Sometimes FSL tools do not immediately find a satisfactory transformation to bring two images in register. In that case, you can give the flirt algorithm a little nudge by (1.) bringing the two images roughly in the same space using itk snap's automatic and manual registration tools and only then (2.) running FSL flirt or epi_reg.
Since itksnap and FSL use different origins for their coordinate systems the transformation matrices that are produced by the two programs are not