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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 Science Library. What does a brain look like?.

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visualizing fiber tracts in the brain using diffusion tensor data

Visualizing Fiber Tractsin the BrainUsing Diffusion Tensor Data

Masters Project Presentation

Yoshihito Yagi

Thursday, July 28th, 10:00 a.m.

499 Dirac Science Library

what does a brain look like
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.
diffusion tensor dt mri
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
glyph based visualization
Glyph-Based Visualization
  • 2D and 3D arrays of glyphs.
fiber tracking
Fiber Tracking
  • Fiber Tracking can visualize the white matter connectivity.
what is a tensor
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.
diffusion of water
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.
eigenvalues and eigenvectors
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 .
anistropic diffusion
Anistropic Diffusion
  • Diffusion can be characterized by three anisotropic diffusion properties.

Westin et.al proposed three measurements: Cl, Cp, Cs.

liner anisotropic diffusion c l
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.
planar anisotropic diffusion c p
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.
spherical anisotropic diffusion c s
Spherical Anisotropic Diffusion, Cs
  • i.e., Isotropic Diffusion.
  • If , then the diffusion occurs in every direction.
  • Define Cs such that:
what do these regions look like
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.
fiber tracking algorithm
Fiber Tracking Algorithm
  • A fiber starts at the point where Cl is large, and it is integrated along e1.
  • e1is the largest diffusion.
problem
Problem
  • Long integration leads you to the point where Cl is small.
tensorline
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.
the goal of this project
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.
realistic illumination
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.
cut away
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.
cut away algorithm
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.
cut away images and movie
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.
density and radius of fibers
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.
changing the density of fibers
Changing the density of fibers
  • The number of fibers are 300, 600, 1200
  • The radius of fibers is 0.3
placing more fibers and shrinking their radius
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.
interactive exploration of data
Interactive exploration of data
  • We implement several interactive tools which enable a user to manipulate data.
  • See a movie.
highlighting fibers
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.
highlighting fibers1
Highlighting fibers
  • Highlighting fibers intersect with triangular meshes.
novel contribution
Novel Contribution
  • Highlighting fibers
  • Intersection of a fiber with a cortex triangular mesh
  • Global illumination
laboratory for mathematics in imaging at harvard medical school
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.
thanks
Thanks
  • Dr. Banks (Adviser)
  • Dr. Ouimet, Dr. Liu (Committee)
  • Beason (Ray Tracer Pane)
  • Ji, Saka,Connor, Reece (Review my report)