Segmentation of dynamic

MR lung images

Abhishek Pandey
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Overview:
Introduction
Snakes
Geodesic Active Contour(GAC)
Region based scheme( Chan Vese)
Hybrid Scheme
3D segementation results
3D 4D segmentation
Results
Future work




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WHY all this ?
We have a method to acquire and reconstruct dynamic MR
lung data in 3D.(Bens Talk Next week).
To verify the acquisition scheme works, we need to compare
and correlate it with spirometer data.
To match the spirometer data with recon data we need to
perform segmentation on recon data.
Manually its time taking.(IMPOSSIBLE !!!)
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4D Lung dataset : (The Problem)
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109ms temporal resolution
7x7x10mm spatial resolution (64x64x26)
Introduction
What is segmentation ?
Subdividing or partitioning an image into its constituent
regions or objects.

Still huge amount of literature being published for
solving segmentation problem.

No GLOBAL solution !!!!

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Introduction: various schemes
Histogram based segmentation

Clustering based segmentation

Active Contour

Edge based scheme(Geodesic active contour)
Region based scheme ( Chan- Vese method)
Hybrid scheme( Combination)
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AC = curve fitted iteratively to an image
based on its shape and the image values
until it stabilizes (ideally on an objects boundary).

curve: polygon = parametric AC
continuous = geometric AC
parametric geometric
Active Contour: Intro
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Types of curves
Parametric AC:
Stored as vertices
Each vertex is moved iteratively

Geometric AC:
Stored as coefficients
Sampled before each iteration
Each sample is moved
New coefficients are computed
(interpolation)
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Snake Model introduced in 1987 by Kass-Witkin-Terzopoulos.

Planar parameterized curve and the cost function is given by:
A cost function defined along that curve



The internal term stands for regularity/smoothness along the curve and has
two components (resisting to stretching and bending)

The image term guides the active contour towards the desired image
properties (strong gradients)

The external term can be used to account for user-defined constraints, or
prior knowledge on the structure to be recovered
The lowest potential of such a cost function refers to an equilibrium of these
terms

Snake model : Active Contour
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Internal Energy (E
int
)
Sum of elastic energy and bending energy.
The contour is defined in the (x, y) plane of an image
as a parametric curve
v(s)=(x(s), y(s))

Elastic Energy (E
elastic
):
The curve is treated as an elastic rubber band
possessing elastic potential energy.
It discourages stretching by introducing tension.



Weight o(s) allows us to control elastic energy along
different parts of the contour. Considered to be
constant o for many applications.
2
1
( ) | |
2
elastic s
E s v ds = o
}
s
( )
s
dv s
v
ds
=
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Bending Energy (E
bending
):

The snake is also considered to behave like a thin metal
strip giving rise to bending energy.

It is defined as sum of squared curvature of the contour.


|(s) plays a similar role to o(s).
Bending energy is minimum for a circle.

Total internal energy of the snake can be defined as

2
1
( ) | |
2
bending ss
s
E s v ds = |
}
2 2
int
1
| | | | )
2
elastic bending s ss
s
E E E v v ds = + = (o +|
}
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External energy of the contour (E
ext
)
It is derived from the image.
Define a function E
image
(x,y) so that it takes on its
smaller values at the features of interest, such as
boundaries.




Key rests on defining E
image
(x,y). Some examples





( ( ))
ext image
s
E E v s ds =
}
2
( , ) | , )|
image
E x y x y = VI(
2
( , ) | ( ( , )* ( , )) |
image
E x y G x y I x y
o
= V
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Weakness of traditional snakes (Kass model)
Extremely sensitive to parameters.
Small capture range.








No external force acts on points which are far away
from the boundary.
Convergence is dependent on initial position.
Difficult to detect concavity.


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Geodesic Active Contour : Intro
A typical external energy coming
from the image:
Positive on homogeneous regions
Near zero on the sharp edges

( )
p
0
0
u G 1
1
u g
- V +
= V
o
MR SEMINAR
Geodesic Active Contours in 2D
2
1
1 | ( * ) | G I
o
+ V
g(x)=
G *I
s
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Geodesic Active Contour(GAC):
Caselles et al.
( ) ( )N N C g C g
dt
dC

), ( V = k
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Level Set Representation (S. Osher - J. Sethian 87)
Inside C
Outside C
Outside C
0 <
0 >
0 >
0 =
C
n

|
|
.
|

\
|
V
V
=
V
V
=
| |
,
| |
Normal

div K Curvature n

Example: mean curvature motion

* Allows automatic topology changes, cusps, merging and breaking.
Originally developed for tracking fluid interfaces.
{ } 0 ) , ( | ) , ( = = y x y x C
C= boundary of an open domain
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Curve expansion and contraction forces:
Active Contour without edge: Chan
Vese et al.
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Active Contour without edges: Chan Vese
region based method

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Chan-Vese method as level set formulation
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Hybrid scheme:
Region based method Edge based method
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Steps to solve:
Hybrid Scheme: Implementation
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Hybrid Scheme: Implementation
Update by solving the PDE
This is solved using Additive Operator Splitting(AOS). AOS is a
stable finite difference method initially proposed for non linear
filtering and then later for GAC.
AOS is used to reduce the data to tridiagonal matrices and Thomas
algorithm or Tridiagonal matrix algorithm (TDMA) is used to solve
the equations.
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Extracting lung out of multiple
boundaries:
Thresholding with -2
Imfill the
step 1
Reverse Thresholding with 0
Lung output
And of step2 and step3
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Results for 4D segmentation:
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Results for 4D segmentation:
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Similar outputs for these ones:
Results from 3D segmentation applied to each point
individually.
Results from variable and constant parameters for 4D
segmentation.
Actual dynamic 3D volume change.

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19
th
slice 4D With time step high
value:
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11
th
slice 4D With time step high
value:
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11
th
slice 4D With time step low
value:
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19
th
slice 4D With time step low
value:
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19
th
slice 4D With time step
variable value:
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19
th
slice 4D With time step
variable value:
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New dataset
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Spirometer outputs:
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Future work:
Standard Spirometer output and segmentation correlation

Using variable parameters for anisotropic image sizes.

3D vs 4D Segmentation data, which is best.

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References:

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