This defines a source space. More...

#include <mne_source_space.h>

Public Types
using	SPtr = std::shared_ptr<MNESourceSpace>
using	ConstSPtr = std::shared_ptr<const MNESourceSpace>
Public Types inherited from MNELIB::MNESurfaceOrVolume
typedef QSharedPointer< MNESurfaceOrVolume >	SPtr
typedef QSharedPointer< const MNESurfaceOrVolume >	ConstSPtr
typedef Eigen::Matrix< float, Eigen::Dynamic, 3, Eigen::RowMajor >	PointsT
typedef Eigen::Matrix< float, Eigen::Dynamic, 3, Eigen::RowMajor >	NormalsT
typedef Eigen::Matrix< int, Eigen::Dynamic, 3, Eigen::RowMajor >	TrianglesT

Public Member Functions
	MNESourceSpace (int np=0)
	~MNESourceSpace () override
virtual MNESourceSpace::SPtr	clone () const
void	enable_all_sources ()
int	is_left_hemi () const
qint32	find_source_space_hemi () const
void	update_inuse (Eigen::VectorXi new_inuse)
int	transform_source_space (const FIFFLIB::FiffCoordTrans &t)
int	add_patch_stats ()
void	rearrange_source_space ()
Public Member Functions inherited from MNELIB::MNESurfaceOrVolume
	MNESurfaceOrVolume ()
	Constructs the MNE Surface or Volume.
virtual	~MNESurfaceOrVolume ()
	Destroys the MNE Surface or Volume description.
	MNESurfaceOrVolume (const MNESurfaceOrVolume &)=default
MNESurfaceOrVolume &	operator= (const MNESurfaceOrVolume &)=default
	MNESurfaceOrVolume (MNESurfaceOrVolume &&)=default
MNESurfaceOrVolume &	operator= (MNESurfaceOrVolume &&)=default
void	add_uniform_curv ()
void	add_triangle_data ()
void	compute_surface_cm ()
void	calculate_vertex_distances ()
int	add_vertex_normals ()
int	add_geometry_info (int do_normals, int check_too_many_neighbors)
int	add_geometry_info (int do_normals)
int	add_geometry_info2 (int do_normals)
Eigen::VectorXi	nearestVertIdx () const
Eigen::VectorXd	nearestDistVec () const
void	setNearestData (const Eigen::VectorXi &nearestIdx, const Eigen::VectorXd &nearestDist)

Static Public Member Functions
static std::unique_ptr< MNESourceSpace >	create_source_space (int np)
static std::unique_ptr< MNESourceSpace >	load_surface (const QString &surf_file, const QString &curv_file)
static std::unique_ptr< MNESourceSpace >	load_surface_geom (const QString &surf_file, const QString &curv_file, int add_geometry, int check_too_many_neighbors)
static MNESourceSpace *	make_volume_source_space (const MNESurface &surf, float grid, float exclude, float mindist)
static int	filter_source_spaces (const MNESurface &surf, float limit, const FIFFLIB::FiffCoordTrans &mri_head_t, std::vector< std::unique_ptr< MNESourceSpace > > &spaces, QTextStream *filtered)
static void	filter_source_space (FilterThreadArg *arg)
static int	filter_source_spaces (float limit, const QString &bemfile, const FIFFLIB::FiffCoordTrans &mri_head_t, std::vector< std::unique_ptr< MNESourceSpace > > &spaces, QTextStream *filtered, bool use_threads)
static int	read_source_spaces (const QString &name, std::vector< std::unique_ptr< MNESourceSpace > > &spaces)
static int	transform_source_spaces_to (int coord_frame, const FIFFLIB::FiffCoordTrans &t, std::vector< std::unique_ptr< MNESourceSpace > > &spaces)
static int	restrict_sources_to_labels (std::vector< std::unique_ptr< MNESourceSpace > > &spaces, const QStringList &labels, int nlabel)
static int	read_label (const QString &label, Eigen::VectorXi &sel)
Static Public Member Functions inherited from MNELIB::MNESurfaceOrVolume
static double	solid_angle (const Eigen::Vector3f &from, const MNELIB::MNETriangle &tri)
static void	compute_cm (const PointsT &rr, int np, float(&cm)[3])

Additional Inherited Members
Public Attributes inherited from MNELIB::MNESurfaceOrVolume
int	type
QString	subject
int	id
int	coord_frame
std::optional< MNEVolGeom >	vol_geom
std::optional< MNEMghTagGroup >	mgh_tags
int	np
PointsT	rr
NormalsT	nn
float	cm [3]
Eigen::VectorXi	inuse
Eigen::VectorXi	vertno
int	nuse
std::vector< Eigen::VectorXi >	neighbor_vert
Eigen::VectorXi	nneighbor_vert
std::vector< Eigen::VectorXf >	vert_dist
float	sigma
int	ntri
std::vector< MNETriangle >	tris
TrianglesT	itris
float	tot_area
int	nuse_tri
std::vector< MNETriangle >	use_tris
TrianglesT	use_itris
std::vector< Eigen::VectorXi >	neighbor_tri
Eigen::VectorXi	nneighbor_tri
std::vector< MNENearest >	nearest
std::vector< std::optional< MNEPatchInfo > >	patches
FIFFLIB::FiffSparseMatrix	dist
float	dist_limit
Eigen::VectorXf	curv
Eigen::VectorXf	val
std::optional< FIFFLIB::FiffCoordTrans >	voxel_surf_RAS_t
int	vol_dims [3]
float	voxel_size [3]
std::optional< FIFFLIB::FiffSparseMatrix >	interpolator
QString	MRI_volume
std::optional< FIFFLIB::FiffCoordTrans >	MRI_voxel_surf_RAS_t
std::optional< FIFFLIB::FiffCoordTrans >	MRI_surf_RAS_RAS_t
int	MRI_vol_dims [3]

Detailed Description

This defines a source space.

Implements the MNE Source Space (Replaces typedef mneSurfaceOrVolume mneSourceSpace; struct of MNE-C mne_types.h).

Definition at line 76 of file mne_source_space.h.

Inheritance diagram for MNELIB::MNESourceSpace:

Member Typedef Documentation

◆ ConstSPtr

using MNELIB::MNESourceSpace::ConstSPtr = std::shared_ptr<const MNESourceSpace>

Const shared pointer type for MNESourceSpace.

Definition at line 80 of file mne_source_space.h.

◆ SPtr

using MNELIB::MNESourceSpace::SPtr = std::shared_ptr<MNESourceSpace>

Shared pointer type for MNESourceSpace.

Definition at line 79 of file mne_source_space.h.

Constructor & Destructor Documentation

◆ MNESourceSpace()

MNESourceSpace::MNESourceSpace ( int np = 0 )

Constructs the MNE Source Space

Definition at line 889 of file mne_source_space.cpp.

◆ ~MNESourceSpace()

MNESourceSpace::~MNESourceSpace ( )

override

Destroys the MNE Source Space

Definition at line 938 of file mne_source_space.cpp.

Member Function Documentation

◆ add_patch_stats()

int MNESourceSpace::add_patch_stats ( )

Compute patch statistics (areas, normals, deviations).

Returns: OK on success, FAIL on error.

Definition at line 1066 of file mne_source_space.cpp.

◆ clone()

MNESourceSpace::SPtr MNESourceSpace::clone ( ) const

virtual

Creates a deep copy of this source space, preserving the actual derived type.

Returns: a shared_ptr to the cloned source space.

Reimplemented in MNELIB::MNEHemisphere.

Definition at line 944 of file mne_source_space.cpp.

◆ create_source_space()

std::unique_ptr< MNESourceSpace > MNESourceSpace::create_source_space ( int np )

static

Create a new source space with np vertices and all associated data initialized to defaults.

Parameters

[in] np Number of vertices.

Returns: Unique pointer to the newly allocated source space.

Definition at line 1168 of file mne_source_space.cpp.

◆ enable_all_sources()

void MNESourceSpace::enable_all_sources ( )

Enable all source points (set inuse to TRUE, nuse = np).

Definition at line 972 of file mne_source_space.cpp.

◆ filter_source_space()

void MNESourceSpace::filter_source_space ( FilterThreadArg * arg )

static

Definition at line 1676 of file mne_source_space.cpp.

◆ filter_source_spaces() [1/2]

int MNESourceSpace::filter_source_spaces	(	const MNESurface &	surf,
		float	limit,
		const FIFFLIB::FiffCoordTrans &	mri_head_t,
		std::vector< std::unique_ptr< MNESourceSpace > > &	spaces,
		QTextStream *	filtered )

static

Definition at line 1585 of file mne_source_space.cpp.

◆ filter_source_spaces() [2/2]

int MNESourceSpace::filter_source_spaces	(	float	limit,
		const QString &	bemfile,
		const FIFFLIB::FiffCoordTrans &	mri_head_t,
		std::vector< std::unique_ptr< MNESourceSpace > > &	spaces,
		QTextStream *	filtered,
		bool	use_threads )

static

Definition at line 1752 of file mne_source_space.cpp.

◆ find_source_space_hemi()

qint32 MNESourceSpace::find_source_space_hemi ( ) const

Returns the hemisphere id (FIFFV_MNE_SURF_LEFT_HEMI or FIFFV_MNE_SURF_RIGHT_HEMI) for this source space, based on the average x-coordinate of all vertices.

Returns: the deduced hemisphere id.

Definition at line 1001 of file mne_source_space.cpp.

◆ is_left_hemi()

int MNESourceSpace::is_left_hemi ( ) const

Determine whether this source space is on the left hemisphere based on the average x-coordinate of all vertices.

Returns: TRUE if left hemisphere, FALSE otherwise.

Definition at line 983 of file mne_source_space.cpp.

◆ load_surface()

std::unique_ptr< MNESourceSpace > MNESourceSpace::load_surface	(	const QString &	surf_file,
		const QString &	curv_file )

static

Load a FreeSurfer surface from disk, adding full geometry information.

Parameters

[in]	surf_file	Path to the FreeSurfer surface file.
[in]	curv_file	Path to the curvature file (may be empty).

Returns: Unique pointer to the loaded source space, or nullptr on error.

Definition at line 1215 of file mne_source_space.cpp.

◆ load_surface_geom()

std::unique_ptr< MNESourceSpace > MNESourceSpace::load_surface_geom	(	const QString &	surf_file,
		const QString &	curv_file,
		int	add_geometry,
		int	check_too_many_neighbors )

static

Load a FreeSurfer surface from disk, optionally adding geometry information.

Parameters

[in]	surf_file	Path to the FreeSurfer surface file.
[in]	curv_file	Path to the curvature file (may be empty).
[in]	add_geometry	Whether to compute full geometry info.
[in]	check_too_many_neighbors	Whether to error on excess neighbors.

Returns: Unique pointer to the loaded source space, or nullptr on error.

Definition at line 1223 of file mne_source_space.cpp.

◆ make_volume_source_space()

MNESourceSpace * MNESourceSpace::make_volume_source_space	(	const MNESurface &	surf,
		float	grid,
		float	exclude,
		float	mindist )

static

Create a volumetric source space by laying out a 3D grid of points within the bounding box of a surface, filtering out points that lie outside the surface or closer than mindist to the surface, and establishing 26-neighbor connectivity.

Parameters

[in]	surf	The bounding surface (e.g. inner skull).
[in]	grid	Grid spacing in meters.
[in]	exclude	Exclusion radius from the center of mass (m).
[in]	mindist	Minimum distance from the surface (m).

Returns: A new volumetric source space, or NULL on failure. Caller takes ownership.

Definition at line 1320 of file mne_source_space.cpp.

◆ read_label()

int MNESourceSpace::read_label	(	const QString &	label,
		Eigen::VectorXi &	sel )

static

Definition at line 2250 of file mne_source_space.cpp.

◆ read_source_spaces()

int MNESourceSpace::read_source_spaces	(	const QString &	name,
		std::vector< std::unique_ptr< MNESourceSpace > > &	spaces )

static

Definition at line 1838 of file mne_source_space.cpp.

◆ rearrange_source_space()

void MNESourceSpace::rearrange_source_space ( )

Rearrange source space after filtering: recount nuse, rebuild vertno, and recompute patch statistics if nearest info is available.

Definition at line 1144 of file mne_source_space.cpp.

◆ restrict_sources_to_labels()

int MNESourceSpace::restrict_sources_to_labels	(	std::vector< std::unique_ptr< MNESourceSpace > > &	spaces,
		const QStringList &	labels,
		int	nlabel )

static

Definition at line 2179 of file mne_source_space.cpp.

◆ transform_source_space()

int MNESourceSpace::transform_source_space ( const FIFFLIB::FiffCoordTrans & t )

Transform this source space into another coordinate frame.

Parameters

[in] t The coordinate transformation to apply.

Returns: OK on success, FAIL on error.

Definition at line 1040 of file mne_source_space.cpp.

◆ transform_source_spaces_to()

int MNESourceSpace::transform_source_spaces_to	(	int	coord_frame,
		const FIFFLIB::FiffCoordTrans &	t,
		std::vector< std::unique_ptr< MNESourceSpace > > &	spaces )

static

Definition at line 2137 of file mne_source_space.cpp.

◆ update_inuse()

void MNESourceSpace::update_inuse ( Eigen::VectorXi new_inuse )

Update the active vertex (inuse) vector and recompute vertno.

Parameters

[in] new_inuse New in-use vector (size np).

Definition at line 1012 of file mne_source_space.cpp.

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

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

Public Types

Public Member Functions

Static Public Member Functions

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ ConstSPtr

◆ SPtr

Constructor & Destructor Documentation

◆ MNESourceSpace()

◆ ~MNESourceSpace()

Member Function Documentation

◆ add_patch_stats()

◆ clone()

◆ create_source_space()

◆ enable_all_sources()

◆ filter_source_space()

◆ filter_source_spaces() [1/2]

◆ filter_source_spaces() [2/2]

◆ find_source_space_hemi()

◆ is_left_hemi()

◆ load_surface()

◆ load_surface_geom()

◆ make_volume_source_space()

◆ read_label()

◆ read_source_spaces()

◆ rearrange_source_space()

◆ restrict_sources_to_labels()

◆ transform_source_space()

◆ transform_source_spaces_to()

◆ update_inuse()