Abstract Over the past two decades, the study of resting-state functional magnetic resonance imaging has revealed that functional connectivity within and between networks are linked to cognitive states and pathologies. However, the white matter connections supporting connectivity remain only partially described. We developed a method to jointly map the white and grey matter contributing to each resting-state network. Using the Human Connectome Project, we generated an atlas of 30 resting-state networks. The method also allows highlighting the overlap between networks, which revealed that most of the brain’s white matter (89%) is shared between multiple networks, with 16% shared by at least 7 resting-state networks. These overlaps, especially the existence of regions shared by numerous networks, suggest that white matter lesions in these areas might strongly impact the correlations and the communication within resting-state networks. We provide an open-source software to explore the joint contribution of white and grey matter to RSNs and facilitate the study of the impact of white matter damage on RSNs. In a first clinical application of the software, we were able to link stroke patients and impacted resting-state networks, showing that their symptoms aligned well with the estimated functions of the networks.

Atlasing white matter and grey matter joint contributions to resting-state networks in the human brain