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
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.
 Files in This Data Supplement
All datasets associated with this publication are available from CIVMSpace, our
Web-based data portal.
| 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 |
| ClrMap_avg8 | 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 |
System Requirements:
CIVMSpace is designed to work on the Microsoft Windows and Mac OS X platforms.
Supported browsers on Windows are Internet Explorer versions 6.0 and above, and Mozilla Firefox versions 1.0 and above.
On the Mac, Safari versions 1.3 and above and Mozilla Firefox versions 1.0 and above are supported.
VoxStation requires a working Java installation. It has been tested with Java 1.4, 1.5 and 1.6 on Windows, and Java 1.4 and 1.5 on Mac OS X.
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
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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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