As early as the end of the 19th century Ernest Bruck declared that the brain is a physical entity and should be studied using the science of mathematics and physics. The brain is an extremely intricate physical entity and we have only recently begun to develop the conceptual tools to decipher this complexity. We can begin to comprehend many of the mental functions and dysfunctions by using insights about brain organization as a developing physical entity of connectivity structures. A comprehensive theoretical framework for the re-conceptualization of mental disorders as real brain-disorders, called "Clinical brain profiling" can be generated to make testable predictions about the etiopathology of psychiatric disorders. If validated, this framework has groundbreaking relevance for psychiatry, not only by providing an etiological diagnostic system, in itself revolutionary, but in its potential to develop effective curative interventions. According to the proposed brain profiling all mental disturbances can be defined in a 3 dimensional space of brain disturbances (1) neural-complexity organization, (2) to neural resilience optimization dynamics and (3) to connectivity constructs for context and internal representations. Neural complexity relates to the ability of the brain to balance connectivity dynamics, neural resilience relates to brain plasticity and changeability for optimizing overall brain dynamics and contextual configurations shape the internal representations of outer world that pattern out reaction and personality styles. Each of these organizational brain functions is predicted to involve a relatively specific neuronal circuitry system in the brain. The circuitry of the nigra-striautum-cortex, are a component of the connectivity balance stabilizers and regulators, a type of neural complexity pacemaker. Thus a patient that rates high on phenomenology related to functional psychosis indicating a disturbance to connectivity balance will have disturbances that will show up in appropriate signal processing imaging of the nigra-striautum-cortex circuitry. The circuitry of thalamus-amygdala-cortex and related pathways are relevant for neuronal matching and constraint frustration. In this respect the patients scoring high on mood and anxiety disorders are predicted to suffer from perturbation shown on appropriate imaging involving the thalamus-amygdala-cortex circuitries. The hippocampus is related to the formation of internal configurations thus those patients rating highest on parameters related to personality organization and maturation will show alterations in the hippocampal organization and activation indicating deficient organizations of internal configurations.