3-Dimensional Diffusion Tensor Imaging (DTI) Atlas of the Rat Brain

Anatomical atlases play an important role in the analysis of neuroimaging data in rodent neuroimaging studies. Having a high resolution, detailed atlas not only can expand understanding of rodent brain anatomy, but also enables automatic segmentation of new images, thus greatly increasing the efficiency of future analysis when applied to new data. These atlases can be used to analyze new scans of individual cases using a variety of automated segmentation methods. This project seeks to develop a set of detailed 3D anatomical atlases of the brain at postnatal day 5 (P5), 14 (P14), and adults (P72) in Sprague-Dawley rats. Our methods consisted of first creating a template image based on fixed scans of control rats, then manually segmenting various individual brain regions on the template. Using itk-SNAP software, subcortical and cortical regions, including both white matter and gray matter structures, were manually segmented in the axial, sagittal, and coronal planes. The P5, P14, and P72 atlases had 39, 45, and 29 regions segmented, respectively. These atlases have been made available to the broader research community

3-dimensional diffusion tensor imaging (DTI) atlas of the rat brain.

Anatomical atlases play an important role in the analysis of neuroimaging data in rodent neuroimaging studies. Having a high resolution, detailed atlas not only can expand understanding of rodent brain anatomy, but also enables automatic segmentation of new images, thus greatly increasing the efficiency of future analysis when applied to new data. These atlases can be used to analyze new scans of individual cases using a variety of automated segmentation methods. This project seeks to develop a set of detailed 3D anatomical atlases of the brain at postnatal day 5 (P5), 14 (P14), and adults (P72) in Sprague-Dawley rats. Our methods consisted of first creating a template image based on fixed scans of control rats, then manually segmenting various individual brain regions on the template. Using itk-SNAP software, subcortical and cortical regions, including both white matter and gray matter structures, were manually segmented in the axial, sagittal, and coronal planes. The P5, P14, and P72 atlases had 39, 45, and 29 regions segmented, respectively. These atlases have been made available to the broader research community

1) 2) The P72 fimbria (pink), fornix (purple), and 3^rd ventricle (blue) in a 3D mesh.

<p>2) The P72 internal capsule (pink) and amygdala (red), with the external capsule (green), body of the corpus callosum (orange), 3^rd ventricle (blue), caudate (light blue), thalamus (brown), and hypothalamus (teal) in the MD.</p

1) The P72 thalamus (brown), ac (yellow), hypothalamus (teal), VTA (navy), central gray (tan), superior (teal) and inferior (purple) colliculi, cerebellum (green), aqueduct, 3^rd, and 4^th ventricle (blue), genu (pink), body of the corpus callosum (orange), splenium (gold), and brain stem (green) in the MD.

<p>2) The P72 neocortex (blue), with the external capsule (green), ac (yellow), and olfactory bulb (pink) in the MD.</p

1) The P5 template MD image.

<p>2) The P5 cerebral peduncle (pink) with the hippocampus (red) and the thalamus (brown) in the MD.</p

1) The P14 template MD image.

<p>2) The P14 medial forebrain bundle (teal) and globus pallidus (lime green), with the caudate (light blue), lateral ventricles (dark blue), external capsule (light green), cingulum (dark green), and ac (yellow) in the MD.</p