The exact shape of every human brain - including its micro- and macroscopic features - is as unique as a human fingerprint, resulting in inter-individual anatomical variability. In the past two decades, the understanding of this variability advanced dramatically not only at the level of sulcal/gyral patterns, anatomical features (e.g. cortical thickness, volume and shape) and extent of cytoarchitectonic areas defined at the microscopic level, but also in the anatomical and functional connectivity of the brain. The core concept within the field of brain mapping is the use of a standardized 3D coordinate frame for data analysis and reporting of findings from neuroimaging experiments. This simple construct allows brain researchers to combine (even structural or functional) data from many subjects to create group-averaged signals. Also, where the signal is robust enough to be detected in individuals, it allows for the exploration of inter-individual variance in the location of that signal. Spatial standardization requires two basic components: (i) the specification of the 3D standard coordinate space, and (ii) a mapping function that transforms a 3D brain image from “native” space to that standard space. The first component is usually expressed by the choice of a representative 3D MR image that serves as target (template or atlas). The native image is re-sampled to standard space under the mapping function that may have few or many degrees of freedom, depending upon the experimental design. The optimal choice of atlas template and mapping function depends upon considerations of age, gender, hemispheric asymmetry, anatomical correspondence, spatial normalization methodology and disease-specificity (1). In our studies we investigated some of these aspects, e.g. 1) how gender and normal aging influences brain morphology, 2) how normal hemispheric asymmetry plays a role in lateralized neurological diseases, such as cluster headache, 3) how progressive neurodegenerative disorders, such as Huntington’s disease affect the brain structure, or 4) how we can deal with inter-individual variability in case of neurosurgical interventions, such as thalamotomy in the therapy of medication resistant tremor.