3T MRI Whole-Brain Microscopy Discrimination of Subcortical Anatomy, Part 1: Brain Stem

AJNR Am J Neuroradiol. 2019 Mar;40(3):401-407. doi: 10.3174/ajnr.A5956. Epub 2019 Jan 31.


Background and purpose: The brain stem is compactly organized with life-sustaining sensorimotor and autonomic structures that can be affected by numerous pathologies but can be difficult to resolve on conventional MR imaging.

Materials and methods: We applied an optimized TSE T2 sequence to washed postmortem brain samples to reveal exquisite and reproducible brain stem anatomic MR imaging contrast comparable with histologic atlases. This resource-efficient approach can be performed across multiple whole-brain samples with relatively short acquisition times (2 hours per imaging plane) using clinical 3T MR imaging systems.

Results: We identified most brain stem structures at 7 canonical axial levels. Multiplanar or oblique planes illustrate the 3D course and spatial relationships of major brain stem white matter pathways. Measurements of the relative position, course, and cross-sectional area of these pathways across multiple samples allow estimation of pathway location in other samples or clinical subjects. Possible structure-function asymmetries in these pathways will require further study-that is, the cross-sectional area of the left corticospinal tract in the midpons appeared 20% larger (n = 13 brains, P < .10).

Conclusions: Compared with traditional atlases, multiplanar MR imaging contrast has advantages for learning and retaining brain stem anatomy for clinicians and trainees. Direct TSE MR imaging sequence discrimination of brain stem anatomy can help validate other MR imaging contrasts, such as diffusion tractography, or serve as a structural template for extracting quantitative MR imaging data in future postmortem investigations.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adult
  • Autopsy
  • Brain Stem / anatomy & histology*
  • Female
  • Humans
  • Image Processing, Computer-Assisted / methods*
  • Magnetic Resonance Imaging / methods*
  • Male
  • Microscopy
  • Neuroimaging / methods*
  • White Matter / anatomy & histology