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Hello and thanks to LBerger who made me take into account the row, columns thing. This is the final code:

 #include <iostream>
 #include <stdio.h>
 #include <opencv2/opencv.hpp>
 using namespace cv;
 using namespace std;

 Mat imageGreen;

 static void onMouse(int event, int x, int y, int f, void*){
cout <<(int)imageGreen.at<unsigned char>(y, x) << endl;
 }

 int main(int argc, char** argv) {
Mat inputImage = imread("/home/diego/Humanoids/imageGreen0.png");
imageGreen = Mat::zeros(inputImage.size(), CV_8UC1);

   //Getting the green channel value and putting it into a one channel value.

Vec3b result;

for (int i = 0; i < inputImage.rows ; i++)
{
    for (int j = 0; j < inputImage.cols ; j++)
    {
        result = inputImage.at<cv::Vec3b>(i,j);
        int value = result[1];
        imageGreen.at<uchar>(i, j) = value;
    }
}

cout <<imageGreen.channels()<<endl;

namedWindow( "imageGreen", CV_WINDOW_NORMAL);
imshow("imageGreen", imageGreen);
setMouseCallback("imageGreen", onMouse, 0);
waitKey(0);
return 0;

}