Inner SPACE: 400-Micron Isotropic Resolution MRI of the Human Brain.

Mary Bruno,Arline Faustin,Timothy M Shepherd,Michael J Hoch,Stephen E Jones,Thomas Wisniewski,Orrin Devinsky,Antonios Papaioannou

doi:10.3389/fnana.2020.00009

Abstract

ObjectivesClinically relevant neuroanatomy is challenging to teach, learn and remember since many functionally important structures are visualized best using histology stains from serial 2D planar sections of the brain. In clinical patients, the locations of specific structures then must be inferred from spatial position and surface anatomy. A 3D MRI dataset of neuroanatomy has several advantages including simultaneous multi-planar visualization in the same brain, direct end-user manipulation of the data and image contrast identical to clinical MRI. We created 3D MRI datasets of the postmortem brain with high spatial and contrast resolution for simultaneous multi-planar visualization of complex neuroanatomy.Materials and MethodsWhole human brains (N = 6) were immersion-fixed in 4% formaldehyde for 4 weeks, then washed continuously in water for 48 h. The brains were imaged on a clinical 3-T MRI scanner with a 64-channel head and neck coil using a 3D T2-weighted sequence with 400-micron isotropic resolution (voxel = 0.064 mm3; time = 7 h). Besides resolution, this sequence has multiple adjustments to improve contrast compared to a clinical protocol, including 93% reduced turbo factor and 77% reduced effective echo time.ResultsThis MRI microscopy protocol provided excellent contrast resolution of small nuclei and internal myelinated pathways within the basal ganglia, thalamus, brainstem, and cerebellum. Contrast was sufficient to visualize the presence and variation of horizontal layers in the cerebral cortex. 3D isotropic resolution datasets facilitated simultaneous multi-planar visualization and efficient production of specific tailored oblique image orientations to improve understanding of complex neuroanatomy.ConclusionWe created an unlabeled high-resolution digital 3D MRI dataset of neuroanatomy as an online resource for readers to download, manipulate, annotate and use for clinical practice, research, and teaching that is complementary to traditional histology-based atlases. Digital MRI contrast is quantifiable, reproducible across brains and could help validate novel MRI strategies for in vivo structure visualization.

Highlights

State-of-the-art clinical MRI provides excellent soft tissue contrast, yet does not resolve much of the complex, intricate internal anatomy of the human brain
We demonstrate using a 3D T2-weighted sequence to characterize the human brain with 400-μm isotropic resolution (0.064 mm3 isotropic voxels)
A systematic annotated atlas of neuroanatomy is beyond the scope of this brief report, but the reader is encouraged to explore the data further

Summary

Introduction

State-of-the-art clinical MRI provides excellent soft tissue contrast, yet does not resolve much of the complex, intricate internal anatomy of the human brain. Stereotactic atlases improve indirect structure localization (Schaltenbrand and Wahren, 1977), but do not account for individual variation and left-right asymmetries (Niemann and van Nieuwenhofen, 1999), or changes from aging and disease This limits our ability to use MRI to recognize pathologic involvement of specific structures in individual clinical patients or quantify subtle changes during research investigations. Indirect anatomic targeting for functional neurosurgery limits our understanding of how this treatment works (Littlechild et al, 2003; Plaha et al, 2006) To help address this problem, several groups have provided labeled, high spatial resolution MRI datasets of individual brains using conventional MRI sequences and contrasts (Shen et al, 2012; Cho et al, 2015; Lusebrink et al, 2017)

Objectives

Methods

Results

Discussion

Conclusion