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Hi - you can't (even in theory) avoid the "undesirable" effects of resampling by doing this - though you can ameliorate this by using a "sharper" interpolation option such as -interp spline Cheers. On 18 Sep 2012, at 17:48, Chris Keown wrote: > Plugging in the anatomical as the reference image when I applied the transform did fix the alignment issues, but it also resampled my voxel sizes to the much higher resolution of the anatomical, which I don't want. When I say I don't want resampling, I realize that registration inherently resamples the data, but I want the voxel sizes to stay the original size they are in the functional in order to minimize any undesirable effects of resampling. Thanks again! > --------------------------------------------------------------------------- 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 ---------------------------------------------------------------------------