UNC-Emory Infant Atlases for Macaque Brain Image Analysis: Postnatal Brain Development through 12 Months

Abstract

Computational anatomical atlases have shown to be of immense value in neuroimaging as they provide age appropriate reference spaces alongside ancillary anatomical information for automated analysis such as subcortical structural definitions, cortical parcellations or white fiber tract regions. Standard workflows in neuroimaging necessitate such atlases to be appropriately selected for the subject population of interest. This is especially of importance in early postnatal brain development, where rapid changes in brain shape and appearance render neuroimaging workflows sensitive to the appropriate atlas choice. We present here a set of novel computation atlases for structural MRI and Diffusion Tensor Imaging as crucial resource for the analysis of MRI data from non-human primate rhesus monkey (Macaca mulatta) data in early postnatal brain development. Forty socially-housed infant macaques were scanned longitudinally at ages 2 weeks, 3, 6, and 12 months in order to create cross-sectional structural and DTI atlases via unbiased atlas building at each of these ages. Probabilistic spatial prior definitions for the major tissue classes were trained on each atlas with expert manual segmentations. In this article we present the development and use of these atlases with publicly available tools, as well as the atlases themselves, which are publicly disseminated to the scientific community.

Population-averaged macaque brain atlas with high-resolution ex vivo DTI integrated into in vivo space

“…The higher resolution of this atlas, in contrast to those from in vivo DTI (e.g. Adluru et al, 2012; Zakszewski et al, 2014; Liu et al, 2015; Shi et al, 2017), is likely to offer anatomical information in finer detail. For example, the delineation of multiple tracts in a small region is clearly demonstrated in the most right panel of Fig 2a.…”

“…Huang et al, 2008) which are especially severe with the big sinuses in the macaque head. However, there are several tradeoffs with the high resolution postmortem DTI, compared to the macaque brain atlases based on in vivo DTI (Adluru et al, 2012; Zakszewski et al, 2014; Liu et al, 2015, Shi et al, 2017). The postmortem samples were shrunk due to the fixation process.…”

Postnatal Zika virus infection is associated with persistent abnormalities in brain structure, function, and behavior in infant macaques

“…Image processing steps included: 1) averaging T1 and T2 images to improve signal-to-noise ratio, 2) intensity inhomogeneity correction, 3) rigid body registration of the subject MRI to the three or the six months UNC-Emory infant RM atlases (35), 4) tissue segmentation and skull-stripping, 5) registration of the atlas to the subject’s brain to generate cortical parcellations (affine followed by deformable SyN/ANTS registration), 6) manual editing of the amygdala and hippocampus was done on all scans using previously published neuroanatomical boundaries (31). For more detailed description of the structural MRI analysis, see (87, 88).…”

“…After the EPI functional time series were concatenated and rigid-body registered to the subject’s T1-weighted structural image, this was transformed to conform to age-specific T1-weighted RM infant atlases (35) using non-linear registration methods in FSL (FNIRT). These atlases were registered to the 112RM-SL atlas in F99 space (96, 97).…”

“… (A) Depiction of Amygdala-Hippocampus resting state functional connectivity (FC) measured by rs-fMRI at six months of age displayed in the UNC-Emory RM infant atlas (35). Images show the same two coronal slice series in each subject with the seed (green) placed in the left amygdala and the FC r-values in the hippocampus colored according to the scale provided.…”