Atlas-Guided Segmentation of Vervet Monkey Brain MRI

Andriy Fedorov*, 1, Xiaoxing Li 2, Kilian M Pohl 4, Sylvain Bouix 5, Martin Styner 6, Merideth Addicott 7, Chris Wyatt 3, James B Daunais 8, William M Wells 1, Ron Kikinis 1
1 Surgical Planning Laboratory, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115
2 General Electric Global Research, Niskayuna, NY 12309
3 Bioimaging Systems Laboratory, Bradley Dept of Electrical and Computer Engineering, Virginia Tech, Blacksburg, VA 24061
4 Department of Radiology, University of Pennsylvania, Philadelphia, PA 19104
5 Psychiatry Neuroimaging Laboratory, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115
6 Neuro Image Research and Analysis Laboratories, Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
7 Department of Psychiatry, Duke University, Durham, NC 27708
8 Department of Physiology & Pharmacology, Wake Forest University Health Sciences, Winston-Salem, NC 27157, USA

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© Fedorov et al; Licensee Bentham Open

open-access license: This is an open access article licensed under the terms of the Creative Commons Attribution Non-Commercial License ( which permits unrestricted, non-commercial use, distribution and reproduction in any medium, provided the work is properly cited.

* Address correspondence to this author at the Brigham and Women's Hospital, Harvard Medical School, 75 Francis Street, Boston, MA 02115, USA; Tel: 617) 525-6258; E-mail:


The vervet monkey is an important nonhuman primate model that allows the study of isolated environmental factors in a controlled environment. Analysis of monkey MRI often suffers from lower quality images compared with human MRI because clinical equipment is typically used to image the smaller monkey brain and higher spatial resolution is required. This, together with the anatomical differences of the monkey brains, complicates the use of neuroimage analysis pipelines tuned for human MRI analysis. In this paper we developed an open source image analysis framework based on the tools available within the 3D Slicer software to support a biological study that investigates the effect of chronic ethanol exposure on brain morphometry in a longitudinally followed population of male vervets. We first developed a computerized atlas of vervet monkey brain MRI, which was used to encode the typical appearance of the individual brain structures in MRI and their spatial distribution. The atlas was then used as a spatial prior during automatic segmentation to process two longitudinal scans per subject. Our evaluation confirms the consistency and reliability of the automatic segmentation. The comparison of atlas construction strategies reveals that the use of a population-specific atlas leads to improved accuracy of the segmentation for subcortical brain structures. The contribution of this work is twofold. First, we describe an image processing workflow specifically tuned towards the analysis of vervet MRI that consists solely of the open source software tools. Second, we develop a digital atlas of vervet monkey brain MRIs to enable similar studies that rely on the vervet model.

Keywords: Vervet monkey, brain MRI, brain morphology, image segmentation, image registration, open source software, 3D Slicer.