An ontologically consistent MRI-based atlas of the mouse diencephalon

Charles Watson; Andrew L Janke; Carlo Hamalainen; Shahrzad M Bagheri; George Paxinos; David C Reutens; Jeremy F P Ullmann

doi:10.1016/j.neuroimage.2017.05.057

An ontologically consistent MRI-based atlas of the mouse diencephalon

Neuroimage. 2017 Aug 15:157:275-287. doi: 10.1016/j.neuroimage.2017.05.057. Epub 2017 May 31.

Authors

Charles Watson¹, Andrew L Janke², Carlo Hamalainen³, Shahrzad M Bagheri³, George Paxinos⁴, David C Reutens², Jeremy F P Ullmann⁵

Affiliations

¹ The Australian Mouse Brain Mapping Consortium, The University of Queensland, Brisbane, Australia; Health Sciences, Curtin University, Perth, Western Australia, Australia; Neuroscience Research Australia and The University of New South Wales, Sydney, Australia. Electronic address: c.watson@curtin.edu.au.
² The Australian Mouse Brain Mapping Consortium, The University of Queensland, Brisbane, Australia; Centre for Advanced Imaging, The University of Queensland, Brisbane, Australia.
³ Centre for Advanced Imaging, The University of Queensland, Brisbane, Australia.
⁴ Neuroscience Research Australia and The University of New South Wales, Sydney, Australia.
⁵ The Australian Mouse Brain Mapping Consortium, The University of Queensland, Brisbane, Australia; Centre for Advanced Imaging, The University of Queensland, Brisbane, Australia; Department of Neurology, Boston Children's Hospital, Boston, MA, USA.

PMID: 28578128
DOI: 10.1016/j.neuroimage.2017.05.057

Abstract

In topological terms, the diencephalon lies between the hypothalamus and the midbrain. It is made up of three segments, prosomere 1 (pretectum), prosomere 2 (thalamus), and prosomere 3 (the prethalamus). A number of MRI-based atlases of different parts of the mouse brain have already been published, but none of them displays the segments the diencephalon and their component nuclei. In this study we present a new volumetric atlas identifying 89 structures in the diencephalon of the male C57BL/6J 12 week mouse. This atlas is based on an average of MR scans of 18 mouse brains imaged with a 16.4T scanner. This atlas is available for download at www.imaging.org.au/AMBMC. Additionally, we have created an FSL package to enable nonlinear registration of novel data sets to the AMBMC model and subsequent automatic segmentation.

Keywords: Diencephalon; MRI; Pretectum; Prethalamus; Segmentation; Thalamus.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Animals
Atlases as Topic*
Diencephalon / anatomy & histology*
Diencephalon / diagnostic imaging*
Magnetic Resonance Imaging / methods*
Male
Mice / anatomy & histology*
Mice, Inbred C57BL