A diffusion tensor MRI atlas of the post-mortem rhesus macaque brain

Supplemental Material for:

A diffusion tensor MRI atlas of the postmortem rhesus macaque brain

Evan Calabresea,b, Alexandra Badeaa, Christopher L. Coec, Gabriele R. Lubachc, Martin A. Stynerd, Yundi Shid, G. Allan Johnsona,b

  1. Center for In Vivo Microscopy, Department of Radiology, Duke University Medical Center
  2. Department of Biomedical Engineering, Duke University
  3. Harlow Center for Biological Psychology, University of Wisconsin-Madison
  4. Department of Computer Science, Department of Psychiatry, University of North Carolina-Chapel Hill


The rhesus macaque (Macaca mulatta) is the most widely used non-human primate for modeling the structure and function of the brain. Brain atlases, and particularly those based on magnetic resonance imaging (MRI), have become important tools for understanding normal brain structure, and for identifying structural abnormalities resulting from disease states, exposures, and/or aging. Diffusion tensor imaging (DTI)-based MRI brain atlases are widely used in both human and macaque brain imaging studies because of the unique contrasts, quantitative diffusion metrics, and diffusion tractography that they can provide. Previous MRI and DTI atlases of the rhesus brain have been limited by low contrast and/or low spatial resolution imaging. Here we present a microscopic resolution MRI/DTI atlas of the rhesus brain based on 10 post-mortem brain specimens. The atlas includes both structural MRI and DTI image data, a detailed three-dimensional segmentation of 242 anatomic structures, diffusion tractography, cortical thickness estimates, and maps of anatomic variability amongst atlas specimens. This atlas incorporates many useful features from previous work, including anatomic label nomenclature and ontology, data orientation, and stereotaxic reference frame, and further extends prior analyses with the inclusion of high-resolution multi-contrast image data.

Published in Neuroimage 117: 408-416, 2015. PMCID: PMC4512905


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Please use the following acknowledgement: Imaging data provided by the Duke Center for In Vivo Microscopy NIH/NIBIB (P41 EB015897).


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All work was performed at the Duke Center for In Vivo Microscopy, an NIH /NIBIB Biomedical Technology Resource Center (P41 EB015897).
Other support was provided by NA-MIC Roadmap for Medical Research (U54 EB005149-01), NIMH (R01 MH091645), NICHD (U54 HD079124), and NIA (K01 AG041211). Brain specimens were provided by the Wisconsin National Primate Research Center (P51 OD011106).We thank Sally Gewalt and James Cook for assistance with the imaging pipelines; Dr. Yi Qi and Gary Cofer for assistance in specimen preparation and scanning; John Lee and David Joseph Lee for assistance with labeling; and Sally Zimney for assistance in editing.