Hippocampus Diencephalon


AMBMC » Cerebellum

Segmentation of the C57BL/6J mouse cerebellum in magnetic resonance images

The cerebellum is a major brain structure central for the voluntary control of the motor system and is implicated in a range of movement disorders. Mice are a well validated models for studying the human cerebellum and creation of digital atlases that can capture biological variability in control and diseased mice are critical for understanding the underlying basis of human neurological disease. As a result in this study we present a methodology for systematic delineation of the vermal and hemispheric lobules of the C57BL/6J mouse cerebellum in magnetic resonance images. We have successfully delineated 38 cerebellar and cerebellar-related structures.


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., Keller, M.D., Watson, C., Janke, A.L., Kurniawan, N.D., Yang, Z., Richards, K., Paxinos, G., Egan, G.F., Petrou, S., Bartlett, P., Galloway, G.J., Reutens, D.C. (2012) Segmentation of the C57BL/6J mouse cerebellum in magnetic resonance images. NeuroImage 62: 1408-1414.

Pubmed Link

There is also an ISMRM poster from 2012 here: Model Poster

Download the data in MINC or NiFTI format here:


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

Label files (including index)

   ambmc-c57bl6-label-cerebellum_v0.8 [ mnc | nii ]

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