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Atlases can only be applied to images if they have the same resolution and show the anatomy with the same geometry. Therefore, images originating from real experiments first need a normalization step for the atlas to be applied. This is done by calculating a normalization transform between the subject image and a "template" image representing the standard anatomy imaged with a certain modality, and using it for warping the VOIs to the subject anatomy.
The PNROD tool supports four methods as described in Normalization of the Anatomical Image.