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>
using	UPtr = std::unique_ptr<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 ()
bool	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 ()
int	writeToStream (FIFFLIB::FiffStream::SPtr &stream, bool selected_only) const
Public Member Functions inherited from MNELIB::MNESurfaceOrVolume
	MNESurfaceOrVolume ()
	Constructs the MNE FsSurface or Volume.
virtual	~MNESurfaceOrVolume ()
	Destroys the MNE FsSurface 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 (bool do_normals, bool check_too_many_neighbors)
int	add_geometry_info (bool do_normals)
int	add_geometry_info2 (bool do_normals)
Eigen::VectorXi	nearestVertIdx () const
Eigen::VectorXd	nearestDistVec () const
void	setNearestData (const Eigen::VectorXi &nearestIdx, const Eigen::VectorXd &nearestDist)
Eigen::Map< const Eigen::Vector3f >	point (int k) const
Eigen::Map< Eigen::Vector3f >	point (int k)
Eigen::Map< const Eigen::Vector3f >	normal (int k) const

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, bool add_geometry, bool check_too_many_neighbors)
static std::unique_ptr< 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 MNEHemisphere	icoDownsample (const MNEHemisphere &hemi, int icoGrade)
static QList< Eigen::VectorXi >	gradeToVertices (const QString &subjectsDir, const QString &subject, int grade)
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 68 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 72 of file mne_source_space.h.

◆ SPtr

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

Shared pointer type for MNESourceSpace.

Definition at line 71 of file mne_source_space.h.

◆ UPtr

using MNELIB::MNESourceSpace::UPtr = std::unique_ptr<MNESourceSpace>

Unique pointer type for MNESourceSpace.

Definition at line 73 of file mne_source_space.h.

Constructor & Destructor Documentation

◆ MNESourceSpace()

MNESourceSpace::MNESourceSpace ( int np = 0 )

Constructs the MNE Source Space

Parameters

[in] np Number of vertices; positions, normals and in-use flags are zero-initialized to this size.

Definition at line 780 of file mne_source_space.cpp.

◆ ~MNESourceSpace()

MNESourceSpace::~MNESourceSpace ( )

override

Destroys the MNE Source Space

Definition at line 829 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 956 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 835 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 1057 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 863 of file mne_source_space.cpp.

◆ filter_source_space()

void MNESourceSpace::filter_source_space ( FilterThreadArg * arg )

static

Definition at line 1519 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 1433 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 1590 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 892 of file mne_source_space.cpp.

◆ gradeToVertices()

QList< Eigen::VectorXi > MNESourceSpace::gradeToVertices	(	const QString &	subjectsDir,
		const QString &	subject,
		int	grade )

static

Vertices of a subject's surfaces nearest to an icosahedron of the given grade (mne.grade_to_vertices), found on surf/lh.sphere.reg and surf/rh.sphere.reg.

Parameters

[in]	subjectsDir	The FreeSurfer subjects directory.
[in]	subject	The subject.
[in]	grade	Icosahedral subdivision grade.

Returns: Sorted vertex numbers for lh and rh, or an empty list if a sphere cannot be read or the grade maps two icosahedron vertices onto the same surface vertex.

Definition at line 2351 of file mne_source_space.cpp.

◆ icoDownsample()

MNEHemisphere MNESourceSpace::icoDownsample	(	const MNEHemisphere &	hemi,
		int	icoGrade )

static

Downsample a hemisphere source space to an icosahedral subdivision of the given grade.

For each vertex of the icosahedron at the requested grade, the nearest vertex in the hemisphere is found and marked as in-use.

Parameters

[in]	hemi	The hemisphere to downsample.
[in]	icoGrade	Icosahedral subdivision grade (0-7).

Returns: A new MNEHemisphere with the downsampled vertex selection.

Since: 2.2.0

Definition at line 2378 of file mne_source_space.cpp.

◆ is_left_hemi()

bool 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 874 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 1104 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,
		bool	add_geometry,
		bool	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 1112 of file mne_source_space.cpp.

◆ make_volume_source_space()

std::unique_ptr< 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 nullptr on failure.

Definition at line 1188 of file mne_source_space.cpp.

◆ read_label()

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

static

Definition at line 2055 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 1672 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 1034 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 1989 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 930 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 1950 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 903 of file mne_source_space.cpp.

◆ writeToStream()

int MNESourceSpace::writeToStream	(	FIFFLIB::FiffStream::SPtr &	stream,
		bool	selected_only ) const

Write this source space to a FIFF stream.

Parameters

[in]	stream	The FIFF output stream.
[in]	selected_only	If true, write only the vertices that are in use.

Returns: FIFF_OK on success, FIFF_FAIL on error.

Definition at line 2192 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

◆ UPtr

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()

◆ gradeToVertices()

◆ icoDownsample()

◆ 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()

◆ writeToStream()