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Hi thank you Jesper for your reply, i have just to inform you that i will use the transformation matrix i produced using flirt (12 dof) between the diffusion space and the T1 space as an affine starting guess, but for the other parameters (subsamp, warpre, lambda ...), i want ask if you have an optimised script for such situations (registering diffusion volume of 256x256x56 to T1 256x256x256) Thanks a lot --- En date de : Mer 5.6.13, Jesper Andersson <[log in to unmask]> a écrit : De: Jesper Andersson <[log in to unmask]> Objet: Re: [FSL] FLIRT problem À: [log in to unmask] Date: Mercredi 5 juin 2013, 11h50 Dear Laouchedi, i run flirt with 12 dof to register diffusion datasets to their T1 datasets and i noticed that for the brainstem (pons) the results are not as good as for the brain. does non linear (fnirt) improve the registration results ? or is there any other mean adapted for this purpose ? Fnirt often will improve that so I think that should be your first option to try. Jesper