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Stereo Camera Calibration Problems

I am trying to calibrate my stereo camera with the OpenCV Samples/stereo_calib.cpp file. I am getting a high rms error as well as a nonsensical rectified image output. I am entering the width,height,square size(side in cm),and the list of input left and right images. Is there any other parameter I should be wary of? What is the best procedure to calibrate it?

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