_operator.h.

◆ getKernel() [2/2]

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

inline

Returns the current kernel

Returns: the current kernel.

◆ isFixedOrient()

bool MNELIB::MNEInverseOperator::isFixedOrient ( ) const

inline

Has inverse operator fixed orientation?

Returns: true if inverse operator has fixed orientation, false otherwise.

Definition at line 403 of file mne_inverse_operator.h.

◆ make_inverse_operator()

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

static

Assembles the inverse operator.

Parameters

[in]	info	The measurement info to specify the channels to include. Bad channels in info['bads'] are not used.
[in]	forward	Forward operator.
[in]	p_noise_cov	The noise covariance matrix.
[in]	loose	float in [0, 1]. Value that weights the source variances of the dipole components defining the tangent space of the cortical surfaces.
[in]	depth	float in [0, 1]. Depth weighting coefficients. If None, no depth weighting is performed.
[in]	fixed	Use fixed source orientations normal to the cortical mantle. If True, the loose parameter is ignored.
[in]	limit_depth_chs	If True, use only grad channels in depth weighting (equivalent to MNE C code). If grad chanels aren't present, only mag channels will be used (if no mag, then eeg). If False, use all channels.

Returns: the assembled inverse operator.

Definition at line 682 of file mne_inverse_operator.cpp.

◆ prepare_inverse_operator()

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

mne_prepare_inverse_operator

MNE toolbox root function

Prepare for actually computing the inverse

Parameters

[in]	nave	Number of averages (scales the noise covariance).
[in]	lambda2	The regularization factor.
[in]	dSPM	Compute the noise-normalization factors for dSPM?.
[in]	sLORETA	Compute the noise-normalization factors for sLORETA?.

Returns: the prepared inverse operator.

Definition at line 926 of file mne_inverse_operator.cpp.

◆ read_inverse_operator()

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

static

mne_read_inverse_operator

MNE toolbox root function

Reads the inverse operator decomposition from a fif file

Parameters

[in]	p_IODevice	A fiff IO device like a fiff QFile or QTCPSocket.
[in,out]	inv	The read inverse operator.

Returns: true if succeeded, false otherwise.

Definition at line 1100 of file mne_inverse_operator.cpp.

◆ write()

void MNEInverseOperator::write ( QIODevice & p_IODevice )

write_inverse_operator

Writes an inverse operator to a fif file

Parameters

[in] p_IODevice IO device to write the inverse operator to.

Definition at line 1345 of file mne_inverse_operator.cpp.

◆ writeToStream()

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

Writes the inverse operator to a FIFF stream

Parameters

[in] p_pStream The stream to write to.

Definition at line 1360 of file mne_inverse_operator.cpp.

Friends And Related Function Documentation

◆ operator<<

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

friend

overloading the stream out operator<<

Parameters

[in]	out	The stream to which the fiff covariance should be assigned to.
[in]	p_MNEInverseOperator	MNEInverseOperator which should be assigned to the stream.

Returns: the stream with the attached fiff covariance matrix.

Definition at line 410 of file mne_inverse_operator.h.

Member Data Documentation

◆ coord_frame

FIFFLIB::fiff_int_t MNELIB::MNEInverseOperator::coord_frame

Coordinate system definition.

Definition at line 361 of file mne_inverse_operator.h.

◆ depth_prior

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

Depth priors.

Definition at line 370 of file mne_inverse_operator.h.

◆ eigen_fields

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

Eigen fields.

Definition at line 366 of file mne_inverse_operator.h.

◆ eigen_leads

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

Eigen leads.

Definition at line 365 of file mne_inverse_operator.h.

◆ eigen_leads_weighted

bool MNELIB::MNEInverseOperator::eigen_leads_weighted

If eigen lead are weighted.

Definition at line 364 of file mne_inverse_operator.h.

◆ fmri_prior

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

fMRI priors.

Definition at line 371 of file mne_inverse_operator.h.

◆ info

FIFFLIB::FiffInfoBase MNELIB::MNEInverseOperator::info

light weighted measurement info.

Definition at line 356 of file mne_inverse_operator.h.

◆ methods

FIFFLIB::fiff_int_t MNELIB::MNEInverseOperator::methods

MEG, EEG or both.

Definition at line 357 of file mne_inverse_operator.h.

◆ mri_head_t

FIFFLIB::FiffCoordTrans MNELIB::MNEInverseOperator::mri_head_t

MRI head coordinate transformation.

Definition at line 373 of file mne_inverse_operator.h.

◆ nave

FIFFLIB::fiff_int_t MNELIB::MNEInverseOperator::nave

Number of averages used to regularize the solution. Set to 1 on single Epoch by default.

Definition at line 374 of file mne_inverse_operator.h.

◆ nchan

FIFFLIB::fiff_int_t MNELIB::MNEInverseOperator::nchan

Number of channels.

Definition at line 360 of file mne_inverse_operator.h.

◆ noise_cov

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

Noise covariance matrix.

Definition at line 367 of file mne_inverse_operator.h.

◆ noisenorm

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

These are the noise-normalization factors.

Definition at line 379 of file mne_inverse_operator.h.

◆ nsource

FIFFLIB::fiff_int_t MNELIB::MNEInverseOperator::nsource

Number of source points.

Definition at line 359 of file mne_inverse_operator.h.

◆ orient_prior

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

Orientation priors.

Definition at line 369 of file mne_inverse_operator.h.

◆ proj

Eigen::MatrixXd MNELIB::MNEInverseOperator::proj

The projector to apply to the data.

Definition at line 376 of file mne_inverse_operator.h.

◆ projs

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

SSP operator.

Definition at line 375 of file mne_inverse_operator.h.

◆ reginv

Eigen::VectorXd MNELIB::MNEInverseOperator::reginv

The diagonal matrix implementing. regularization and the inverse.

Definition at line 378 of file mne_inverse_operator.h.

◆ sing

Eigen::VectorXd MNELIB::MNEInverseOperator::sing

Singular values.

Definition at line 363 of file mne_inverse_operator.h.

◆ source_cov

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

Source covariance matrix.

Definition at line 368 of file mne_inverse_operator.h.

◆ source_nn

Eigen::MatrixXf MNELIB::MNEInverseOperator::source_nn

Source normals.

Definition at line 362 of file mne_inverse_operator.h.

◆ source_ori

FIFFLIB::fiff_int_t MNELIB::MNEInverseOperator::source_ori

Source orientation: f.

Definition at line 358 of file mne_inverse_operator.h.

◆ src

MNESourceSpace MNELIB::MNEInverseOperator::src

Source Space.

Definition at line 372 of file mne_inverse_operator.h.

◆ whitener

Eigen::MatrixXd MNELIB::MNEInverseOperator::whitener

Whitens the data.

Definition at line 377 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()

MNE toolbox root function

◆ read_inverse_operator()

MNE toolbox root function

◆ write()

◆ writeToStream()

Friends And Related Function 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