How do I shear one image such that its dimensions match another similar image?

I am trying to shear one ROI image over another in order to compare intensity values, however it appears that doing an affine shears moves the image such that the intensity values overlap. I need the two images to overlap in their boundaries as opposed to their intensities.

[Walter Roberson]

Perhaps create a mask the same shape as their boundaries, in which case the "intensity" that it would be calculating over would just be a constant 1, resulting in a shear that is just boundary based.

[Image Analyst]

Attach images as an example.