Inferring brain connectivity from inter-individual correlations has been applied across various neuroimaging modalities, including positron emission tomography (PET) and MRI. The variability underlying these inter-individual correlations is generally attributed to factors such as genetics, life experiences, and long-term influences like aging. This study leveraged two unique longitudinal datasets to examine intra-individual correlations of structural and functional brain measures across an extended time span. By focusing on intra-individual correlations, we aimed to minimize individual differences and investigate how aging and state-like effects contribute to brain connectivity patterns. Additionally, we compared intra-individual correlations with inter-individual correlations to better understand their relationship. In the first dataset, which included repeated scans from a single individual over 15 years, we found that intra-individual correlations in both regional homogeneity (ReHo) during resting-state and gray matter volumes (GMV) from structural MRI closely resembled resting-state functional connectivity. However, ReHo correlations were primarily driven by state-like variability, whereas GMV correlations were mainly influenced by aging. The second dataset, comprising multiple participants with longitudinal Fludeoxyglucose (18F) FDG-PET and MRI scans, replicated these findings. Both intra- and inter-individual correlations were strongly associated with resting-state functional connectivity, with functional measures (i.e., ReHo and FDG-PET) exhibiting greater similarity to resting-state connectivity than structural measures. This study demonstrated that controlling for various factors can enhance the interpretability of brain correlation structures. While inter- and intra-individual correlation patterns showed similarities, accounting for additional variables may improve our understanding of inter-individual connectivity measures.