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If you can create a checkerboard visible by both the kinect rgb camera and the thermal camera, then you would be able to feed that into the stereo calibration package. When we were calibrating the kinect RGB camera to the kinect depth camera, we pasted black squares on a large glass pane, and held the pane between the kinect and a white wall. The result was that both cameras "saw" black squares on a white background.

I'm not sure about the details of the thermal imaging camera, but would something similar work? If glass is transparent to it, you might be able to trick it to see squares of different temperatures.