An abnormal brain development due to a neuropsychiatric disorder can influence the shape and the anatomical organization of both white and grey matter structures. An example is the syndrome of Gilles de la Tourette (GTS) which is thought to be associated with dysfunctions of the cortico-striato-pallido-thalamic circuits [6]. These anatomical complexes should be studied as a whole, analysing both the shape and the relative position of their structures.Atlas constructions permit to estimate an average shape complex of a given population, called template, and its deformations towards the shape complexes of each subject. The template represents the morphological invariants of the population whereas the deformations capture its variability.Previous works defined these deformations as single diffeomorphisms acting on the entire 3D space, so that ending points of fiber bundles could not move independently of grey matter structures [1,2,4,5]. This implicitly assumes that fiber bundles connect the same areas of grey matter structures across subjects. This assumption is not compatible with the aforementioned hypothesis about GTS [6] which relates the syndrome to atypical configurations of neural circuits. We propose a new atlas construction method which can handle both fibers and surfaces and which is based on a double diffeomorphism. This permits to analyse the morphological variations of each structure and the changes in the relative position between fiber bundles and grey matter structures, namely the variations in structural connectivity.