In-memory FreeSurfer triangular cortical surface for one hemisphere. More...

#include <fs_surface.h>

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

Public Member Functions
	FsSurface ()
	FsSurface (const QString &p_sFile)
	FsSurface (const QString &subject_id, qint32 hemi, const QString &surf, const QString &subjects_dir)
	FsSurface (const QString &path, qint32 hemi, const QString &surf)
	~FsSurface ()
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, FsSurface &p_Surface, bool p_bLoadCurvature=true)
static bool	read (const QString &path, qint32 hemi, const QString &surf, FsSurface &p_Surface, bool p_bLoadCurvature=true)
static bool	read (const QString &p_sFileName, FsSurface &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)
static qint32	fread3 (QDataStream &stream)
static qint32	fread3 (std::iostream &stream)
static Eigen::VectorXi	fread3_many (QDataStream &stream, qint32 count)
static Eigen::VectorXi	fread3_many (std::iostream &stream, qint32 count)

Detailed Description

In-memory FreeSurfer triangular cortical surface for one hemisphere.

Owns the vertex coordinate matrix (n_vertices × 3, Tk-surface RAS mm), the triangle index matrix (n_faces × 3, zero-based into the vertex array) and the hemisphere id (0 = lh, 1 = rh). Construction is purely an I/O operation: each constructor either takes a direct path to a lh.pial / rh.white / lh.inflated style binary surface file, or the subject_id / hemi / surf shorthand resolved against $SUBJECTS_DIR. The instance is intended to be paired with an FsAnnotation or FsLabel sharing the same vertex indexing.

Definition at line 91 of file fs_surface.h.

Member Typedef Documentation

◆ ConstSPtr

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

Const shared pointer type for FsSurface class.

Definition at line 95 of file fs_surface.h.

◆ SPtr

typedef QSharedPointer<FsSurface> FSLIB::FsSurface::SPtr

Shared pointer type for FsSurface class.

Definition at line 94 of file fs_surface.h.

Constructor & Destructor Documentation

◆ FsSurface() [1/4]

FsSurface::FsSurface ( )

Default constructor

Definition at line 41 of file fs_surface.cpp.

◆ FsSurface() [2/4]

FsSurface::FsSurface ( const QString & p_sFile )

explicit

Construts the surface by reading it of the given file.

Parameters

[in] p_sFile FsSurface file name with path.

Definition at line 52 of file fs_surface.cpp.

◆ FsSurface() [3/4]

FsSurface::FsSurface	(	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 64 of file fs_surface.cpp.

◆ FsSurface() [4/4]

FsSurface::FsSurface	(	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 76 of file fs_surface.cpp.

◆ ~FsSurface()

FsSurface::~FsSurface ( )

Destroys the FsSurface class.

Definition at line 88 of file fs_surface.cpp.

Member Function Documentation

◆ clear()

void FsSurface::clear ( )

Initializes the FsSurface.

Definition at line 94 of file fs_surface.cpp.

◆ compute_normals()

MatrixX3f FsSurface::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 108 of file fs_surface.cpp.

◆ curv()

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

inline

FreeSurfer curvature

Returns: the FreeSurfer curvature data.

Definition at line 397 of file fs_surface.h.

◆ fileName()

QString FSLIB::FsSurface::fileName ( ) const

inline

surf file name

Returns: the surf file name.

Definition at line 425 of file fs_surface.h.

◆ filePath()

QString FSLIB::FsSurface::filePath ( ) const

inline

path to surf directuryt

Returns: the path to surf directory.

Definition at line 418 of file fs_surface.h.

◆ fread3() [1/2]

qint32 FsSurface::fread3 ( QDataStream & stream )

static

Reads a 3-byte integer out of a QDataStream (FreeSurfer format).

Parameters

[in] stream Stream to read from.

Returns: the read 3-byte integer.

Definition at line 439 of file fs_surface.cpp.

◆ fread3() [2/2]

qint32 FsSurface::fread3 ( std::iostream & stream )

static

Reads a 3-byte integer out of a std::iostream (FreeSurfer format).

Parameters

[in] stream Stream to read from.

Returns: the read 3-byte integer.

Definition at line 448 of file fs_surface.cpp.

◆ fread3_many() [1/2]

VectorXi FsSurface::fread3_many	(	QDataStream &	stream,
		qint32	count )

static

Reads multiple 3-byte integers out of a QDataStream (FreeSurfer format).

Parameters

[in]	stream	Stream to read from.
[in]	count	Number of elements to read.

Returns: the read 3-byte integers.

Definition at line 457 of file fs_surface.cpp.

◆ fread3_many() [2/2]

VectorXi FsSurface::fread3_many	(	std::iostream &	stream,
		qint32	count )

static

Reads multiple 3-byte integers out of a std::iostream (FreeSurfer format).

Parameters

[in]	stream	Stream to read from.
[in]	count	Number of elements to read.

Returns: the read 3-byte integers.

Definition at line 467 of file fs_surface.cpp.

◆ hemi()

qint32 FSLIB::FsSurface::hemi ( ) const

inline

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

Returns: hemisphere id.

Definition at line 355 of file fs_surface.h.

◆ isEmpty()

bool FSLIB::FsSurface::isEmpty ( ) const

inline

Returns whether FsSurface is empty.

Returns: true if is empty, false otherwise.

Definition at line 362 of file fs_surface.h.

◆ nn()

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

inline

Normalized surface normals for each vertex

Returns: surface normals.

Definition at line 390 of file fs_surface.h.

◆ offset() [1/2]

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

inline

Vector offset

Returns: the offset vector.

Definition at line 411 of file fs_surface.h.

◆ offset() [2/2]

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

inline

Vector offset

Returns: the offset vector.

Definition at line 404 of file fs_surface.h.

◆ read() [1/3]

bool FsSurface::read	(	const QString &	p_sFileName,
		FsSurface &	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 183 of file fs_surface.cpp.

◆ read() [2/3]

bool FsSurface::read	(	const QString &	path,
		qint32	hemi,
		const QString &	surf,
		FsSurface &	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 171 of file fs_surface.cpp.

◆ read() [3/3]

bool FsSurface::read	(	const QString &	subject_id,
		qint32	hemi,
		const QString &	surf,
		const QString &	subjects_dir,
		FsSurface &	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 159 of file fs_surface.cpp.

◆ read_curv()

VectorXf FsSurface::read_curv ( const QString & p_sFileName )

static

reads a binary curvature file into a vector

Returns: the read curvature.

Definition at line 385 of file fs_surface.cpp.

◆ rr()

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

inline

Coordinates of vertices (rr)

Returns: coordinates of vertices.

Definition at line 376 of file fs_surface.h.

◆ surf()

QString FSLIB::FsSurface::surf ( ) const

inline

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

Returns: the surface.

Definition at line 369 of file fs_surface.h.

◆ tris()

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

inline

The triangle descriptions

Returns: triangle descriptions.

Definition at line 383 of file fs_surface.h.

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

src/libraries/fs/fs_surface.h
src/libraries/fs/fs_surface.cpp

Public Types

Public Member Functions

Static Public Member Functions

Detailed Description

Member Typedef Documentation

◆ ConstSPtr

◆ SPtr

Constructor & Destructor Documentation

◆ FsSurface() [1/4]

◆ FsSurface() [2/4]

◆ FsSurface() [3/4]

◆ FsSurface() [4/4]

◆ ~FsSurface()

Member Function Documentation

◆ clear()

◆ compute_normals()

◆ curv()

◆ fileName()

◆ filePath()

◆ fread3() [1/2]

◆ fread3() [2/2]

◆ fread3_many() [1/2]

◆ fread3_many() [2/2]

◆ hemi()

◆ isEmpty()

◆ nn()

◆ offset() [1/2]

◆ offset() [2/2]

◆ read() [1/3]

◆ read() [2/3]

◆ read() [3/3]

◆ read_curv()

◆ rr()

◆ surf()

◆ tris()