This extracts a ROI from images that are 16bits per pixel.

extract_roi.cpp

void extractRoi(cv::Mat& inImage, cv::Mat& outImage, cv::Rect roi)
{
    /* Create the image */
    outImage = cv::Mat(roi.height, roi.width, inImage.type());

    /* Populate the image */
    for (int i = roi.y; i < (roi.y+roi.height); i++)
    {
        uint16_t* inP = inImage.ptr<uint16_t>(i);
        uint16_t* outP = outImage.ptr<uint16_t>(i-roi.y);
        for (int j = roi.x; j < (roi.x+roi.width); j++)
        {
            outP[j-roi.x] = inP[j];
        }
    }
}