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

Nat Commun. 2019 Dec 13;10(1):5699. doi: 10.1038/s41467-019-13575-7.


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 [Formula: see text]-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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Atlases as Topic*
  • Brain Mapping / methods*
  • Cerebrospinal Fluid / diagnostic imaging
  • Cerebrospinal Fluid / physiology
  • Gray Matter / anatomy & histology
  • Gray Matter / diagnostic imaging
  • Gray Matter / physiology
  • Imaging, Three-Dimensional / methods*
  • Magnetic Resonance Imaging*
  • Male
  • Models, Animal
  • Rats
  • Rats, Wistar
  • Software
  • White Matter / anatomy & histology
  • White Matter / diagnostic imaging
  • White Matter / physiology