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

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 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.

Histologically derived fiber response functions for diffusion MRI vary across white matter fibers—An ex vivo validation study in the squirrel monkey brain

“…Different response functions can lead to different tractography results. A, Tractography is compared with an atlas of known connections (atlas and histology described in References and ; see Figure from reference and Figure B from reference for visualization of the ground truth pathways), by calculating the true positive and true negative rate of connections to various regions of interest. B, C, the sensitivity and specificity of the tractography results from Figure are plotted in a receiver operating characteristic curve using the default FOD threshold (B) and no FOD threshold (C).…”

“…The anatomical accuracy of tractography connections to labeled regions of interest was assessed by comparing results with known connections derived from histology and defined in the squirrel monkey atlas. 46,47 The atlas contains 71 white matter and gray matter ROIs, 44 of which are known to be connected to the left hemisphere primary motor cortex and 27 of which are not connected (ie do not show evidence of tracer after injection into the primary motor cortex). Following procedures similar to References 48 and 49, tractography results were binarized, and the presence or absence of streamlines in each ROI (both white and gray matter) was determined.…”

A Web-Based Atlas Combining MRI and Histology of the Squirrel Monkey Brain

“…Functionality includes scrolling, zooming, and panning throughout the atlas-space as well as overlays of labels and differing contrasts. VALiDATe29 data are made available with all other data content (https://www.nitrc.org/projects/smatlas/), as well as downloadable separately at https://www.nitrc.org/projects/validate29/ (K. G. Schilling et al 2017).…”

“…However, these are printed atlases and, unlike digital atlases, do not facilitate spatial normalization of new image information for quantitative comparisons of brains across subjects, time, or differing experimental conditions. In other species, atlases based on magnetic resonance imaging (MRI) have become valuable tools to reference the anatomy of the brain (Hsiao et al 2011; Sunkin et al 2013; Ding et al 2017; Woodward et al 2018; Frey et al 2011; Toga et al 1989) (http://observatory.brain-map.org/visualcoding, https://brainknowledge.mricloud.org/map%3Fmapname=wholebrain, http://www.thehumanbrain.info/brain/brain_navigator.php) Recently, we have introduced the first MRI atlas of the squirrel monkey brain to facilitate three-dimensional (3D) anatomical localization or segmentation, and to enable comparisons of experimental data across different subjects (K. G. Schilling et al 2017).…”

High angular resolution diffusion MRI reveals conserved and deviant programs in the paths that guide human cortical circuitry

“…To that end, we use structural MRI and atlases to measure the corpus callosum area from mid-sagittal sections in small-brained monkeys and largebrained rodents in order to control for variation in overall brain size. We supplement these data with previously published data (Charvet et al, 2019;Manger et al, 2010;Yuasa and Kohsaka, 2010;Schilling et al, 2017;Charvet et al, 2015). We use phylogeny-generalized-least-squares statistics (PGLS) to obtain phylogenetically-controlled slopes of the logged values of the area of corpus callosum versus the logged values of brain size (Pagel, 1999;Freckleton et al, 2000).…”