A segmentation protocol and MRI atlas of the C57BL/6J mouse neocortex

The neocortex is the largest component of the mammalian cerebral cortex. It integrates sensory inputs with experiences and memory, to produce sophisticated responses to an organism’s internal and external environment. While areal patterning of the mouse neocortex has been mapped using histological techniques, the neocortex has not been comprehensively segmented in magnetic resonance images. This study presents a method for systematic segmentation of the C57BL/6J mouse neocortex. We created a minimum deformation atlas, which was placed into Waxholm space and has been hierarchically segmented into 74 neocortical and cortical-related regions, making it the most detailed atlas of the mouse neocortex currently available. In addition, we provide mean volumes and contrast intensities for each structure as well as a nomenclature comparison between the two most cited histological atlases of the mouse brain. This MR atlas is available for download, and it should enable researchers to perform automated segmentation in genetic models of cortical disorders.

Method linked here


Download the data in MINC or NiFTI format here


ambmc-c57bl6-model-symmet_v0.8 [ mnc | nii ]

Label files (including index)

ambmc-c57bl6-label-cortex_v0.8 [ mnc | nii ]


If you use this data please cite

Ullmann, J.F.P., Watson, C., Janke, A.L., Kurniawan, N.D., Reutens, D.C. (2013) A segmentation protocol and MRI atlas of the C57BL/6J mouse neocortex. NeuroImage

For more details about the segmentation please see Pubmed Link