3D Exploration of the Brainstem in 50-Micron Resolution MRI

Abstract

The brainstem, a structure of vital importance in mammals, is currently becoming a principal focus in cognitive, affective, and clinical neuroscience. Midbrain, pontine and medullary structures serve as the conduit for signals between the forebrain and spinal cord, are the epicenter of cranial nerve-circuits and systems, and subserve such integrative functions as consciousness, emotional processing, pain, and motivation. In this study, we parcellated the nuclear masses and the principal fiber pathways that were visible in a high-resolution T2-weighted MRI dataset of 50-micron isotropic voxels of a postmortem human brainstem. Based on this analysis, we generated a detailed map of the human brainstem. To assess the validity of our maps, we compared our observations with histological maps of traditional human brainstem atlases. Given the unique capability of MRI-based morphometric analysis in generating and preserving the morphology of 3D objects from individual 2D sections, we reconstructed the motor, sensory and integrative neural systems of the brainstem and rendered them in 3D representations. We anticipate the utilization of these maps by the neuroimaging community for applications in basic neuroscience as well as in neurology, psychiatry, and neurosurgery, due to their versatile computational nature in 2D and 3D representations in a publicly available capacity.

A Topographic Atlas of the Human Brainstem in the Ponto-Mesencephalic Junction Plane

“…In this atlas, sections of the brainstem were numbered based on their distance from the obex. More recently, numerous human brainstem descriptions from MRI have been published (Naidich et al, 2007;Deistung et al, 2013;Bianciardi et al, 2015;Tang et al, 2018;Rushmore et al, 2020). Among these, the Duvernoy's non-stereotaxic atlas of the human brainstem correlates transverse histological brainstem sections with corresponding clinical 3T and 9.4T MRI (Naidich et al, 2007) and is still widely used.…”

“…Among these, the Duvernoy's non-stereotaxic atlas of the human brainstem correlates transverse histological brainstem sections with corresponding clinical 3T and 9.4T MRI (Naidich et al, 2007) and is still widely used. The recent work of Rushmore and collaborators offers a detailed map of the human brainstem based on MRI dataset composed of 50-micron isotropic voxels from a post-mortem human brain (Rushmore et al, 2020).…”

The Distributional Characteristics of Multiple Sclerosis Lesions on Quantitative Susceptibility Mapping and Their Correlation With Clinical Severity

“…In subtentorial areas, we found a positive correlation between ARR and the burden of rim-lesions, although their clinical consequences, based on supratentorial comparison with rim+ lesions, were modest. The infratentorial brain consists of abundant nuclei and compact fiber tracts ascending or descending to functionally connect the forebrain and spinal cord (38). In our study, the volume of lesions in subtentorial areas was relatively large compared with the lesion volumes in other regions, which may lead to the simultaneous involvement of multiple neural pathways and brainstem or cerebellum dysfunction (limb weakness, sensory loss, ataxia, etc.).…”

Structural Connectivity of Human Inferior Colliculus Subdivisions Using in vivo and post mortem Diffusion MRI Tractography

“…Three unique datasets were included in this study. The first is a post mortem human brainstem of a 65-year-old male who died of non-neurological natural causes ( Calabrese et al, 2015 ; Sitek et al, 2019 ; Rushmore et al, 2020 ; Adil et al, 2021 ). The tissue was removed approximately 24 h post mortem and fixed with 10% formalin solution for 2 weeks.…”