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In the EyeX Select Display setup, we use the physical display size reported by the monitor to draw an image of the eye tracker that we believe corresponds to the physical size of the eye tracker. Since we know some monitors report incorrect values for their physical size, the size of the displayed eye tracker image can be corrected by the user by clicking and dragging the handles on the dotted lines and the center mark on the image until they all line up with the marks on the actual eye tracker device.
Optimally the eye tracker should be positioned so that is vertically aligned with the bottom of the display area it is calibrated and used for. In your case you will have an vertical offset between the eye tracker and the displayed screen. The calibration process will compensate for some of this offset, but not completely.