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Had input xml used instead of output xml, which was causing the stitching transform to be applied to the bdv xml instead of the actual output xml (since it writes in-place)..
Had input xml used instead of output xml, which was causing the stitching transform to be applied to the bdv xml instead of the actual output xml (since it writes in-place)..
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Had input xml used instead of output xml, which was causing the stitching transform to be applied to the bdv xml instead of the actual output xml (since it writes in-place)..