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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.


Eighteen animals were perfused and fixed with 4% paraformaldehyde and 0.1% Magnevist®. Brains were extracted and incubated in 0.1% Magnevist/PB for 4 days, placed in Fomblin and imaged on a 16.4T (89mm) Bruker micro-imaging system using a 15 mm SAW coil (M2M Imaging, USA). MRI data were acquired using a 3D gradient echo sequence with TR/TE/FA= 50ms/12ms/30°, 82 KHz spectral bandwidth, and 8 excitations with an acquisition time of 5h 15mins to produce T1/T2*-weighted images at 30µm3 isotropic resolution. A complete protocol can be downloaded here.

For more details about the segmentation please see:

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

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 ]

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