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Conformal radiotherapy planning needs accurate delineations of the critical structures. Atlas-based segmentation has been shown to be very efficient to delineate brain structures. It would therefore be very interesting to develop an atlas for the head and neck region where 7 % of the cancers arise. However, the construction of an atlas in this region is very difficult due to the high variability of the anatomies. This can generate segmentation errors and over-segmented structures in the atlas. To overcome this drawback, we present an alternative method to build a template locally adapted to the patient’s anatomy. This is done first by selecting in a database the images that are the most similar to the patient on predefined regions of interest, using on a distance between transformations. The first major contribution is that we do not compute every patient-to-image registration to find the most similar image, but only …