HumanBrainAtlas: an in vivo MRI dataset for detailed segmentations

Abstract

We introduce HumanBrainAtlas, an initiative to construct a highly detailed, open-access atlas of the living human brain that combines high-resolution in vivo MR imaging and detailed segmentations previously possible only in histological preparations. Here, we present and evaluate the first step of this initiative: a comprehensive dataset of two healthy male volunteers reconstructed to a 0.25 mm3 isotropic resolution for T1w, T2w and DWI contrasts. Multiple high-resolution acquisitions were collected for each contrast and each participant, followed by averaging using symmetric group-wise normalisation (Advanced Normalisation Tools). The resulting image quality permits structural parcellations rivalling histology-based atlases, while maintaining the advantages of in vivo MRI. For example, components of the thalamus, hypothalamus, and hippocampus - difficult or often impossible to identify using standard MRI protocols, can be identified within the present data. Our data are virtually distortion free, fully 3D, and compatible with existing in vivo Neuroimaging analysis tools. The dataset is suitable for teaching and is publicly available via our website (www.hba.neura.edu.au), which also provides data processing scripts. Instead of focusing on coordinates in an averaged brain space, our approach focuses on providing an example segmentation at great detail in the high quality individual brain, this serves as an illustration on what features contrasts and relations can be used to interpret MRI datasets, in research, clinical and education settings.

Advances in Neuroanatomy through Brain Atlasing

“…In the modality category, the major advancement has been from postmortem to in vivo data enabled by neuroimaging allowing to accomplish a "living neuroanatomy". Furthermore, more detailed neuroanatomical images with better quality are feasible in brain atlasing due to the increased teslage of the acquired MRI neuroimages, namely, from 1.5T [78] to 3T [45,53] to 7T [52,[79][80][81][82][83] to 9.4T [84].…”

Mesoscopic in vivo human T2* dataset acquired using quantitative MRI at 7 Tesla

“…Recently, MRI at ultra-high magnetic field strength (≥7 Tesla) has breached the mesoscopic scale, which we define as resolutions between 0.1 mm and 0.5 mm (Edwards et al, 2018). Particularly, openly accessible datasets by Bollmann et al (2022), Federau and Gallichan (2016), Lüsebrink et al (2021), and Lüsebrink et al (2017), Schira et al (2022) have facilitated the incorporation of mesoscopic MRI into the toolkit of practicing neuroscientists. However, despite the rich variety of MRI contrasts acquired by the previous work (Barbier et al, 2002; Bollmann et al, 2022; Bridge et al, 2005; Budde et al, 2011; Dinse et al, 2015; Duyn et al, 2007; Federau & Gallichan, 2016; Fracasso et al, 2016; Kemper et al, 2018; Lüsebrink et al, 2021; Lüsebrink et al, 2017; Mattern et al, 2018; Petridou et al, 2010; Sanchez Panchuelo et al, 2021a; Sánchez-Panchuelo et al, 2012; Schira et al, 2022; Tardif et al, 2015; Trampel et al, 2011; Turner et al, 2008; Zwanenburg et al, 2011), there has been no openly accessible quantitative in vivo human T 2 * measurements at mesoscopic resolution (see Supplementary Table 1) .…”