Rhesus Macaque Brain Atlas Regions Aligned to an MRI Template

  • Jeffrey M. Moirano
  • Gleb Y. Bezgin
  • Elizabeth O. Ahlers
  • Rolf Kötter
  • Alexander K. ConverseEmail author
Original Article


To aid in the analysis of rhesus macaque brain images, we aligned digitized anatomical regions from the widely used atlas of Paxinos et al. to a published magnetic resonance imaging (MRI) template based on a large number of subjects. Digitally labelled atlas images were aligned to the template in 2D and then in 3D. The resulting grey matter regions appear qualitatively to be well registered to the template. To quantitatively validate the procedure, MR brain images of 20 rhesus macaques were aligned to the template along with regions drawn by hand in striatal and cortical areas in each subject’s MRI. There was good geometric overlap between the hand drawn regions and the template regions. Positron emission tomography (PET) images of the same subjects showing uptake of a dopamine D2 receptor ligand were aligned to the template space, and good agreement was found between tracer binding measures calculated using the hand drawn and template regions. In conclusion, an anatomically defined set of rhesus macaque brain regions has been aligned to an MRI template and has been validated for analysis of PET imaging in a subset of striatal and cortical areas. The entire set of over 200 regions is publicly available at

Graphical Abstract


Rhesus macaque Brain Atlas Regions of interest Positron emission tomography (PET) Magnetic resonance imaging (MRI) 



This work was primarily funded by NIH grant R21EB004482 to A.K.C. with additional support from R01AA012277, P50MH100031, and U54HD090256. G.Y.B. acknowledges JS McDonnell Collaborative Research Grant 220020255. The authors are grateful to Mary L. Schneider for the use of PET and MR images. The authors are grateful to Max Albiero, Erin Crain, Shilpa Cyriac, Sabrina Koehler, Parker Johnson, and Alysha Rameshk for assistance drawing and analyzing ROIs for validation.

Supplementary material

12021_2018_9400_MOESM1_ESM.pdf (718 kb)
ESM 1 (PDF 718 kb)


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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Waisman CenterUniversity of Wisconsin-MadisonMadisonUSA
  2. 2.Montreal Neurological InstituteMcGill UniversityMontrealCanada
  3. 3.Department of Neuroinformatics, Donders Institute for Brain, Cognition and BehaviourRadboud University NijmegenNijmegenThe Netherlands
  4. 4.C.& O. Vogt Brain Research InstituteHeinrich Heine UniversityDüsseldorfGermany
  5. 5.Institute of Anatomy IIHeinrich Heine UniversityDüsseldorfGermany

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