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4426

Medical Imaging

Computed Tomography

(Part 1)

Yao Wang

Polytechnic School of Engineering

New York University, Brooklyn, NY 11201

Based on Prince and Links, Medical Imaging Signals and Systems and

Lecture Notes by Prince. Figures are from the book.

Lecture Outline

Instrumentation

CT Generations

X-ray source and collimation

CT detectors

Image Formation

Line integrals

Parallel Ray Reconstruction

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Radon transform

Back projection

Filtered backprojection

Convolution backprojection

Implementation issues

Projection radiography

Projection of a 2D slice along one direction only

Can only see the shadow of the 3D body

When the angle spacing is sufficiently small, can reconstruct the

2D slice very well

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2nd Generation

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Much faster than 2G

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4G

Fast

Cannot use

collimator at

detector, hence

affected by

scattering

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Used for fast (cine) whole heart imaging

Source of x-ray moves around by steering an electron

beam around X-ray tube anode.

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6G: Helical CT

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7G: Multislice

From http://www.kau.edu.sa/Files/0008512/Files/19500_2nd_presentation_final.pdf

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10

From http://www.kau.edu.sa/Files/0008512/Files/19500_2nd_presentation_final.pdf

Reduced scan time and increased Z-resolution (thin slices)

Most modern MSCT systems generates 64 slices per rotation, can image

whole body (1.5 m) in 30 sec.

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Generation

Source

Source Collimation

Detector

1st

Pencil Beam

Single

2nd

Multiple

3rd

Many

Stationary

Ring of

Detectors

4th

5th

Many tungsten

anodes in single

large tube

Fan Beam

Stationary

Ring of

Detectors

6th

3G/4G

3G/4G

3G/4G

Cone Beam

Multiple

array of

detectors

7th

From http://www.kau.edu.sa/Files/0008512/Files/19500_2nd_presentation_final.pdf

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12

From http://www.kau.edu.sa/Files/0008512/Files/19500_2nd_presentation_final.pdf

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X-ray Source

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Dual Energy CT

Recall that linear attenuation coefficient depends on the

X-ray energy

Dual energy CT enables simultanious acquisition to two

images of the organ, reflecting their attenuation profiles

corresponding to different energies

The scanner has two x-ray tubes using two different

voltage levels to generate the x-rays.

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15

X-ray Detectors

Convert detected photons to lights

Convert light to electric current

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CT Measurement Model

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attenuating objects

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CT Number

Godfrey Hounsfield, together with Alan Cormack, invented X-ray CT!

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Parameterization of a Line

Each projection line is

defined by (l,)

y

be specified with two options

x

Option 2:

=l

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What is g(l,)?

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Example

Example 1: Consider an image slice which contains a

single square in the center. What is its projections along

0, 45, 90, 135 degrees?

Example 2: Instead of a square, we have a rectangle.

Repeat.

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Sinogram

Bottom row: =0 (vertical proj), middle =/2 (horizontal proj), top =-d

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Backprojection

The simplest method for reconstructing an image from a

projection along an angle is by backprojection

Assigning every point in the image along the line defined by (l,) the

projected value g(l, ), repeat for all l for the given

s

x

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Example

Continue with the example of the image with a square in

the center. Determine the backprojected image from

each projection and the reconstruction by summing

different number of backprojections

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Option 1: assigning value of g(l, ) to all points on the line (l, )

g(l, ) is only measured at certain l: ln=n l

If l is coarsely sampled (l is large), many points in an image will not be

assigned a value

Many points on the line may not be a sample point in a digital image

image, find its corresponding l=x cos +y sin , take the g value

for (l, )

g(l, ) is only measured at certain l: ln=n l

must interpolate g(l, ) for any l from given g(ln, )

assigned a value

For more accurate results, the backprojected value at each point

should be divided by the length of the underlying image in the

projection direction (if known)

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Backprojection Summation

Replaced by a

sum in practice

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Implementation Issues

g(:,phi) stores the projection data at angle phi corresponding to excentricities stored in s_n

From L. Parra at CUNY, http://bme.ccny.cuny.edu/faculty/parra/teaching/med-imaging/lecture4.pdf

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Implementation: Projection

Possible l and are both quantized. If you first specify (l,), then find (x,y)

that are on this line. It is not easy. Instead, for given , you can go through

all (x,y) and determine corresponding l, quantize l to one of those you want

to collect data.

Sample matlab code (for illustration purpose only)

f(x,y) stores the original image data

G(l,phi) stores projection data, ql is the desired quantization stepsize for l.

N=ceil(sqrt(I*I+J*J))+1; %(assume image size IxJ), N0 is maximum lateral distance

N0= floor((N-1)/2);

ql=1;

G=zeros(N,180);

for phi=0:179

for (x=-J/2:J/2-1; y=-I/2:I/2-1)

l=x*cos(phi*pi/180)+y*sin(phi*pi/180);

l=round(l/ql)+N0+1;

If (l>=1) && (l<=N)

G(l,phi+1)=G(l,phi+1)+f(x+J/2+1,y+I/2+1);

End

end

end

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Blurring

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G( , ) = g (l , ) exp{ j 2l}dl

Fourier transform of the image at the same angle.

If (l,) are sampled sufficiently dense, then from g (l,) we

essentially know F(u,v) (on the polar coordinate), and by inverse

transform we can obtain f(x,y)!

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Theorem

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Proof

Go through on the board

Using the set form of the line integral

See Prince&Links, P. 203 (2nd edition)

G( , ) = g (l , ) exp{ j 2l}dl

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37

The projection slice theorem leads to the following

conceptually simple reconstruction method

Take 1D FT of each projection to obtain G(,) for all

Convert G(,) to Cartesian grid F(u,v)

Take inverse 2D FT to obtain f(x,y)

Difficult to interpolate polar data onto a Cartesian grid

Inverse 2D FT is time consuming

Take inverse 2D FT on G(,) on the polar coordinate leads to

the widely used Filtered Backprojection algorithm

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Filtered Backprojection

Inverse 2D FT in Cartesian coordinate:

f ( x, y ) =

F (u , v)e j 2 ( xu + yv ) dudv

f ( x, y) =

=G(,)

=l

0 > 2 0 >

Inverse FT

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39

Algorithm:

For each

Frequency domain filtering: G(,) -> Q(,)=||G(,)

Take inverse 1D FT: Q(,) -> q(l,)

Backprojecting q(l,) to image domain -> b(x,y)

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Filter response:

c() =||

High pass filter

sampled when is small, and

vice verse

The ramp filter compensate

for the sparser sampling at

higher

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Convolution Backprojection

The Filtered backprojection method requires taking 2 Fourier

transforms (forward and inverse) for each projection

Instead of performing filtering in the FT domain, perform convolution

in the spatial domain

Assuming c(l) is the spatial domain filter

|| <-> c(l)

||G(,) <-> c(l) * g(l,)

For each :

Convolve projection g(l,) with c(l): q(l,)= g(l,) * c(l)

Backprojecting q(l,) to image domain -> b(x,y)

Add b(x,y) to the backprojection sum

Used in most commercial CT scanners

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Step 1: Convolution

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Step 2: Backprojection

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Step 3: Summation

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Common Filters

Ram-Lak: using the rectangular window

Tend to amplify noise

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Cosine: using a cosine window

Hamming: using a generalized Hamming window

See Fig. B.5 in A. Webb, Introduction to biomedical

imaging

49

Practical Implementation

l=n;

chosen based on maximum frequency in G(,), W

1/ >=2W or <=1/2W (Nyquist Sampling Theorem)

W can be estimated by the number of cycles/cm in the projection direction in the most detailed

area in the slice to be scanned

Fourier transform G(,) is obtained via FFT using samples g(n, )

If N sample are available in g, 2N point FFT is taken by zero padding g(n, )

The ramp-filter is sampled at l=n

Sampled Ram-Lak Filter

1 / 4 2 ;

2

c(n) = 1 / (n ) ;

0;

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n=0

n = odd

n = even

50

Matlab Implementation

MATLAB (image toolbox) has several built-in functions:

phantom: create phantom images of size NxN

I = PHANTOM(DEF,N) DEF=Shepp-Logan,Modified Shepp-Logan

Can also construct your own phantom, or use an arbitrary image

Can specify sampling of

R = RADON(I,THETA)

The number of samples per projection angle = sqrt(2) N

Uses the filtered backprojection method

Can choose different filters and different interpolation methods for

performing backprojection

[I,H]=IRADON(R,THETA,INTERPOLATION,FILTER,FREQUENCY_SCALING,OUTPUT_SIZE)

Other useful command:

imshow, imagesc, colormap

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using different parameter settings

More vs. less projection angles

Different filters

I=phantom(def,N),

DEF='Shepp-Logan, 'Modified Shepp-Logan (default)

R = RADON(I,THETA), e.g. THETA=0:179 or 0:2:179

I = IRADON(R,THETA,INTERPOLATION,FILTER)

Interpoltation filters: used for backprojection

'nearest' - nearest neighbor interpolation,

'linear' - linear interpolation (default),

'spline' - spline interpolation

Reconstruction filter: Ram-Lak (default), 'Shepp-Logan, 'Cosine

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52

Middle: 90 projections

Bottom: 45 projections

MATLAB code:

>> I=imread('lena.jpg');

>> r180=radon(I,0:179); % 0:2:179;

>> p180=iradon(r180,0:179,spline,cosine);

>> subplot(1,3,1),imagesc(I);

>> subplot(1,3,2),imagesc(r180);

>> subplot(1,3,3),imagesc(p180);

>> truesize

>> colormap(gray)

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53

Summary

Different generations of CT machines:

Difference and pros and cons of each

Require (close-to) monogenic x-ray source

imaged slice

Line integral of absorption coefficients (Radon transform)

Reconstruction methods

Backprojection summation

Fourier method (projection slice theorem)

Filtered backprojection

Convolution backprojection

computation

quality

Matlab implementations

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54

Reference

Prince and Links, Medical Imaging Signals and Systems,

Chap 6.

Webb, Introduction to biomedical imaging, Appendix B.

Kak and Slanley, Principles of Computerized

Tomographic Imaging, IEEE Press, 1988. Chap. 3

Electronic copy available at

http://www.slaney.org/pct/pct-toc.html

machines

http://www.kau.edu.sa/Files/0008512/Files/

19500_2nd_presentation_final.pdf

http://bme.ccny.cuny.edu/faculty/parra/teaching/med-imaging/

lecture4.pdf

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55

Homework

Reading:

Prince and Links, Medical Imaging Signals and Systems, Chap

6, Sec.6.1-6.3.3

the textbook based on the provided errata.

Problems for Chap 6 of the text book:

1. P6.5

2. P6.14 (Note that you can leave the solution of part (a) in the

form of the convolution of two functions without deriving the

actual convolution. For part (b) you could describe in terms of

intuition.)

3. P6.17

4. The added problem in the following page

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Added problem

Consider a 4x4 discrete image that contains a diagonal line

I=[1,0,0,0;0,1,0,0;0,0,1,0;0,0,0,1];

a) determine its projections in the directions: 0, 45,90,135 degrees.

b) determine the backprojected image from each projection;

c) determine the reconstructed images by using projections in the 0 and 90

degrees only.

d) determine the reconstructed images by using all projections. Comment on

the difference from c).

Note that for back-projection, you should normalize the backprojection in

each direction based on the total length of projection along that direction in

the square area.

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57

Computer Assignment

Due: Two weeks from lecture date

1.

2.

3.

4.

F14

functionalities. Type demos on the command line, then select toolbox > image processing -> transform -> reconstructing an image from

projection data. Alternatively, you can use help for each particular

function.

Write a MATLAB program that 1) generate a phantom image (you can use

a standard phantom provided by MATLAB or construct your own), 2)

produce projections in a specified number of angle, 3) reconstruct the

phantom using backprojection summation; Your program should allow the

user to specify the number of projection angle. Run your program with

different number of projections for the same view angle, and the different

view angles, and compare the quality. You should NOT use the radon( )

and iradon() function in MATLAB.

Repeat 1 but uses filter backprojection method for step 3). In addition to

the number of projection angles, you should be able to specify the filter

among several filters provided by Matlab and the interpolation filters used

for backprojection. Compare the reconstructed image quality obtained with

different filters and interpolation methods for the same view angle and

number of projections. You can use the iradon() function in MATLAB

(Optional) Repeat 3 but uses convolution backprojection method. You

have to do your own program.

Yao Wang @ NYU

58

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