Forward operator. More...

#include <mne_forwardsolution.h>

Public Types
typedef QSharedPointer< MNEForwardSolution >	SPtr

typedef QSharedPointer< const MNEForwardSolution >	ConstSPtr

Public Member Functions
	MNEForwardSolution ()

	MNEForwardSolution (QIODevice &p_IODevice, bool force_fixed=false, bool surf_ori=false, const QStringList &include=FIFFLIB::defaultQStringList, const QStringList &exclude=FIFFLIB::defaultQStringList, bool bExcludeBads=false)

	MNEForwardSolution (const MNEForwardSolution &p_MNEForwardSolution)

	~MNEForwardSolution ()

void	clear ()

MNEForwardSolution	cluster_forward_solution (const FSLIB::AnnotationSet &p_AnnotationSet, qint32 p_iClusterSize, Eigen::MatrixXd &p_D=defaultD, const FIFFLIB::FiffCov &p_pNoise_cov=defaultCov, const FIFFLIB::FiffInfo &p_pInfo=defaultInfo, QString p_sMethod="cityblock") const

FIFFLIB::FiffCov	compute_orient_prior (float loose=0.2)

bool	isClustered () const

bool	isEmpty () const

bool	isFixedOrient () const

MNEForwardSolution	pick_channels (const QStringList &include=FIFFLIB::defaultQStringList, const QStringList &exclude=FIFFLIB::defaultQStringList) const

MNEForwardSolution	pick_regions (const QList< FSLIB::Label > &p_qListLabels) const

MNEForwardSolution	pick_types (bool meg, bool eeg, const QStringList &include=FIFFLIB::defaultQStringList, const QStringList &exclude=FIFFLIB::defaultQStringList) const

void	prepare_forward (const FIFFLIB::FiffInfo &p_info, const FIFFLIB::FiffCov &p_noise_cov, bool p_pca, FIFFLIB::FiffInfo &p_outFwdInfo, Eigen::MatrixXd &gain, FIFFLIB::FiffCov &p_outNoiseCov, Eigen::MatrixXd &p_outWhitener, qint32 &p_outNumNonZero) const

Eigen::VectorXi	tripletSelection (const Eigen::VectorXi &p_vecIdxSelection) const

MNEForwardSolution	reduce_forward_solution (qint32 p_iNumDipoles, Eigen::MatrixXd &p_D) const

void	to_fixed_ori ()

Eigen::MatrixX3f	getSourcePositionsByLabel (const QList< FSLIB::Label > &lPickedLabels, const FSLIB::SurfaceSet &tSurfSetInflated)

Static Public Member Functions
static FIFFLIB::FiffCov	compute_depth_prior (const Eigen::MatrixXd &Gain, const FIFFLIB::FiffInfo &gain_info, bool is_fixed_ori, double exp=0.8, double limit=10.0, const Eigen::MatrixXd &patch_areas=FIFFLIB::defaultConstMatrixXd, bool limit_depth_chs=false)

static bool	read (QIODevice &p_IODevice, MNEForwardSolution &fwd, bool force_fixed=false, bool surf_ori=false, const QStringList &include=FIFFLIB::defaultQStringList, const QStringList &exclude=FIFFLIB::defaultQStringList, bool bExcludeBads=true)

static void	restrict_gain_matrix (Eigen::MatrixXd &G, const FIFFLIB::FiffInfo &info)

Public Attributes
FIFFLIB::FiffInfoBase	info

FIFFLIB::fiff_int_t	source_ori

bool	surf_ori

FIFFLIB::fiff_int_t	coord_frame

FIFFLIB::fiff_int_t	nsource

FIFFLIB::fiff_int_t	nchan

FIFFLIB::FiffNamedMatrix::SDPtr	sol

FIFFLIB::FiffNamedMatrix::SDPtr	sol_grad

FIFFLIB::FiffCoordTrans	mri_head_t

MNESourceSpace	src

Eigen::MatrixX3f	source_rr

Eigen::MatrixX3f	source_nn

Friends
std::ostream &	operator<< (std::ostream &out, const MNELIB::MNEForwardSolution &p_MNEForwardSolution)

bool	operator== (const MNEForwardSolution &a, const MNEForwardSolution &b)

Detailed Description

Forward operator.

Forward operator

Definition at line 170 of file mne_forwardsolution.h.

Member Typedef Documentation

◆ ConstSPtr

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

Const shared pointer type for MNEForwardSolution.

Definition at line 174 of file mne_forwardsolution.h.

◆ SPtr

typedef QSharedPointer<MNEForwardSolution> MNELIB::MNEForwardSolution::SPtr

Shared pointer type for MNEForwardSolution.

Definition at line 173 of file mne_forwardsolution.h.

Constructor & Destructor Documentation

◆ MNEForwardSolution() [1/3]

MNEForwardSolution::MNEForwardSolution ( )

Default constructor.

Definition at line 82 of file mne_forwardsolution.cpp.

◆ MNEForwardSolution() [2/3]

MNEForwardSolution::MNEForwardSolution	(	QIODevice &	p_IODevice,
		bool	force_fixed = `false`,
		bool	surf_ori = `false`,
		const QStringList &	include = `FIFFLIB::defaultQStringList`,
		const QStringList &	exclude = `FIFFLIB::defaultQStringList`,
		bool	bExcludeBads = `false`
	)

Constructs a forward operator, by reading from a IO device.

Parameters

[in]	p_IODevice	IO device to read from the forward operator.
[in]	force_fixed	Force fixed source orientation mode? (optional).
[in]	surf_ori	Use surface based source coordinate system? (optional).
[in]	include	Include these channels (optional).
[in]	exclude	Exclude these channels (optional).
[in]	bExcludeBads	If true bads are also read; default = false (optional).

Definition at line 99 of file mne_forwardsolution.cpp.

◆ MNEForwardSolution() [3/3]

MNEForwardSolution::MNEForwardSolution ( const MNEForwardSolution & p_MNEForwardSolution )

Copy constructor.

Parameters

[in] p_MNEForwardSolution MNE forward solution.

Definition at line 121 of file mne_forwardsolution.cpp.

◆ ~MNEForwardSolution()

MNEForwardSolution::~MNEForwardSolution ( )

Destroys the MNEForwardSolution.

Definition at line 139 of file mne_forwardsolution.cpp.

Member Function Documentation

◆ clear()

void MNEForwardSolution::clear ( )

Initializes the MNE forward solution.

Definition at line 145 of file mne_forwardsolution.cpp.

◆ cluster_forward_solution()

MNEForwardSolution MNEForwardSolution::cluster_forward_solution	(	const FSLIB::AnnotationSet &	p_AnnotationSet,
		qint32	p_iClusterSize,
		Eigen::MatrixXd &	p_D = `defaultD`,
		const FIFFLIB::FiffCov &	p_pNoise_cov = `defaultCov`,
		const FIFFLIB::FiffInfo &	p_pInfo = `defaultInfo`,
		QString	p_sMethod = `"cityblock"`
	)		const

Cluster the forward solution and stores the result to p_fwdOut. The clustering is done by using the provided annotations

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_pNoise_cov.
[in]	p_pInfo.
[in]	p_sMethod	"cityblock" or "sqeuclidean".

Returns: clustered MNE forward solution.

Definition at line 163 of file mne_forwardsolution.cpp.

◆ compute_depth_prior()

FiffCov MNEForwardSolution::compute_depth_prior	(	const Eigen::MatrixXd &	Gain,
		const FIFFLIB::FiffInfo &	gain_info,
		bool	is_fixed_ori,
		double	exp = `0.8`,
		double	limit = `10.0`,
		const Eigen::MatrixXd &	patch_areas = `FIFFLIB::defaultConstMatrixXd`,
		bool	limit_depth_chs = `false`
	)

static

Compute weighting for depth prior. ToDo move this to FiffCov

Parameters

[in]	Gain	gain matrix.
[in]	gain_info	The measurement info to specify the channels to include.
[in]	is_fixed_ori	Fixed orientation?.
[in]	exp	float in [0, 1]. Depth weighting coefficients. If None, no depth weighting is performed. (optional; default = 0.8).
[in]	limit	(optional; default = 10.0).
[in]	patch_areas	(optional).
[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. (optional).

Returns: the depth prior.

Definition at line 807 of file mne_forwardsolution.cpp.

◆ compute_orient_prior()

FiffCov MNEForwardSolution::compute_orient_prior ( float loose = 0.2 )

Compute orientation prior

Parameters

[in] loose The loose orientation parameter.

Returns: Orientation priors.

Definition at line 916 of file mne_forwardsolution.cpp.

◆ getSourcePositionsByLabel()

MatrixX3f MNEForwardSolution::getSourcePositionsByLabel	(	const QList< FSLIB::Label > &	lPickedLabels,
		const FSLIB::SurfaceSet &	tSurfSetInflated
	)

Returns the positions of the specified sources based on their beloning labels

Parameters

[in]	lPickedLabels	The stream to which the MNE forward solution should be assigned to.
[in]	tSurfSetInflated	The surface used to pick the source from, based on their index specified bzy this forward solution.

Returns: the source position in 3D space.

Definition at line 1835 of file mne_forwardsolution.cpp.

◆ isClustered()

bool MNELIB::MNEForwardSolution::isClustered ( ) const

inline

Indicates whether fwd conatins a clustered forward solution.

Returns: true if forward solution is clustered, false otherwise.

Definition at line 538 of file mne_forwardsolution.h.

◆ isEmpty()

bool MNELIB::MNEForwardSolution::isEmpty ( ) const

inline

True if FIFF measurement file information is empty.

Returns: true if FIFF measurement file information is empty.

Definition at line 545 of file mne_forwardsolution.h.

◆ isFixedOrient()

bool MNELIB::MNEForwardSolution::isFixedOrient ( ) const

inline

Has forward operator fixed orientation?

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

Definition at line 552 of file mne_forwardsolution.h.

◆ pick_channels()

MNEForwardSolution MNEForwardSolution::pick_channels	(	const QStringList &	include = `FIFFLIB::defaultQStringList`,
		const QStringList &	exclude = `FIFFLIB::defaultQStringList`
	)		const

mne.fiff.pick_channels_forward

Pick channels from forward operator

Parameters

[in]	include	List of channels to include. (if None, include all available).
[in]	exclude	Channels to exclude (if None, do not exclude any).

Returns: Forward solution restricted to selected channel types.

Definition at line 965 of file mne_forwardsolution.cpp.

◆ pick_regions()

MNEForwardSolution MNEForwardSolution::pick_regions ( const QList< FSLIB::Label > & p_qListLabels ) const

Reduces a forward solution to selected regions

Parameters

[in] p_qListLabels ROIs.

Returns: the reduced forward solution.

Definition at line 1029 of file mne_forwardsolution.cpp.

◆ pick_types()

MNEForwardSolution MNEForwardSolution::pick_types	(	bool	meg,
		bool	eeg,
		const QStringList &	include = `FIFFLIB::defaultQStringList`,
		const QStringList &	exclude = `FIFFLIB::defaultQStringList`
	)		const

mne.fiff.pick_types_forward

Pick by channel type and names from a forward operator

Parameters

[in]	meg	Include MEG channels.
[in]	eeg	Include EEG channels.
[in]	include	Additional channels to include (if empty, do not add any).
[in]	exclude	Channels to exclude (if empty, do not exclude any).

Returns: Forward solution restricted to selected channel types.

Definition at line 1080 of file mne_forwardsolution.cpp.

◆ prepare_forward()

void MNEForwardSolution::prepare_forward	(	const FIFFLIB::FiffInfo &	p_info,
		const FIFFLIB::FiffCov &	p_noise_cov,
		bool	p_pca,
		FIFFLIB::FiffInfo &	p_outFwdInfo,
		Eigen::MatrixXd &	gain,
		FIFFLIB::FiffCov &	p_outNoiseCov,
		Eigen::MatrixXd &	p_outWhitener,
		qint32 &	p_outNumNonZero
	)		const

Prepare forward for assembling the inverse operator

Parameters

[in]	p_info	The measurement info to specify the channels to include. Bad channels in info['bads'] are not used.
[in]	p_noise_cov	The noise covariance matrix.
[in]	p_pca	Calculate pca or not.
[out]	ch_names	Selected channel names.
[out]	gain	Gain matrix.
[out]	p_outNoiseCov	noise covariance matrix.
[out]	p_outWhitener	Whitener.
[out]	p_outNumNonZero	the rank (non zeros).

Definition at line 1093 of file mne_forwardsolution.cpp.

◆ read()

bool MNEForwardSolution::read	(	QIODevice &	p_IODevice,
		MNEForwardSolution &	fwd,
		bool	force_fixed = `false`,
		bool	surf_ori = `false`,
		const QStringList &	include = `FIFFLIB::defaultQStringList`,
		const QStringList &	exclude = `FIFFLIB::defaultQStringList`,
		bool	bExcludeBads = `true`
	)

static

MNE toolbox root function ###: Definition of the mne_read_forward_solution function

Reads a forward solution from a fif file

Parameters

[in]	p_IODevice	A fiff IO device like a fiff QFile or QTCPSocket.
[out]	fwd	A forward solution from a fif file.
[in]	force_fixed	Force fixed source orientation mode? (optional).
[in]	surf_ori	Use surface based source coordinate system? (optional).
[in]	include	Include these channels (optional).
[in]	exclude	Exclude these channels (optional).
[in]	bExcludeBads	If true bads are also read; default = false (optional).

Returns: true if succeeded, false otherwise.

Definition at line 1192 of file mne_forwardsolution.cpp.

◆ reduce_forward_solution()

MNEForwardSolution MNEForwardSolution::reduce_forward_solution	(	qint32	p_iNumDipoles,
		Eigen::MatrixXd &	p_D
	)		const

reduces the forward solution and stores the result to p_fwdOut.

Parameters

[in]	p_iNumDipoles	Desired number of dipoles.
[out]	p_D	The reduction operator.

Returns: reduced MNE forward solution.

Definition at line 702 of file mne_forwardsolution.cpp.

◆ restrict_gain_matrix()

void MNEForwardSolution::restrict_gain_matrix	(	Eigen::MatrixXd &	G,
		const FIFFLIB::FiffInfo &	info
	)

static

Restrict gain matrix entries for optimal depth weighting

Parameters

[in,out]	G	Gain matrix to be restricted; result is stored in place.
[in]	info	Fiff information.

Definition at line 1772 of file mne_forwardsolution.cpp.

◆ to_fixed_ori()

void MNEForwardSolution::to_fixed_ori ( )

Helper to convert the forward solution to fixed ori from free

Definition at line 1817 of file mne_forwardsolution.cpp.

Friends And Related Function Documentation

◆ operator<<

std::ostream& operator<<	(	std::ostream &	out,
		const MNELIB::MNEForwardSolution &	p_MNEForwardSolution
	)

friend

overloading the stream out operator<<

Parameters

[in]	out	The stream to which the MNE forward solution should be assigned to.
[in]	p_MNEForwardSolution	MNE forward solution which should be assigned to the stream.

Returns: the stream with the attached fiff projector.

Definition at line 559 of file mne_forwardsolution.h.

◆ operator==

bool operator==	(	const MNEForwardSolution &	a,
		const MNEForwardSolution &	b
	)

friend

Overloaded == operator to compare an object to this instance.

Parameters

[in] object The object which should be compared to.

Returns: true if equal, false otherwise.

Definition at line 575 of file mne_forwardsolution.h.

Member Data Documentation

◆ coord_frame

FIFFLIB::fiff_int_t MNELIB::MNEForwardSolution::coord_frame

Coil coordinate system definition.

Definition at line 523 of file mne_forwardsolution.h.

◆ info

FIFFLIB::FiffInfoBase MNELIB::MNEForwardSolution::info

light weighted measurement info.

Definition at line 520 of file mne_forwardsolution.h.

◆ mri_head_t

FIFFLIB::FiffCoordTrans MNELIB::MNEForwardSolution::mri_head_t

MRI head coordinate transformation.

Definition at line 528 of file mne_forwardsolution.h.

◆ nchan

FIFFLIB::fiff_int_t MNELIB::MNEForwardSolution::nchan

Number of channels.

Definition at line 525 of file mne_forwardsolution.h.

◆ nsource

FIFFLIB::fiff_int_t MNELIB::MNEForwardSolution::nsource

Number of source dipoles.

Definition at line 524 of file mne_forwardsolution.h.

◆ sol

FIFFLIB::FiffNamedMatrix::SDPtr MNELIB::MNEForwardSolution::sol

Forward solution.

Definition at line 526 of file mne_forwardsolution.h.

◆ sol_grad

FIFFLIB::FiffNamedMatrix::SDPtr MNELIB::MNEForwardSolution::sol_grad

ToDo...

Definition at line 527 of file mne_forwardsolution.h.

◆ source_nn

Eigen::MatrixX3f MNELIB::MNEForwardSolution::source_nn

Source normals (number depends on fixed or free orientation).

Definition at line 531 of file mne_forwardsolution.h.

◆ source_ori

FIFFLIB::fiff_int_t MNELIB::MNEForwardSolution::source_ori

Source orientation: fixed or free.

Definition at line 521 of file mne_forwardsolution.h.

◆ source_rr

Eigen::MatrixX3f MNELIB::MNEForwardSolution::source_rr

Source locations.

Definition at line 530 of file mne_forwardsolution.h.

◆ src

MNESourceSpace MNELIB::MNEForwardSolution::src

Geometric description of the source spaces (hemispheres).

Definition at line 529 of file mne_forwardsolution.h.

◆ surf_ori

bool MNELIB::MNEForwardSolution::surf_ori

If surface oriented.

Definition at line 522 of file mne_forwardsolution.h.

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

src/libraries/mne/mne_forwardsolution.h
src/libraries/mne/mne_forwardsolution.cpp

Public Types

Public Member Functions

Static Public Member Functions

Public Attributes

Friends

Detailed Description

Member Typedef Documentation

◆ ConstSPtr

◆ SPtr

Constructor & Destructor Documentation

◆ MNEForwardSolution() [1/3]

◆ MNEForwardSolution() [2/3]

◆ MNEForwardSolution() [3/3]

◆ ~MNEForwardSolution()

Member Function Documentation

◆ clear()

◆ cluster_forward_solution()

◆ compute_depth_prior()

◆ compute_orient_prior()

◆ getSourcePositionsByLabel()

◆ isClustered()

◆ isEmpty()

◆ isFixedOrient()

◆ pick_channels()

◆ pick_regions()

◆ pick_types()

◆ prepare_forward()

◆ read()

MNE toolbox root function ###: Definition of the mne_read_forward_solution function

◆ reduce_forward_solution()

◆ restrict_gain_matrix()

◆ to_fixed_ori()

Friends And Related Function Documentation

◆ operator<<

◆ operator==

Member Data Documentation

◆ coord_frame

◆ info

◆ mri_head_t

◆ nchan

◆ nsource

◆ sol

◆ sol_grad

◆ source_nn

◆ source_ori

◆ source_rr

◆ src

◆ surf_ori