Skip to main content

MNEBem

Namespace: MNELIB  ·  Library: MNE Library

Python equivalent

mne.make_bem_model in MNE-Python.

#include <mne/mne_bem.h>

class MNELIB::MNEBem

Boundary element model: aggregates the inner-skull, outer-skull and scalp MNEBemSurface objects of a head conductor model.

Aggregated boundary element model loaded from a -bem.fif file.

Public Methods​

MNEBem()​

Default constructor.

MNEBem(p_MNEBem)​

Copy constructor.

Parameters:

  • p_MNEBem : const MNEBem & MNE BEM.

MNEBem(p_IODevice)​

Default constructor.

~MNEBem()​

Destroys the MNE Bem.

clear()​

Initializes MNE Bem.

isEmpty()​

True if MNE Bem is empty.

Returns:

  • bool — true if MNE Bem is empty.

size()​

Returns the number of stored bem surfaces.

Returns:

  • qint32 — number of stored bem surfaces.

write(p_IODevice)​

MNE Toolbox function mne_write_bem_surfaces_block.

Write the Bem to a FIF file

Parameters:

  • p_IODevice : QIODevice & IO device to write the bem to.

writeToStream(p_pStream)​

MNE Toolbox function mne_write_bem_surfaces_block.

Write the Bem to a FIF stream

Parameters:

  • p_pStream : *FiffStream ** The stream to write to.

operator​

Subscript operator [] to access bem_surface by index.

Parameters:

  • idx : qint32 the surface index (0,1 or 2).

Returns:

operator​

Subscript operator [] to access bem_surface by index.

Parameters:

  • idx : qint32 the surface index (0,1 or 2).

Returns:

operator<<(surf)​

Subscript operator << to add a new bem_surface.

Parameters:

Returns:

operator<<(surf)​

Subscript operator << to add a new bem_surface.

Parameters:

Returns:

warp(sLm, dLm)​

Warp the Bem.

Parameters:

  • sLm : const Eigen::MatrixXf & 3D Landmarks of the source geometry.

  • dLm : const Eigen::MatrixXf & 3D Landmarks of the destination geometry.

transform(trans)​

Transform the Bem.

Parameters:

invtransform(trans)​

Transform the Bem using the inverse.

Parameters:

Static Methods​

readFromStream(p_pStream, add_geom, p_Bem)​

Parameters:

  • p_pStream : FIFFLIB::FiffStream::SPtr & The opened fif file.

  • add_geom : bool Add geometry information to the Bem FsSurface.

Returns:

  • bool — true if succeeded, false otherwise.

Example​

Source: src/examples/ex_read_bem/main.cpp

#include <iostream>

#include <mne/mne.h>

#include <utils/ioutils.h>
#include <utils/generics/mne_logger.h>

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

#include <QtCore/QCoreApplication>
#include <QCommandLineParser>

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

using namespace MNELIB;
using namespace UTILSLIB;

//=============================================================================================================
// 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[])
{
    qInstallMessageHandler(MNELogger::customLogWriter);
    QCoreApplication app(argc, argv);

    // Command Line Parser
    QCommandLineParser parser;
    parser.setApplicationDescription("Read BEM Example");
    parser.addHelpOption();
    QCommandLineOption bemFileInOption("bem", "Path to BEM <file>.", "file", QCoreApplication::applicationDirPath() + "/../resources/data/MNE-sample-data/subjects/sample/bem/sample-head.fif");
    QCommandLineOption bemFileOutOption("bemOut", "Path to BEM <file>, which is to be written.", "file", "./sample-head-test.fif");

//    QCoreApplication::applicationDirPath() + "/../resources/data/MNE-sample-data/subjects/sample/bem/sample-5120-5120-5120-bem.fif"
//    QCoreApplication::applicationDirPath() + "/../resources/data/MNE-sample-data/subjects/sample/bem/sample-all-src.fif"
//    QCoreApplication::applicationDirPath() + "/../resources/data/MNE-sample-data/subjects/sample/bem/sample-5120-bem-sol.fif"
//    QCoreApplication::applicationDirPath() + "/../resources/data/MNE-sample-data/subjects/sample/bem/sample-5120-bem.fif"

    parser.addOption(bemFileInOption);
    parser.addOption(bemFileOutOption);
    parser.process(app);

    // Read the BEM
    QFile t_fileBem(parser.value(bemFileInOption));
    MNEBem t_Bem(t_fileBem);

    if( t_Bem.size() > 0 )
    {
        qDebug() << "Loaded BEM";
        qDebug() << "t_Bem[0].tri_nn:" << t_Bem[0].tri_nn(0,0) << t_Bem[0].tri_nn(0,1) << t_Bem[0].tri_nn(0,2);
        qDebug() << "t_Bem[0].tri_nn:" << t_Bem[0].tri_nn(2,0) << t_Bem[0].tri_nn(2,1) << t_Bem[0].tri_nn(2,2);
        qDebug() << "t_Bem[0].rr:" << t_Bem[0].rr(2,0) << t_Bem[0].rr(2,1) << t_Bem[0].rr(2,2);
    }

    // Write the BEM
    QFile t_fileBemTest(parser.value(bemFileOutOption));
    t_Bem.write(t_fileBemTest);
    t_fileBemTest.close();

    MNEBem t_BemTest (t_fileBemTest) ;

    if( t_BemTest.size() > 0 )
    {
        qDebug() << "Loaded written BEM";
        qDebug() << "t_BemTest[0].tri_nn:" << t_BemTest[0].tri_nn(0,0) << t_BemTest[0].tri_nn(0,1) << t_BemTest[0].tri_nn(0,2);
        qDebug() << "t_BemTest[0].tri_nn:" << t_BemTest[0].tri_nn(2,0) << t_BemTest[0].tri_nn(2,1) << t_BemTest[0].tri_nn(2,2);
        qDebug() << "t_BemTest[0].rr:" << t_BemTest[0].rr(2,0) << t_BemTest[0].rr(2,1) << t_BemTest[0].rr(2,2);
    }

    return app.exec();
}

Authors of this file​