Brain is a complex system that contains multiple localized groups each of which performs independent tasks. Nevertheless, the brain can also run as a unique system that its function depends on different localized groups. These two principles of the brain are called functional segregation and integration, respectively, and there should be a balance between them for the brain to act properly. In this thesis, we hypothesized that sleep deprivation might have a negative effect on these principles which results in loss of sustained attention and having difficulty performing tasks. Moreover, we investigated the effects of the circadian rhythm and homeostatic sleep pressure on functional integration. Another hypothesis was that if a part of the fMRI time-series is not stationary, the results of the functional integration might not be reliable. Total integration, between-network integration and within-network integration were measured using the fMRI data set provided by our colleagues from University of Liège. Our results show that global integration increased after sleep deprivation while the segregation decreased, and integration’s maximum level was around the peak of the melatonin curve for each subject. Furthermore, in a non-stationary fMRI signal, numerous fluctuations were found in the integration results compared to when the signal was stationary.