Hi Sourena,
Thanks a lot for your reply. It's not only the binary mask which is taken into account by the cost function, it is also the background.
In addition, smoothing of the fixed and floating image (regularization) makes the boarder of the mask to have a variability which guides the registration of the mask boarders. I'm doing this with ANTS and the results are perfect. However, for the purpose of my work I can't do diffiomorphic transformation, so I was wondering if any one has done this with fnirt previously so I can use the same parameters set instead of examining them one by one. For some reason fnirt takes forever to run a simple registration.
Best,
Ray,
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