Higher cognitive functions, such as the reading of intentionality in someone's face, or the judgment about an unexpected harmony in a song, are based on a complex neuronal interaction between multiple regions across the brain. These interactions can be traced by functional brain imaging techniques, and considerable effort has been given to describe normal and altered brain networks during cognitive tasks, as well as in the brain at rest. Here I present several studies that establish the structural and functional connectivity underlying selected higher cognitive tasks, as well as pathologically altered connectivity in patients at rest, with an application to multiple sclerosis. These results provide additional information about the state of the disease in every single patient, and this information can be used to additionally characterize the patient's condition. The results offer new perspectives to describe, monitor or stratify patients according to the individual profile of the altered pattern of functional networks using different modalities of functional and structural brain imaging.