Visualization of subcortical structures in non-human primates in vivo by Quantitative Susceptibility Mapping at 3T MRI

Magnetic resonance imaging (MRI) is now an essential tool in the field of neuroscience involving non-human primates (NHP). Structural MRI scanning using T1-weighted (T1w) or T2-weighted (T2w) images provides anatomical information, particularly for experiments involving deep structures such as the basal ganglia and cerebellum. However, for certain subcortical structures, T1w and T2w images fail to reveal important anatomical details. To better visualize such structures in the macaque brain, we applied a relatively new method called quantitative susceptibility mapping (QSM), which enhances tissue contrast based on the local tissue magnetic susceptibility. To evaluate the visualization of important structures, we quantified the the contrast-to-noise ratios (CNRs) of the ventral pallidum (VP), globus pallidus external and internal segments (GPe and GPi), substantia nigra (SN), subthalamic nucleus (STN) in the basal ganglia and the dentate nucleus (DN) in the cerebellum. For these structures, the QSM method significantly increased the CNR, and thus the visibility, beyond that in either the T1w or T2w images. In addition, QSM values of some structures were correlated to the age of the macaque subjects. These results indicate that the QSM method can enable the clear identification of certain subcortical structures that are invisible in more traditional scanning sequences. Highlights ### Competing Interest Statement The authors have declared no competing interest. * AC : anterior commissure CNR : contrast-to-noise ratio CdB : body of caudate nucleus CdH : head of caudate nucleus CdT : tail of caudate nucleus DBS : deep brain stimulation DN : dentate nucleus GPe : globus pallidus external segment GPi : globus pallidus internal segment IC : internal capsule GRE : gradient echo MCP : middle cerebellar peduncle MPRAGE : magnetization prepared rapid gradient echo MRI : magnetic resonance imaging NHP : non-human primate NMT : NIMH macaque template OT : optic tract Put : putamen QSM : quantitative susceptibility mapping ROI : region of interest SARM : subcortical atlas of the rhesus macaque SN : substantia nigra SPACE : sampling perfection with application optimized contrasts using different flip angle evolution STN : subthalamic nucleus T1w : T1-weighted T2w : T2-weighted TE : echo time TR : repetition time 3D : three-dimensional VP : ventral pallidum