Visualizing Fiber Tracts in the Brain Using Diffusion Tensor Data

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Visualizing Fiber Tractsin the BrainUsing
Diffusion Tensor Data

• Masters Project Presentation
• Yoshihito Yagi
• Thursday, July 28th, 1000 a.m.
• 499 Dirac Science Library

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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.

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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

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Glyph-Based Visualization

• 2D and 3D arrays of glyphs.

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Fiber Tracking

• Fiber Tracking can visualize the white matter
  connectivity.

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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.

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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.

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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 .

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Anistropic Diffusion

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

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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.

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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.

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Spherical Anisotropic Diffusion, Cs

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

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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.

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Fiber Tracking Algorithm

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

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Problem

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

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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.

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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.

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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.

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Global vs. Local
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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.

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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.

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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.

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Global vs. Local
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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.

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Changing the density of fibers

• The number of fibers are 300, 600, 1200
• The radius of fibers is 0.3

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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.

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Interactive exploration of data

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

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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.

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Highlighting fibers

• Highlighting fibers intersect with triangular
  meshes.

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Novel Contribution

• Highlighting fibers
• Intersection of a fiber with a cortex triangular
  mesh
• Global illumination

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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.

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Thanks

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