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Supplemental Material for:

Microscopic Diffusion Tensor Atlas of the Mouse Brain

Yi Jiang, G. Allan Johnson
NeuroImage 56(3): 1235-1243, 1 June 2011



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 6540 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.

Files in This Data Supplement

All datasets associated with this publication are available from CIVMSpace, our Web-based data portal.

Data downloaded from this site is for academic use only. If you use this data in a publication please send us a request for copyright permission and appropriate acknowledgements. Licenses can be granted for commercial use.
Contact the Center for permission.



T1_avg8T1 contrast, 2-byte (unsigned int), little-endian, 256x256x512, 43 micron/voxel
T2_avg8T2* contrast, 2-byte (unsigned int), little-endian, 256x256x512, 43 micron/voxel
ClrMap_avg8RGB color map, 3x1 byte/voxel, 256x256x512, 43 micron/voxel
AD_avg8_meanmean 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_meanmean map of fractional anisotropy, 4-byte (float), little-endian, 256x256x512, 43 micron/voxel
FA_avg8_cvcoefficient of variation map of fractional anisotropy, 4-byte (float), little-endian, 256x256x512, 43 micron/voxel
ev0_angle_avg8_meanmean map of angular deviation of the primary eigenvector, 4-byte (float), little-endian, 256x256x512, 43 micron/voxel
WMatlas8probabilistic white matter map, 4-byte (float), little-endian, 256x256x512, 43 micron/voxel

System Requirements:
CIVMSpace is designed to work on most platforms and is supported in most browsers.

VoxStation requires a working Java installation.



From CIVMSpace, select any thumbnail to browse slices from the corresponding dataset. To view structure labels, select "Open in VoxStation" from the pull-down menu at the upper right corner of the CIVMSpace page, then select the "Go" button; this will launch VoxStation, a Java Web Start application that lets you view datasets in three planes.

Below is an example of a volume dataset (ClrMap_avg8.jpg) that can be found in CIVMSpace.

      

Acknowledgement

  • 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).

 

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