If you know what regions of the images you have noise that needs filtering why not just filter those regions? Something like this (one-region example):
regN = [i11,i12,i21,i22];
ImgN = Im_full((regN(1)-1):(regN(2)+1),(regN(3)-1):(regN(4)+1)); Will break down for regions that extends to image edges, fix to suit needs
ImgN = wiener2(ImgN,[3,3]);
Im_full(regN(1):regN(2),regN(3):regN(4)) = ImgN(2:end-1,2:end-1);
To me it sounds strange that you need to reduce noise in what seems to be "medically uninteresting" parts of images, while the parts of the images with organs and tissue should be left unfiltered with noise intact. Why not simply tell the doctors that the noisy parts of the images are left noisy to make them aware of the general noise characteristics of the images, that should be information that should help image interpretation.
HTH
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