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Hi Joana, I got an OK registration with the following command: flirt -dof 6 -in example_func.nii.gz -ref MPRAGE_reori_brain.nii.gz -out example_func2highres However, I can't tell if you have a lot signal dropout in the VMPFC area or if the brain is slightly tilted upward. Is that what you're talking about? If you have field maps, it would be good to include those. In addition, it looks like your functional data is highly anisotropic, which can lead to suboptimal registrations (and maybe more signal dropout, though I'm not sure). pixdim1 3.5156250000 pixdim2 3.5156250000 pixdim3 6.9997386932 I'm not sure if you can improve this registration, but maybe others have better ideas. Cheers, David On Apr 22, 2013, at 3:00 PM, Joana Pinto <[log in to unmask]> wrote: > Dear FSL experts, > > I’m trying to use FLIRT to register some EPI images to the corresponding individual T1 images (one example in the links below). However, my EPI slice prescription was significantly angled relative to the axial orientation (of the T1 images). I believe that, for this reason, I am not succeeding in obtaining a good registration. I have already tried some different options, including using 6 DOF or BBR, and using -usesqform –applyxfm. > > I would be grateful for your help! > > Thanks for the attention. > Best regards, > > Joana Pinto > > https://www.dropbox.com/s/6a9dr4v39gwwc36/example_func.nii.gz > https://www.dropbox.com/s/fvykd20zdic39qu/MPRAGE_reori_brain.nii.gz ---------------------------------------------- David V. Smith, Ph.D. Postdoctoral Fellow, Delgado Lab Department of Psychology Rutgers University Newark, NJ 07102 ----------------------------------------------