Mapping structural changes in subcortical brain regions is crucial for understanding their functions in both health and disease. We developed a method to quantify microstructure profiles in vivo within a single human brain. Our findings show that spatial profiles in the putamen, caudate, and globus pallidus are consistently reproducible across individuals, clinical conditions, and datasets. Using multiparametric quantitative MRI, we identified distinct, spatially dependent, aging-related changes in water content and iron concentration. In Parkinson’s disease (PD) patients, we observed abnormal profiles in the putamen, particularly in the posterior putamen, which correlate with patients' dopaminergic loss and motor dysfunction.