Multi-contrast anatomical subcortical structures parcellation

Pierre-Louis Bazin,Anneke Alkemade,Birte U Forstmann,Amanda G Henry,Martijn J Mulder

doi:10.7554/elife.59430

Abstract

The human subcortex is comprised of more than 450 individual nuclei which lie deep in the brain. Due to their small size and close proximity, up until now only 7% have been depicted in standard MRI atlases. Thus, the human subcortex can largely be considered as terra incognita. Here, we present a new open-source parcellation algorithm to automatically map the subcortex. The new algorithm has been tested on 17 prominent subcortical structures based on a large quantitative MRI dataset at 7 Tesla. It has been carefully validated against expert human raters and previous methods, and can easily be extended to other subcortical structures and applied to any quantitative MRI dataset. In sum, we hope this novel parcellation algorithm will facilitate functional and structural neuroimaging research into small subcortical nuclei and help to chart terra incognita.

Highlights

Subcortical brain structures are often neglected in neuroimaging studies due to their small size, limited inter-regional contrast, and weak signal-to-noise ratio in functional imaging (Forstmann et al, 2016; Johansen-Berg, 2013)
Evolutionary genetics even uncovered that in modern humans, Neanderthal-inherited alleles were preferentially down-regulated in subcortical and cerebellar regions compared to other brain regions (McCoy et al, 2017), suggesting these structures to be essential in making us human
Experience-based plasticity continuously remodels myelin (Tardif et al, 2016; Hill et al, 2018; Turner, 2019), iron and other magnetic substances accumulate with age or pathology (Andersen et al, 2014; Zhang et al, 2018), both bringing changes in the MRI appearance of subcortical regions with diverse tissue characteristics (Draganski et al, 2011; Keuken et al, 2017)

Summary

Introduction

Subcortical brain structures are often neglected in neuroimaging studies due to their small size, limited inter-regional contrast, and weak signal-to-noise ratio in functional imaging (Forstmann et al, 2016; Johansen-Berg, 2013) These small and diverse structures are prominent nodes in functional networks (Marquand et al, 2017; Ji et al, 2019), and they undergo pathological alterations already at early stages of neurodegenerative diseases (Andersen et al, 2014; Koshiyama et al, 2018). Evolutionary genetics even uncovered that in modern humans, Neanderthal-inherited alleles were preferentially down-regulated in subcortical and cerebellar regions compared to other brain regions (McCoy et al, 2017), suggesting these structures to be essential in making us human Despite their importance, these areas are difficult to image. Experience-based plasticity continuously remodels myelin (Tardif et al, 2016; Hill et al, 2018; Turner, 2019), iron and other magnetic substances accumulate with age or pathology (Andersen et al, 2014; Zhang et al, 2018), both bringing changes in the MRI appearance of subcortical regions with diverse tissue characteristics (Draganski et al, 2011; Keuken et al, 2017)

Methods

Results

Conclusion