Functional magnetic resonance and diffusion weighted imaging have so far made a major contribution to delineation of the brain connectome at the macroscale. While functional connectivity (FC) was shown to be related to structural connectivity (SC) to a certain degree, their spatial overlap is unknown. Even less clear are relations of SC with estimates of connectivity from inter-subject covariance of regional F18-fluorodeoxyglucose uptake (FDG_cov) and grey matter volume (GMV_cov). Here, we asked to what extent SC underlies three proxy estimates of brain connectivity: FC, FDG_cov and GMV_cov. Simultaneous PET/MR acquisitions were performed in 56 healthy middle-aged individuals. Similarity between four networks was assessed using Spearman correlation and convergence ratio (CR), a measure of spatial overlap. Spearman correlation coefficient was 0.27 for SC-FC, 0.40 for SC-FDG_cov, and 0.15 for SC-GMV_cov. Mean CRs were 51% for SC-FC, 48% for SC-FDG_cov, and 37% for SC-GMV_cov. These results proved to be reproducible and robust against image processing steps. In sum, we found a relevant similarity of SC with FC and FDG_cov, while GMV_cov consistently showed the weakest similarity. These findings indicate that white matter tracts underlie FDG_cov to a similar degree as FC, supporting FDG_cov as estimate of functional brain connectivity.