An ontologically consistent MRI-based atlas of the mouse diencephalon

• Published in: NeuroImage (Orlando, Fla.) Vol. 157; pp. 275 - 287
• Main Authors: Watson, Charles, Janke, Andrew L., Hamalainen, Carlo, Bagheri, Shahrzad M., Paxinos, George, Reutens, David C., Ullmann, Jeremy F.P.
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 15.08.2017; Elsevier Limited; Elsevier
• Subjects: Algorithms; Animals; Atlases as Topic; Brain; Diencephalon; Diencephalon - anatomy & histology; Diencephalon - diagnostic imaging; Gene expression; Hypothalamus; Image processing; Magnetic resonance imaging; Magnetic Resonance Imaging - methods; Male; Mesencephalon; Mice - anatomy & histology; Mice, Inbred C57BL; MRI; Neuroimaging; NMR; Nuclear magnetic resonance; Ontology; Pretectum; Prethalamus; Rodents; Segmentation; Thalamus; United States > US; Thalamus; Pretectum; Segmentation; Diencephalon; MRI; Prethalamus
• ISSN: 1053-8119; 1095-9572
• DOI: 10.1016/j.neuroimage.2017.05.057

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. •A detailed atlas of high resolution images of the diencephalon of the C57Bl/6J mouse.•The atlas is based on data from an average of 18 brains imaged with a 16.4T MR scanner.•The MRI atlas is the first to employ a modern developmental ontology of the diencephalon.•This atlas is available for download at www.imaging.org.au/AMBMC.•We offer an FSL package to enable nonlinear registration of novel data sets to our model.