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Hi, I'm really surprised to hear about your "shrinkage". We would not expect anything like this. If any of your original images look distorted then this is either due to real scanner-induced distortion (which occurs in the EPI images but not significantly in the structurals) or a problem in your conversion to NIFTI. So check the conversion if this is the case. If, instead, you only see strange looking images _after_ registration, then this indicates that the registration has gone wrong. In that case I would double-check your brain extraction (of the structural) and that you've used the appropriate degrees of freedom (12 DOF to standard space, but never between functional and structural of the same subject). I hope this helps. All the best, Mark On 17 Aug 2012, at 14:09, Varina Wolf <[log in to unmask]> wrote: > Dear FSL Experts, > > My goal is to register my statistical image to a subject original whole brain T1. > > 1. At some point in my rs-fmri analysis the images undergo a shrinking process, and I understand this has something to do with affine transformation. This is why when I look at the subjects standard anatomical MRI the brain looks longer than the BETed and registered images used in FSL. Is this true? And/Or does it have something to do with converting from DICOM to Nifti format? > > 2. To get the statistical image overlaid back onto the original "unshrunk" anatomical image, what would be the best steps? Would it be: > > > Most Appreciatively, > Varina >