Hi @Aldo_Camargo,
It is not necessary to normalize to MNI space, in fact, is it advised to do all the connectivity analysis in diffusion native space.
Ideally you should correct the distortions of your diffusion image, if you don’t have reverse phase encoding direction you can use the T1w with SynB0, have a look at this thread. Then coregister your T1w to your B0 and perform the connectivity analysis in the diffusion space.
Best regards,
Manuel