ex_evoked_grad_amp

Compute tangential gradient amplitudes from planar gradiometer data.

Libraries: MNE Core, FIFF I/O, Utilities

Options

Option	Description
`--ave`	Path to the evoked/average <file>.
`--doBaseline`	Do baseline correction.

Build and run

cmake --build build/developer-dynamic --target ex_evoked_grad_amp
./out/Release/examples/ex_evoked_grad_amp --help

The default inputs come from the MNE sample dataset.

Source

src/examples/ex_evoked_grad_amp/main.cpp
//=============================================================================================================
/**
 * SPDX-License-Identifier: BSD-3-Clause
 * Copyright (c) 2012-2026 MNE-CPP Authors
 *
 * @file     main.cpp
 * @author   Gabriel Motta <gabrielbenmotta@gmail.com>;
 *           Christoph Dinh <christoph.dinh@mne-cpp.org>;
 *           Lorenz Esch <lorenz.esch@tu-ilmenau.de>
 * @since    0.1.0
 * @date     July, 2012
 * @brief     Compute tangential gradient amplitudes from planar gradiometer data
 */

//=============================================================================================================
// INCLUDES
//=============================================================================================================

#include <iostream>
#include <vector>
#include <math.h>

#include <utils/generics/mne_logger.h>

#include <fiff/fiff.h>
#include <mne/mne.h>

#include <Eigen/Core>

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

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

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

using namespace FIFFLIB;
using namespace MNELIB;
using namespace UTILSLIB;
using namespace Eigen;

//=============================================================================================================
// 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 a(argc, argv);

    // Command Line Parser
    QCommandLineParser parser;
    parser.setApplicationDescription("Evoked Grad Amp Example");
    parser.addHelpOption();

    QCommandLineOption evokedFileOption("ave", "Path to the evoked/average <file>.", "file", QCoreApplication::applicationDirPath() + "/../resources/data/MNE-sample-data/MEG/sample/sample_audvis-ave.fif");
    QCommandLineOption doBaselineption("doBaseline", "Do baseline correction.", "doBaseline", "false");

    parser.addOption(evokedFileOption);
    parser.addOption(doBaselineption);

    parser.process(a);

    //generate FiffEvokedSet
    QFile t_sampleFile(parser.value(evokedFileOption));
    FiffEvokedSet p_FiffEvokedSet(t_sampleFile);

    //mne_ex_evoked_grad_amp.m example
    fiff_int_t coil1, coil2;
    QString one, two;
    QChar lastone, lasttwo;
    qint32 npair = 0;
    MatrixXi pairs(p_FiffEvokedSet.info.nchan, 2);
    fiff_double_t base1, base2;

    QStringList ch_sel_names;

    //settings
    bool do_baseline = false;
    if (parser.value(doBaselineption) == "false" || parser.value(doBaselineption) == "0") {
        do_baseline = false;
    } else if (parser.value(doBaselineption) == "true" || parser.value(doBaselineption) == "1") {
        do_baseline = true;
    }

    fiff_int_t b1 = 1;
    fiff_int_t b2 = 1;
    fiff_double_t bmin = 0;
    fiff_double_t bmax = 0.231;

    for (qint32 i = 0; i < p_FiffEvokedSet.info.nchan - 1; ++i) {
        //First check the coil types
        coil1 = p_FiffEvokedSet.info.chs.at(i).chpos.coil_type;
        coil2 = p_FiffEvokedSet.info.chs.at(i + 1).chpos.coil_type;
        if (coil1 == coil2 && (coil1 == 2 || coil1 == 3012 || coil1 == 3013)) {
            one = p_FiffEvokedSet.info.ch_names[i];
            two = p_FiffEvokedSet.info.ch_names[i + 1];
            lastone = one.at(one.size() - 1);
            lasttwo = one.at(two.size() - 1);

            //Then the channel names
            if ((one.left(3) == "MEG") && (two.left(3) == "MEG") && (one.left(one.size() - 1) == two.left(two.size() - 1)) && ((one.right(1) == "2" && two.right(1) == "3") || (one.right(1) == "3" && two.right(1) == "2"))) {
                pairs(npair, 0) = (int)i;
                pairs(npair, 1) = i + 1;
                ++npair;
                ++i;
            }
        }
    }

    printf("\nComputing the amplitudes");
    if (do_baseline) {
        printf("(Baseline = %7.1f ... %7.1f ms)',1000*bmin,1000*bmax)", 1000 * bmin, 1000 * bmax);
    }
    printf("...");

    for (qint32 i = 0; i < p_FiffEvokedSet.evoked.size() - 1; ++i) {
        if (b2 > b1) {
            b1 = (p_FiffEvokedSet.info.sfreq * bmin) - p_FiffEvokedSet.evoked[i].first;
            b2 = (p_FiffEvokedSet.info.sfreq * bmax) - p_FiffEvokedSet.evoked[i].last;
            if (b1 < 1)
                b1 = 1;
            if (b2 > p_FiffEvokedSet.evoked[i].data.cols())
                b2 = p_FiffEvokedSet.evoked[i].data.cols();
        } else {
            b1 = 1;
            b2 = 1;
        }

        //go through all pairs
        qint16 p0, p1;
        ArrayXd tmparray;

        for (qint32 p = 0; p < npair; ++p) {
            p0 = pairs(p, 0);
            p1 = pairs(p, 1);

            if (b2 > b1) {
                Matrix<double, 1, Dynamic> tmpbase1;
                Matrix<double, 1, Dynamic> tmpbase2;

                tmpbase1 = p_FiffEvokedSet.evoked[i].data.block(pairs(p, 0), (b2 - b1), 1, p_FiffEvokedSet.evoked[i].data.cols());
                base1 = tmpbase1.sum() / tmpbase1.rows();
                tmpbase2 = p_FiffEvokedSet.evoked[i].data.block(pairs(p, 1), (b2 - b1), 1, p_FiffEvokedSet.evoked[i].data.cols());
                base2 = tmpbase2.sum() / tmpbase2.rows();

                tmparray = ((p_FiffEvokedSet.evoked[i].data.row(p0).array() - base1).square()) + ((p_FiffEvokedSet.evoked[i].data.row(p1).array() - base2).square()).square();
                p_FiffEvokedSet.evoked[i].data.row(p0) = tmparray.matrix();
            } else {
                tmparray = ((p_FiffEvokedSet.evoked[i].data.row(p0).array()).square()) + ((p_FiffEvokedSet.evoked[i].data.row(p1).array()).square());
                p_FiffEvokedSet.evoked[i].data.row(p0) = tmparray.matrix();
            }
        }
        printf(".");
    }
    printf("[done]\n");

    //Compose the selection name list
    for (qint32 i = 0; i < npair; ++i) {
        ch_sel_names.append(p_FiffEvokedSet.info.ch_names.at(i));
    }

    //Omit MEG channels but include others
    for (qint32 p = 0; p < p_FiffEvokedSet.info.nchan; ++p) {
        if ((p_FiffEvokedSet.info.channel_type(p) == "grad") || (p_FiffEvokedSet.info.channel_type(p) == "mag")) {
            ch_sel_names.append(p_FiffEvokedSet.info.ch_names.at(p));
        }
    }

    //Modify the bad channel list
    if (!p_FiffEvokedSet.info.bads.isEmpty()) {
        QString firstOfPair, secondOfPair;

        for (qint32 i = 0; i < npair; ++i) {
            firstOfPair = p_FiffEvokedSet.info.ch_names.at(pairs(i, 0));
            secondOfPair = p_FiffEvokedSet.info.ch_names.at(pairs(i, 1));

            //If one channel of the planar gradiometer is marked bad, add the other to the bad channel list
            if (!p_FiffEvokedSet.info.bads.contains(firstOfPair) && p_FiffEvokedSet.info.bads.contains(secondOfPair))
                p_FiffEvokedSet.info.bads.append(secondOfPair);
            if (p_FiffEvokedSet.info.bads.contains(firstOfPair) && !p_FiffEvokedSet.info.bads.contains(secondOfPair))
                p_FiffEvokedSet.info.bads.append(firstOfPair);
        }
    }

    //Do the picking
    p_FiffEvokedSet.pick_channels(ch_sel_names);

    //Optionally write an output file
    //ToDo: implement MNE root function fiff_write_evoked

    return a.exec();
}

//=============================================================================================================
// STATIC DEFINITIONS
//=============================================================================================================

Options​

Build and run​

Source​

Options

Build and run

Source