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Hi FSLers - I think we might have come across a subtle bug in applywarp. It seems that the tool sets the "intent_code" in the NIfTI header of the output image to the value found in the "reference" image. Since the "intent" refers to the meaning of the data, not the geometry though, and the data come from the input image, it would seem more logical that the latter is where the intent_code should be coming from also. Best, Torsten