Dear Filiberto,
It is only important that the orientation of the images is similar so the intra-patient registration is able to correctly align them to the T1c image. Yes, you can have isotropic or anisotropic acquisition mixed.
Regarding slice thickness, we haven’t tested the limits of it, but up to slice thickness of 6mm it should work without problems.
Let me know if you experiences problems
Regards,
Mauricio