The VALiDATe29 MRI Based Multi-Channel Atlas of the Squirrel Monkey Brain

Neuroinformatics. 2017 Oct;15(4):321-331. doi: 10.1007/s12021-017-9334-0.


We describe the development of the first digital atlas of the normal squirrel monkey brain and present the resulting product, VALiDATe29. The VALiDATe29 atlas is based on multiple types of magnetic resonance imaging (MRI) contrast acquired on 29 squirrel monkeys, and is created using unbiased, nonlinear registration techniques, resulting in a population-averaged stereotaxic coordinate system. The atlas consists of multiple anatomical templates (proton density, T1, and T2* weighted), diffusion MRI templates (fractional anisotropy and mean diffusivity), and ex vivo templates (fractional anisotropy and a structural MRI). In addition, the templates are combined with histologically defined cortical labels, and diffusion tractography defined white matter labels. The combination of intensity templates and image segmentations make this atlas suitable for the fundamental atlas applications of spatial normalization and label propagation. Together, this atlas facilitates 3D anatomical localization and region of interest delineation, and enables comparisons of experimental data across different subjects or across different experimental conditions. This article describes the atlas creation and its contents, and demonstrates the use of the VALiDATe29 atlas in typical applications. The atlas is freely available to the scientific community.

Keywords: Atlas; Brain; Diffusion MRI; Magnetic Resonance Imaging; Segmentation; Squirrel monkey; Template.

MeSH terms

  • Animals
  • Anisotropy
  • Brain / anatomy & histology*
  • Diffusion Magnetic Resonance Imaging / methods*
  • Female
  • Male
  • Saimiri / anatomy & histology*