Visualizing Fiber Tracts in the Brain Using Diffusion Tensor Data

1. Visualizing Fiber Tractsin the BrainUsing Diffusion Tensor Data Masters Project Presentation Yoshihito Yagi Thursday, July 28th, 10:00 a.m. 499 Dirac Science Library

2. What does a brain look like? • A brain is composed of fibers, which connect the cortex to other parts of the brain and the spinal chord. • When lesions or tumors appear in the interior of the white matter of the brain, fibers might go around them, and it makes lesions and tumors visible. • Until now, in order to see fibers we had to cut into a brain.

3. Diffusion Tensor (DT) MRI • DT-MRI can be used to reconstruct fibers inside brain noninvasively. • There are two visualization methods using DT-MRI. • Glyph-based visualization • Fiber tracking method

4. Glyph-Based Visualization • 2D and 3D arrays of glyphs.

5. Fiber Tracking • Fiber Tracking can visualize the white matter connectivity.

6. What is a tensor? • A tensor with rank 2, dimension 3 is just a 3x3 matrix. • A matrix is used to represent the diffusion of water inside tissue.

7. Diffusion of Water • How the diffusion MRI relates to the diffusion of water is not fully understood. • The diffusion of microstructures is limited by the boundary of the long structure. • The diffusion is more along one direction than the others.

8. eigenvalues and eigenvectors • In this project, a matrix is symmetric positive definite. • There are only six distinct values. • A matrix has 3 eigenvectors, , and 3 positive real number eigenvalues, , where .

9. Anistropic Diffusion • Diffusion can be characterized by three anisotropic diffusion properties. Westin et.al proposed three measurements: Cl, Cp, Cs.

10. Liner Anisotropic Diffusion, Cl • If , then the diffusion occurs almost entirely along the e1 direction. • Define Cl that is 1 when the previous situation holds, and is less than 1 otherwise.

11. Planar Anisotropic Diffusion, Cp • If , then the diffusion is along 2 directions, e1 and e2. • Define Cp that is 1 when the previous situation holds, and is less than 1 otherwise.

12. Spherical Anisotropic Diffusion, Cs • i.e., Isotropic Diffusion. • If , then the diffusion occurs in every direction. • Define Cs such that:

13. What do these regions look like? • The regions of large Cl, Cp, Cs. • The region of white matter, like the corpus callosum, has a large Cl. • Fibers exist where Cl is large, and they are parallel due to a linear diffusion.

14. Fiber Tracking Algorithm • A fiber starts at the point where Cl is large, and it is integrated along e1. • e1is the largest diffusion.

15. Problem • Long integration leads you to the point where Cl is small.

16. Tensorline • This is proposed by Weinstein et al. • This used two additional vectors, Vinand Vout to calculate a propagation vector. • If Cl is small, then Vin has more weight.

17. The Goal of This Project • Our goal is to make pictures which look like those of dissected brains in the book. • We are improving realism in the display.

18. Realistic Illumination • Realistic illumination means global illumination (GI) which is the technique used to simulate indirect illumination. • Problem – GI uses surfaces instead of lines. • Solution – Around each line, create a polygonal mesh.

19. Global vs. Local

20. Cut-away • In all the preparations of the brains, we see that the brain has been cut into, in order to see the interior. • We use the same strategy.

21. Cut-away algorithm • We create an isosurface mesh of the basic anatomical MRI data, which yields the cortex of the brain. • There are a mesh S and two planes H1 and H2.

22. Cut-away images and movie • We clip the isosurface of the cortex in order to see inside the isosurfaces of Cl and Cp. • See a movie.

23. Global vs. Local

24. Density and radius of fibers • Since these fibers are merely suggestive of the actual anatomy of the white matter, their density and radius are free parameters.

25. Changing the density of fibers • The number of fibers are 300, 600, 1200 • The radius of fibers is 0.3

26. Placing more fibers and shrinking their radius • The number of fibers are 300, 600, 1200. • The radius of fibers are 0.6, 0.3, 0.15.

27. Interactive exploration of data • We implement several interactive tools which enable a user to manipulate data. • See a movie.

28. Highlighting fibers • If fibers are passing through active regions of the cortex, then they are highlighted. • The activated regions can be found from functional MRI.

29. Highlighting fibers • Highlighting fibers intersect with triangular meshes.

30. Novel Contribution • Highlighting fibers • Intersection of a fiber with a cortex triangular mesh • Global illumination

31. Laboratory for Mathematics in Imaging at Harvard Medical School. • We have collaborated with Gordon Kindleman at LMI. In fact, We use his brain data to construct 3D images. • Next year, Dr. Banks will spend fall 2005 at LMI in order to integrate the tools from this project into their clinical protocols.

32. Thanks • Dr. Banks (Adviser) • Dr. Ouimet, Dr. Liu (Committee) • Beason (Ray Tracer Pane) • Ji, Saka,Connor, Reece (Review my report)