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Hi Giuseppe, I suspect that what is happening is that FLIRT is giving you a close-to-optimal affine (global) registration, i.e. doing the best possible job of aligning the images globally - but that the EPI contains distortions relative to the structural, which an affine transformation cannot fix. Probably the best way to undistort the EPI is to use a B0 fieldmap, along with PRELUDE/FUGUE. Cheers, Steve. On Tue, 27 Apr 2004, Giuseppe Pagnoni wrote: > Hi all > > I am trying to get an EPI registered to a T1 (both preprocessed with BET) > and no matter how many parameters I try to change, the results are not good: > the global whole-brain overlapping of the resulting images does not look bad > at first, but at a closer inspection, checking the ventricles and the gyry > overlapping, the registered EPI always ends up lying around 10 mm below the > T1. The images are of reasonable quality (at least to my eye), they cover > most of the brain and have a fairly high resolution (EPI=3x3x3mm, > T1=1x1x1mm). I could try and make a mask out of the ventricles, but I really > see no reason why the registration would fail with normal parameters under > such a standard situation. Did anybody come across the same problem? I'd > hate to have to resort to 'manual' registration....! > > thanks for any help > > giuseppe > Stephen M. Smith DPhil Associate Director, FMRIB and Analysis Research Coordinator Oxford University Centre for Functional MRI of the Brain John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK +44 (0) 1865 222726 (fax 222717) [log in to unmask] http://www.fmrib.ox.ac.uk/~steve