solved the problem simply by swapping my x and y around
for( y =0; y < 480 ; y++)
{
//getting in to each pixel in a row
for( x = 0; x < 640; x++)
{
if (depthpixels[i]>1500)
{
grey.at<unsigned char >(y,x) = 0;
}
if (depthpixels[i] <500)
{
grey.at<unsigned char >(y,x) = 0;
}
i++;
}
}