In-memory representation of an -fwd.fif forward solution. More...

#include <mne_forward_solution.h>

Public Types
typedef QSharedPointer< MNEForwardSolution >	SPtr
typedef QSharedPointer< const MNEForwardSolution >	ConstSPtr
typedef std::unique_ptr< MNEForwardSolution >	UPtr

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 &	operator= (const MNEForwardSolution &other)
	MNEForwardSolution (MNEForwardSolution &&other)=default
MNEForwardSolution &	operator= (MNEForwardSolution &&other)=default
	~MNEForwardSolution ()
void	clear ()
MNEForwardSolution	cluster_forward_solution (const FSLIB::FsAnnotationSet &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::FsLabel > &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
bool	write (QIODevice &p_IODevice) const
MNEForwardSolution	reduce_forward_solution (qint32 p_iNumDipoles, Eigen::MatrixXd &p_D) const
void	to_fixed_ori ()
void	convert_to_surf_ori ()
Eigen::MatrixX3f	getSourcePositionsByLabel (const QList< FSLIB::FsLabel > &lPickedLabels, const FSLIB::FsSurfaceSet &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=false)
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
QString	mri_filename
FIFFLIB::FiffId	mri_id
MNELIB::MNESourceSpaces	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

In-memory representation of an -fwd.fif forward solution.

Forward solution: leadfield matrix mapping source-space dipoles to sensor measurements, together with the source spaces, coordinate transforms and SSP/CTF state it was computed under.

Definition at line 157 of file mne_forward_solution.h.

Member Typedef Documentation

◆ ConstSPtr

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

Const shared pointer type for MNEForwardSolution.

Definition at line 161 of file mne_forward_solution.h.

◆ SPtr

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

Shared pointer type for MNEForwardSolution.

Definition at line 160 of file mne_forward_solution.h.

◆ UPtr

typedef std::unique_ptr<MNEForwardSolution> MNELIB::MNEForwardSolution::UPtr

Unique pointer type for MNEForwardSolution.

Definition at line 162 of file mne_forward_solution.h.

Constructor & Destructor Documentation

◆ MNEForwardSolution() [1/4]

MNEForwardSolution::MNEForwardSolution ( )

Default constructor.

Definition at line 126 of file mne_forward_solution.cpp.

◆ MNEForwardSolution() [2/4]

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	Drop the channels marked bad in the file; mne.read_forward_solution keeps them.

Definition at line 141 of file mne_forward_solution.cpp.

◆ MNEForwardSolution() [3/4]

MNEForwardSolution::MNEForwardSolution ( const MNEForwardSolution & p_MNEForwardSolution )

Copy constructor.

Parameters

[in] p_MNEForwardSolution MNE forward solution.

Definition at line 160 of file mne_forward_solution.cpp.

◆ MNEForwardSolution() [4/4]

MNELIB::MNEForwardSolution::MNEForwardSolution ( MNEForwardSolution && other )

default

Move constructs an MNEForwardSolution.

Parameters

[in,out] other Forward solution to move from; left in a valid but unspecified state.

◆ ~MNEForwardSolution()

MNEForwardSolution::~MNEForwardSolution ( )

Destroys the MNEForwardSolution.

Definition at line 203 of file mne_forward_solution.cpp.

Member Function Documentation

◆ clear()

void MNEForwardSolution::clear ( )

Initializes the MNE forward solution.

Definition at line 209 of file mne_forward_solution.cpp.

◆ cluster_forward_solution()

MNEForwardSolution MNEForwardSolution::cluster_forward_solution	(	const FSLIB::FsAnnotationSet &	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	FsAnnotation 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	Noise covariance used to whiten the gain matrix before clustering (optional).
[in]	p_pInfo	Measurement info matching the noise covariance (optional).
[in]	p_sMethod	"cityblock" or "sqeuclidean".

Returns: clustered MNE forward solution.

Definition at line 422 of file mne_forward_solution.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) Cortical patch area of each source position (m²); the source gain is divided by it, as in mne.forward.compute_depth_prior.
[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 798 of file mne_forward_solution.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 895 of file mne_forward_solution.cpp.

◆ convert_to_surf_ori()

void MNEForwardSolution::convert_to_surf_ori ( )

Rotates a free-orientation solution into local surface coordinates (two tangential components, then the normal), using average patch normals when the source spaces carry them. Equivalent of mne.convert_forward_solution(fwd, surf_ori=True). Does nothing if already surface-oriented or fixed.

Definition at line 1533 of file mne_forward_solution.cpp.

◆ getSourcePositionsByLabel()

MatrixX3f MNEForwardSolution::getSourcePositionsByLabel	(	const QList< FSLIB::FsLabel > &	lPickedLabels,
		const FSLIB::FsSurfaceSet &	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 1642 of file mne_forward_solution.cpp.

◆ isClustered()

bool MNEForwardSolution::isClustered ( ) const

Indicates whether fwd conatins a clustered forward solution.

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

Definition at line 1634 of file mne_forward_solution.cpp.

◆ 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 539 of file mne_forward_solution.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 546 of file mne_forward_solution.h.

◆ operator=() [1/2]

MNEForwardSolution & MNEForwardSolution::operator= ( const MNEForwardSolution & other )

Copy assignment operator. Copies public data fields only (not computation state).

Parameters

[in] other MNE forward solution to copy from.

Returns: Reference to this.

Definition at line 180 of file mne_forward_solution.cpp.

◆ operator=() [2/2]

MNEForwardSolution & MNELIB::MNEForwardSolution::operator= ( MNEForwardSolution && other )

default

Move assignment operator.

Parameters

[in,out] other Forward solution to move from; left in a valid but unspecified state.

Returns: Reference to this object.

◆ 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 936 of file mne_forward_solution.cpp.

◆ pick_regions()

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

Reduces a forward solution to selected regions

Parameters

[in] p_qListLabels ROIs.

Returns: the reduced forward solution.

Definition at line 998 of file mne_forward_solution.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 1044 of file mne_forward_solution.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]	p_outFwdInfo	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 1057 of file mne_forward_solution.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 = false )

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	Drop the channels marked bad in the file; mne.read_forward_solution keeps them.

Returns: true if succeeded, false otherwise.

Definition at line 1144 of file mne_forward_solution.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 744 of file mne_forward_solution.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 1497 of file mne_forward_solution.cpp.

◆ to_fixed_ori()

void MNEForwardSolution::to_fixed_ori ( )

Helper to convert the forward solution to fixed ori from free

Definition at line 1611 of file mne_forward_solution.cpp.

◆ tripletSelection()

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

inline

Definition at line 383 of file mne_forward_solution.h.

◆ write()

bool MNEForwardSolution::write ( QIODevice & p_IODevice ) const

Write the forward solution to a FIFF file.

Formerly write_solution (SVN MNE).

Splits the combined MEG/EEG forward matrix back into separate blocks for FIFF storage, writes source spaces, coordinate transforms, and parent file provenance.

Parameters

[in] p_IODevice The I/O device (e.g. QFile) to write to.

Returns: True if succeeded, false otherwise.

Definition at line 229 of file mne_forward_solution.cpp.

◆ 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 553 of file mne_forward_solution.h.

◆ operator==

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

friend

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

Parameters

[in]	a	The object which should be compared to.
[in]	b	Right-hand forward solution.

Returns: true if equal, false otherwise.

Definition at line 569 of file mne_forward_solution.h.

Member Data Documentation

◆ coord_frame

FIFFLIB::fiff_int_t MNELIB::MNEForwardSolution::coord_frame

Coil coordinate system definition.

Definition at line 522 of file mne_forward_solution.h.

◆ info

FIFFLIB::FiffInfoBase MNELIB::MNEForwardSolution::info

light weighted measurement info.

Definition at line 519 of file mne_forward_solution.h.

◆ mri_filename

QString MNELIB::MNEForwardSolution::mri_filename

MRI file name (parent provenance).

Definition at line 528 of file mne_forward_solution.h.

◆ mri_head_t

FIFFLIB::FiffCoordTrans MNELIB::MNEForwardSolution::mri_head_t

MRI head coordinate transformation.

Definition at line 527 of file mne_forward_solution.h.

◆ mri_id

FIFFLIB::FiffId MNELIB::MNEForwardSolution::mri_id

MRI file ID (parent provenance).

Definition at line 529 of file mne_forward_solution.h.

◆ nchan

FIFFLIB::fiff_int_t MNELIB::MNEForwardSolution::nchan

Number of channels.

Definition at line 524 of file mne_forward_solution.h.

◆ nsource

FIFFLIB::fiff_int_t MNELIB::MNEForwardSolution::nsource

Number of source dipoles.

Definition at line 523 of file mne_forward_solution.h.

◆ sol

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

Forward solution.

Definition at line 525 of file mne_forward_solution.h.

◆ sol_grad

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

ToDo...

Definition at line 526 of file mne_forward_solution.h.

◆ source_nn

Eigen::MatrixX3f MNELIB::MNEForwardSolution::source_nn

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

Definition at line 532 of file mne_forward_solution.h.

◆ source_ori

FIFFLIB::fiff_int_t MNELIB::MNEForwardSolution::source_ori

Source orientation: fixed or free.

Definition at line 520 of file mne_forward_solution.h.

◆ source_rr

Eigen::MatrixX3f MNELIB::MNEForwardSolution::source_rr

Source locations.

Definition at line 531 of file mne_forward_solution.h.

◆ src

MNELIB::MNESourceSpaces MNELIB::MNEForwardSolution::src

Geometric description of the source spaces (hemispheres).

Definition at line 530 of file mne_forward_solution.h.

◆ surf_ori

bool MNELIB::MNEForwardSolution::surf_ori

If surface oriented.

Definition at line 521 of file mne_forward_solution.h.

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

src/libraries/mne/mne_forward_solution.h
src/libraries/mne/mne_forward_solution.cpp

Public Types

Public Member Functions

Static Public Member Functions

Public Attributes

Friends

Detailed Description

Member Typedef Documentation

◆ ConstSPtr

◆ SPtr

◆ UPtr

Constructor & Destructor Documentation

◆ MNEForwardSolution() [1/4]

◆ MNEForwardSolution() [2/4]

◆ MNEForwardSolution() [3/4]

◆ MNEForwardSolution() [4/4]

◆ ~MNEForwardSolution()

Member Function Documentation

◆ clear()

◆ cluster_forward_solution()

◆ compute_depth_prior()

◆ compute_orient_prior()

◆ convert_to_surf_ori()

◆ getSourcePositionsByLabel()

◆ isClustered()

◆ isEmpty()

◆ isFixedOrient()

◆ operator=() [1/2]

◆ operator=() [2/2]

◆ 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()

◆ tripletSelection()

◆ write()

Friends And Related Symbol Documentation

◆ operator<<

◆ operator==

Member Data Documentation

◆ coord_frame

◆ info

◆ mri_filename

◆ mri_head_t

◆ mri_id

◆ nchan

◆ nsource

◆ sol

◆ sol_grad

◆ source_nn

◆ source_ori

◆ source_rr

◆ src

◆ surf_ori