The Rat (Waxholm-80um) atlas is based on the brain of a 397.6 g male Sprague-Dawley rat. The brain was imaged with MR ex vivo, resulting in T2-weighted gradient echo images with 40 um isotropic spatial resolution. 76 brain structures were segmented [1, 2].
E. A. Papp prepared a version suitable for PMOD and made it available for download on nitrc.org: https://www.nitrc.org/projects/whs-sd-atlas/
An adapted version of this atlas is distributed with PMOD as a convenience to our users. Because the original 40um isotropic resolution is beyond typical in vivo MR and far beyond the resolution applicable for PET image analysis, it was down-sampled to 80um. The original text file associated with the atlas was re-organized to consecutively number the regions. Note: down-sampling left no actual voxels in regions 6,33,47,49,60,63 as numbered in the atlas text file.
Atlas Label Map and MR Normalization Template
3D Rendering of Atlas Regions
 Papp EA, Leergaard TB, Calabrese E, Johnson GA, JG (2014). Waxholm Space atlas of the Sprague Dawley rat brain. NeuroImage 97:374-386. doi: 10.1016/j.neuroimage.2014.04.001
 Kjonigsen LJ, Lillehaug S, Bjaalie JG, Witter MP, Leergaard TB (2015). Waxholm Space atlas of the rat brain hippocampal region: Three-dimensional delineations based on magnetic resonance and diffusion tensor imaging. NeuroImage 108:441-449. doi: 10.1016/j.neuroimage.2014.12.080