Hi, It's very normal to have to calibrate two cameras of different resolution when working in Multi-modal imaging. It's always the case that you have two different sensors with different technologies and highly unlikely that they have same resolution. Kinect is of course a very common example. Unfortunately, the official matlab app doesn't support this. There are some codes which make this possible for kinect 1 which you can google. But if you're looking for something with kinect 2, you can try first using the detectCheckerboardPoints from matlab for each set of images (check the matlab manual) and then when you have the points use : imagePoints = cat(4, poitnsRGB, pointsIR); Then feed these to the estimateCameraParameters (check the manual for more info). The catch is that I've done this for a HD camera and the kinect IR and I get terrible amount of error. I'm still trying to fix this. Worst case, one can use Kinect 1 with one of the available calibration codes.
Regarding what you said about cropping the images, that's a calibration sin ! If you look up info on how to calibrate cameras, they always tell you not to do that because that messes up everything.