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Dear FSL users/developers, I am new of FSL and I am trying to register an MRI diffusion weigthed on a MRI T1 weighted. I am using fnirt but I read in the documentation that the only cost function avaible is the sum of squared differences. In my opinion the mutual information (in theory) should be the best choise in this case...Am I wrong? Is there a way to use a different cost function instead of the SSD? Thank you very much. Regards. Paolo