The region of interest is shifted in one of the images. In the other image, the region of interest is at the center of the image. So how to map the pixels of the region of interest of the shifted image with the other one? Finally the aim is performing coregistration of the two images.
Did you try imregister() in the Image Processing Toolbox. This is exactly what it's meant for. Please try it.
Then try normxcorr2() (in the Image Processing Toolbox) and imtranslate() (in the File Exchange).
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