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An MRI atlas of the mouse Basal Ganglia

The basal ganglia are group of subpallial nuclei that play an important role inmotor, emotional, and cognitive functions. Morphological changes and disrupted afferent/efferent connections in the basal ganglia have been associated with a variety of neurological disorders including psychiatric and movement disorders. While high-resolution magnetic resonance imaging has been used to characterize changes in brain structure in mouse models of these disorders no systematicmethod for segmentation of the C57BL/6J mouse basal ganglia exists. In thisstudy we have used high-resolution MR images of ex-vivo C57BL/6J mouse brain to create a detailed protocol for segmenting the basal ganglia. We created a three-dimensional minimum deformation atlas, which includes the segmentation of 35 striatal, pallidal, and basal ganglia-related structures. In addition, we provide mean volumes, mean T2 contrast intensities and mean FA and ADC values for each structure. This MR atlas is available for download, and enables researchers to perform automated segmentation in genetic models of basal ganglia 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.

If you use this data please cite:

Ullmann, J.F.P., Watson, C., Janke, A.L., Kurniawan, N.D., Paxinos, G. Reutens, D.C. A segmentation protocol and MRI atlas of the C57BL/6J mouse basal ganglia. Brain Structure Function, 2013, DOI: 10.1007/s00429-013-0572-0

Download the data in MINC or NiFTI format here:


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

Label files (including index)

   ambmc-c57bl6-label-basalganglia_v0.8 [ mnc | nii ]

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