FreeSurfer surface mesh. More...

#include <surface.h>

Public Types
typedef QSharedPointer< Surface >	SPtr
typedef QSharedPointer< const Surface >	ConstSPtr

Public Member Functions
	Surface ()
	Surface (const QString &p_sFile)
	Surface (const QString &subject_id, qint32 hemi, const QString &surf, const QString &subjects_dir)
	Surface (const QString &path, qint32 hemi, const QString &surf)
	~Surface ()
void	clear ()
qint32	hemi () const
bool	isEmpty () const
QString	surf () const
const Eigen::MatrixX3f &	rr () const
const Eigen::MatrixX3i &	tris () const
const Eigen::MatrixX3f &	nn () const
const Eigen::VectorXf &	curv () const
const Eigen::Vector3f &	offset () const
Eigen::Vector3f &	offset ()
QString	filePath () const
QString	fileName () const

Static Public Member Functions
static bool	read (const QString &subject_id, qint32 hemi, const QString &surf, const QString &subjects_dir, Surface &p_Surface, bool p_bLoadCurvature=true)
static bool	read (const QString &path, qint32 hemi, const QString &surf, Surface &p_Surface, bool p_bLoadCurvature=true)
static bool	read (const QString &p_sFileName, Surface &p_Surface, bool p_bLoadCurvature=true)
static Eigen::VectorXf	read_curv (const QString &p_sFileName)
static Eigen::MatrixX3f	compute_normals (const Eigen::MatrixX3f &rr, const Eigen::MatrixX3i &tris)

Detailed Description

FreeSurfer surface mesh.

A FreeSurfer surface mesh in triangular format

Definition at line 75 of file surface.h.

Member Typedef Documentation

◆ ConstSPtr

typedef QSharedPointer<const Surface> FSLIB::Surface::ConstSPtr

Const shared pointer type for Surface class.

Definition at line 79 of file surface.h.

◆ SPtr

typedef QSharedPointer<Surface> FSLIB::Surface::SPtr

Shared pointer type for Surface class.

Definition at line 78 of file surface.h.

Constructor & Destructor Documentation

◆ Surface() [1/4]

Surface::Surface ( )

Default constructor

Definition at line 66 of file surface.cpp.

◆ Surface() [2/4]

Surface::Surface ( const QString & p_sFile )

explicit

Construts the surface by reading it of the given file.

Parameters

[in] p_sFile Surface file name with path.

Definition at line 77 of file surface.cpp.

◆ Surface() [3/4]

Surface::Surface	(	const QString &	subject_id,
		qint32	hemi,
		const QString &	surf,
		const QString &	subjects_dir )

explicit

Construts the surface by reading it of the given file.

Parameters

[in]	subject_id	Name of subject.
[in]	hemi	Which hemisphere to load {0 -> lh, 1 -> rh}.
[in]	surf	Name of the surface to load (eg. inflated, orig ...).
[in]	subjects_dir	Subjects directory.

Definition at line 89 of file surface.cpp.

◆ Surface() [4/4]

Surface::Surface	(	const QString &	path,
		qint32	hemi,
		const QString &	surf )

explicit

Construts the surface by reading it of the given file.

Parameters

[in]	path	path to surface directory.
[in]	hemi	Which hemisphere to load {0 -> lh, 1 -> rh}.
[in]	surf	Name of the surface to load (eg. inflated, orig ...).

Returns: true if read sucessful, false otherwise.

Definition at line 101 of file surface.cpp.

◆ ~Surface()

Surface::~Surface ( )

Destroys the Surface class.

Definition at line 113 of file surface.cpp.

Member Function Documentation

◆ clear()

void Surface::clear ( )

Initializes the Surface.

Definition at line 119 of file surface.cpp.

◆ compute_normals()

MatrixX3f Surface::compute_normals	(	const Eigen::MatrixX3f &	rr,
		const Eigen::MatrixX3i &	tris )

static

Efficiently compute vertex normals for triangulated surface

Parameters

[in]	rr	Vertex coordinates in meters.
[out]	tris	The triangle descriptions.

Returns: The computed normals.

Definition at line 133 of file surface.cpp.

◆ curv()

const Eigen::VectorXf & FSLIB::Surface::curv ( ) const

inline

FreeSurfer curvature

Returns: the FreeSurfer curvature data.

Definition at line 343 of file surface.h.

◆ fileName()

QString FSLIB::Surface::fileName ( ) const

inline

surf file name

Returns: the surf file name.

Definition at line 371 of file surface.h.

◆ filePath()

QString FSLIB::Surface::filePath ( ) const

inline

path to surf directuryt

Returns: the path to surf directory.

Definition at line 364 of file surface.h.

◆ hemi()

qint32 FSLIB::Surface::hemi ( ) const

inline

Returns the hemisphere id (0 = lh; 1 = rh)

Returns: hemisphere id.

Definition at line 301 of file surface.h.

◆ isEmpty()

bool FSLIB::Surface::isEmpty ( ) const

inline

Returns whether Surface is empty.

Returns: true if is empty, false otherwise.

Definition at line 308 of file surface.h.

◆ nn()

const Eigen::MatrixX3f & FSLIB::Surface::nn ( ) const

inline

Normalized surface normals for each vertex

Returns: surface normals.

Definition at line 336 of file surface.h.

◆ offset() [1/2]

Eigen::Vector3f & FSLIB::Surface::offset ( )

inline

Vector offset

Returns: the offset vector.

Definition at line 357 of file surface.h.

◆ offset() [2/2]

const Eigen::Vector3f & FSLIB::Surface::offset ( ) const

inline

Vector offset

Returns: the offset vector.

Definition at line 350 of file surface.h.

◆ read() [1/3]

bool Surface::read	(	const QString &	p_sFileName,
		Surface &	p_Surface,
		bool	p_bLoadCurvature = true )

static

mne_read_surface

Reads a FreeSurfer surface file

Parameters

[in]	p_sFileName	The file to read.
[out]	p_Surface	The read surface.
[in]	p_bLoadCurvature	True if the curvature should be read (optional, default = true).

Returns: true if read sucessful, false otherwise.

Definition at line 208 of file surface.cpp.

◆ read() [2/3]

bool Surface::read	(	const QString &	path,
		qint32	hemi,
		const QString &	surf,
		Surface &	p_Surface,
		bool	p_bLoadCurvature = true )

static

mne_read_surface

Reads a FreeSurfer surface file

Parameters

[in]	path	path to surface directory.
[in]	hemi	Which hemisphere to load {0 -> lh, 1 -> rh}.
[in]	surf	Name of the surface to load (eg. inflated, orig ...).
[out]	p_Surface	The read surface.
[in]	p_bLoadCurvature	True if the curvature should be read (optional, default = true).

Returns: true if read sucessful, false otherwise.

Definition at line 196 of file surface.cpp.

◆ read() [3/3]

bool Surface::read	(	const QString &	subject_id,
		qint32	hemi,
		const QString &	surf,
		const QString &	subjects_dir,
		Surface &	p_Surface,
		bool	p_bLoadCurvature = true )

static

mne_read_surface

Reads a FreeSurfer surface file

Parameters

[in]	subject_id	Name of subject.
[in]	hemi	Which hemisphere to load {0 -> lh, 1 -> rh}.
[in]	surf	Name of the surface to load (eg. inflated, orig ...).
[in]	subjects_dir	Subjects directory.
[out]	p_Surface	The read surface.
[in]	p_bLoadCurvature	True if the curvature should be read (optional, default = true).

Returns: true if read sucessful, false otherwise.

Definition at line 184 of file surface.cpp.

◆ read_curv()

VectorXf Surface::read_curv ( const QString & p_sFileName )

static

reads a binary curvature file into a vector

Returns: the read curvature.

Definition at line 410 of file surface.cpp.

◆ rr()

const Eigen::MatrixX3f & FSLIB::Surface::rr ( ) const

inline

Coordinates of vertices (rr)

Returns: coordinates of vertices.

Definition at line 322 of file surface.h.

◆ surf()

QString FSLIB::Surface::surf ( ) const

inline

Loaded surface (eg. inflated, orig ...)

Returns: the surface.

Definition at line 315 of file surface.h.

◆ tris()

const Eigen::MatrixX3i & FSLIB::Surface::tris ( ) const

inline

The triangle descriptions

Returns: triangle descriptions.

Definition at line 329 of file surface.h.

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

src/libraries/fs/surface.h
src/libraries/fs/surface.cpp

Public Types

Public Member Functions

Static Public Member Functions

Detailed Description

Member Typedef Documentation

◆ ConstSPtr

◆ SPtr

Constructor & Destructor Documentation

◆ Surface() [1/4]

◆ Surface() [2/4]

◆ Surface() [3/4]

◆ Surface() [4/4]

◆ ~Surface()

Member Function Documentation

◆ clear()

◆ compute_normals()

◆ curv()

◆ fileName()

◆ filePath()

◆ hemi()

◆ isEmpty()

◆ nn()

◆ offset() [1/2]

◆ offset() [2/2]

◆ read() [1/3]

◆ read() [2/3]

◆ read() [3/3]

◆ read_curv()

◆ rr()

◆ surf()

◆ tris()