The SIGMA rat brain templates and atlases for multimodal MRI data analysis and visualization

T M Jay,F Boumezbeur,R Magalhães,A Novais,S Mériaux,P Marques,M Bottlaender,E Selingue,J C Sousa,A Cachia,F Marques,J Cerqueira,D A Barrière,F Geffroy,N Sousa

doi:10.1038/s41467-019-13575-7

Abstract

Preclinical imaging studies offer a unique access to the rat brain, allowing investigations that go beyond what is possible in human studies. Unfortunately, these techniques still suffer from a lack of dedicated and standardized neuroimaging tools, namely brain templates and descriptive atlases. Here, we present two rat brain MRI templates and their associated gray matter, white matter and cerebrospinal fluid probability maps, generated from ex vivo {mathrm{T}}_2^ ast-weighted images (90 µm isotropic resolution) and in vivo T2-weighted images (150 µm isotropic resolution). In association with these templates, we also provide both anatomical and functional 3D brain atlases, respectively derived from the merging of the Waxholm and Tohoku atlases, and analysis of resting-state functional MRI data. Finally, we propose a complete set of preclinical MRI reference resources, compatible with common neuroimaging software, for the investigation of rat brain structures and functions.

Highlights

Preclinical imaging studies offer a unique access to the rat brain, allowing investigations that go beyond what is possible in human studies
We were able to confirm that our Multiple Gradient Echo (MGE) imaging strategy, especially the parametrization of echoes and acquisition matrix, results in a high contrast-tonoise ratio (CNR) between the two main tissue classes (WM and GM) and has a spatial resolution simultaneously capable of capturing anatomical detail while limiting the influence of magnetic susceptibility artifacts present in TÃ2-weighted images (Supplementary Fig. 1)
It is noteworthy that the Waxholm template corresponding to a single anatomical image does not provide any tissue probability maps (TPMs), and the DPABI template defines only two of the three tissue classes and as such is unable to distinguish GM and WM

Summary

Introduction

Preclinical imaging studies offer a unique access to the rat brain, allowing investigations that go beyond what is possible in human studies These techniques still suffer from a lack of dedicated and standardized neuroimaging tools, namely brain templates and descriptive atlases. We present two rat brain MRI templates and their associated gray matter, white matter and cerebrospinal fluid probability maps, generated from ex vivo TÃ2-weighted images (90 μm isotropic resolution) and in vivo T2-weighted images (150 μm isotropic resolution). In association with these templates, we provide both anatomical and functional 3D brain atlases, respectively derived from the merging of the Waxholm and Tohoku atlases, and analysis of resting-state functional MRI data. We propose a complete set of preclinical MRI reference resources, compatible with common neuroimaging software, for the investigation of rat brain structures and functions

Objectives

Methods

Results

Conclusion