Microscopic Diffusion Tensor Atlas of the Mouse Brain
Yi Jiang, G. Allan Johnson
NeuroImage 56(3): 1235-1243, 1 June 2011. PCMID: PMC3085633
Eight diffusion tensor imaging (DTI) datasets of normal adult mouse brains were acquired at 43-micron isotropic resolution (voxel volume ~80 pl) by using a streamlined protocol, including specimen fixation and staining, image acquisition, reconstruction, and normalization to a common reference space (called Waxholm Space). The precision of the registration was established by measuring displacement of 80 different landmarks in individual brains from the reference brain. The precision was better than 130 microns for 95% of the landmarks (overall landmark displacement is 65±40 microns, n=640). After confirming normalization accuracy, mean, and coefficient of variation atlases of DTI indices (anisotropy and diffusivity) were generated with potential application for both voxel-based and region of interest-based analysis. To examine consistency of DTI data among individual subjects in this study and difference in diffusion indices between separate brain structures within each subject, averaged values of DTI indices were computed in 9 white matter structures in each brain. The variation of the DTI indices across the population was very small, e.g., ~5% for axial diffusivity for each white matter structure, enabling confident differentiation of these structures within each subject. ANOVA tests indicated that the current protocol is able to provide consistent DTI data of individual brains, and also distinguish difference of diffusion indices between white matters. The data provide a critical addition to Waxholm Space, our online comprehensive atlas of the mouse brain.
CIVM makes many types of data acquired for published and yet unpublished studies available through our CIVM VoxPort application. Use of VoxPort is free. Registration is required. Register for VoxPort access now. A new browser window or tab will open.
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Instructions: Click on a link below. A new browser window or tab will open where you will be prompted to login to CIVMVoxPort. If you do not have login credentials, follow the instructions to register for access. After you login, come back to this page and re-click on a link below to go directly to the desired page.
| T1_avg8 | T1 contrast, 2-byte (unsigned int), little-endian, 256x256x512, 43 micron/voxel |
| T2_avg8 | T2* contrast, 2-byte (unsigned int), little-endian, 256x256x512, 43 micron/voxel |
| RGB color map, 3x1 byte/voxel, 256x256x512, 43 micron/voxel | |
| AD_avg8_mean | mean map of axial diffusivity, 4-byte (float), little-endian, 256x256x512, 43 micron/voxel |
| AD_avg8_cv | coefficient of variation map of axial diffusivity, 4-byte (float), little-endian, 256x256x512, 43 micron/voxel |
| RD_avg8_mean | mean map of radial diffusivity, 4-byte (float), little-endian, 256x256x512, 43 micron/voxel |
| RD_avg8_cv | coefficient of variation map of radial diffusivity, 4-byte (float), little-endian, 256x256x512, 43 micron/voxel |
| FA_avg8_mean | mean map of fractional anisotropy, 4-byte (float), little-endian, 256x256x512, 43 micron/voxel |
| FA_avg8_cv | coefficient of variation map of fractional anisotropy, 4-byte (float), little-endian, 256x256x512, 43 micron/voxel |
| ev0_angle_avg8_mean | mean map of angular deviation of the primary eigenvector, 4-byte (float), little-endian, 256x256x512, 43 micron/voxel |
| WMatlas8 | probabilistic white matter map, 4-byte (float), little-endian, 256x256x512, 43 micron/voxel |
Below is an example of a volume dataset (ClrMap_avg8.jpg) that can be found in CIVMVoxPort.
Acknowledgements
We are grateful to Boma Fubara for assistance in specimen preparation and anatomical region definition, Gary Cofer for assistance in MR acquisition, Alexandra Badea for assistance in anatomical region definition, and Sally Zimney for assistance in manuscript preparation. All work was performed at the Duke Center for In Vivo Microscopy, an NCRR National Biomedical Technology Research Center (P41 RR005959) and Small Animal Imaging Resource Program (U24 CA092656), with specific support from the Mouse Bioinformatics Research Network (U24 RR021760).
