The VALiDATe29 MRI Based Multi-Channel Atlas of the Squirrel Monkey Brain
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ORIGINAL ARTICLE
The VALiDATe29 MRI Based Multi-Channel Atlas of the Squirrel Monkey Brain Kurt G. Schilling 1,2 & Yurui Gao 1,2 & Iwona Stepniewska 3 & Tung-Lin Wu 1,2 & Feng Wang 1,4 & Bennett A. Landman 1,2,4,5 & John C. Gore 1,2,4 & Li Min Chen 1,4 & Adam W. Anderson 1,2,4
# Springer Science+Business Media, LLC 2017
Abstract 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 populationaveraged 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
* Kurt G. Schilling [email protected]
1
Vanderbilt University Institute of Imaging Science, Vanderbilt University, Nashville, TN, USA
2
Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
3
Department of Psychology, Vanderbilt University, Nashville, TN, USA
4
Radiology and Radiological Sciences, Vanderbilt University, Nashville, TN, USA
5
Department of Electrical Engineering, Vanderbilt University, Nashville, TN, USA
the use of the VALiDATe29 atlas in typical applications. The atlas is freely available to the scientific community. Keywords Brain . Atlas . Squirrel monkey . Magnetic Resonance Imaging . Template . Diffusion MRI . Segmentation
Introduction The creation and application of image-based brain atlases is widespread in neuroanatomy and neuroscience research. Atlases are used as reference spaces to describe brain anatomy, and are frequently composed of two types of images: intensity images (or Btemplates^), and segmented images (or Blabels^) (Cabezas et al. 2011). The template images establish a standard coordinate system which provides a common framework for reporting findings from neuroimaging experiments (Toga 1999). In a process called spatial normalization, new images are aligned with the templates and comparisons of brains can be made across subjects, time, or differing experimental conditions. In addition, the labelled images can be propagated from the atlas to the new data to identify regions of interest in a pro
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