Correlations in spontaneous brain activity provide powerful access to large-scale organizational principles of the CNS. However, making inferences about cognitive processes requires a detailed understanding of the link between these couplings and the structural integrity of the CNS. We studied the impact of multiple sclerosis, which leads to the severe disintegration of the central white matter, on functional connectivity patterns in spontaneous cortical activity. Using a data driven approach based on the strength of a salient pattern of cognitive pathology, we identified distinct networks that exhibit increases in functional connectivity despite the presence of strong and diffuse reductions of the central white-matter integrity. The default mode network emerged as a core target of these connectivity modulations, showing enhanced functional coupling in bilateral inferior parietal cortex, posterior cingulate, and medial prefrontal cortex. These findings imply a complex and diverging relation of anatomical and functional connectivity in early multiple sclerosis and, thus, add an important observation for understanding how cognitive abilities and CNS integrity may be reflected in the intrinsic covariance of functional signals.resting state | BOLD fMRI | diffusion tensor imaging | fractional anisotropy | neurological U nderstanding how disease processes affect functional interactions in the CNS is a core challenge of neuroscience research. fMRI connectivity has become an important tool for revealing large-scale network interactions by analyzing correlations in intrinsic fluctuations of the BOLD signal (1). This method is sensitive to plastic as well as developmental changes of the functional architecture (2-5), and has successfully linked specific cognitive syndromes to the pathology of distinct functional systems (e.g., spatial neglect after stroke, different forms of dementias, and healthy aging) (6-8). The structural wiring of the brain plays an essential role in shaping the spatial patterns of functional interactions (9, 10). However, the activity correlations are not fully determined by the anatomical connections and, thus, provide complementary information about network organization (11). Especially in the context of neurological damage, the functional covariance structure may document pathological effects well beyond focal damage, indicating the complex changes of interactions that occur in distributed networks (12)(13)(14). Commonly, the coupling strength of spontaneous brain activity is thought to be a direct proxy for the functioning of brain networks, with stronger interactions also reflecting a stronger computational capacity (15,16).In this study we have investigated how cognitive pathology due to neurological damage in multiple sclerosis (MS) is reflected in changes of structural and functional connectivity. Compared with other CNS pathologies, MS stands out due to the prominent involvement of the central white matter. During the disease process, the immune system exerts inflammatory insults to neurona...