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Atlas-guided Segmentation of Vervet Monkey Brain MRI

1Surgical Planning Laboratory, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
2General Electric Global Research, Niskayuna, NY, USA.
3Bioimaging Systems Laboratory, Bradley Department of Electrical and Computer Engineering, Virginia Tech, Blacksburg, VA, USA.
4Department of Radiology, University of Pennsylvania, Philadelphia, PA, USA.
5Psychiatry Neuroimaging Laboratory, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
6Neuro Image Research and Analysis Laboratories, Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
7Department of Psychiatry, Duke University, Durham, NC, USA.
8Department of Physiology & Pharmacology, Wake Forest University Health Sciences, Winston-Salem, NC, USA.
Betham Open
Publication Date:
Open Neuroimag J.
Volume Number:
Issue Number:
Open Neuroimag J. 2011 Dec;5:186-97.
PubMed ID:
Vervet monkey, brain MRI, brain morphology, image segmentation, image registration, open source software, 3D Slicer
Appears in Collections:
R01 AG019771/AG/NIA NIH HHS/United States
U24 AG021886/AG/NIA NIH HHS/United States
R03 EB008674/EB/NIBIB NIH HHS/United States
U01 AG024904/AG/NIA NIH HHS/United States
U54 EB005149/EB/NIBIB NIH HHS/United States
R01 CA101318/CA/NCI NIH HHS/United States
T15 LM007117/LM/NLM NIH HHS/United States
ARRA supplement to P41 RR013218/RR/NCRR NIH HHS/United States
Generated Citation:
Fedorov A., Li X., Pohl K.M., Bouix S., Styner M., Addicott M., Wyatt C., Daunais J.B., Wells III W.M., Kikinis R. Atlas-guided Segmentation of Vervet Monkey Brain MRI. Open Neuroimag J. 2011 Dec;5:186-97. PMID: 22253661. PMCID: PMC3256578.
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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 analy-sis 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 seg-mentation. The comparison of atlas construction strategies reveals that the use of a population-specific atlas leads to im-proved 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.

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