Mapping the human subcortical auditory system using histology, postmortem MRI and in vivo MRI at 7T

Abstract

Studying the human subcortical auditory system non-invasively is challenging due to its small, densely packed structures deep within the brain. Additionally, the elaborate three-dimensional (3-D) structure of the system can be difficult to understand based on currently available 2-D schematics and animal models. Wfe addressed these issues using a combination of histological data, post mortem magnetic resonance imaging (MRI), and in vivo MRI at 7 Tesla. We created anatomical atlases based on state-of-the-art human histology (BigBrain) and postmortem MRI (50 µm). We measured functional MRI (fMRI) responses to natural sounds and demonstrate that the functional localization of subcortical structures is reliable within individual participants who were scanned in two different experiments. Further, a group functional atlas derived from the functional data locates these structures with a median distance below 2 mm. Using diffusion MRI tractography, we revealed structural connectivity maps of the human subcortical auditory pathway both in vivo (1050 µm isotropic resolution) and post mortem (200 µm isotropic resolution). This work captures current MRI capabilities for investigating the human subcortical auditory system, describes challenges that remain, and contributes novel, openly available data, atlases, and tools for researching the human auditory system.

What are the gray and white matter volumes of the human spinal cord?

“…The analysis of post-mortem tissue where scanning time is no restriction opens up new possibilities. The combination of high-strength magnetic fields in a smaller bore absent of mechanical movement artifacts and where the tissue, in a signal-free, non-distorting fluid, can be advanced through the smaller scanning region with strong gradients allows for unprecedented spatial resolutions (Atik et al, 2019;Sitek et al, 2019;Calabrese et al, 2018;Colon-Perez et al, 2015;Lundell et al, 2011). In the present study, we use a small bore strong field (9.4T) scanner where a post-mortem ex-vivo spinal cord is advanced using a stepping motor through a small region of about 2 cm of scanning area with constant field strength and homogeneous gradient.…”

Improving a probabilistic cytoarchitectonic atlas of auditory cortex using a novel method for inter-individual alignment

“…We have used the dataset 2 described in ( Sitek et al, 2019 ). This dataset includes: (I) T 1 weighted (T 1 w), proton density weighted (PDw) and weighted anatomical images collected (using a modified MPRAGE sequence) at a resolution of 0.7 mm isotropic (whole brain); (II) functional images at collected at a resolution of 1.1 mm isotropic (partial coverage, coronal-oblique slab, multi band factor=2; GRAPPA = 3) in response to the presentation of natural sounds (168 natural sounds; 24 runs divided in four cross validation splits of 18 training and 6 testing runs each (126 training sounds and 42 testing sounds per split).…”

Multi-contrast Anatomical Subcortical Structures Parcellation

“…Besides serious difficulties in obtaining adequate measures of subcortical neural activity in functional MRI (de Hollander et al, 2017;Miletic et al, 2020), atlases and techniques for labeling accurately and reliably individual subcortical structures have also been scarce (Frazier et al, 2005;Chakravarty et al, 2006;Ahsan et al, 2007;Yelnik et al, 2007;Qiu et al, 2010;Patenaude et al, 2011), typically labelling the thalamus, striatum (or its subdivision into caudate and putamen), and globus pallidus (internal and external segments combined), sometimes the amygdala. However, recent advances in anatomical MRI, combining multiple contrasts and/or quantitative MRI mapping and utilizing the higher resolution achievable with 7 Tesla (7T) and above have started to reduce the gap, each mapping a few additional structures or sub-structures, primarily the iron-rich substantia nigra, red nucleus and sub-thalamic nucleus (Keuken et al, 2014;Xiao et al, 2015;Visser et al, 2016a;Visser et al, 2016b;Wang et al, 2016;Makowski et al, 2018;Ewert et al, 2018;Iglesias et al, 2018;Pauli et al, 2018;Sitek et al, 2019). While these efforts generated valuable atlases, they do not yet enable to identify many subcortical structures in individual subjects.…”