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Hi - you can create a flirt matrix like 1 0 0 xshift-in-mm 0 1 0 y 0 0 1 z 0 0 0 1 Cheers. On 29 Apr 2010, at 16:30, Allen Kline wrote: > I’m doing SEMS DTI on ex vivo mouse brains and using a high b- > value. Thus my reference images have a very different intensity > pattern from the diffusion images. I can use eddy_correct or a 2D > version of it to improve the alignment of the diffusion images, but > these programs always do a poor job with the reference. I have > shuffled along by choosing the diffusion image which best aligns to > my reference, then using that one to align the other images. After > I get the aligned images, I then replace the reference image with > the original and that gives reasonable DTI data. But I’ve noticed > that my reference is often off by 3-4 pixels from the aligned set of > diffusion images. Since this is consistent in all of my slices, I > wanted to know if there was a way to translate a set of images by an > arbitrary number of data points. A circular shift would work fine. > > Thanks, Allen > --------------------------------------------------------------------------- Stephen M. Smith, Professor of Biomedical Engineering Associate Director, Oxford University FMRIB Centre FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK +44 (0) 1865 222726 (fax 222717) [log in to unmask] http://www.fmrib.ox.ac.uk/~steve ---------------------------------------------------------------------------