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answered 2017-11-28 13:51:10 -0600

sjhalayka gravatar image

The following code reads the .nii header and then the .nii body. It writes PNG images. Make sure that you mark this answer as correct if you find that it works for you.

#include <fstream>
#include <iostream>
#include <vector>
#include <string>
#include <strstream>
using namespace std;

#include <opencv2/opencv.hpp>
using namespace cv;
#pragma comment(lib, "opencv_world331.lib")

int main(void)
{
    // https://brainder.org/2012/09/23/the-nifti-file-format/
    ifstream infile("example_func.nii", std::ios::binary);

    if (infile.fail())
    {
        cout << "Could not read file example_func.nii" << endl;
        return 0;
    }

    size_t bytes_read = 0;

    cout << "Reading header" << endl;

    int sizeof_header;
    infile.read(reinterpret_cast<char*>(&sizeof_header), sizeof(sizeof_header));
    bytes_read += infile.gcount();

    if (sizeof_header != 348)
    {
        cout << "Invalid header size: should be 348 bytes" << endl;
        return -1;
    }

    char data_type[10];
    infile.read(reinterpret_cast<char*>(&data_type), sizeof(data_type));
    bytes_read += infile.gcount();

    char db_name[18];
    infile.read(reinterpret_cast<char*>(&db_name), sizeof(db_name));
    bytes_read += infile.gcount();

    int extents;
    infile.read(reinterpret_cast<char*>(&extents), sizeof(extents));
    bytes_read += infile.gcount();

    short session_error;
    infile.read(reinterpret_cast<char*>(&session_error), sizeof(session_error));
    bytes_read += infile.gcount();

    char regular;
    infile.read(reinterpret_cast<char*>(&regular), sizeof(regular));
    bytes_read += infile.gcount();

    char dim_info;
    infile.read(reinterpret_cast<char*>(&dim_info), sizeof(dim_info));
    bytes_read += infile.gcount();

    short dim[8];
    infile.read(reinterpret_cast<char*>(&dim), sizeof(dim));
    bytes_read += infile.gcount();

    cout << dim[0] << " dimensions" << endl;
    cout << "Dim 1: " << dim[1] << endl;
    cout << "Dim 2: " << dim[2] << endl;
    cout << "Dim 3: " << dim[3] << endl;
    cout << "Dim 4: " << dim[4] << endl;
    cout << "Dim 5: " << dim[5] << endl;
    cout << "Dim 6: " << dim[6] << endl;
    cout << "Dim 7: " << dim[7] << endl;

    float intent_p1;
    infile.read(reinterpret_cast<char*>(&intent_p1), sizeof(intent_p1));
    bytes_read += infile.gcount();

    float intent_p2;
    infile.read(reinterpret_cast<char*>(&intent_p2), sizeof(intent_p2));
    bytes_read += infile.gcount();

    float intent_p3;
    infile.read(reinterpret_cast<char*>(&intent_p3), sizeof(intent_p3));
    bytes_read += infile.gcount();

    short intent_code;
    infile.read(reinterpret_cast<char*>(&intent_code), sizeof(intent_code));
    bytes_read += infile.gcount();

    short datatype;
    infile.read(reinterpret_cast<char*>(&datatype), sizeof(datatype));
    bytes_read += infile.gcount();

    if (datatype != 16)
    {
        cout << "Data type must be float" << endl;
        return -1;
    }
    else
    {
        cout << "Data type: float" << endl;
    }

    short bitpix;
    infile.read(reinterpret_cast<char*>(&bitpix), sizeof(bitpix));
    bytes_read += infile.gcount();

    if (bitpix != 32)
    {
        cout << "Bits per pixel must be 32-bit" << endl;
        return -1;
    }
    else
    {
        cout << "Bits per pixel: " << bitpix << endl;
    }

    short slice_start;
    infile.read(reinterpret_cast<char*>(&slice_start), sizeof(slice_start));
    bytes_read += infile.gcount();

    float pixdim[8];
    infile.read(reinterpret_cast<char*>(&pixdim), sizeof(pixdim));
    bytes_read += infile.gcount();

    float vox_offset;
    infile.read(reinterpret_cast<char*>(&vox_offset), sizeof(vox_offset));
    bytes_read += infile.gcount();

    float scl_slope;
    infile.read(reinterpret_cast<char*>(&scl_slope), sizeof(scl_slope));
    bytes_read += infile.gcount();

    float scl_inter;
    infile.read(reinterpret_cast<char*>(&scl_inter), sizeof(scl_inter));
    bytes_read += infile.gcount();

    short slice_end;
    infile.read(reinterpret_cast<char*>(&slice_end), sizeof(slice_end));
    bytes_read += infile.gcount();

    char slice_code;
    infile.read(reinterpret_cast<char*>(&slice_code), sizeof(slice_code));
    bytes_read += infile.gcount();

    char xyzt_units;
    infile.read(reinterpret_cast<char*>(&xyzt_units), sizeof(xyzt_units));
    bytes_read += infile.gcount();

    float cal_max;
    infile.read(reinterpret_cast<char*>(&cal_max), sizeof(cal_max));
    bytes_read += infile.gcount();

    float cal_min;
    infile.read(reinterpret_cast<char*>(&cal_min), sizeof(cal_min));
    bytes_read += infile.gcount();

    float slice_duration;
    infile.read(reinterpret_cast<char*>(&slice_duration), sizeof(slice_duration));
    bytes_read += infile.gcount();

    float toffset;
    infile.read(reinterpret_cast<char*>(&toffset), sizeof(toffset));
    bytes_read += infile.gcount();

    int glmax;
    infile.read(reinterpret_cast<char*>(&glmax), sizeof(glmax));
    bytes_read += infile.gcount();

    int glmin;
    infile.read(reinterpret_cast<char*>(&glmin), sizeof(glmin));
    bytes_read += infile.gcount();

    char descrip[80];
    infile.read(reinterpret_cast<char*>(&descrip), sizeof(descrip));
    bytes_read += infile.gcount();

    char aux_file[24];
    infile.read(reinterpret_cast<char*>(&aux_file), sizeof(aux_file));
    bytes_read += infile.gcount();

    short qform_code;
    infile.read(reinterpret_cast<char*>(&qform_code), sizeof(qform_code));
    bytes_read += infile.gcount();

    short sform_code;
    infile.read(reinterpret_cast<char*>(&sform_code), sizeof(sform_code));
    bytes_read += infile.gcount();

    float quatern_b;
    infile.read(reinterpret_cast<char*>(&quatern_b), sizeof(quatern_b));
    bytes_read += infile.gcount();

    float quatern_c;
    infile.read(reinterpret_cast<char*>(&quatern_c), sizeof(quatern_c));
    bytes_read += infile.gcount();

    float quatern_d;
    infile.read(reinterpret_cast<char*>(&quatern_d), sizeof(quatern_d));
    bytes_read += infile.gcount();

    float qoffset_x;
    infile.read(reinterpret_cast<char*>(&qoffset_x), sizeof(qoffset_x));
    bytes_read += infile.gcount();

    float qoffset_y;
    infile.read(reinterpret_cast<char*>(&qoffset_y), sizeof(qoffset_y));
    bytes_read += infile.gcount();

    float qoffset_z;
    infile.read(reinterpret_cast<char*>(&qoffset_z), sizeof(qoffset_z));
    bytes_read += infile.gcount();

    float srow_x[4];
    infile.read(reinterpret_cast<char*>(&srow_x), sizeof(srow_x));
    bytes_read += infile.gcount();

    float srow_y[4];
    infile.read(reinterpret_cast<char*>(&srow_y), sizeof(srow_y));
    bytes_read += infile.gcount();

    float srow_z[4];
    infile.read(reinterpret_cast<char*>(&srow_z), sizeof(srow_z));
    bytes_read += infile.gcount();

    char intent_name[16];
    infile.read(reinterpret_cast<char*>(&intent_name), sizeof(intent_name));
    bytes_read += infile.gcount();

    char magic[4];
    infile.read(reinterpret_cast<char*>(&magic), sizeof(magic));
    bytes_read += infile.gcount();

    cout << "Read " << bytes_read << " bytes" << endl;

    if (bytes_read != 348)
    {
        cout << "Error reading header" << endl;
        return -1;
    }

    long unsigned int num_voxels = dim[1] * dim[2] * dim[3] * dim[4] * dim[5] * dim[6] * dim[7];
    cout << "Reading " << num_voxels << " voxels" << endl;

    vector<float> data(num_voxels, 0);
    infile.read(reinterpret_cast<char*>(&data[0]), sizeof(float)*num_voxels);
    bytes_read = infile.gcount();

    if (bytes_read != sizeof(float)*num_voxels)
    {
        cout << "Error reading file" << endl;
        return -1;
    }

    for (int i = 0; i < dim[7]; i++)
    {
        for (int j = 0; j < dim[6]; j++)
        {
            for (int k = 0; k < dim[5]; k++)
            {
                for (int l = 0; l < dim[4]; l++)
                {
                    for (int m = 0; m < dim[3]; m++)
                    {
                        string file_name = "output_";
                        ostringstream oss;
                        oss << i << "_" << j << "_" << k << "_" << l << "_" << m;
                        file_name += oss.str();
                        file_name += ".png";

                        cv::Mat img = Mat::zeros(Size(dim[1], dim[2]), CV_8UC3);

                        for (int n = 0; n < dim[2]; n++)
                        {
                            for (int o = 0; o < dim[1]; o++)
                            {
                                size_t index = i*dim[6] * dim[5] * dim[4] * dim[3] * dim[2] * dim[1];
                                      index += j*dim[5] * dim[4] * dim[3] * dim[2] * dim[1];
                                      index += k*dim[4] * dim[3] * dim[2] * dim[1];
                                      index += l*dim[3] * dim[2] * dim[1];
                                      index += m*dim[2] * dim[1];
                                      index += n*dim[1];
                                      index += o;

                                float f = data[index];

                                img.at<Vec3b>(n, o)[0] = static_cast<unsigned char>(f/255.0f);
                                img.at<Vec3b>(n, o)[1] = static_cast<unsigned char>(f/255.0f);
                                img.at<Vec3b>(n, o)[2] = static_cast<unsigned char>(f/255.0f);
                            }
                        }

                        cout << "Writing " << dim[1] << "x" << dim[2] << " file " << file_name.c_str() << endl;
                        imwrite(file_name.c_str(), img);
                    }
                }
            }
        }
    }

    return 0;
}

The following code reads the .nii header and then the .nii body. It writes PNG images. Make sure that you mark this answer as correct if you find that it works for you.

#include <fstream>
#include <iostream>
#include <vector>
#include <string>
#include <strstream>
using namespace std;

#include <opencv2/opencv.hpp>
using namespace cv;
#pragma comment(lib, "opencv_world331.lib")

int main(void)
{
    // https://brainder.org/2012/09/23/the-nifti-file-format/
    ifstream infile("example_func.nii", std::ios::binary);

    if (infile.fail())
    {
        cout << "Could not read file example_func.nii" << endl;
        return 0;
    }

    size_t bytes_read = 0;

    cout << "Reading header" << endl;

    int sizeof_header;
    infile.read(reinterpret_cast<char*>(&sizeof_header), sizeof(sizeof_header));
    bytes_read += infile.gcount();

    if (sizeof_header != 348)
    {
        cout << "Invalid header size: should be 348 bytes" << endl;
        return -1;
    }

    char data_type[10];
    infile.read(reinterpret_cast<char*>(&data_type), sizeof(data_type));
    bytes_read += infile.gcount();

    char db_name[18];
    infile.read(reinterpret_cast<char*>(&db_name), sizeof(db_name));
    bytes_read += infile.gcount();

    int extents;
    infile.read(reinterpret_cast<char*>(&extents), sizeof(extents));
    bytes_read += infile.gcount();

    short session_error;
    infile.read(reinterpret_cast<char*>(&session_error), sizeof(session_error));
    bytes_read += infile.gcount();

    char regular;
    infile.read(reinterpret_cast<char*>(&regular), sizeof(regular));
    bytes_read += infile.gcount();

    char dim_info;
    infile.read(reinterpret_cast<char*>(&dim_info), sizeof(dim_info));
    bytes_read += infile.gcount();

    short dim[8];
    infile.read(reinterpret_cast<char*>(&dim), sizeof(dim));
    bytes_read += infile.gcount();

    cout << dim[0] << " dimensions" << endl;
    cout << "Dim 1: " << dim[1] << endl;
    cout << "Dim 2: " << dim[2] << endl;
    cout << "Dim 3: " << dim[3] << endl;
    cout << "Dim 4: " << dim[4] << endl;
    cout << "Dim 5: " << dim[5] << endl;
    cout << "Dim 6: " << dim[6] << endl;
    cout << "Dim 7: " << dim[7] << endl;

    float intent_p1;
    infile.read(reinterpret_cast<char*>(&intent_p1), sizeof(intent_p1));
    bytes_read += infile.gcount();

    float intent_p2;
    infile.read(reinterpret_cast<char*>(&intent_p2), sizeof(intent_p2));
    bytes_read += infile.gcount();

    float intent_p3;
    infile.read(reinterpret_cast<char*>(&intent_p3), sizeof(intent_p3));
    bytes_read += infile.gcount();

    short intent_code;
    infile.read(reinterpret_cast<char*>(&intent_code), sizeof(intent_code));
    bytes_read += infile.gcount();

    short datatype;
    infile.read(reinterpret_cast<char*>(&datatype), sizeof(datatype));
    bytes_read += infile.gcount();

    if (datatype != 16)
    {
        cout << "Data type must be float" << endl;
        return -1;
    }
    else
    {
        cout << "Data type: float" << endl;
    }

    short bitpix;
    infile.read(reinterpret_cast<char*>(&bitpix), sizeof(bitpix));
    bytes_read += infile.gcount();

    if (bitpix != 32)
    {
        cout << "Bits per pixel must be 32-bit" << endl;
        return -1;
    }
    else
    {
        cout << "Bits per pixel: " << bitpix << endl;
    }

    short slice_start;
    infile.read(reinterpret_cast<char*>(&slice_start), sizeof(slice_start));
    bytes_read += infile.gcount();

    float pixdim[8];
    infile.read(reinterpret_cast<char*>(&pixdim), sizeof(pixdim));
    bytes_read += infile.gcount();

    float vox_offset;
    infile.read(reinterpret_cast<char*>(&vox_offset), sizeof(vox_offset));
    bytes_read += infile.gcount();

    float scl_slope;
    infile.read(reinterpret_cast<char*>(&scl_slope), sizeof(scl_slope));
    bytes_read += infile.gcount();

    float scl_inter;
    infile.read(reinterpret_cast<char*>(&scl_inter), sizeof(scl_inter));
    bytes_read += infile.gcount();

    short slice_end;
    infile.read(reinterpret_cast<char*>(&slice_end), sizeof(slice_end));
    bytes_read += infile.gcount();

    char slice_code;
    infile.read(reinterpret_cast<char*>(&slice_code), sizeof(slice_code));
    bytes_read += infile.gcount();

    char xyzt_units;
    infile.read(reinterpret_cast<char*>(&xyzt_units), sizeof(xyzt_units));
    bytes_read += infile.gcount();

    float cal_max;
    infile.read(reinterpret_cast<char*>(&cal_max), sizeof(cal_max));
    bytes_read += infile.gcount();

    float cal_min;
    infile.read(reinterpret_cast<char*>(&cal_min), sizeof(cal_min));
    bytes_read += infile.gcount();

    float slice_duration;
    infile.read(reinterpret_cast<char*>(&slice_duration), sizeof(slice_duration));
    bytes_read += infile.gcount();

    float toffset;
    infile.read(reinterpret_cast<char*>(&toffset), sizeof(toffset));
    bytes_read += infile.gcount();

    int glmax;
    infile.read(reinterpret_cast<char*>(&glmax), sizeof(glmax));
    bytes_read += infile.gcount();

    int glmin;
    infile.read(reinterpret_cast<char*>(&glmin), sizeof(glmin));
    bytes_read += infile.gcount();

    char descrip[80];
    infile.read(reinterpret_cast<char*>(&descrip), sizeof(descrip));
    bytes_read += infile.gcount();

    char aux_file[24];
    infile.read(reinterpret_cast<char*>(&aux_file), sizeof(aux_file));
    bytes_read += infile.gcount();

    short qform_code;
    infile.read(reinterpret_cast<char*>(&qform_code), sizeof(qform_code));
    bytes_read += infile.gcount();

    short sform_code;
    infile.read(reinterpret_cast<char*>(&sform_code), sizeof(sform_code));
    bytes_read += infile.gcount();

    float quatern_b;
    infile.read(reinterpret_cast<char*>(&quatern_b), sizeof(quatern_b));
    bytes_read += infile.gcount();

    float quatern_c;
    infile.read(reinterpret_cast<char*>(&quatern_c), sizeof(quatern_c));
    bytes_read += infile.gcount();

    float quatern_d;
    infile.read(reinterpret_cast<char*>(&quatern_d), sizeof(quatern_d));
    bytes_read += infile.gcount();

    float qoffset_x;
    infile.read(reinterpret_cast<char*>(&qoffset_x), sizeof(qoffset_x));
    bytes_read += infile.gcount();

    float qoffset_y;
    infile.read(reinterpret_cast<char*>(&qoffset_y), sizeof(qoffset_y));
    bytes_read += infile.gcount();

    float qoffset_z;
    infile.read(reinterpret_cast<char*>(&qoffset_z), sizeof(qoffset_z));
    bytes_read += infile.gcount();

    float srow_x[4];
    infile.read(reinterpret_cast<char*>(&srow_x), sizeof(srow_x));
    bytes_read += infile.gcount();

    float srow_y[4];
    infile.read(reinterpret_cast<char*>(&srow_y), sizeof(srow_y));
    bytes_read += infile.gcount();

    float srow_z[4];
    infile.read(reinterpret_cast<char*>(&srow_z), sizeof(srow_z));
    bytes_read += infile.gcount();

    char intent_name[16];
    infile.read(reinterpret_cast<char*>(&intent_name), sizeof(intent_name));
    bytes_read += infile.gcount();

    char magic[4];
    infile.read(reinterpret_cast<char*>(&magic), sizeof(magic));
    bytes_read += infile.gcount();

    cout << "Read " << bytes_read << " bytes" << endl;

    if (bytes_read != 348)
    {
        cout << "Error reading header" << endl;
        return -1;
    }

    long unsigned int num_voxels = dim[1] * dim[2] * dim[3] * dim[4] * dim[5] * dim[6] * dim[7];
    cout << "Reading " << num_voxels << " voxels" << endl;

    vector<float> data(num_voxels, 0);
    infile.read(reinterpret_cast<char*>(&data[0]), sizeof(float)*num_voxels);
    bytes_read = infile.gcount();

    if (bytes_read != sizeof(float)*num_voxels)
    {
        cout << "Error reading file" << endl;
        return -1;
    }

    for (int i = 0; i < dim[7]; i++)
    {
        for (int j = 0; j < dim[6]; j++)
        {
            for (int k = 0; k < dim[5]; k++)
            {
                for (int l = 0; l < dim[4]; l++)
                {
                    for (int m = 0; m < dim[3]; m++)
                    {
                        string file_name = "output_";
                        ostringstream oss;
                        oss << i << "_" << j << "_" << k << "_" << l << "_" << m;
                        file_name += oss.str();
                        file_name += ".png";

                        cv::Mat img = Mat::zeros(Size(dim[1], dim[2]), CV_8UC3);

                        for (int n = 0; n < dim[2]; n++)
                        {
                            for (int o = 0; o < dim[1]; o++)
                            {
                                size_t index = i*dim[6] * dim[5] * dim[4] * dim[3] * dim[2] * dim[1];
                                      index += j*dim[5] * dim[4] * dim[3] * dim[2] * dim[1];
                                      index += k*dim[4] * dim[3] * dim[2] * dim[1];
                                      index += l*dim[3] * dim[2] * dim[1];
                                      index += m*dim[2] * dim[1];
                                      index += n*dim[1];
                                      index += o;

                                float f = data[index];

                                img.at<Vec3b>(n, o)[0] = static_cast<unsigned char>(f/255.0f);
char>(f/cal_max *255.0f);
                                img.at<Vec3b>(n, o)[1] = static_cast<unsigned char>(f/255.0f);
char>(f/cal_max*255.0f);
                                img.at<Vec3b>(n, o)[2] = static_cast<unsigned char>(f/255.0f);
char>(f/cal_max*255.0f);
                            }
                        }

                        cout << "Writing " << dim[1] << "x" << dim[2] << " file " << file_name.c_str() << endl;
                        imwrite(file_name.c_str(), img);
                    }
                }
            }
        }
    }

    return 0;
}

The following code reads the .nii header and then the .nii body. It writes PNG images. Make sure that you mark this answer as correct if you find that it works for you.

#include <fstream>
#include <iostream>
#include <vector>
#include <string>
#include <strstream>
using namespace std;

#include <opencv2/opencv.hpp>
using namespace cv;
#pragma comment(lib, "opencv_world331.lib")

int main(void)
{
    // https://brainder.org/2012/09/23/the-nifti-file-format/
    ifstream infile("example_func.nii", std::ios::binary);

    if (infile.fail())
    {
        cout << "Could not read file example_func.nii" << endl;
        return 0;
    }

    size_t bytes_read = 0;

    cout << "Reading header" << endl;

    int sizeof_header;
    infile.read(reinterpret_cast<char*>(&sizeof_header), sizeof(sizeof_header));
    bytes_read += infile.gcount();

    if (sizeof_header != 348)
    {
        cout << "Invalid header size: should be 348 bytes" << endl;
        return -1;
    }

    char data_type[10];
    infile.read(reinterpret_cast<char*>(&data_type), sizeof(data_type));
    bytes_read += infile.gcount();

    char db_name[18];
    infile.read(reinterpret_cast<char*>(&db_name), sizeof(db_name));
    bytes_read += infile.gcount();

    int extents;
    infile.read(reinterpret_cast<char*>(&extents), sizeof(extents));
    bytes_read += infile.gcount();

    short session_error;
    infile.read(reinterpret_cast<char*>(&session_error), sizeof(session_error));
    bytes_read += infile.gcount();

    char regular;
    infile.read(reinterpret_cast<char*>(&regular), sizeof(regular));
    bytes_read += infile.gcount();

    char dim_info;
    infile.read(reinterpret_cast<char*>(&dim_info), sizeof(dim_info));
    bytes_read += infile.gcount();

    short dim[8];
    infile.read(reinterpret_cast<char*>(&dim), sizeof(dim));
    bytes_read += infile.gcount();

    cout << dim[0] << " dimensions" << endl;
    cout << "Dim 1: " << dim[1] << endl;
    cout << "Dim 2: " << dim[2] << endl;
    cout << "Dim 3: " << dim[3] << endl;
    cout << "Dim 4: " << dim[4] << endl;
    cout << "Dim 5: " << dim[5] << endl;
    cout << "Dim 6: " << dim[6] << endl;
    cout << "Dim 7: " << dim[7] << endl;

    float intent_p1;
    infile.read(reinterpret_cast<char*>(&intent_p1), sizeof(intent_p1));
    bytes_read += infile.gcount();

    float intent_p2;
    infile.read(reinterpret_cast<char*>(&intent_p2), sizeof(intent_p2));
    bytes_read += infile.gcount();

    float intent_p3;
    infile.read(reinterpret_cast<char*>(&intent_p3), sizeof(intent_p3));
    bytes_read += infile.gcount();

    short intent_code;
    infile.read(reinterpret_cast<char*>(&intent_code), sizeof(intent_code));
    bytes_read += infile.gcount();

    short datatype;
    infile.read(reinterpret_cast<char*>(&datatype), sizeof(datatype));
    bytes_read += infile.gcount();

    if (datatype != 16)
    {
        cout << "Data type must be float" << endl;
        return -1;
    }
    else
    {
        cout << "Data type: float" << endl;
    }

    short bitpix;
    infile.read(reinterpret_cast<char*>(&bitpix), sizeof(bitpix));
    bytes_read += infile.gcount();

    if (bitpix != 32)
    {
        cout << "Bits per pixel must be 32-bit" << endl;
        return -1;
    }
    else
    {
        cout << "Bits per pixel: " << bitpix << endl;
    }

    short slice_start;
    infile.read(reinterpret_cast<char*>(&slice_start), sizeof(slice_start));
    bytes_read += infile.gcount();

    float pixdim[8];
    infile.read(reinterpret_cast<char*>(&pixdim), sizeof(pixdim));
    bytes_read += infile.gcount();

    float vox_offset;
    infile.read(reinterpret_cast<char*>(&vox_offset), sizeof(vox_offset));
    bytes_read += infile.gcount();

    float scl_slope;
    infile.read(reinterpret_cast<char*>(&scl_slope), sizeof(scl_slope));
    bytes_read += infile.gcount();

    float scl_inter;
    infile.read(reinterpret_cast<char*>(&scl_inter), sizeof(scl_inter));
    bytes_read += infile.gcount();

    short slice_end;
    infile.read(reinterpret_cast<char*>(&slice_end), sizeof(slice_end));
    bytes_read += infile.gcount();

    char slice_code;
    infile.read(reinterpret_cast<char*>(&slice_code), sizeof(slice_code));
    bytes_read += infile.gcount();

    char xyzt_units;
    infile.read(reinterpret_cast<char*>(&xyzt_units), sizeof(xyzt_units));
    bytes_read += infile.gcount();

    float cal_max;
    infile.read(reinterpret_cast<char*>(&cal_max), sizeof(cal_max));
    bytes_read += infile.gcount();

    float cal_min;
    infile.read(reinterpret_cast<char*>(&cal_min), sizeof(cal_min));
    bytes_read += infile.gcount();

    float slice_duration;
    infile.read(reinterpret_cast<char*>(&slice_duration), sizeof(slice_duration));
    bytes_read += infile.gcount();

    float toffset;
    infile.read(reinterpret_cast<char*>(&toffset), sizeof(toffset));
    bytes_read += infile.gcount();

    int glmax;
    infile.read(reinterpret_cast<char*>(&glmax), sizeof(glmax));
    bytes_read += infile.gcount();

    int glmin;
    infile.read(reinterpret_cast<char*>(&glmin), sizeof(glmin));
    bytes_read += infile.gcount();

    char descrip[80];
    infile.read(reinterpret_cast<char*>(&descrip), sizeof(descrip));
    bytes_read += infile.gcount();

    char aux_file[24];
    infile.read(reinterpret_cast<char*>(&aux_file), sizeof(aux_file));
    bytes_read += infile.gcount();

    short qform_code;
    infile.read(reinterpret_cast<char*>(&qform_code), sizeof(qform_code));
    bytes_read += infile.gcount();

    short sform_code;
    infile.read(reinterpret_cast<char*>(&sform_code), sizeof(sform_code));
    bytes_read += infile.gcount();

    float quatern_b;
    infile.read(reinterpret_cast<char*>(&quatern_b), sizeof(quatern_b));
    bytes_read += infile.gcount();

    float quatern_c;
    infile.read(reinterpret_cast<char*>(&quatern_c), sizeof(quatern_c));
    bytes_read += infile.gcount();

    float quatern_d;
    infile.read(reinterpret_cast<char*>(&quatern_d), sizeof(quatern_d));
    bytes_read += infile.gcount();

    float qoffset_x;
    infile.read(reinterpret_cast<char*>(&qoffset_x), sizeof(qoffset_x));
    bytes_read += infile.gcount();

    float qoffset_y;
    infile.read(reinterpret_cast<char*>(&qoffset_y), sizeof(qoffset_y));
    bytes_read += infile.gcount();

    float qoffset_z;
    infile.read(reinterpret_cast<char*>(&qoffset_z), sizeof(qoffset_z));
    bytes_read += infile.gcount();

    float srow_x[4];
    infile.read(reinterpret_cast<char*>(&srow_x), sizeof(srow_x));
    bytes_read += infile.gcount();

    float srow_y[4];
    infile.read(reinterpret_cast<char*>(&srow_y), sizeof(srow_y));
    bytes_read += infile.gcount();

    float srow_z[4];
    infile.read(reinterpret_cast<char*>(&srow_z), sizeof(srow_z));
    bytes_read += infile.gcount();

    char intent_name[16];
    infile.read(reinterpret_cast<char*>(&intent_name), sizeof(intent_name));
    bytes_read += infile.gcount();

    char magic[4];
    infile.read(reinterpret_cast<char*>(&magic), sizeof(magic));
    bytes_read += infile.gcount();

    cout << "Read " << bytes_read << " bytes" << endl;

    if (bytes_read != 348)
    {
        cout << "Error reading header" << endl;
        return -1;
    }

    long unsigned int num_voxels = dim[1] * dim[2] * dim[3] * dim[4] * dim[5] * dim[6] * dim[7];
    cout << "Reading " << num_voxels << " voxels" << endl;

    vector<float> data(num_voxels, 0);
    infile.read(reinterpret_cast<char*>(&data[0]), sizeof(float)*num_voxels);
    bytes_read = infile.gcount();

    if (bytes_read != sizeof(float)*num_voxels)
    {
        cout << "Error reading file" << endl;
        return -1;
    }

    for (int i = 0; i < dim[7]; i++)
    {
        for (int j = 0; j < dim[6]; j++)
        {
            for (int k = 0; k < dim[5]; k++)
            {
                for (int l = 0; l < dim[4]; l++)
                {
                    for (int m = 0; m < dim[3]; m++)
                    {
                        string file_name = "output_";
                        ostringstream oss;
                        oss << i << "_" << j << "_" << k << "_" << l << "_" << m;
                        file_name += oss.str();
                        file_name += ".png";

                        cv::Mat Mat img = Mat::zeros(Size(dim[1], dim[2]), CV_8UC3);

                        for (int n = 0; n < dim[2]; n++)
                        {
                            for (int o = 0; o < dim[1]; o++)
                            {
                                size_t index = i*dim[6] * dim[5] * dim[4] * dim[3] * dim[2] * dim[1];
                                      index += j*dim[5] * dim[4] * dim[3] * dim[2] * dim[1];
                                      index += k*dim[4] * dim[3] * dim[2] * dim[1];
                                      index += l*dim[3] * dim[2] * dim[1];
                                      index += m*dim[2] * dim[1];
                                      index += n*dim[1];
                                      index += o;

                                float f = data[index];

                                img.at<Vec3b>(n, o)[0] = static_cast<unsigned char>(f/cal_max *255.0f);
                                img.at<Vec3b>(n, o)[1] = static_cast<unsigned char>(f/cal_max*255.0f);
                                img.at<Vec3b>(n, o)[2] = static_cast<unsigned char>(f/cal_max*255.0f);
                            }
                        }

                        cout << "Writing " << dim[1] << "x" << dim[2] << " file " << file_name.c_str() << endl;
                        imwrite(file_name.c_str(), img);
                    }
                }
            }
        }
    }

    return 0;
}

The following code reads the .nii header and then the .nii body. It writes PNG images. Make sure that you mark this answer as correct if you find that it works for you.you. It handles input files of dimensions up to 7.

#include <fstream>
#include <iostream>
#include <vector>
#include <string>
#include <strstream>
using namespace std;

#include <opencv2/opencv.hpp>
using namespace cv;
#pragma comment(lib, "opencv_world331.lib")

int main(void)
{
    // https://brainder.org/2012/09/23/the-nifti-file-format/
    ifstream infile("example_func.nii", std::ios::binary);

    if (infile.fail())
    {
        cout << "Could not read file example_func.nii" << endl;
        return 0;
    }

    size_t bytes_read = 0;

    cout << "Reading header" << endl;

    int sizeof_header;
    infile.read(reinterpret_cast<char*>(&sizeof_header), sizeof(sizeof_header));
    bytes_read += infile.gcount();

    if (sizeof_header != 348)
    {
        cout << "Invalid header size: should be 348 bytes" << endl;
        return -1;
    }

    char data_type[10];
    infile.read(reinterpret_cast<char*>(&data_type), sizeof(data_type));
    bytes_read += infile.gcount();

    char db_name[18];
    infile.read(reinterpret_cast<char*>(&db_name), sizeof(db_name));
    bytes_read += infile.gcount();

    int extents;
    infile.read(reinterpret_cast<char*>(&extents), sizeof(extents));
    bytes_read += infile.gcount();

    short session_error;
    infile.read(reinterpret_cast<char*>(&session_error), sizeof(session_error));
    bytes_read += infile.gcount();

    char regular;
    infile.read(reinterpret_cast<char*>(&regular), sizeof(regular));
    bytes_read += infile.gcount();

    char dim_info;
    infile.read(reinterpret_cast<char*>(&dim_info), sizeof(dim_info));
    bytes_read += infile.gcount();

    short dim[8];
    infile.read(reinterpret_cast<char*>(&dim), sizeof(dim));
    bytes_read += infile.gcount();

    cout << dim[0] << " dimensions" << endl;
    cout << "Dim 1: " << dim[1] << endl;
    cout << "Dim 2: " << dim[2] << endl;
    cout << "Dim 3: " << dim[3] << endl;
    cout << "Dim 4: " << dim[4] << endl;
    cout << "Dim 5: " << dim[5] << endl;
    cout << "Dim 6: " << dim[6] << endl;
    cout << "Dim 7: " << dim[7] << endl;

    float intent_p1;
    infile.read(reinterpret_cast<char*>(&intent_p1), sizeof(intent_p1));
    bytes_read += infile.gcount();

    float intent_p2;
    infile.read(reinterpret_cast<char*>(&intent_p2), sizeof(intent_p2));
    bytes_read += infile.gcount();

    float intent_p3;
    infile.read(reinterpret_cast<char*>(&intent_p3), sizeof(intent_p3));
    bytes_read += infile.gcount();

    short intent_code;
    infile.read(reinterpret_cast<char*>(&intent_code), sizeof(intent_code));
    bytes_read += infile.gcount();

    short datatype;
    infile.read(reinterpret_cast<char*>(&datatype), sizeof(datatype));
    bytes_read += infile.gcount();

    if (datatype != 16)
    {
        cout << "Data type must be float" << endl;
        return -1;
    }
    else
    {
        cout << "Data type: float" << endl;
    }

    short bitpix;
    infile.read(reinterpret_cast<char*>(&bitpix), sizeof(bitpix));
    bytes_read += infile.gcount();

    if (bitpix != 32)
    {
        cout << "Bits per pixel must be 32-bit" << endl;
        return -1;
    }
    else
    {
        cout << "Bits per pixel: " << bitpix << endl;
    }

    short slice_start;
    infile.read(reinterpret_cast<char*>(&slice_start), sizeof(slice_start));
    bytes_read += infile.gcount();

    float pixdim[8];
    infile.read(reinterpret_cast<char*>(&pixdim), sizeof(pixdim));
    bytes_read += infile.gcount();

    float vox_offset;
    infile.read(reinterpret_cast<char*>(&vox_offset), sizeof(vox_offset));
    bytes_read += infile.gcount();

    float scl_slope;
    infile.read(reinterpret_cast<char*>(&scl_slope), sizeof(scl_slope));
    bytes_read += infile.gcount();

    float scl_inter;
    infile.read(reinterpret_cast<char*>(&scl_inter), sizeof(scl_inter));
    bytes_read += infile.gcount();

    short slice_end;
    infile.read(reinterpret_cast<char*>(&slice_end), sizeof(slice_end));
    bytes_read += infile.gcount();

    char slice_code;
    infile.read(reinterpret_cast<char*>(&slice_code), sizeof(slice_code));
    bytes_read += infile.gcount();

    char xyzt_units;
    infile.read(reinterpret_cast<char*>(&xyzt_units), sizeof(xyzt_units));
    bytes_read += infile.gcount();

    float cal_max;
    infile.read(reinterpret_cast<char*>(&cal_max), sizeof(cal_max));
    bytes_read += infile.gcount();

    float cal_min;
    infile.read(reinterpret_cast<char*>(&cal_min), sizeof(cal_min));
    bytes_read += infile.gcount();

    float slice_duration;
    infile.read(reinterpret_cast<char*>(&slice_duration), sizeof(slice_duration));
    bytes_read += infile.gcount();

    float toffset;
    infile.read(reinterpret_cast<char*>(&toffset), sizeof(toffset));
    bytes_read += infile.gcount();

    int glmax;
    infile.read(reinterpret_cast<char*>(&glmax), sizeof(glmax));
    bytes_read += infile.gcount();

    int glmin;
    infile.read(reinterpret_cast<char*>(&glmin), sizeof(glmin));
    bytes_read += infile.gcount();

    char descrip[80];
    infile.read(reinterpret_cast<char*>(&descrip), sizeof(descrip));
    bytes_read += infile.gcount();

    char aux_file[24];
    infile.read(reinterpret_cast<char*>(&aux_file), sizeof(aux_file));
    bytes_read += infile.gcount();

    short qform_code;
    infile.read(reinterpret_cast<char*>(&qform_code), sizeof(qform_code));
    bytes_read += infile.gcount();

    short sform_code;
    infile.read(reinterpret_cast<char*>(&sform_code), sizeof(sform_code));
    bytes_read += infile.gcount();

    float quatern_b;
    infile.read(reinterpret_cast<char*>(&quatern_b), sizeof(quatern_b));
    bytes_read += infile.gcount();

    float quatern_c;
    infile.read(reinterpret_cast<char*>(&quatern_c), sizeof(quatern_c));
    bytes_read += infile.gcount();

    float quatern_d;
    infile.read(reinterpret_cast<char*>(&quatern_d), sizeof(quatern_d));
    bytes_read += infile.gcount();

    float qoffset_x;
    infile.read(reinterpret_cast<char*>(&qoffset_x), sizeof(qoffset_x));
    bytes_read += infile.gcount();

    float qoffset_y;
    infile.read(reinterpret_cast<char*>(&qoffset_y), sizeof(qoffset_y));
    bytes_read += infile.gcount();

    float qoffset_z;
    infile.read(reinterpret_cast<char*>(&qoffset_z), sizeof(qoffset_z));
    bytes_read += infile.gcount();

    float srow_x[4];
    infile.read(reinterpret_cast<char*>(&srow_x), sizeof(srow_x));
    bytes_read += infile.gcount();

    float srow_y[4];
    infile.read(reinterpret_cast<char*>(&srow_y), sizeof(srow_y));
    bytes_read += infile.gcount();

    float srow_z[4];
    infile.read(reinterpret_cast<char*>(&srow_z), sizeof(srow_z));
    bytes_read += infile.gcount();

    char intent_name[16];
    infile.read(reinterpret_cast<char*>(&intent_name), sizeof(intent_name));
    bytes_read += infile.gcount();

    char magic[4];
    infile.read(reinterpret_cast<char*>(&magic), sizeof(magic));
    bytes_read += infile.gcount();

    cout << "Read " << bytes_read << " bytes" << endl;

    if (bytes_read != 348)
    {
        cout << "Error reading header" << endl;
        return -1;
    }

    long unsigned int num_voxels = dim[1] * dim[2] * dim[3] * dim[4] * dim[5] * dim[6] * dim[7];
    cout << "Reading " << num_voxels << " voxels" << endl;

    vector<float> data(num_voxels, 0);
    infile.read(reinterpret_cast<char*>(&data[0]), sizeof(float)*num_voxels);
    bytes_read = infile.gcount();

    if (bytes_read != sizeof(float)*num_voxels)
    {
        cout << "Error reading file" << endl;
        return -1;
    }

    for (int i = 0; i < dim[7]; i++)
    {
        for (int j = 0; j < dim[6]; j++)
        {
            for (int k = 0; k < dim[5]; k++)
            {
                for (int l = 0; l < dim[4]; l++)
                {
                    for (int m = 0; m < dim[3]; m++)
                    {
                        string file_name = "output_";
                        ostringstream oss;
                        oss << i << "_" << j << "_" << k << "_" << l << "_" << m;
                        file_name += oss.str();
                        file_name += ".png";

                        Mat img = Mat::zeros(Size(dim[1], dim[2]), CV_8UC3);

                        for (int n = 0; n < dim[2]; n++)
                        {
                            for (int o = 0; o < dim[1]; o++)
                            {
                                size_t index = i*dim[6] * dim[5] * dim[4] * dim[3] * dim[2] * dim[1];
                                      index += j*dim[5] * dim[4] * dim[3] * dim[2] * dim[1];
                                      index += k*dim[4] * dim[3] * dim[2] * dim[1];
                                      index += l*dim[3] * dim[2] * dim[1];
                                      index += m*dim[2] * dim[1];
                                      index += n*dim[1];
                                      index += o;

                                float f = data[index];

                                img.at<Vec3b>(n, o)[0] = static_cast<unsigned char>(f/cal_max *255.0f);
                                img.at<Vec3b>(n, o)[1] = static_cast<unsigned char>(f/cal_max*255.0f);
                                img.at<Vec3b>(n, o)[2] = static_cast<unsigned char>(f/cal_max*255.0f);
                            }
                        }

                        cout << "Writing " << dim[1] << "x" << dim[2] << " file " << file_name.c_str() << endl;
                        imwrite(file_name.c_str(), img);
                    }
                }
            }
        }
    }

    return 0;
}
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