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![Page 1: Visualizing Fiber Tracts in the Brain Using Diffusion Tensor Data Masters Project Presentation Yoshihito Yagi Thursday, July 28 th, 10:00 a.m. 499 Dirac.](https://reader030.fdocuments.us/reader030/viewer/2022032709/56649eb65503460f94bbf62f/html5/thumbnails/1.jpg)
Visualizing Fiber Tractsin the Brain
Using Diffusion Tensor Data
Masters Project Presentation
Yoshihito Yagi
Thursday, July 28th, 10:00 a.m.
499 Dirac Science Library
![Page 2: Visualizing Fiber Tracts in the Brain Using Diffusion Tensor Data Masters Project Presentation Yoshihito Yagi Thursday, July 28 th, 10:00 a.m. 499 Dirac.](https://reader030.fdocuments.us/reader030/viewer/2022032709/56649eb65503460f94bbf62f/html5/thumbnails/2.jpg)
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.
![Page 3: Visualizing Fiber Tracts in the Brain Using Diffusion Tensor Data Masters Project Presentation Yoshihito Yagi Thursday, July 28 th, 10:00 a.m. 499 Dirac.](https://reader030.fdocuments.us/reader030/viewer/2022032709/56649eb65503460f94bbf62f/html5/thumbnails/3.jpg)
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
![Page 4: Visualizing Fiber Tracts in the Brain Using Diffusion Tensor Data Masters Project Presentation Yoshihito Yagi Thursday, July 28 th, 10:00 a.m. 499 Dirac.](https://reader030.fdocuments.us/reader030/viewer/2022032709/56649eb65503460f94bbf62f/html5/thumbnails/4.jpg)
Glyph-Based Visualization
• 2D and 3D arrays of glyphs.
![Page 5: Visualizing Fiber Tracts in the Brain Using Diffusion Tensor Data Masters Project Presentation Yoshihito Yagi Thursday, July 28 th, 10:00 a.m. 499 Dirac.](https://reader030.fdocuments.us/reader030/viewer/2022032709/56649eb65503460f94bbf62f/html5/thumbnails/5.jpg)
Fiber Tracking
• Fiber Tracking can visualize the white matter connectivity.
![Page 6: Visualizing Fiber Tracts in the Brain Using Diffusion Tensor Data Masters Project Presentation Yoshihito Yagi Thursday, July 28 th, 10:00 a.m. 499 Dirac.](https://reader030.fdocuments.us/reader030/viewer/2022032709/56649eb65503460f94bbf62f/html5/thumbnails/6.jpg)
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.
zzzyzx
yzyyyx
xzxyxx
DDD
DDD
DDD
![Page 7: Visualizing Fiber Tracts in the Brain Using Diffusion Tensor Data Masters Project Presentation Yoshihito Yagi Thursday, July 28 th, 10:00 a.m. 499 Dirac.](https://reader030.fdocuments.us/reader030/viewer/2022032709/56649eb65503460f94bbf62f/html5/thumbnails/7.jpg)
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.
![Page 8: Visualizing Fiber Tracts in the Brain Using Diffusion Tensor Data Masters Project Presentation Yoshihito Yagi Thursday, July 28 th, 10:00 a.m. 499 Dirac.](https://reader030.fdocuments.us/reader030/viewer/2022032709/56649eb65503460f94bbf62f/html5/thumbnails/8.jpg)
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 .
zzzyzx
yzyyyx
xzxyxx
DDD
DDD
DDD
zyyzzxxzyxxy DDDDDD ,,where
321 ,, eee
321 ,, 321
![Page 9: Visualizing Fiber Tracts in the Brain Using Diffusion Tensor Data Masters Project Presentation Yoshihito Yagi Thursday, July 28 th, 10:00 a.m. 499 Dirac.](https://reader030.fdocuments.us/reader030/viewer/2022032709/56649eb65503460f94bbf62f/html5/thumbnails/9.jpg)
Anistropic Diffusion
• Diffusion can be characterized by three anisotropic diffusion properties.
Westin et.al proposed three measurements: Cl, Cp, Cs.
.,, 332211 ebeger
![Page 10: Visualizing Fiber Tracts in the Brain Using Diffusion Tensor Data Masters Project Presentation Yoshihito Yagi Thursday, July 28 th, 10:00 a.m. 499 Dirac.](https://reader030.fdocuments.us/reader030/viewer/2022032709/56649eb65503460f94bbf62f/html5/thumbnails/10.jpg)
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.
0321
1)00(
)0(
)(
)(
1
1
321
21
lC
![Page 11: Visualizing Fiber Tracts in the Brain Using Diffusion Tensor Data Masters Project Presentation Yoshihito Yagi Thursday, July 28 th, 10:00 a.m. 499 Dirac.](https://reader030.fdocuments.us/reader030/viewer/2022032709/56649eb65503460f94bbf62f/html5/thumbnails/11.jpg)
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.
0321
1)0(
)0(2
)(
)(2
22
2
321
32
pC
![Page 12: Visualizing Fiber Tracts in the Brain Using Diffusion Tensor Data Masters Project Presentation Yoshihito Yagi Thursday, July 28 th, 10:00 a.m. 499 Dirac.](https://reader030.fdocuments.us/reader030/viewer/2022032709/56649eb65503460f94bbf62f/html5/thumbnails/12.jpg)
Spherical Anisotropic Diffusion, Cs
• i.e., Isotropic Diffusion.
• If , then the diffusion occurs in every direction.
• Define Cs such that:
321
1)(
3
)(
3
333
3
321
3
sC
![Page 13: Visualizing Fiber Tracts in the Brain Using Diffusion Tensor Data Masters Project Presentation Yoshihito Yagi Thursday, July 28 th, 10:00 a.m. 499 Dirac.](https://reader030.fdocuments.us/reader030/viewer/2022032709/56649eb65503460f94bbf62f/html5/thumbnails/13.jpg)
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.
![Page 14: Visualizing Fiber Tracts in the Brain Using Diffusion Tensor Data Masters Project Presentation Yoshihito Yagi Thursday, July 28 th, 10:00 a.m. 499 Dirac.](https://reader030.fdocuments.us/reader030/viewer/2022032709/56649eb65503460f94bbf62f/html5/thumbnails/14.jpg)
Fiber Tracking Algorithm
• A fiber starts at the point where Cl is large, and it is integrated along e1.
• e1 is the largest diffusion.
![Page 15: Visualizing Fiber Tracts in the Brain Using Diffusion Tensor Data Masters Project Presentation Yoshihito Yagi Thursday, July 28 th, 10:00 a.m. 499 Dirac.](https://reader030.fdocuments.us/reader030/viewer/2022032709/56649eb65503460f94bbf62f/html5/thumbnails/15.jpg)
Problem
• Long integration leads you to the point where Cl is small.
![Page 16: Visualizing Fiber Tracts in the Brain Using Diffusion Tensor Data Masters Project Presentation Yoshihito Yagi Thursday, July 28 th, 10:00 a.m. 499 Dirac.](https://reader030.fdocuments.us/reader030/viewer/2022032709/56649eb65503460f94bbf62f/html5/thumbnails/16.jpg)
Tensorline
• This is proposed by Weinstein et al.
• This used two additional vectors, Vin and Vout to calculate a propagation vector.
• If Cl is small, then Vin has more weight.
inout VDV ))1(()1(1 outinllprop VwVwCeCV
where weightwvectornpropagatiopreviousVin :,:
![Page 17: Visualizing Fiber Tracts in the Brain Using Diffusion Tensor Data Masters Project Presentation Yoshihito Yagi Thursday, July 28 th, 10:00 a.m. 499 Dirac.](https://reader030.fdocuments.us/reader030/viewer/2022032709/56649eb65503460f94bbf62f/html5/thumbnails/17.jpg)
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.
![Page 18: Visualizing Fiber Tracts in the Brain Using Diffusion Tensor Data Masters Project Presentation Yoshihito Yagi Thursday, July 28 th, 10:00 a.m. 499 Dirac.](https://reader030.fdocuments.us/reader030/viewer/2022032709/56649eb65503460f94bbf62f/html5/thumbnails/18.jpg)
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.
![Page 19: Visualizing Fiber Tracts in the Brain Using Diffusion Tensor Data Masters Project Presentation Yoshihito Yagi Thursday, July 28 th, 10:00 a.m. 499 Dirac.](https://reader030.fdocuments.us/reader030/viewer/2022032709/56649eb65503460f94bbf62f/html5/thumbnails/19.jpg)
Global vs. Local
![Page 20: Visualizing Fiber Tracts in the Brain Using Diffusion Tensor Data Masters Project Presentation Yoshihito Yagi Thursday, July 28 th, 10:00 a.m. 499 Dirac.](https://reader030.fdocuments.us/reader030/viewer/2022032709/56649eb65503460f94bbf62f/html5/thumbnails/20.jpg)
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.
![Page 21: Visualizing Fiber Tracts in the Brain Using Diffusion Tensor Data Masters Project Presentation Yoshihito Yagi Thursday, July 28 th, 10:00 a.m. 499 Dirac.](https://reader030.fdocuments.us/reader030/viewer/2022032709/56649eb65503460f94bbf62f/html5/thumbnails/21.jpg)
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.
![Page 22: Visualizing Fiber Tracts in the Brain Using Diffusion Tensor Data Masters Project Presentation Yoshihito Yagi Thursday, July 28 th, 10:00 a.m. 499 Dirac.](https://reader030.fdocuments.us/reader030/viewer/2022032709/56649eb65503460f94bbf62f/html5/thumbnails/22.jpg)
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.
![Page 23: Visualizing Fiber Tracts in the Brain Using Diffusion Tensor Data Masters Project Presentation Yoshihito Yagi Thursday, July 28 th, 10:00 a.m. 499 Dirac.](https://reader030.fdocuments.us/reader030/viewer/2022032709/56649eb65503460f94bbf62f/html5/thumbnails/23.jpg)
Global vs. Local
![Page 24: Visualizing Fiber Tracts in the Brain Using Diffusion Tensor Data Masters Project Presentation Yoshihito Yagi Thursday, July 28 th, 10:00 a.m. 499 Dirac.](https://reader030.fdocuments.us/reader030/viewer/2022032709/56649eb65503460f94bbf62f/html5/thumbnails/24.jpg)
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.
![Page 25: Visualizing Fiber Tracts in the Brain Using Diffusion Tensor Data Masters Project Presentation Yoshihito Yagi Thursday, July 28 th, 10:00 a.m. 499 Dirac.](https://reader030.fdocuments.us/reader030/viewer/2022032709/56649eb65503460f94bbf62f/html5/thumbnails/25.jpg)
Changing the density of fibers
• The number of fibers are 300, 600, 1200
• The radius of fibers is 0.3
![Page 26: Visualizing Fiber Tracts in the Brain Using Diffusion Tensor Data Masters Project Presentation Yoshihito Yagi Thursday, July 28 th, 10:00 a.m. 499 Dirac.](https://reader030.fdocuments.us/reader030/viewer/2022032709/56649eb65503460f94bbf62f/html5/thumbnails/26.jpg)
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.
![Page 27: Visualizing Fiber Tracts in the Brain Using Diffusion Tensor Data Masters Project Presentation Yoshihito Yagi Thursday, July 28 th, 10:00 a.m. 499 Dirac.](https://reader030.fdocuments.us/reader030/viewer/2022032709/56649eb65503460f94bbf62f/html5/thumbnails/27.jpg)
Interactive exploration of data
• We implement several interactive tools which enable a user to manipulate data.
• See a movie.
![Page 28: Visualizing Fiber Tracts in the Brain Using Diffusion Tensor Data Masters Project Presentation Yoshihito Yagi Thursday, July 28 th, 10:00 a.m. 499 Dirac.](https://reader030.fdocuments.us/reader030/viewer/2022032709/56649eb65503460f94bbf62f/html5/thumbnails/28.jpg)
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.
![Page 29: Visualizing Fiber Tracts in the Brain Using Diffusion Tensor Data Masters Project Presentation Yoshihito Yagi Thursday, July 28 th, 10:00 a.m. 499 Dirac.](https://reader030.fdocuments.us/reader030/viewer/2022032709/56649eb65503460f94bbf62f/html5/thumbnails/29.jpg)
Highlighting fibers
• Highlighting fibers intersect with triangular meshes.
![Page 30: Visualizing Fiber Tracts in the Brain Using Diffusion Tensor Data Masters Project Presentation Yoshihito Yagi Thursday, July 28 th, 10:00 a.m. 499 Dirac.](https://reader030.fdocuments.us/reader030/viewer/2022032709/56649eb65503460f94bbf62f/html5/thumbnails/30.jpg)
Novel Contribution
1. Highlighting fibers
2. Intersection of a fiber with a cortex triangular mesh
3. Global illumination
![Page 31: Visualizing Fiber Tracts in the Brain Using Diffusion Tensor Data Masters Project Presentation Yoshihito Yagi Thursday, July 28 th, 10:00 a.m. 499 Dirac.](https://reader030.fdocuments.us/reader030/viewer/2022032709/56649eb65503460f94bbf62f/html5/thumbnails/31.jpg)
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.
![Page 32: Visualizing Fiber Tracts in the Brain Using Diffusion Tensor Data Masters Project Presentation Yoshihito Yagi Thursday, July 28 th, 10:00 a.m. 499 Dirac.](https://reader030.fdocuments.us/reader030/viewer/2022032709/56649eb65503460f94bbf62f/html5/thumbnails/32.jpg)
Thanks
• Dr. Banks (Adviser)
• Dr. Ouimet, Dr. Liu (Committee)
• Beason (Ray Tracer Pane)
• Ji, Saka,Connor, Reece (Review my report)