Align 2 matrices to find the minimum difference

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Hi,
I want to find the difference between two matrices but there might be a rotation misalignment between them. These matrices are simuations of a surface from different sources and both contain some NaN values. Is there a function in Matlab or a way I can find the rotation angle that best aligns the matrices so the difference between them is the minimum possible? Many thanks!
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Jan
Jan 2019-3-20

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