KJ. If the skull fits: magnetic resonance imaging and microcomputed tomography for combined analysis of brain and skull phenotypes in the mouse. Physiol Genomics 44: 992-1002. First published September 4, 2012 doi:10.1152/physiolgenomics.00093.2012.-The mammalian brain and skull develop concurrently in a coordinated manner, consistently producing a brain and skull that fit tightly together. It is common that abnormalities in one are associated with related abnormalities in the other. However, this is not always the case. A complete characterization of the relationship between brain and skull phenotypes is necessary to understand the mechanisms that cause them to be coordinated or divergent and to provide perspective on the potential diagnostic or prognostic significance of brain and skull phenotypes. We demonstrate the combined use of magnetic resonance imaging and microcomputed tomography for analysis of brain and skull phenotypes in the mouse. Co-registration of brain and skull images allows comparison of the relationship between phenotypes in the brain and those in the skull. We observe a close fit between the brain and skull of two genetic mouse models that both show abnormal brain and skull phenotypes. Application of these three-dimensional image analyses in a broader range of mouse mutants will provide a map of the relationships between brain and skull phenotypes generally and allow characterization of patterns of similarities and differences. craniofacial development; mouse phenotyping; mouse imaging; oculodentodigital dysplasia; Dandy-Walker malformation THE DEVELOPMENT OF THE BRAIN and skull is an intricate and coordinated process that results in two complex structures fitting tightly together. Both physical and genetic factors participate in the direction of this process, and changes in either may result in an altered brain and/or skull morphometry. Characterization of such alterations, and of how brain and skull alterations relate to one another, will provide insight into the process of normal brain and skull development and into conditions where this development is perturbed.It is recognized that the physical interaction between structures in the developing brain and skull can induce covariation in their shape (61). Premature fusion of a cranial suture, for example, results in an abnormal skull shape due to growth restriction in one direction (51). Brain growth is also physically constrained in these circumstances, and the brain is similarly altered in shape (5,6,77). Fear of increased intracranial pressure and abnormal craniofacial development motivates corrective surgery in these patients to partly normalize anatomical outcome (71). Furthermore, simple geometric measurements of the skull, such as the angle between the skull base and the front of the brain or landmarks on the facial bones, show a high degree of correlation with the total volume of the brain (16,59,81,82). This observation seems to hold true in multiple species of mammals, a fact that informs some studies in anthropology and evoluti...