BMEG 3320: Biomedical Imaging

Magnetic Resonance Imaging

Prof. Weitian Chen

Imaging and Interventional Radiology

The Chinese University of Hong Kong
E-mail: [email protected]
November 2023
Outline
• Hardware of MRI system
• MR Image Formation
• Gradient Echo vs. Spin Echo
• Contrast, Field of View, Resolution, and SNR in MRI

2
https://www.youtube.com/watch?v=3nIXRPuFK5U
MRI scanner

4
Typical floor layout of MRI system

5
MRI Hardware System
• Magnet room:
• Main Magnet: Generate B0 field
• Gradient coils: Generate gradient
of magnetic field in the direction
of B0
• RF Coils: Generate Radiofrequency
waveforms to excite the protons
and detect the signal from the
protons after excitation
• Equipment room:
• System electronics
• Control room:
• Viewing Console

6
Main Magnet

7
Main and shielding coils of a The six primary coils (1–6) and two shield coils (7,
superconducting magnet before being 8) mounted on an aluminium alloy bobbin
enclosed in a cryostat.
8
The invisible force

https://youtu.be/6BBx8BwLhqg 9
Gradient Coils

Gradient coil with distributed windings etched into

copper conducting sheets (courtesy GEMS)

Gradient coil with thin metallic strips being10

applied in a
fingerprint pattern to a former (courtesy Siemens)
 RF coils
• RF transmit coils: produce a time-varying excitation field B1(t) with
the following characteristics:
• B1(t) must have components that rotate near the resonant frequency
• B1(t) must have components perpendicular to the static magnetic field

Generation of rotating B1 field

(green arrow) by a birdcage
coil. Sinusoidal current is
applied sequentially to rungs
1-6, each of which generates a
local field in directions shown.
A phase shift of 360°/6 = 60°
between the successive rungs
produces a resonantly rotating
B1 field.

Helmholz coil configuration The birdcage coil is the most commonly used RF-
transmit device used in clinical MRI today http://mri-q.com/ 11
RF coils
• Receiver only RF coils
• RF transmission and reception functions have been largely separated and delegated to
two different types of coils.
• In the typical arrangement, RF-transmission is performed by a body RF-coil located just
beneath the inner wall of the scanner bore. RF-reception is delegated to one or more
surface coils placed close to the patient's body as illustrated in the diagram above.

A variety of simple loop

receive-only coils (courtesy
Toshiba)
• RF transceiver coils http://mri-q.com/ 12
 RF coils
• Different RF receiver coils for different part of the body

• RF receiver chain:
Coil Decoupling → Preamplification → ADC → Demodulation → Image Processing

http://mri-q.com/
13
Put all together The essential components of
a typical clinical MRI system
"An MR scanner is a coil within a coil within a coil within a coil . . . "

Schematic cross-section
through a typical
superconducting clinical MR
scanner.

• Within the cryostat are the superconducting coils of the

primary magnet and active shield.
• In the bore of the magnet there are passive shim rods,
active shim coils, gradient coils, body RF coils and 14
patient bed.
Home Made MRI

https://hackaday.io/project/182802-home-made-mri
https://tabletop.martinos.org/index.php? 15
Outline
• Hardware of MRI system
• MR Image Formation
• Gradient Echo vs. Spin Echo
• Contrast, Field of View, Resolution, and SNR in MRI

16
 Data acquisition

Image reconstruction

Post-processing
Signal Acquisition
• Receive sum of signals from each spin.

18
 Reconstruction
• Received signal is a sum of each waveform
• Each waveform has its own frequency
• Fourier Transform can be used to obtain each frequency component

Fourier
Transform

Received Signal Frequency

19
Magnetic Field Gradient
• If spins at each spatial location precess at a different frequency, we
can determine the location of the spins by its frequency
• The precessing frequency is proportional to the magnetic field
• In MRI, we use gradient of magnetic field to cause resonant frequency
to vary with position.
Bz

Position

20
Gx a linear gradient Gy a linear gradient
along x along y
Bz=B0 +xGx Bz=B0 +yGy

z
z
y
y

x
x

Bz Bz

21
• Why do we use gradient?
• Why not use other non-linear magnetic field variations?

22
MR Signal
The received signal is proportional to the vector sum of the
magnetization within the imaging volume:

𝑆 ( 𝑡 )=∫ 𝑚 ( 𝑟
𝑗 𝜑 (𝑟
⃗ ,𝑡 )
⃗ )𝑒 𝑑⃗
𝑟
𝑉

= (x, y) is spatial location;

: spin density;

: the phase of spins at time t;

Remember the phase is time integral of precession frequency.

23
MR Signal
Remember the phase is time integral of precession frequency.

The precession frequency is:

𝑓 (⃗
𝑟 , 𝑡 ) =𝛾 ( 𝐵 0 + 𝑥 𝐺𝑥 (𝑡 )+ 𝑦 𝐺 𝑦 (𝑡 ))

Thus =

Therefore 𝑡

𝑗 2 𝜋 𝛾 ∫ ( 𝑥 𝐺𝑥 (𝜏 )+ 𝑦 𝐺 𝑦 (𝜏 )) 𝑑 𝜏
𝑆 ( 𝑡 )=𝑒 𝑗 2 𝜋𝛾 𝐵 0𝑡
∫ 𝑚 (𝑟⃗ ) 𝑒 0
𝑑⃗
𝑟
𝑉 24
k-space
Define

The term can be removed by demodulation. We have:

𝑆 ( 𝑡 )= 𝑠 ( 𝑘𝑥 , 𝑘 𝑦 ) =∫ 𝑚 ( ⃗
𝑗 2 𝜋 (𝑥 𝑘 + 𝑦 𝑘 𝑦)
𝑟)𝑒 𝑥
⃗
𝑑𝑟
𝑉

Thus the acquired signal and the image are Fourier transform of
each other:

 
s kx , k y  F  m x, y 
( k x ,k y )
25
 t t
 
k x (t )  Gx  d , k y (t )  G y  d
2 0 2 0

ky

b) t=T c) t=2T d) t=3T

Gy

a) t=0 kx

Gx

Data Acquisition
a) t=0 b) t=T c) t=2T d) t=3T
26
2D MR imaging
ky

kx

k-space Image space

(frequency-space)
27
2D MR imaging
• Slice Selection
• Phase Encoding and Frequency Encoding

28
Selective Excitation

29
 Selective Excitation
After we apply gradient Gz along z direction, the Larmor frequency at location z is

𝜔 0 +𝛾 𝐺𝑧 𝑧

If the RF pulse rotates at frequency then it excites a slice at location z:

𝜔 − 𝜔0
𝜔= 𝜔 0 +𝛾 𝐺 𝑧 𝑧 → 𝑧=
𝛾 𝐺𝑧

The RF pulse usually has a bandwidth , which means its rotation frequency has a range
Thus, the RF pulse will excite a slice with thickness

The slice thickness can be decreased either by decreasing RF bandwidth or by increasing

gradient strength
30
Selective Excitation
1
Slope =

Position
gG

Frequency
(a)
(b)

RF Amplitude
Magnitude

Frequency Time
(c) (d)
31
2D MR imaging - Phase Encoding and Frequency
Encoding

• Phase Encoding:
• Apply gradient to impose a spatially dependent
Phase encoding phase on the signal from the precessing protons
• The gradient is turned on and off before data
acquisition
• A number of different values of the phase-
encoding gradient must be used.
• Frequency Encoding:
Frequency encoding • Apply a gradient to create a spatially dependent
precessional frequency during signal acquisition
Data acquisition
• The gradient is turned on during data acquisition

32
 K-space
trajectory
Spins in
Transverse
plane Frequency
encoding

Phase
encoding

33
Pulse Sequences
• Excitation and imaging are separate.
• Pulse sequence controls:
• RF excitation
• Gradient waveforms
• Acquisition
• Reconstruction information as well.

34
2DFT - Pulse Sequence
RF

Gz

Gx

Gy

Acq.
TR, TE

Excitation Imaging 35
 TE and TR
• The echo time (TE) represents the time from the center of the RF-pulse
to the center of the echo.

• The repetition time (TR) is the length of time between corresponding

consecutive points on a repeating series of pulses and echoes.

36
Outline
• Hardware of MRI system
• MR Image Formation
• Gradient Echo vs. Spin Echo
• Contrast, Field of View, Resolution, and SNR in MRI

37
Gradient Echo
• Undoing of phase shifts from gradient fields
𝑡

900 Phase 𝜑 ( 𝑥,𝑡 ) =∫ 𝜔 ( 𝑥 ,𝜏 ) 𝑑 𝜏=𝛾 𝑥 𝐺𝑥 𝑡

0
RF t

Gx
Location x1
Location x2

t
S(t) t=T t=2T

t=T t=2T
38
Spin echo
• Undoing of phase shift from field inhomogeneities and chemical shift
• Ideally, the magnetic field should be homogeneous in the MR scanner, but there are imperfections in
reality. The field inhomogeneity causes protons resonant at different frequencies even there is no
gradient turned on.

The spin-echo is achieved by applying a 180 degree

RF pulse after the 90 degree excitation RF pulse

39
Four Basic Types of Signals in MRI

Type of Signal Method

Free Induction Decay (FID) 1 RF pulse

Gradient Echo 1 RF pulse and gradient reversal

Spin Echo 2 RF pulses

Stimulated Echo 3 or more RF pulses

40
Outline
• Hardware of MRI system
• MR Image Formation
• Gradient Echo vs. Spin Echo
• Contrast, Field of View, Resolution, and SNR in MRI

41
Contrast
• Contrast is the difference in appearance of different tissues in an image.

X-ray contrast is based on transmission.

42
Contrast in MRI
• Three main contrasts in MRI
• Contrast based on T2 relaxation time (T2-weighted)
• Contrast based on T1 relaxation time (T1-weighted)
• Contrast based on proton density (PD-weighted)
• We achieve these contrasts by controlling Echo Time (TE) and
Repetition Time (TR)

43
T2 Contrast (long TE, long TR)
Short Echo-Time Long Echo-Time

CSF
Signal

White/Gray Matter
Time
44
T1 Contrast (short TE, short TR)
Short Repetition Long Repetition

White/Gray Matter
Signal

Time Signal CSF Time 45

Proton Density (Short TE, long TR)

46
Short TR long TR long TR
Short TE long TE short TE
47
 Sampling in frequency domain
Field of View corresponds to replication in
the image domain
F.T
.

Frequency Image

F.T.

Frequency FOV Image

49
 Field of View

https://www.youtube.com/watch?v=qn5WhQ0jIY0&feature=youtu.be
50
 Tp

∆ 𝐺𝑦
Phase encoding
Gy

Gx
Frequency encoding T

T: sampling rate along readout;

Tp: duration of phase encoding
gradient
Gx: the amplitude of readout
gradient;
step of phase encoding gradient
51
 Field of View

Samplin Image
g
Pattern
in k-
space

Samplin
g Image
Pattern
in k-
space
52
Resolution
• Image resolution increases as higher spatial frequencies are acquired.
1 mm 2 mm 4 mm

ky ky ky

kx kx kx

53
Image Noise and SNR
Low Signal-to-Noise Ratio High Signal-to-Noise Ratio

54
Example
We want to acquire a 256x256 image with a pixel resolution of 1mm. Thus FOV is
25.6cm. We know that Gx = 40mT/m.
1. What is the sampling step (sampling rate) T ? What is the duration of the
readout gradient Ts?
2. If the duration of the phase encoding gradient Tp = Ts/10, what is the value ?

Answer:
1 1
1. 𝑇= = =2.29 𝜇 𝑠
𝛾 𝐺 𝑥 𝐹𝑂𝑉 𝑥 6
10 𝐻𝑧 −3
42.58 × ×0.256 𝑚 × 40 ∗10 /𝑚
𝑇
Duration of readout gradient Ts = 256*T = 0.586ms

1 1
∆ 𝐺 𝑦= = =1.57 mT / m
2. 𝛾 𝑇𝑝 ∙ 𝐹𝑂𝑉 𝑦 6
10 𝐻𝑧 −3
42.58 × × 0.256 𝑚 ×0.0586 × 10 𝑠𝑒𝑐
𝑇
55
Acknowledgement
• Prof. Thierry Blu
• Prof. Brian Hargreaves, Stanford University

References:
• Dwight G. Nishimura, Principles of Magnetic Resonance Imaging
• Bernstein, King, Zhou, Handbook of MRI pulse sequences
• http://mri-q.com/

56