Quantitative MRI maps of human neocortex explored using cell type-specific gene expression analysis

Quantitative magnetic resonance imaging (qMRI) allows extraction of reproducible and robust parameter maps. However, the connection to underlying biological substrates remains murky, especially in the complex, densely packed cortex. We investigated associations in human neocortex between qMRI parameters and neocortical cell types by comparing the spatial distribution of the qMRI parameters longitudinal relaxation rate ([Formula: see text]), effective transverse relaxation rate ([Formula: see text]), and magnetization transfer saturation (MTsat) to gene expression from the Allen Human Brain Atlas, then combining this with lists of genes enriched in specific cell types found in the human brain. As qMRI parameters are magnetic field strength-dependent, the analysis was performed on MRI data at 3T and 7T. All qMRI parameters significantly covaried with genes enriched in GABA- and glutamatergic neurons, i.e. they were associated with cytoarchitecture. The qMRI parameters also significantly covaried with the distribution of genes enriched in astrocytes ([Formula: see text] at 3T, [Formula: see text] at 7T), endothelial cells ([Formula: see text] and MTsat at 3T), microglia ([Formula: see text] and MTsat at 3T, [Formula: see text] at 7T), and oligodendrocytes and oligodendrocyte precursor cells ([Formula: see text] at 7T). These results advance the potential use of qMRI parameters as biomarkers for specific cell types.