In this research report, we present a general scheme for building entirely automatically a morphometric anatomical atlas from 3D medical images (CT-Scan, Magnetic Resonance Imagery). We detail each step of the method, including the non-rigid registration algorithm, 3D feature lines averaging, and statistical processes. We apply the method to obtain a quantitative atlas of crest lines of the skull. Finally, we use the resulting atlas to study a craniofacial disease: we show how we can obtain qualitative and quantitative medical results by contrasting a skull affected by Crouzon's disease with the atlas.