The Functional CNS Model - Rat (FMrat) ( Swanson-2004) is one of three hierarchical models representing the internal organization of the central nervous system (CNS). The others are the Structural CNS Model - Human (SThmn) and the Functional CNS Model - Human (FMhmn). The FMrat model represents the basic organization of the mouse ( Hof-2000 AMBA-2024 ) and, presumably, other rodents. Functional CNS models differ from structural models in that structures are defined and named by connectivity rather than by proximity to other structures at the same level. Functional models are more useful for representing longitudinal components of are grouped based on information drawn from multiple neuroscientific disciplines. such as connections, neurochemical characteristics, and role in physiogical and behavioral processes. While the Functional Model was developed primarily for an atlas of the rat brain ( Swanson-2004 ), the hierarchical organization of structures is for the most part applicable to the human, macaque, mouse and other mammalian brains as well. Structures at lower levels of the Functional CNS hierarchy are largely the same as in the Classical and Developmental Models, i.e., they were originally identified by stains for gray matter (Nissl substance) and white matter (myelin). At the next higher level they are grouped into basic connectional and functional systems of the CNS, such as the subcortical sensory systems, the brainstem motor system and the behavioral state system. At the highest levels CNS structures are grouped on the basis of dissection and embryologic precursors into cerebrum ( cerebral cortex and cerebral nuclei ), cerebellum, and cerebrospinal trunk.

The Classical Vertebrate Central Nervous System is a hierarchical model of gray matter structures that are common to the brain and spinal cord of all vertebrates. As in other classical models, structures are grouped by proximity as observed on dissection, and the upper levels correspond roughly to their organization in the embryo. The hierarchical organization is based on the Basic Partts List for Adult Nervous System in All Animals ( Swanson-2104 ), the nomenclature on NeuroNames ( Bowden-2012 ).