The MNE class provides wrapper functions to stay consistent with mne matlab toolbox. More...

#include <mne.h>

Public Member Functions
virtual	~MNE ()

Static Public Member Functions
static Eigen::VectorXd *	combine_xyz (const Eigen::VectorXd &vec)
static qint32	find_source_space_hemi (MNEHemisphere &p_Hemisphere)
static qint32	get_current_comp (FIFFLIB::FiffInfo *info)
static Eigen::SparseMatrix< double > *	make_block_diag (const Eigen::MatrixXd &A, qint32 n)
static bool	make_compensator (const FIFFLIB::FiffInfo &info, FIFFLIB::fiff_int_t from, FIFFLIB::fiff_int_t to, FIFFLIB::FiffCtfComp &ctf_comp, bool exclude_comp_chs=false)
static FIFFLIB::fiff_int_t	make_projector (const QList< FIFFLIB::FiffProj > &projs, const QStringList &ch_names, Eigen::MatrixXd &proj, const QStringList &bads=FIFFLIB::defaultQStringList, Eigen::MatrixXd &U=FIFFLIB::defaultMatrixXd)
static qint32	make_projector (FIFFLIB::FiffInfo &info, Eigen::MatrixXd &proj)
static bool	patch_info (MNEHemisphere &p_Hemisphere)
static MNEInverseOperator	prepare_inverse_operator (MNEInverseOperator &orig, qint32 nave, float lambda2, bool dSPM, bool sLORETA=false)
static bool	read_events (const QString &t_sEventName, const QString &t_fileRawName, Eigen::MatrixXi &events)
static bool	read_events_from_fif (QIODevice &p_IODevice, Eigen::MatrixXi &eventlist)
static bool	read_events_from_ascii (QIODevice &p_IODevice, Eigen::MatrixXi &eventlist)
static bool	write_events_to_fif (QIODevice &p_IODevice, const Eigen::MatrixXi &eventlist)
static bool	write_events_to_ascii (QIODevice &p_IODevice, const Eigen::MatrixXi &eventlist, float sfreq=0.0f)
static FIFFLIB::FiffCov	compute_epoch_covariance (const FIFFLIB::FiffRawData &raw, const Eigen::MatrixXi &events, const QList< int > &eventCodes, float tmin, float tmax, float bmin=0.0f, float bmax=0.0f, bool doBaseline=false, bool removeMean=true)
static QList< FIFFLIB::FiffProj >	compute_proj (const FIFFLIB::FiffRawData &raw, const Eigen::MatrixXi &events, int eventCode, float tmin, float tmax, int nGrad, int nMag, int nEeg, const QMap< QString, double > &mapReject=QMap< QString, double >())
static bool	save_raw (const FIFFLIB::FiffRawData &raw, QIODevice &p_IODevice, const Eigen::RowVectorXi &picks=Eigen::RowVectorXi(), int decim=1, int from=-1, int to=-1)
static void	setup_compensators (FIFFLIB::FiffRawData &raw, FIFFLIB::fiff_int_t dest_comp, bool keep_comp)
static bool	read_cov (FIFFLIB::FiffStream::SPtr &p_pStream, const FIFFLIB::FiffDirNode::SPtr &p_Node, FIFFLIB::fiff_int_t cov_kind, FIFFLIB::FiffCov &p_covData)
static bool	read_inverse_operator (QIODevice &p_pIODevice, MNEInverseOperator &inv)
static bool	read_forward_solution (QIODevice &p_IODevice, MNEForwardSolution &fwd, bool force_fixed=false, bool surf_ori=false, const QStringList &include=FIFFLIB::defaultQStringList, const QStringList &exclude=FIFFLIB::defaultQStringList)
static bool	read_source_spaces (FIFFLIB::FiffStream::SPtr &p_pStream, bool add_geom, MNESourceSpaces &p_SourceSpace)
static QList< FIFFLIB::FiffChInfo >	set_current_comp (QList< FIFFLIB::FiffChInfo > &chs, FIFFLIB::fiff_int_t value)
static bool	transform_source_space_to (MNESourceSpaces &p_pMNESourceSpaces, FIFFLIB::fiff_int_t dest, FIFFLIB::FiffCoordTrans &trans)
static void	transpose_named_matrix (FIFFLIB::FiffNamedMatrix &mat)

Detailed Description

The MNE class provides wrapper functions to stay consistent with mne matlab toolbox.

DECLARE MNE WRAPPER CLASS

Definition at line 89 of file mne.h.

Constructor & Destructor Documentation

◆ ~MNE()

virtual MNELIB::MNE::~MNE ( )

inlinevirtual

dtor

Definition at line 98 of file mne.h.

Member Function Documentation

◆ combine_xyz()

Eigen::VectorXd * MNELIB::MNE::combine_xyz ( const Eigen::VectorXd & vec )

inlinestatic

mne_combine_xyz

MNE toolbox root function

Wrapper for the MNEMath::combine_xyz static function

Compute the three Cartesian components of a vector together

Parameters

[in] vec Input row vector [ x1 y1 z1 ... x_n y_n z_n ].

Returns: Output vector [x1^2+y1^2+z1^2 ... x_n^2+y_n^2+z_n^2 ].

Definition at line 115 of file mne.h.

◆ compute_epoch_covariance()

FIFFLIB::FiffCov MNELIB::MNE::compute_epoch_covariance	(	const FIFFLIB::FiffRawData &	raw,
		const Eigen::MatrixXi &	events,
		const QList< int > &	eventCodes,
		float	tmin,
		float	tmax,
		float	bmin = 0.0f,
		float	bmax = 0.0f,
		bool	doBaseline = false,
		bool	removeMean = true )

inlinestatic

compute_epoch_covariance

MNE toolbox root function

Wrapper for the FiffCov::compute_from_epochs static function

Compute a noise covariance matrix from raw data based on event-locked epochs. Ported from compute_cov.c (MNE-C).

Parameters

[in]	raw	The raw data.
[in]	events	Event matrix (nEvents x 3): [sample, before, after].
[in]	eventCodes	Which event codes to include.
[in]	tmin	Start of time window relative to event (seconds).
[in]	tmax	End of time window relative to event (seconds).
[in]	bmin	Baseline start (seconds, relative to event). Only used if doBaseline is true.
[in]	bmax	Baseline end (seconds, relative to event). Only used if doBaseline is true.
[in]	doBaseline	Whether to apply baseline correction before covariance computation.
[in]	removeMean	Whether to remove sample mean from the covariance estimate.

Returns: The computed noise covariance matrix, or empty FiffCov on failure.

Definition at line 434 of file mne.h.

◆ compute_proj()

QList< FIFFLIB::FiffProj > MNELIB::MNE::compute_proj	(	const FIFFLIB::FiffRawData &	raw,
		const Eigen::MatrixXi &	events,
		int	eventCode,
		float	tmin,
		float	tmax,
		int	nGrad,
		int	nMag,
		int	nEeg,
		const QMap< QString, double > &	mapReject = QMap<QString,double>() )

inlinestatic

compute_proj

MNE toolbox root function

Create SSP (Signal-Space Projection) operators from raw data via SVD. Ported from make_ssp.c (MNE-C).

Parameters

[in]	raw	The raw data.
[in]	events	Event matrix (nEvents x 3).
[in]	eventCode	Which event code to select epochs for.
[in]	tmin	Start of epoch relative to event (seconds).
[in]	tmax	End of epoch relative to event (seconds).
[in]	nGrad	Number of gradiometer projection vectors.
[in]	nMag	Number of magnetometer projection vectors.
[in]	nEeg	Number of EEG projection vectors.
[in]	mapReject	Rejection thresholds (key = channel type string, value = threshold).

Returns: List of FiffProj items, or empty list on failure.

Definition at line 468 of file mne.h.

◆ find_source_space_hemi()

qint32 MNELIB::MNE::find_source_space_hemi ( MNEHemisphere & p_Hemisphere )

inlinestatic

mne_block_diag - decoding part

MNE toolbox root function

Wrapper for the MNEForwardSolution::extract_block_diag static function mne_find_source_space_hemi

MNE toolbox root function

Wrapper for the MNESourceSpaces::find_source_space_hemi static function

Returns the hemisphere id (FIFFV_MNE_SURF_LEFT_HEMI or FIFFV_MNE_SURF_RIGHT_HEMI) for a source space.

Parameters

[in] p_Hemisphere The hemisphere to investigate.

Returns: the deduced hemisphere id.

Definition at line 144 of file mne.h.

◆ get_current_comp()

qint32 MNELIB::MNE::get_current_comp ( FIFFLIB::FiffInfo * info )

inlinestatic

mne_get_current_comp

MNE toolbox root function

Wrapper for the FiffInfo get_current_comp member function

Get the current compensation in effect in the data

Parameters

[in] info Fiff measurement info.

Returns: the current compensation.

Definition at line 163 of file mne.h.

◆ make_block_diag()

Eigen::SparseMatrix< double > * MNELIB::MNE::make_block_diag	(	const Eigen::MatrixXd &	A,
		qint32	n )

inlinestatic

mne_block_diag - encoding part

MNE toolbox root function

Wrapper for the MNEForwardSolution::make_block_diag static function

Make a sparse block diagonal matrix

Returns a sparse block diagonal, diagonalized from the elements in "A". "A" is ma x na, comprising bdn=(na/"n") blocks of submatrices. Each submatrix is ma x "n", and these submatrices are placed down the diagonal of the matrix.

Parameters

[in,out]	A	Matrix which should be diagonlized.
[in,out]	n	Columns of the submatrices.

Returns: A sparse block diagonal, diagonalized from the elements in "A".

Definition at line 188 of file mne.h.

◆ make_compensator()

bool MNELIB::MNE::make_compensator	(	const FIFFLIB::FiffInfo &	info,
		FIFFLIB::fiff_int_t	from,
		FIFFLIB::fiff_int_t	to,
		FIFFLIB::FiffCtfComp &	ctf_comp,
		bool	exclude_comp_chs = false )

inlinestatic

mne_make_compensator

MNE toolbox root function

Wrapper for the FiffInfo make_compensator member function

Create a compensation matrix to bring the data from one compensation state to another

Parameters

[in]	info	measurement info as returned by the fif reading routines.
[in]	from	compensation in the input data.
[in]	to	desired compensation in the output.
[out]	ctf_comp	Compensation Matrix.
[in]	exclude_comp_chs	exclude compensation channels from the output (optional).

Returns: true if succeeded, false otherwise.

Definition at line 211 of file mne.h.

◆ make_projector() [1/2]

FIFFLIB::fiff_int_t MNELIB::MNE::make_projector	(	const QList< FIFFLIB::FiffProj > &	projs,
		const QStringList &	ch_names,
		Eigen::MatrixXd &	proj,
		const QStringList &	bads = FIFFLIB::defaultQStringList,
		Eigen::MatrixXd &	U = FIFFLIB::defaultMatrixXd )

inlinestatic

make_projector

MNE toolbox root function

Wrapper for the FiffInfo::make_projector static function There exists also a member function which should be preferred: make_projector(MatrixXd& proj, Eigen::MatrixXd& U = defaultUMatrix)

Make an SSP operator

Parameters

[in]	projs	A set of projection vectors.
[in]	ch_names	A cell array of channel names.
[out]	proj	The projection operator to apply to the data.
[in]	bads	Bad channels to exclude.
[out]	U	The orthogonal basis of the projection vectors (optional).

Returns: nproj - How many items in the projector.

Definition at line 240 of file mne.h.

◆ make_projector() [2/2]

qint32 MNELIB::MNE::make_projector	(	FIFFLIB::FiffInfo &	info,
		Eigen::MatrixXd &	proj )

inlinestatic

mne_make_projector_info

MNE toolbox root function

Wrapper for the FiffInfo make_projector_info(MatrixXd& proj) member function

Make a SSP operator using the meas info

Parameters

[in]	info	Fiff measurement info.
[out]	proj	The projection operator to apply to the data.

Returns: nproj - How many items in the projector.

Definition at line 268 of file mne.h.

◆ patch_info()

bool MNELIB::MNE::patch_info ( MNEHemisphere & p_Hemisphere )

inlinestatic

mne_patch_info

MNE toolbox root function

Wrapper for the MNESourceSpaces::patch_info static function

Parameters

[in,out] p_Hemisphere The source space.

Returns: true if succeeded, false otherwise.

Definition at line 286 of file mne.h.

◆ prepare_inverse_operator()

MNEInverseOperator MNELIB::MNE::prepare_inverse_operator	(	MNEInverseOperator &	orig,
		qint32	nave,
		float	lambda2,
		bool	dSPM,
		bool	sLORETA = false )

inlinestatic

mne_prepare_inverse_operator

MNE toolbox root function

Wrapper for the MNEInverseOperator prepare_inverse_operator member function

Prepare for actually computing the inverse

Parameters

[in]	orig	The inverse operator structure read from a file.
[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 309 of file mne.h.

◆ read_cov()

bool MNELIB::MNE::read_cov	(	FIFFLIB::FiffStream::SPtr &	p_pStream,
		const FIFFLIB::FiffDirNode::SPtr &	p_Node,
		FIFFLIB::fiff_int_t	cov_kind,
		FIFFLIB::FiffCov &	p_covData )

inlinestatic

mne_read_cov

MNE toolbox root function

Wrapper for the FiffStream read_cov member function

Reads a covariance matrix from a fiff file

Parameters

[in]	p_pStream	an open fiff file.
[in]	p_Node	look for the matrix in here.
[in]	cov_kind	what kind of a covariance matrix do we want?.
[in,out]	p_covData	the read covariance matrix.

Returns: true if succeeded, false otherwise.

Definition at line 532 of file mne.h.

◆ read_events()

bool MNELIB::MNE::read_events	(	const QString &	t_sEventName,
		const QString &	t_fileRawName,
		Eigen::MatrixXi &	events )

inlinestatic

Definition at line 318 of file mne.h.

◆ read_events_from_ascii()

bool MNELIB::MNE::read_events_from_ascii	(	QIODevice &	p_IODevice,
		Eigen::MatrixXi &	eventlist )

inlinestatic

read_events

Read a list of events from an eve file

Parameters

[in]	p_IODevice	The I/O device to read from.
[in,out]	eventList	List of events.

Returns: true if succeeded, false otherwise.

Definition at line 361 of file mne.h.

◆ read_events_from_fif()

bool MNELIB::MNE::read_events_from_fif	(	QIODevice &	p_IODevice,
		Eigen::MatrixXi &	eventlist )

inlinestatic

mne_read_events

Read an event list from a fif file

Parameters

[in]	p_IODevice	The I/O device to read from.
[in,out]	eventlist	The read eventlist m x 3; with m events; colum: 1 - position in samples, 3 - eventcode.

Returns: true if succeeded, false otherwise.

Definition at line 340 of file mne.h.

◆ read_forward_solution()

bool MNELIB::MNE::read_forward_solution	(	QIODevice &	p_IODevice,
		MNEForwardSolution &	fwd,
		bool	force_fixed = false,
		bool	surf_ori = false,
		const QStringList &	include = FIFFLIB::defaultQStringList,
		const QStringList &	exclude = FIFFLIB::defaultQStringList )

inlinestatic

mne_read_forward_solution

MNE toolbox root function

Wrapper for the MNEForwardSolution::read_forward_solution static function

Reads a forward solution from a fif file

Parameters

[in]	p_IODevice	A fiff IO device like a fiff QFile or QTCPSocket.
[in,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).

Returns: true if succeeded, false otherwise.

Definition at line 583 of file mne.h.

◆ read_inverse_operator()

bool MNELIB::MNE::read_inverse_operator	(	QIODevice &	p_pIODevice,
		MNEInverseOperator &	inv )

inlinestatic

mne_read_inverse_operator

MNE toolbox root function

Wrapper for the MNEInverseOperator::read_inverse_operator static function

Reads the inverse operator decomposition from a fif file

Parameters

[in]	p_pIODevice	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 557 of file mne.h.

◆ read_source_spaces()

bool MNELIB::MNE::read_source_spaces	(	FIFFLIB::FiffStream::SPtr &	p_pStream,
		bool	add_geom,
		MNESourceSpaces &	p_SourceSpace )

inlinestatic

mne_read_forward_solution

MNE toolbox root function

Wrapper for the MNESourceSpaces::read_source_spaces static function

Reads source spaces from a fif file

Parameters

[in]	p_pStream	The open fiff file.
[in]	add_geom	Add geometry information to the source spaces.
[in,out]	p_SourceSpace	The read source spaces.

Returns: true if succeeded, false otherwise.

Definition at line 615 of file mne.h.

◆ save_raw()

bool MNELIB::MNE::save_raw	(	const FIFFLIB::FiffRawData &	raw,
		QIODevice &	p_IODevice,
		const Eigen::RowVectorXi &	picks = Eigen::RowVectorXi(),
		int	decim = 1,
		int	from = -1,
		int	to = -1 )

inlinestatic

save_raw

MNE toolbox root function

Wrapper for the FiffRawData::save member function

Save raw data to a FIFF file, optionally with decimation and channel picking. Ported from save.c (MNE-C).

Parameters

[in]	raw	The raw data to save.
[in]	p_IODevice	Output device to write to.
[in]	picks	Channel indices to include (empty = all channels).
[in]	decim	Decimation factor (1 = no decimation).
[in]	from	First sample to save (-1 = from start of raw data).
[in]	to	Last sample to save (-1 = to end of raw data).

Returns: true on success.

Definition at line 501 of file mne.h.

◆ set_current_comp()

QList< FIFFLIB::FiffChInfo > MNELIB::MNE::set_current_comp	(	QList< FIFFLIB::FiffChInfo > &	chs,
		FIFFLIB::fiff_int_t	value )

inlinestatic

mne_set_current_comp

MNE toolbox root function

Wrapper for the FiffInfo::set_current_comp static function Consider taking the member function of a FiffInfo set_current_comp(fiff_int_t value), when compensation should be applied to the channels of FiffInfo

Set the current compensation value in the channel info structures

Parameters

[in]	chs	fiff channel info list.
[in]	value	compensation value.

Returns: the current compensation.

Definition at line 642 of file mne.h.

◆ setup_compensators()

void MNE::setup_compensators	(	FIFFLIB::FiffRawData &	raw,
		FIFFLIB::fiff_int_t	dest_comp,
		bool	keep_comp )

static

Definition at line 68 of file mne.cpp.

◆ transform_source_space_to()

bool MNELIB::MNE::transform_source_space_to	(	MNESourceSpaces &	p_pMNESourceSpaces,
		FIFFLIB::fiff_int_t	dest,
		FIFFLIB::FiffCoordTrans &	trans )

inlinestatic

mne_transform_source_space_to

MNE toolbox root function

Wrapper for the MNESourceSpaces transform_source_space_to member function

Transforms source space data to the desired coordinate system

Parameters

[in,out]	p_pMNESourceSpaces	the source space which is should be transformed.
[in]	dest	destination check code.
[in]	trans	transformation information.

Returns: true if succeeded, false otherwise.

Definition at line 665 of file mne.h.

◆ transpose_named_matrix()

void MNELIB::MNE::transpose_named_matrix ( FIFFLIB::FiffNamedMatrix & mat )

inlinestatic

mne_transpose_named_matrix

MNE toolbox root function

Wrapper for the FiffNamedMatrix transpose_named_matrix member function

Transpose a named matrix (FiffNamedMatrix)

Parameters

[in,out] mat FiffNamedMatrix which shoul be transposed.

Definition at line 686 of file mne.h.

◆ write_events_to_ascii()

bool MNELIB::MNE::write_events_to_ascii	(	QIODevice &	p_IODevice,
		const Eigen::MatrixXi &	eventlist,
		float	sfreq = 0.0f )

inlinestatic

write_events_to_ascii

Write an event list to a text file (MNE-C compatible format).

Parameters

[in]	p_IODevice	The I/O device to write to.
[in]	eventlist	The event list (nEvents x 3): [sample, before, after].
[in]	sfreq	Sampling frequency for time column computation.

Returns: true if succeeded, false otherwise.

Definition at line 402 of file mne.h.

◆ write_events_to_fif()

bool MNELIB::MNE::write_events_to_fif	(	QIODevice &	p_IODevice,
		const Eigen::MatrixXi &	eventlist )

inlinestatic

write_events_to_fif

Write an event list to a FIFF file.

Parameters

[in]	p_IODevice	The I/O device to write to.
[in]	eventlist	The event list (nEvents x 3): [sample, before, after].

Returns: true if succeeded, false otherwise.

Definition at line 382 of file mne.h.

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

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

Public Member Functions

Static Public Member Functions

Detailed Description

Constructor & Destructor Documentation

◆ ~MNE()

Member Function Documentation

◆ combine_xyz()

MNE toolbox root function

◆ compute_epoch_covariance()

MNE toolbox root function

◆ compute_proj()

MNE toolbox root function

◆ find_source_space_hemi()

MNE toolbox root function

MNE toolbox root function

◆ get_current_comp()

MNE toolbox root function

◆ make_block_diag()

MNE toolbox root function

◆ make_compensator()

MNE toolbox root function

◆ make_projector() [1/2]

MNE toolbox root function

◆ make_projector() [2/2]

MNE toolbox root function

◆ patch_info()

MNE toolbox root function

◆ prepare_inverse_operator()

MNE toolbox root function

◆ read_cov()

MNE toolbox root function

◆ read_events()

◆ read_events_from_ascii()

◆ read_events_from_fif()

◆ read_forward_solution()

MNE toolbox root function

◆ read_inverse_operator()

MNE toolbox root function

◆ read_source_spaces()

MNE toolbox root function

◆ save_raw()

MNE toolbox root function

◆ set_current_comp()

MNE toolbox root function

◆ setup_compensators()

◆ transform_source_space_to()

MNE toolbox root function

◆ transpose_named_matrix()

MNE toolbox root function

◆ write_events_to_ascii()

◆ write_events_to_fif()