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The recent discovery of an intricate and nontrivial interaction topology among the elements of a wide range of natural systems has altered the manner we understand complexity. For example, the axonal fibres transmitting electrical information between cortical regions form a network which is neither regular nor completely random. Their structure seems to follow functional principles to balance between segregation (functional specialisation) and integration. Cortical regions are clustered into modules specialised in processing different kinds of information, e.g. visual or auditory. However, in order to generate a global perception of the real world, the brain needs to integrate the distinct types of information. Where this integration happens, nobody knows. We have performed an extensive and detailed graph theoretical analysis of the cortico-cortical organisation in the brain of cats, trying to relate the individual and collective topological properties of the cortical areas to their function. We conclude that the cortex possesses a very rich communication structure, composed of a mixture of parallel and serial processing paths capable of accommodating dynamical processes with a wide variety of time scales. The communication paths between the sensory systems are not random, but largely mediated by a small set of areas. Far from acting as mere transmitters of information, these central areas are densely connected to each other, strongly indicating their functional role as integrators of the multisensory information. In the quest of uncovering the structure-function relationship of cortical networks, the peculiarities of this network have led us to continuously reconsider the stablished graph measures. For example, a normalised formalism to identify the “functional roles” of vertices in networks with community structure is proposed. The tools developed for this purpose open the door to novel community detection techniques which may also characterise the overlap between modules. The concept of integration has been revisited and adapted to the necessities of the network under study. Additionally, analytical and numerical methods have been introduced to facilitate understanding of the complicated statistical interrelations between the distinct network measures. These methods are helpful to construct new significance tests which may help to discriminate the relevant properties of real networks from side-effects of the evolutionary-growth processes.