I'm not sure about doing this to the raw data, but if you want to tidy the appearance of the images output from dtifit (FA, etc) you could try nudging them?
Type Nudge at the command line to get the nudge GUI - this allows you to "rotate" an image in x, y or z.
If you want the corpus callosum nicely oriented to the midline, you could try rotating by 5-20 degrees in the z plane. Put your subject FA image as the input, and as the reference, and click View. A rotated image will appear on top in red-yellow. If you like the appearance of the nudged image, you can save it, e.g. as "subject1_dti_FA_nudged.nii.gz".
Charlotte
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MRC Cognition and Brain Sciences Unit
Cambridge, UK
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