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> http://www.mathworks.com/matlabcentral/fileexchange/26186-absolute-orientation-horns-method

Yes, hunt around on the FEX: there are various functions for this sort of thing. 

If you have a small number of image pairs then there are landmark-based ways of doing image registration. Look at the image processing toolbox. These are hard to automate, however, if you have large numbers of image pairs.