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Dear FSL experts, I have a question about my registration pipeline. Image summarizing the registration can be found here <https://www.dropbox.com/s/w9cwqdnveiewx0h/registration_example.png?dl=0> (dropbox-folder). I'm trying to register EPI data (TR=2s, 3mm isotropic) to MNI space using the standard FSL way as implemented through FEAT. That means I use the BBR cost-function to co-register my functional (middle image) to my structural image and I calculate the final structural to MNI registration by first using FLIRT (12 dof, affine transformation) followed by FNIRT (10mm warp). As you can see in the linked image the result of the registration procedure for the functional to MNI looks rather odd (there is a 'horn' of matter outside the MNI's brain shape). This one data set performed especially bad but some of the other data sets look comparably (bad) in terms of their final registration. Do you maybe have some ideas/insights why this might be happening and how to fix it? Cheers, Paul