Hippocampal formation: MR image segmentation guide

High-resolution MR images were acquired using a 16.4T imaging system and the hippocampal formation was segmented using DISPLAY (1). To assist segmentation of the hippocampal formation, MR images of an adult male C57BL/6 mouse brain are provided as a series of unsegmented and segmented images in the coronal plane (example below). The 25 image sets at 300µm intervals commence approximately 0.80 mm caudal to bregma and ending 4.80 mm caudal to bregma. Follow the links to view series of segmented MR images. Details of the operational guidelines used for systematic segmentation of the hippocampal formation please refer to the segmentation guide.


Segmentation was based chiefly on the atlases of Franklin and Paxinos (2008), and Dong (2008). Please note, segmentation includes correction to region defined as perirhinal cortex in mouse, not shown in these atlases.


Download the data in MINC or NiFTI format here


ambmc-c57bl6-model-nonsym_v0.8 [ mnc | nii ]

Label files (including index)

ambmc-c57bl6-label-hippocampus_v0.8 [ mnc | nii ]


If you use this data please cite

Richards K, Watson C, Buckley RF, Kurniawan ND, Yang Z, Keller MD, Beare R, Bartlett PF, Egan GF, Galloway GJ, Paxinos G, Petrou S, Reutens DC. Segmentation of the mouse hippocampal formation in magnetic resonance images. Neuroimage. 2011 Oct 1;58(3):732-40. doi: 10.1016/j.neuroimage.2011.06.025. Epub 2011 Jun 17.

For more details about the segmentation please see Pubmed Link