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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!