I'd like to find a transformation that projects the image from the Left camera onto the image from the Right camera so that the two become aligned. I already managed to do that with two similar cameras (IGB and RGB), by using the disparity map and shifting each pixel by the corresponding disparity value. My problem is that this doesn't work for other cameras that I'm using (for example multispectral and infrared sensors), because the calculated disparity maps have very little detail. I am currently using the Matlab Computer Vision Tool Box, and I suspect that the problem is the poor correlation of information in the images (little correspondences found by the disparity algorithm). I would like to know if there is another way of doing this transformation, for example just by using the Extrinsic and Intrinsic Parameters of the cameras (the are already calibrated).
The disparity IS the transformation you are looking for. Any sensible left-right mapping depends on 3D information, which the disparity provides. Anything else is just hallucinating some values based on assumptions that may or may not make sense.