BP8113

Advanced Medical Imaging

Instructor: Yuan Xu
Office: KHS-331-D
Email: yxu@ryerson.ca
 Outline
• Course administration and course outline
• Math review
• Fourier series and transform
• Textbook
– Webb: concise, fundamental
– Bushberg: comprehensive, practical, clinical, good
for Med Phy ABR
– Kak: good for linear system, FT, reconstruction
– Weishaupt: excellent, but MRI only
– Prince: modelling of imaging system
 Course Objectives
• Linear system theory
• Image reconstruction techniques for parallel beam
CT, and ultrasound
• Nuclear medicine imaging
• Ultrasound
• MRI

• Fourier transform is an important tool that will be

used in studying all imaging modalities.
 Evaluation Scheme

Assignments 10%
Test 20%
Final exam 25%
Five labs 25%
Course project and presentation 20 %

Test/exam format
 Course project and presentation
• discuss with the instructor to select a
method/technique or paper related to any of
the following topics:
– image reconstruction or inverse problem
– Signal processing
– Application to a specific disease
– Others to be discussed
 Math review
• Functions , scaling, and shifting
• Fourier series
• Fourier transform and its properties
 Functions
• Rect(x)
• Sinc(x)
 Functions
• Delta or Dirac, representing a point object.
Sifting property of Delta function
Clicker question 1
What is the unit of the 1-D delta function defined in space?

(a) m
(b) m-1
(c) m-2
(d)m2
Clicker question 2

(a) -3
(b) 3
(c) -5
(d)5
 Manipulating functions
• Shift
– When you shift a function f(x) to the right by x0, it
becomes f(x- x0 ).

• Scale
– When you stretch/compress a function f(x) (or
the x-axis while the function is fixed on the axis)
by a factor of a, it becomes f(x/a).

• Combined:
Clicker question 3
Which of the following functions describe the following plot?

(a)2 rect(x/3 -2.5)

(b) 2 rect(3x -2.5)
(c) 2 rect(x/3 -0.833)
(d)2 rect(3x -7.5)
Clicker question 4
Which of the following plots show rect(x/2-1)?
Clicker question 5
If we define f1(x) as follows, Which of the following functions
describe the following plot on f2(x)?

(a)f1(-1-x)
(b) f1(-1+x)
(c) f1(1-x)
(d)f1(2-x)
 Fourier transform
• Why Fourier transform
• Fourier analysis of periodic functions
• MTF and LSF
• Fourier transform in Matlab (1D and 2D)
– fft function
– Find the frequency in the spectrum in MATLAB
 Continuous Spectrum

Continuous
Spectrum of
sunlight

The sunlight can be decomposed into waves with

different colors, or frequencies.
 Why Fourier transform
• Represent a signal as a summation of sinusoidal
functions
– sinusoidal functions are still sinusoidal functions after
going through a LSI (linear shift-invariant) system.
– Frequency domain, a new perspective to understand
the signal
– New methods to process signals
• Widely used in medical imaging
– A new way to understand the convolution and PSF
– Image resolution
– CT reconstruction
– Ultrasound
– MRI
 Representation of functions in sinusoids
A periodic function with
period L can be
represented by the
summation of harmonic
sine and cosine
functions.

frequency f0 = 1/L
(fundamental frequency)

Harmonic frequency:
f=nf0. n=0,1,2…
 Cos and sin functions and
harmonics
fundamental frequency u0 =1/L

Harmonic: waves with frequency of nu0

DC component, u=0, the average of a function

Fourier Series: example
For the function shown below with a period of 1, what kind of harmonics does it
have?

A. 2 and 3
B. 1 and 11
C. 1 and 3
D. 2 and 11
 Fourier series: formulas
A Fourier series decomposes periodic functions or periodic
signals f(t) with a period of L into the sum of a (possibly infinite)
set of simple oscillating functions, namely sines and cosines (or
complex exponentials).

n>0
What is the DC term (the
first term of the Fourier
series) for the periodic
functions on the left?

n>0

A. 1
B. 2
C. 4
D. 8
Fourier series in complex exponentials
Cosine and sine functions can be expressed by complex
exponentials of positive and negative frequencies

Consequently, the Fourier series can be expressed as

If f(x) is a real function, is a complex conjugate of , which

means there is a symmetry between the positive and the negative
frequency components.
 Example of Fourier series: a single
frequency Single-Sided Amplitude Spectrum of y(t)
1 1

0.8 0.9

0.6 0.8

0.4 0.7

0.2 0.6

|Y(f)|
0 0.5

-0.2 0.4

-0.4 0.3

-0.6 0.2

-0.8 0.1

-1 0
0 5 10 15 20 25 30 35 40 45 50 0 50 100 150 200 250 300 350 400 450 500
time (milliseconds) Frequency (Hz)
 Example of Fourier series : Two
frequencies
Signal Corrupted with Zero-Mean Random Noise Single-Sided Amplitude Spectrum of y(t)
1.5 1

0.9
1
0.8

0.7
0.5

0.6

|Y(f)|
0.5

0.4
-0.5
0.3

-1 0.2

0.1
-1.5
0 5 10 15 20 25 30 35 40 45 50 0
time (milliseconds) 0 50 100 150 200 250 300 350 400 450 500
Frequency (Hz)
Assuming the fundamental frequency is 0.5 Hz, the coefficients of
Fourier series of the 3cos(2πx) + sin(2πx) in the format of [c0, c1,
c2, …] is

A.[ 0, 3 – i, 0, 0 …]
B. [0, 1.5-0.5i, 0, 0, …]
C. [ 1.5, -0.5i, 0, …]
D. [ 0, 0, 1.5-0.5i, 0, …]
E. [ 0, 1.5, 0.5, …]
Assuming the fundamental frequency is 0.5 Hz, the coefficients of
Fourier series of the 1+ 3cos(2πx) + sin(2πx)+ 6sin(6πx) in the
format of [c0, c1, c2, c3, …] is

A. [ 1, 1.5-0.5i, -3i, 0, …]
B. [ 0, 1.5-0.5i, -3i, 0, …]
C. [ 0, 1.5-0.5i, -3i, 0 …]
D. [ 1, 1.5-0.5i, -3i, 0, …]
E. [ 1, 0,1.5-0.5i, 0,0,0, -3i, …]
Assuming the fundamental frequency is 2 Hz, the coefficients of
Fourier series of a function in the format of [c0, c1, c2, c3, …] is
[ 1, 1.5, -i, 0, 0 .…].

A. 1+ 1.5cos(4πx) +2sin(4πx)
B. 1+ 3cos(2πx) +2sin(4πx)
C. 2+ 3cos(4πx) +2sin(8πx)
D. 1+ 3cos(4πx)+2sin(8πx)
E. 1+ 1.5cos(2πx) +2sin(4πx)
 Find the amplitudes and frequencies
of your digital signal in computer
You measured a signal segment, which are discrete sampling
points in your computer. How can you fit it to cosine and sine
functions with Matlab?
 Sampling of a continuous function
A continuous function is sampled at periodic sampling points to
be processed by computers, [0, Δx, 2Δx, 3Δx…].
Sampling interval, Δx , the distance between two closest sampling
points.
Sampling frequency: the inverse of the sampling interval.

Assume we have a segment of signal with length L and sampling

interval Δx. The number of sampling points is:

The signal can be represented in a vector y

 Finite Discrete Fourier transform (finite DFT)
Finite DFT change a spatial domain vector y(n) into a spectral
domain vector Y(k), where k is an integer, the index of the
spectrum vector Y. The frequency at the k-th position of Y
uk = (k-1)f0, k=1…N.

The value at the k-th position of Y is the finite DFT coefficients,

similar to the ck-1 in the Fourier series. Function fft in MATLAB
will do DFT.
Y(k) =

Y(k) is a complex-valued vector. You need to use abs(Y(k)) to

plot it.
The inverse DFT is
Relation between C and DFT vector Y

ck=Yk+1/N, for k=0,..N-1

Ck: the complex coefficient in the Fourier series representation of the data.
Yk+1: is the (k+1)-th element of the spectrum vector in Matlab
Finite DFT summary
 Find the frequency of each point in the spectrum vector Y
Read Kak 2.1.7 for DFT frequency interpretation

• Nyquist criteria
magnitude of spectrum
6

The maximum frequency of the data is 5

half of the sampling frequency usamp.
4

0
0 5 10 15 20 25 30 35 40
Clicker question
You got the following data Signal=[ 1 2 3 4 5 6 7] from your
data acquisition card. The sampling rate is 100 Hz. Then You
have the following matlab program to find out the spectrum
of the signal:
signal=[ 1 2 3 4 5 6 7];
spec=fft(signal);

What is the frequencies corresponding to first point of the

vector spec?

(a) 10 Hz
(b) 20 Hz
(c)50 Hz
(d)0 Hz
Clicker question
You got the following data Signal=[ 1 2 3 4 5 6 7 8 9 10] from
your data acquisition card. The sampling rate is 100 Hz.
Then You have the following matlab program to find out the
spectrum of the signal:
signal=[ 1 2 3 4 5 6 7 8 9 10];
spec=fft(signal);

What is the frequencies corresponding to fourth point of the

vector spec?

(a) 30 Hz
(b) 20 Hz
(c)-20 Hz
(d)0 Hz
Clicker question
You got the following data Signal=[ 1 2 3 4 5 6 7 8 9 10] from
your data acquisition card. The sampling rate is 100 Hz.
Then You have the following matlab program to find out the
spectrum of the signal:
signal=[ 1 2 3 4 5 6 7 8 9 10];
spec=fft(signal);

What is the frequencies corresponding to the 8-th point of the

vector spec?

(a) -30 Hz
(b) 20 Hz
(c)-20 Hz
(d)30 Hz
 Find the amplitudes and frequencies
of your signal
Signal Corrupted with Zero-Mean Random Noise
6 You measured a signal segment.
4
You want to fit it to cosine and
sine functions.
2

0 1. Use fft in MATLAB to get Y(k)

2. Get ck, then ak and bk.
-2

-4

-6
0 5 10 15 20 25 30 35 40 45 50
time (milliseconds)

3. Represent the data with ak

and bk.
Definition of Fourier Transform
 Reading material
• Chapter 2 of A. C. Kak and Malcolm Slaney,
Principles of Computerized Tomographic
Imaging, Society of Industrial and Applied
Mathematics, 2001.(Available on-line)
•