DW-MRI, Tractography,

and Connectivity: what

Machine Learning can do?

Ting-Shuo Yo

Max Planck Institute

for Human Cognitive and Brain Sciences
Leipzig, Germany

Max Planck Institute for Human Cognitive and Brain Sciences

 Where the story begins
● Diffusion Weighted MRI (DWI) is a newly
developed MR scanning protocol, which can
detect the movement/displacement of water
molecules in tissues.
● So far, the techniques used in DWI analysis are
mostly deterministic and mechanical. The
stochastic approaches (ML related) can bring
new insights to this field.

Max Planck Institute for Human Cognitive and Brain Sciences

 Outline
● MPG/MPIs
● A brief introduction of DWI
● What DWI can do
● A comparison of different tractography algorithms
● What ML can do in DWI

Max Planck Institute for Human Cognitive and Brain Sciences

 Outline
● MPG/MPIs
– Max Planck Society
– Objective and Organization
– MPI - CBS
● A brief introduction of DWI
● What DWI can do
● A comparison of different tractography algorithms
● What ML can do in DWI
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Max Planck Institute for Human Cognitive and Brain Sciences

 The Max Planck Society
● The Max Planck Society for the
Advancement of Science is an independent,
non-profit research organization.
● In particular, the Max Planck Society takes up
new and innovative and interdisciplinary
research areas that German universities are
not in a position to accommodate or deal with
adequately.

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 The Max Planck Institutes
● The research institutes
of the Max Planck
Society perform basic
research in the interest
of the general public in
the natural sciences,
life sciences, social
sciences, and the
humanities.
● Currently there are 81
MPIs.

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The MPI for CBS

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 Outline
● MPG/MPIs
● An Introduction of DWI tractography
– Local modelling
– Fibre tracking
● What DWI can do
● A comparison of different tractography algorithms
● What ML can do in DWI

Max Planck Institute for Human Cognitive and Brain Sciences

 Diffusion Weighted MRI
● MRI can detect the
movement of water
molecules.
● The movement is
constrained by the
neural fibers.

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Max Planck Institute for Human Cognitive and Brain Sciences

 Diffusion Weighted MRI
● By posing a gradient magnetic field, the
displacement in the corresponding direction
can be measured.

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Tractography (1)

● Local modelling:
➢ Reconstruct the fibre
orientation within each voxel

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 Tractography (2)

● Diffusion propagator
– Diffusion Tensor (DT)
– Multiple compartment models
– Persistent Angular Structure (PAS)

● Fibre Orientation Distribution Function

– Spherical Deconvolution

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 Tractography (3)

● Fiber tracking:
➢ Reconstruct fibre tracts by
integrating the reconstructed
local information

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 Tractography (4)

● Streamline approach
– Deterministic
– Probabilistic

● Optimization for a larger region

– Spin tracking
– Gibbs tracking

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 Tractography (5)

● Deterministic tracking
– At each step, only
consider the most likely
direction
● Curvature threshold
● Step size
● Interpolation
● ......

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 Tractography (6)

● Probabilistic tracking
– Perform deterministic tracking for multiple times
– Allow uncertainty at each step

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 Tractography (7)

● Probabilistic tracking and tractogram

– Probability of connection

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 Tractography (8)

● Optimization for a larger region

– Spin tracking
– Gibbs tracking

From Kreher et al. 2008

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 Outline
● MPG/MPIs
● A brief introduction of DWI
● What DWI can do
– To reveal anatomical structure in white matter
– To construct the general brain network
– In vivo
● A comparison of different tractography algorithms
● What ML can do in DWI
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 White matter structure from DWI
● Product of tractography

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 Brain Network from DWI
● Hagmann 2008

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 What DWI can do
● fMRI shows "where" is working.
– The "nodes" in a graph/network
● DWI shows the structure of the fiber bundles.
– The “edges" in a graph/network
– With further analysis, can also show "strength of
edges".
● The brain network:
– The amount of nodes: 10^2
– The amount of edges: 10^3
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Max Planck Institute for Human Cognitive and Brain Sciences

 Outline
● MPG/MPIs
● A brief introduction of DWI
● What DWI can do
● A comparison of different tractography
algorithms
– Selected algorithms
– Procedure
– Results
● What ML can do in DWI
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Selected Algorithms

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Procedure

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Results (1)

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Results (2)

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Results (3)

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Results (4)

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Results (5)

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Results (6)

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Results (7)

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Results (8)

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 Quick Summary
● More connections
– Local models which allow multiple fibres
– Probabilistic tracking
● Consistent patterns across methods
– Strong connections within a lobe
– Strong connections to corpus callosum
– Weak trans-callosum connections

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Results (9)

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 Outline
● MPG/MPIs
● A brief introduction of DWI
● What DWI can do
● A comparison of different tractography algorithms
● What ML can do in DWI
– Local model reconstruction
– Fiber tracking
– Further application
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 ML in DWI

● Local modeling: deconvolution approach

– Assume the signals are convolution of neural
fibers and noises.
– Need to “learn" the deconvolution kernel from
data defined as "one single fiber".
– So far only GLM (2nd order polynomial) is used.
– More sophisticated kernel methods can be used.

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 ML in DWI
● Fiber tracking
– Speed up the optimization process.
– Different fiber reconstruction method.

● Probabilistic modeling of fiber tracts

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 MICCAI'09 Fiber Cup
● 6 datasets:
– 3 of resolution 3x3x3mm (image size: 64x64x3) and
3 b-values (650, 1500 and 2000)
– 3 of resolution 6x6x6mm (image size: 64x64x1) and
3 b-values (650, 1500, 2650)
● Participants have to return one single fiber per
spatial position selected.

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MICCAI'09 Fiber Cup

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A Very Brief Review of Tractography
● Local modeling
● Fiber tracking

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 Why are we doing this?
● Streamline-based tractography:
– Each simulation (a fiber) is a possible trajectory in
the given vector field.
● What is the probability of one given fiber?
● How to select the most representative fibers?

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 Probability of a Fiber Tract (1)

● Fiber tract, t = { x1, x2, ...., xl }

● P(t) = P( x1, x2, ...., xl )

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 Probability of a Fiber Tract (2)

● Conditional Probability and Joint Probability

– P(A|B) = P(A,B) / P(B)
– P(A,B) = P(A|B) P(B)

● P(t) = P( x1, x2, ...., xl )

= P(xl| x1, ...., xl-1) P(x1, ...., xl-1)
= P(xl| x1, ...., xl-1) P(xl-1|x1, ...., xl-2) P(x1, ...., xl-2)
= P(xl| x1, ...., xl-1) P(xl-1|x1, ...., xl-2) ......P(x2|x1) P(x1)

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 Probability of a Fiber Tract (3)

●
Assumption: fiber tracking is a 1st order Markov
process
– P(xi| x1, ...., xi-1) = P(xl|xi-1)
– P(t) = P( x1, x2, ...., xl )
= P(xl| x1, ...., xl-1) P(xl-1|x1, ...., xl-2) ......P(x2|x1) P(x1)
= P(xl|xl-1) P(xl-1|xl-2) ......P(x2|x1) P(x1)
l−1
= P  x 1 ∏ P  x i1∣x i 
i=1

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 Probability of a Fiber Tract (4)

● How do we define P(xi+1|xi) and P(xi) ?

– C: connection probability map
– P(xi) ~ C(xi)
– P(xi+1|xi) ~ C(xi+1|xi) ~ C(xi+1,xi)

l−1
P t=P  x1  ∏ P  x i1∣x i 
i=1

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 Finite State Automata (1)

● Each step of fiber tracking can lead to next

middle point or the terminal point.

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Finite State Automata (2)

t={x 1 , ... , x l }
l−1
P t=P0  x l  ∏ 1−P 0  x i 
i=1

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 Finite State Automata (3)

● How to define P0?

– # of fibers in the neighboring voxels, NB(x)
– (1-P0(xi)) ~ C(NB(xi))
P 0  x=1−C  x k

– C(NB(xi))~ C(xi) K = 20, 10, 5

l−1
P t=P0  x l  ∏ 1−P 0  x i 
i=1

l −1
P t≃∏ 1−1−C  xi k
i=1
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 Finite State Automata (4)

● Likelihood and Log-likelihood

l−1
P t=P0  x l  ∏ 1−P 0  x i 
i=1

l −1
P t≃∏ 1−1−C  xi  k

i=1

l−1 l−1
L t≃∑ ln 1−1−C  x i k ≃∑ −1−C  xi k
i=1 i=1

Approximation with 1st order Taylor's expansion

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 Entropy of a Fiber Tract (1)

● Entropy
l
H t =∑ C  x i ⋅lnC  x i 
i=1

● Can be seen as the log-likelihood of

l l

∑ C  xi ⋅lnC  xi =ln ∏ C  x i  C xi 

i=1 i =1

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 Fiber Cup Results (2)

Max. Entropy Max. Likelihood

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 ML in DWI
● Connectivity based clustering
– Brain parcellation
– Brain tissue is mostly
continuous without clear
segmentation, how to
define regions on it?
– Perform clustering based
on the connectivity
matrices.

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Leipzig, Germany Saclay, Gif-sur-Yvette, France

A. Anwander M. Descoteaux
T.R. Knösche P. Fillard
T. Yo C. Poupon

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Questions

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Doing what the brain does - how
computers learn to listen

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 Thank You

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