FsSurface

Namespace: FSLIB · Library: FreeSurfer Library

Python equivalent

mne.read_surface in MNE-Python.

#include <fs/fs_surface.h>

class FSLIB::FsSurface

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.

Public Methods

FsSurface()

Default constructor.

FsSurface(p_sFile)

Construts the surface by reading it of the given file.

Parameters:

p_sFile : const QString & FsSurface file name with path.

FsSurface(subject_id, hemi, surf, subjects_dir)

Construts the surface by reading it of the given file.

Parameters:

subject_id : const QString & Name of subject.
hemi : qint32 Which hemisphere to load {0 -> lh, 1 -> rh}.
surf : const QString & Name of the surface to load (eg. inflated, orig ...).
subjects_dir : const QString & Subjects directory.

FsSurface(path, hemi, surf)

Construts the surface by reading it of the given file.

Parameters:

path : const QString & path to surface directory.
hemi : qint32 Which hemisphere to load {0 -> lh, 1 -> rh}.
surf : const QString & Name of the surface to load (eg. inflated, orig ...).

Returns:

true if read sucessful, false otherwise.

~FsSurface()

Destroys the FsSurface class.

clear()

Initializes the FsSurface.

hemi()

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

Returns:

qint32 — hemisphere id.

isEmpty()

Returns whether FsSurface is empty.

Returns:

bool — true if is empty, false otherwise.

surf()

Loaded surface (eg.

inflated, orig ...)

Returns:

QString — the surface.

rr()

Coordinates of vertices (rr).

Returns:

const Eigen::MatrixX3f & — coordinates of vertices.

tris()

The triangle descriptions.

Returns:

const Eigen::MatrixX3i & — triangle descriptions.

nn()

Normalized surface normals for each vertex.

Returns:

const Eigen::MatrixX3f & — surface normals.

curv()

FreeSurfer curvature.

Returns:

const Eigen::VectorXf & — the FreeSurfer curvature data.

offset()

Vector offset.

Returns:

const Eigen::Vector3f & — the offset vector.

offset()

Vector offset.

Returns:

Eigen::Vector3f & — the offset vector.

filePath()

path to surf directuryt

Returns:

QString — the path to surf directory.

fileName()

surf file name

Returns:

QString — the surf file name.

Static Methods

read(subject_id, hemi, surf, subjects_dir, p_Surface, p_bLoadCurvature)

mne_read_surface

Reads a FreeSurfer surface file

Parameters:

subject_id : const QString & Name of subject.
hemi : qint32 Which hemisphere to load {0 -> lh, 1 -> rh}.
surf : const QString & Name of the surface to load (eg. inflated, orig ...).
subjects_dir : const QString & Subjects directory.
p_Surface : FsSurface & The read surface.
p_bLoadCurvature : bool True if the curvature should be read (optional, default = true).

Returns:

bool — true if read sucessful, false otherwise.

read(path, hemi, surf, p_Surface, p_bLoadCurvature)

mne_read_surface

Reads a FreeSurfer surface file

Parameters:

path : const QString & path to surface directory.
hemi : qint32 Which hemisphere to load {0 -> lh, 1 -> rh}.
surf : const QString & Name of the surface to load (eg. inflated, orig ...).
p_Surface : FsSurface & The read surface.
p_bLoadCurvature : bool True if the curvature should be read (optional, default = true).

Returns:

bool — true if read sucessful, false otherwise.

read(p_sFileName, p_Surface, p_bLoadCurvature)

mne_read_surface

Reads a FreeSurfer surface file

Parameters:

p_sFileName : const QString & The file to read.
p_Surface : FsSurface & The read surface.
p_bLoadCurvature : bool True if the curvature should be read (optional, default = true).

Returns:

bool — true if read sucessful, false otherwise.

read_curv(p_sFileName)

reads a binary curvature file into a vector

Returns:

Eigen::VectorXf — the read curvature.

compute_normals(rr, tris)

Efficiently compute vertex normals for triangulated surface.

Parameters:

rr : const Eigen::MatrixX3f & Vertex coordinates in meters.
tris : const Eigen::MatrixX3i & The triangle descriptions.

Returns:

Eigen::MatrixX3f — The computed normals.

fread3(stream)

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

Parameters:

stream : QDataStream & Stream to read from.

Returns:

qint32 — the read 3-byte integer.

fread3(stream)

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

Parameters:

stream : std::iostream & Stream to read from.

Returns:

qint32 — the read 3-byte integer.

fread3_many(stream, count)

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

Parameters:

stream : QDataStream & Stream to read from.
count : qint32 Number of elements to read.

Returns:

Eigen::VectorXi — the read 3-byte integers.

fread3_many(stream, count)

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

Parameters:

stream : std::iostream & Stream to read from.
count : qint32 Number of elements to read.

Returns:

Eigen::VectorXi — the read 3-byte integers.

Example

Source: src/examples/ex_fs_surface/main.cpp

#include <disp3D/view/brainview.h>
#include <disp3D/model/braintreemodel.h>

#include <fs/fs_surfaceset.h>

#include <utils/generics/mne_logger.h>

//=============================================================================================================
// QT INCLUDES
//=============================================================================================================

#include <QApplication>
#include <QCommandLineParser>

//=============================================================================================================
// USED NAMESPACES
//=============================================================================================================

using namespace FSLIB;

//=============================================================================================================
// MAIN
//=============================================================================================================

//=============================================================================================================
/**
 * The function main marks the entry point of the program.
 * By default, main has the storage class extern.
 *
 * @param[in] argc (argument count) is an integer that indicates how many arguments were entered on the command line when the program was started.
 * @param[in] argv (argument vector) is an array of pointers to arrays of character objects. The array objects are null-terminated strings, representing the arguments that were entered on the command line when the program was started.
 * @return the value that was set to exit() (which is 0 if exit() is called via quit()).
 */
int main(int argc, char *argv[])
{
    #ifdef STATICBUILD
    // Q_INIT_RESOURCE(mne_disp3d);
    #endif
    
    qInstallMessageHandler(UTILSLIB::MNELogger::customLogWriter);
    QApplication a(argc, argv);

    // Command Line Parser
    QCommandLineParser parser;
    parser.setApplicationDescription("Fs FsSurface Example");
    parser.addHelpOption();

    QCommandLineOption hemiOption("hemi", "Selected hemisphere <hemi>.", "hemi", "2");
    QCommandLineOption subjectOption("subject", "Selected subject <subject>.", "subject", "sample");
    QCommandLineOption subjectPathOption("subjectPath", "Selected subject path <subjectPath>.", "subjectPath", QCoreApplication::applicationDirPath() + "/../resources/data/MNE-sample-data/subjects");

    parser.addOption(hemiOption);
    parser.addOption(subjectOption);
    parser.addOption(subjectPathOption);

    parser.process(a);

    int hemi = parser.value(hemiOption).toInt();
    QString subject = parser.value(subjectOption);
    QString subjectPath = parser.value(subjectPathOption);

    //
    // pial
    //
    FsSurfaceSet tSurfSetPial (subject, hemi, "pial", subjectPath);

    BrainView *pBrainView = new BrainView();
    BrainTreeModel *pModel = new BrainTreeModel();
    pBrainView->setModel(pModel);

    for (auto it = tSurfSetPial.data().constBegin(); it != tSurfSetPial.data().constEnd(); ++it) {
        QString hemi = (it.value().hemi() == 0) ? "lh" : "rh";
        pModel->addSurface(subject, hemi, "pial", it.value());
    }

    //
    // inflated
    //
    FsSurfaceSet tSurfSetInflated (subject, hemi, "inflated", subjectPath);
    for (auto it = tSurfSetInflated.data().constBegin(); it != tSurfSetInflated.data().constEnd(); ++it) {
        QString hemi = (it.value().hemi() == 0) ? "lh" : "rh";
        pModel->addSurface(subject, hemi, "inflated", it.value());
    }

    //
    // orig
    //
    FsSurfaceSet tSurfSetOrig (subject, hemi, "orig", subjectPath);
    for (auto it = tSurfSetOrig.data().constBegin(); it != tSurfSetOrig.data().constEnd(); ++it) {
        QString hemi = (it.value().hemi() == 0) ? "lh" : "rh";
        pModel->addSurface(subject, hemi, "orig", it.value());
    }

    //
    // white
    //
    FsSurfaceSet tSurfSetWhite (subject, hemi, "white", subjectPath);
    for (auto it = tSurfSetWhite.data().constBegin(); it != tSurfSetWhite.data().constEnd(); ++it) {
        QString hemi = (it.value().hemi() == 0) ? "lh" : "rh";
        pModel->addSurface(subject, hemi, "white", it.value());
    }

    pBrainView->show();

    return a.exec();
}

Authors of this file

Christoph Dinh <christoph.dinh@mne-cpp.org>

Public Methods​

FsSurface()​

FsSurface(p_sFile)​

FsSurface(subject_id, hemi, surf, subjects_dir)​

FsSurface(path, hemi, surf)​

~FsSurface()​

clear()​

hemi()​

isEmpty()​

surf()​

rr()​

tris()​

nn()​

curv()​

offset()​

offset()​

filePath()​

fileName()​

Static Methods​

read(subject_id, hemi, surf, subjects_dir, p_Surface, p_bLoadCurvature)​

read(path, hemi, surf, p_Surface, p_bLoadCurvature)​

read(p_sFileName, p_Surface, p_bLoadCurvature)​

read_curv(p_sFileName)​

compute_normals(rr, tris)​

fread3(stream)​

fread3(stream)​

fread3_many(stream, count)​

fread3_many(stream, count)​

Example​

Authors of this file​

Public Methods

FsSurface()

FsSurface(p_sFile)

FsSurface(subject_id, hemi, surf, subjects_dir)

FsSurface(path, hemi, surf)

~FsSurface()

clear()

hemi()

isEmpty()

surf()

rr()

tris()

nn()

curv()

offset()

offset()

filePath()

fileName()

Static Methods

read(subject_id, hemi, surf, subjects_dir, p_Surface, p_bLoadCurvature)

read(path, hemi, surf, p_Surface, p_bLoadCurvature)

read(p_sFileName, p_Surface, p_bLoadCurvature)

read_curv(p_sFileName)

compute_normals(rr, tris)

fread3(stream)

fread3(stream)

fread3_many(stream, count)

fread3_many(stream, count)

Example

Authors of this file