How do I get the lowest value of all the non zero value pixels?

edit

You can use mask :

    Mat im = imread("f:/lib/opencv/samples/data/lena.jpg", IMREAD_GRAYSCALE);
    Mat mask = im>0;
    double minc[1], maxc[1];

    minMaxLoc(im, minc, maxc,NULL,NULL,mask);
    cout<<minc[0];

I think,mast is not a must.

int main( int argc, char** argv )
{

Mat im = imread("e:/template/lena.jpg", IMREAD_GRAYSCALE);
double minc[1], maxc[1];
minMaxLoc(im, minc, maxc,NULL,NULL);
cout<<minc[0];
return 0;
}

it works.