Mouse Diffusion Tensor Imaging (DTI) Atlas of developing mouse brains

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Embryonic and adult mouse brain images were acquired using three dimensional diffusion tensor magnetic resonance microimaging technique.


An atlas of developing mouse brains from embryonic and adult mouse brain images. The images were acquired using three dimensional diffusion tensor magnetic resonance microimaging technique. The atlas consists of a viewing software and diffusion tensor MR images from E14, E15, E16, E17, E18 and adult mouse brains.

MR Data Acquisition: Mouse brain specimens were fixed using 4% paraformaldehyde in phosphate-buffered saline (PBS) and stayed in fixation solution for over one month. Before imaging, we placed specimens in PBS for 24 hours, then transferred them into home-built MR-compatible tubes. The tubes were then filled with fombin (Fomblin Profludropolyether, Ausimont, Thorofare, New Jersey, USA) to prevent dehydration. Imaging was performed using a Bruker Biospin 500MHz (11.7 Tesla) spectrometer. Diffusion-weighted images were acquired with the field of view of approximately 12 mm x 9 mm x 9 mm. For diffusion-weighted images, the imaging matrix had a dimension of 128 x 100 x 100, which was zero-filled to 256 x 200 x 200 after the spectral data was apodized by a 10% trapezoidal function. The nominal resolution for embryonic images was approximately 40 ~ 45 micrometer per pixel isotropic. Eight to fourteen diffusion-weighted images were acquired with different diffusion gradient directions and magnitudes. For diffusion-weighted images, 3D fast spin echo imaging sequence was used with a repetition time (TR) of 0.9s, an echo time (TE) of 35 ms, and echo train length of 4, with four signal averages were used, for a total imaging time of 24 hours.

Data Processing: The diffusion tensor was calculated using a multivariant linear fitting method, and three pairs of eigen-values and eigen-vectors were calculated for each pixel. The eigen-vector associated with the largest eigen-value was referred to as the primary eigenvector. For the quantification of anisotropy, fractional anisotropy (FA) was used. Average diffusion weighted images (DW) were the sum of six diffusion weighted images with different diffusion gradient directions. Using primary eigen-vector and FA, color maps (V1FA) were calculated. In the color map images, the R(ed), G(reen), and B(lue) value of each pixel was defined by the orientation of its primary eigen-vector, and the intensity was proportional to the FA. Red was assigned to the fiber orientation along the anterior-posterior axis, green to the right-left axis, and blue to the dorsal-ventral axis.



AtlasView, a data viewer (see figure above), is included with the image data. It is for Windows 2000/XP only. The program can be started by double-clicking on it. AtlasView automatically loads image data and displays three orthogonal view of the image data. User can change the viewpoint by changing the slice number in area 1 in the figure below, and can change to image by selecting from a drop-down list in area 2.

Accession Number



Susumu Mori, Ph.D.
Jiangyang Zhang, Ph.D.
Linda J. Richards, Ph.D.
Paul Yarowksy, Ph.D.
Hangyi Jiang, Ph.D.
Peter C.M. van Zijl, Ph.D.


  • Three-Dimensional Diffusion Tensor Magnetic Resonance Microimaging of Adult Mouse Brain and Hippocampus J. Zhang, P.C.M. van Zijl, S. Mori, NeuroImage, Vol 15, Issue 4, Page 892-901, April 2002
  • Three-dimensional anatomical characterization of the developing mouse brain by diffusion tensor microimaging J. Zhang, L. Richards, P. Yarowsky, H. Huang, P.C.M. van Zijl, S. Mori, Vol. 20, Issue 3, Page 1639-1648, November 2003

Technical Contacts

Susumu Mori (susumu *AT*
Jiangyang Zhang (jzhang3 *AT*


This research was supported by NIH grants RO1 AG20012-01, RO3 HD41407-01A1 and P41 RR15241-01.


This page allows you to download the Mouse DTI Atlas. Due to the size of some of the files, the atlas has been split into individual downloads that are easier to retrieve.

Embryonic Development

  • MORI_embryonic_development [tgz] [zip] 352MB

Postnatal Development

  • msadult_2005 [tgz] [zip] 352MB
  • msp0_04_2002 [tgz] [zip] 49MB
  • msp10_071802 [tgz] [zip] 77MB
BIRN is supported by NIH grants 1U24-RR025736, U24-RR021992, U24-RR021760 and by the Collaborative Tools Support Network Award 1U24-RR026057-01.