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Supplemental Material for:

Microscopic Diffusion Tensor Imaging of the Mouse Brain

Yi Jiang, G. Allan Johnson

NeuroImage, 50(3):465-471.

Diffusion tensor imaging (DTI) data at 43 μm isotropic resolution has been acquired on the intact adult mouse brain in 28-hour scan time by using a streamlined protocol, including specimen fixation and staining, image acquisition, reconstruction, post-processing, and distribution. An intermediate registration of each component image is required to achieve the desired microscopic resolution. Multiple parameters have been derived including fractional anisotropy, axial and radial diffusivity, and a color-coded orientation map of the primary eigenvector. Each DTI dataset was mapped to a common reference space to facilitate future standardized analysis. Fiber tracking has also been demonstrated, providing 3D connection information. This protocol to acquire high-resolution DTI data in a robust and repeatable fashion will serve as a foundation to quantitatively study mouse brain integrity and white matter architecture, at what we believe to be the highest spatial resolution yet attained.

Files in This Data Supplement

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

Tensor_090430_reg_re.dat   tensor, 4-byte (float), little-endian, xyzc, 256x256x512x6, 43 micron/voxel
va0_090430_re.datprimary eigenvalue, axial diffusivity, 4-byte (float), little-endian, 256x256x512, 43 micron/voxel
T2_090430_reg.datT2 contrast, 2-byte (unsigned int), little-endian, 256x256x512, 43 micron/voxel
T1_090430_reg.datT1 contrast, 2-byte (unsigned int), little-endian, 256x256x512, 43 micron/voxel
RD_090430_re.datRadial diffusivity, 4-byte (float), little-endian, 256x256x512, 43 micron/voxel
FA_090430_re.datfractional anisotropy, 4 byte (float), little-endian, 256x256x512, 43 micron/voxel
ev0_090430_re.datprimary eigenvector, 3x4 byte (float), little-endian, cxyz, 3x256x256x512, 43 micron/voxel
ClrMap_0430_re.datRGB color map, 3x1 byte/voxel, 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_0430_re.dat) that can be found in CIVMSpace.



  • We are grateful to Boma Fubara for assistance in specimen preparation and anatomical region definition, Gary Cofer for assistance in MR acquisition, Jeffrey Brandenburg for assistance in 3D visualization, Alexandra Badea for assistance in anatomical region definition and fiber tracking, 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 he Mouse Bioinformatics Research Network (U24 RR021760).



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