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Chapter 5

Magnetic Resonance Imaging

5.1 What is MRI?
5.2 Spin Physics
5.3 MRI Scanner
5.4 MRI Applications
5.5 Functional MRI
5.6 MRI Scan versus CT Scan
5.7 Summary
5.8 References
5.9 Raise Your Grades
5.10 Tutorial
5.1 What is MRI?
Magnetic Resonance Imaging (MRI)
Also termed as nuclear magnetic resonance imaging (NMRI),
or magnetic resonance tomography (MRT)
is a medical imaging technique used in radiology to visualize internal
structures of the body in detail.
makes use of the property of nuclear magnetic resonance (NMR) to
image nuclei of atoms inside the body.
can create more detailed images of the human body than are possible
with X-rays.
This 'nuclear'' refers not to the disintegration of atomic nuclei,
but to their harmless behavior in the presence of a magnetic field.

Unlike CT scanning, which use radiation, MRI examines the body only
with magnetic fields and the pulses of radio waves.

v1_What Is an MRI_1m30s.mp4
MRI A topic of more than 2 Nobel Prizes
Nobel Prize in Physics (1952)
Felix Bloch (1905-1983) Edward Purcell (19121997)

Felix Bloch a Swiss/American professor, Stanford, UC Berkeley

In 1946, he proposed the Bloch equations which determine the time evolution
of nuclear magnetization.
Edward Purcell - an American professor, Harvard, MIT
In December 1946, he discovered nuclear magnetic resonance (NMR) with his
He served as science advisor to 3 Presidents
D.D. Eisenhower, J.F. Kennedy, and L.B. Johnson
Felix Bloch & Edward Purcell
Received Nobel Prize in 1952 for their development of new ways and
methods for nuclear magnetic precision measurements

However, for decades NMR technology was used mainly in NMR

spectrometer for studying the chemical structure of substances.
It wasn't until the 1970s with Lauterbur's and Mansfield's developments that
NMR could be used to produce images of the body.
MRI A topic of more than 2 Nobel Prizes
Nobel Prize in Physiology or Medicine (2003)
Paul Lauterbur (1929-2007) Sir Peter Mansfield (1933 - now)

Paul Lauterbur An American chemist, UIUC

Developed the concept of MRI and got first MRI images (poor quality) with NMR
Unsuccessfully attempted to file patents as his university chose not to pursue patents, with
the rationale that the expense would not pay off in the end. Also attempted to get the federal
government to pay for an early prototype of the MRI machine for years in the 1970s, and the
process took a decade.
The University of Nottingham did file patents which later made Mansfield wealthy.
Sir Peter Mansfield A British physicist, University of Nottingham
Supplied a major step to make Lauterbur's concept a practical reality.
At the age of 15 he was told by a careers teacher that science wasn't for him.
He left school shortly afterwards to work as a printer's assistant.
He developed interest in physics, and his PhD project was on pulsed NMR spectrometer
Mansfield is credited with showing how the radio signals from MRI can be mathematically
analyzed, making interpretation of the signals into a useful image a possibility. He is also
credited with discovering how fast imaging could be possible by developing the MRI
protocol called echo-planar imaging.

5.2 Spin Physics
What is spin?
Spin is a fundamental property of nature like electrical charge or mass.
Spin comes in multiples of 1/2 and can be + or -.
Protons, electrons, and neutrons possess spin.
Individual unpaired electrons, protons, and neutrons each possesses a spin of
Body tissue contains about 60% water ( H2O),
each water molecule has two hydrogen nuclei or protons (1H nuclei)
Each hydrogen proton spins or has a spin.

A water molecule A hydrogen proton spins

5.2.1 Proton
is a subatomic particle with the symbol p or p+ and
a positive electric charge of 1 elementary charge.
One or more protons are present in the nucleus of each atom.
The number of protons in each atom is its atomic number.
A proton has a magnetic moment and spin

Proton spins around its axis like a planet, has

positive charge and electric field around it,
Moving electric field has a magnet field like a bar
Proton alignment
Alignment of protons with the B0 field.
With no external magnetic field, hydrogen protons (+) are
oriented randomly.
When the protons are placed in a strong magnetic field (B0), a net
magnetization will be produced parallel to the main magnetic

5.2.2 Precession
Proton moves in like spinning top in two axis wobbling motion (called
Precession), depends on magnetic field strength

Precession is a change in
the orientation of the
rotational axis of
a rotating body.

Larmor Equation

The protons precession frequency f can be determined by

Larmor Equation

f = B0
f is precession frequency in Hz or MHz
is gyromagnetic ratio of of the particle,
for hydrogen protons =42.58 MHz/T
B0 in magnetic field strength in Tesla (T)

Stronger the external magnetic field, higher the precession frequency

Example: f = 85.16 MHz for hydrogen protons under B = 2 T

Coordinate System

Representation of magnetic force in z-axis, proton vector as red vector

Net magnetic force
Protons pointing in opposite directions cancel each others
magnetic field effect in respective directions
9 protons align up and 5 down, resulting 4 protons up force

Net magnetic force

As there are more

protons aligned parallel
to the external magnetic
field, there is a net
magnetic movement
aligned with or
longitudinal to the
external magnetic field

Human magnetic vector

In a strong external
magnetic field, a new
magnetic vector is
induced in the patient,
who becomes a magnet

This new magnetic

vector is aligned with
the external magnetic

Measuring magnetization

Magnetization along an external magnetic field

cannot be measured.
For this, a magnetization transverse to the external magnetic
field is necessary.

5.2.3 Magnetic Resonance
After protons aligned with the external magnetic force, RF pulse
is sent for energy exchange. Which is only possible if RF pulse
has same frequency as protons precession frequency

Absorption of RF energy
When placed in a magnetic field of strength B0, a particle with a net spin can
absorb a photon of the precession frequency.
The net magnetization points in a direction parallel to the main magnetic field
(also called the longitudinal direction).
As energy is absorbed from the RF pulse, the net magnetization rotates away
from the longitudinal direction.
The amount of rotation (termed the flip angle) depends on the strength and
duration of the RF pulse

Prior to an RF pulse, the net An RF pulse at the Larmor frequency will allow energy to
magnetization (small black be absorbed by the protons, thus causing the net
arrow) is aligned parallel to the magnetization to rotate away from the z axis
main magnetic field and the z
axis EE8094/EE0001/5-16
90 and 180 RF pulses
If the RF pulse rotates the net magnetization into the transverse
plane, that is termed a 90 RF pulse.
If the RF pulse rotates the net magnetization 180 into the z
direction, that is termed a 180 RF pulse.

The strength and/or

duration of the RF pulse
can be controlled to
rotate the net
magnetization to any
90 and 180 RF pulses
are important when
discussing the spin echo

5.2.4 Relaxation
In physics, the spinspin relaxation is the mechanism by which the
transverse component of the magnetization vector, exponentially decays
towards its equilibrium value of zero, in MRI.

Longitudinal Relaxation (T1)
Also termed as T1 relaxation or T1 decay
Application of a 90 RF pulse causes longitudinal
magnetization to become zero.
Over time, the longitudinal magnetization will grow back in a
direction parallel to the main magnetic field

T1 curve
Transverse Relaxation (T2)
Also termed as T2 relaxation or T2 decay
Immediately after application of a 90 RF pulse, transverse
magnetization is maximized;
After the 90 RF pulse is switched off, protons loose phase
coherence, they get out of step (dephase)
The signals from these dephasing protons begin to cancel out, and the MR
signal decreases

T2 curve

v3_T2_decay_12s.mp4 EE8094/EE0001/5-20
5.2.5 Spin Echo (SE)
After a 90 RF pulse, protons that were in phase begin to dephase in
the transverse plane
Application of a 180 RF pulse will allow formation of an echo
at a time TE (time to echo).
Multiple 180 pulses will form multiple echoes.
The 180 pulse refocuses the dephasing
protons which results in a stronger signal,
the spin echo after the time TE.
The protons then dephase again and can be
refocused another time by a 180 pulse and
so on.
Thus it is possible to obtain more than one
spin-echo (MR signal).
The spin-echo, however differ in intensity
due to so-called T2-decay.

The signal intensity reduces but A curve connecting the spin echo intensities is the T2
frequency is constant. This is called curve. If we did not use the 180 pulse, the signal intensity
would decay faster. A curve describing the signal
free induction decay (FID) signal.
intensity in that case the T2* curve.
v4_Spin_Echo_36s.mp4 EE8094/EE0001/5-21
180 Turn
t=0 When a rabbit and a
90 pulse
turtle run in one direction
for a certain time,
then turn around and run
t = TE/2 in the opposite direction
180 pulse with the same speed for
the same time,
they will arrive at the
starting point at the same
t = TE time.

How to differentiate various tissues?
Various tissues can be differentiated based on how quickly they
release energy after pulse is turned off.

It is possible to determine
signal intensity for a tissue
using a spin echo sequence by
combining the T1-and the T2-
curve for that tissue.
T1- and T2-weighted images
may be created with this pulse
G = gradient field.

TR: Time to repeat or repetition time

TE: Time to echo
Different tissues have different T1, T2 rates
Different tissues have different rates Different tissues have different rates
of T1 relaxation. of T2 relaxation.
If an image is obtained at a time If an image is obtained at a time
when the T1 relaxation curves are when the T2 relaxation curves are
widely separated, T1-weighted widely separated, T2-weighted
contrast will be maximized. contrast will be maximized.

(Cerebro-Spinal Fluid)

T1 : 200 2000 msec

T2 : 20 150 msec
Liquids have long T1 & T2; fat has short T1 & T2

T1 weighted image T2 weighted image

(TR=450 msec, TE=14 msec) (TR=5550 msec, TE=105 msec)

MR signal detection

A magnetic field (black arrow)

that is near and perpendicular to
a loop of wire will produce an
electric current in the loop.
The current can be digitized and
stored for later reconstruction
into an MR image.

5.2.6 Magnetic Field Gradient
Constant B0 cannot provide spatial information
The hydrogen spin-flip frequency is the same for all parts of the sample.
Once excited by the RF signal, the hydrogens will tend to return to their lower
state in a process called "relaxation" and will re-emit RF radiation at their Larmor
frequency. This signal is detected as a function of time, and then is converted to
signal strength as a function of frequency by means of a Fourier transformation.
Since the protons in each of the active areas of the sample are subjected to the
same magnetic field, they will produce the same frequency of radiation and the
Fourier transform of the detected signal will have only one peak. This one peak
demonstrates the presence of hydrogen atoms, but gives no information to locate
them in the sample.

Magnetic Field Gradient
Use Gradient Field BG for Spatial Information
Information about the location of the hydrogen atoms can be obtained by adding a
calibrated gradient field across the region of the sample.
With an increasing magnetic field as you move to the right across the sample, the
spin-flip energy and therefore the frequency of the emitted signal increases from
left to right.
When excited by an RF transmitter, the emitted signal contains different
frequencies for the two proton concentration (spin) areas. These frequencies can be
separated by means of the Fourier transform and the example gives two different
regions of frequency for the two sample areas.
In the sketch, it only locates them along the horizontal direction, giving no
indication that they are at different heights.

Using z-gradient to select a slice
To select a particular slice of a body, we can transmit a
pulse of a frequency that would cause the particular slice
to resonate

But the spins cannot de distinguished

f = B0 EE8094/EE0001/5-29
Use y-gradient for phase coding
This gradient is briefly turned on, then quickly turned off, then the
magnetic moments have returned to their base frequency and spin at
the same rate but experience phase shift in y-axis which we can use to
localize spins in y-direction

Use x-gradient for frequency coding
We then tune our system to focus on a particular phase of the
matrix to definitely locate a magnetic moment
Each of the signals has a unique phase and frequency which can be
localized in 3D space

MRI Image Formation
Each voxels are assigned a grey scale value corresponding to the
strength of local signal to create a image

A voxel represents a value on a regular grid in 3D space.

5.3 MRI Scanner

v5_How Does an MRI Work_54s.mp4

MRI Scanner
An MRI scanner is a device in which the patient lies within a
large, powerful magnet where the magnetic field is used to align
the magnetization of some atomic nuclei in the body, and pulsed
radio frequency (RF) magnetic fields are applied to
systematically alter the alignment of this magnetization.
This causes the nuclei to produce a rotating magnetic field detectable
by the scannerand this information is recorded to construct an
image of the scanned area of the body.
Magnetic field gradients cause nuclei at different locations to precess
at different speeds, which allows spatial information to be recovered
using Fourier analysis of the measured signal.
By using gradients in different directions, 2D images or 3D volumes
can be obtained in any arbitrary orientation.

5.4 MRI Applications
MRI can be used to image every part of the body, and is
particularly useful for tissues with many hydrogen nuclei
and little density contrast, such as the brain, muscle,
connective tissue and most tumors.



The Neural Highway
MRI can be used to understand brain structure

5.5 Functional MRI
Functional MRI (fMRI)
is a functional neuroimaging procedure using MRI technology that measures
brain activity by detecting associated changes in blood flow.
This technique relies on the fact that cerebral blood flow and neuronal
activation are coupled. When an area of the brain is in use, blood flow to that
region also increases.
The primary form of fMRI uses the Blood-Oxygen-Level Dependent (BOLD)
This is a type of specialized brain and body scan used to map neural activity
in the brain or spinal cord of humans or other animals by imaging the change
in blood flow (hemodynamic response) related to energy use by brain cells.
Since the early 1990s, fMRI has come to dominate brain mapping research
because it does not require people to undergo shots, surgery, or to ingest
substances, or be exposed to radiation.

Functional MRI
The procedure is similar to MRI but uses the change in
magnetization between oxygen-rich and oxygen-poor blood as its
basic measure.
The resulting brain activation can be presented graphically by color-coding
the strength of activation across the brain or the specific region studied.
The technique can localize activity to within millimeters but, using standard
techniques, no better than within a window of a few seconds.

fMRI Example
These fMRI images are from a study showing parts of the brain lighting up on
seeing houses and other parts on seeing faces.
The 'r' values are correlations, with higher positive or negative values indicating a
better match.

5.6 MRI Scan versus CT Scan
CT Scan MRI Scan

Imaging Uses X-rays for imaging Uses large external field, RF pulse and 3
principle different gradient fields

Time Usually completed within 5 minutes. Scan typically runs for about 30 minutes.
Actual scan time usually less than 30
Cost CT Scan usually costs less than MRIs More expensive than CT Scan, X-rays, and
(e.g., CT brain scan: S$312-S$956) most other examing methods
(e.g., MRI brain scan: S$520-S$1393)
Radiation safety Low ionizing radiation with risk. No radiation.
Usually not recommended for No biological hazards have been reported
pregnant women or children unless with the use of the MRI.
absolutely necessary.

MRI Scan versus CT Scan
CT Scan MRI Scan
Scope of CT can outline bone inside the MRI is more versatile than the X-Ray
applications body very accurately. and is used to examine a large variety of
medical conditions.
Application Suited for bone injuries, Lung and Suited for Soft tissue evaluation, e.g.
Chest imaging, cancer detection. ligament and tendon injury, spinal cord
Widely used on Emergency Room injury, brain tumors etc.
Details of bony Provides good details about bony Less detailed compared to X-ray.
structures structures
Details of soft A major advantage of CT is that it Much higher soft tissue detail as
tissues: is able to image bone, soft tissue compare to CT scan.
and blood vessels all at the same
Limitation for Patients with metal implants can In most cases the examination is safe for
Scanning get CT scan. patients with metal implants, with the
patients: exception of a few types of implants:
Cardiac Pacemakers, ferromagnetic
object which may cause trauma/burn.

Advantages of MRI Scan over CT Scan
A CT scan uses X rays to build up a picture. A MRI scan uses a magnetic
field to do the same and has no known side effects related to radiation
MRI gives higher detail in soft tissues.
One of the greatest advantages of MRI is the ability to change the contrast of
the images.
Small changes in radio waves and magnetic fields can completely change the contrast of
the image.
Different contrast settings will highlight different types of tissue.

Another advantage of MRI is the ability to change the imaging plane

without moving the patient.
Most MRI machines can produce images in any plane.

Contrast agents are also used in MRI but they are not made of iodine.
There are fewer documented cases of reactions to MRI contrast and it is considered to be
safer than X-ray dyes.

Advantages of CT Scan over MRI Scan

CT is very good for imaging bone structures.

Patients with certain metal implants cannot receive an MRI
surgical clips,
metallic fragments,
cardiac monitors or pacemakers.
The time taken for total testing is shorter than taken by MRI.
MRI cannot be done on patients who are claustrophobic as the
patient has to remain inside the noisy machine for about 20-45
CT scan is cheaper than an MRI scan.
A CT scan costs $1,200 to $3,200 while an MRI can cost up to $4,000.

5.7 Summary
Basic concepts
Proton spin
Magnetic resonance
MRI procedure
Patient is put in a magnet
90 and 180 RF pulses are sent
Patient emits a signal (spin-echo) which is recorded and used for
Reconstruction of image
MRI Scan versus CT Scan
In terms of safety, scope of applications, cost,

5.8 References
What is an MRI (1m30s, for slide 2)

Understanding MRIs (5m22s, slide 34)

MRI Physics Tutorial (many small animations, slides 19, 20, 21)

The Basics of MRI

5.9 Raise Your Grades
Do you understand ?
Basic concepts of MRI physics
Proton spin
Magnetic resonance
Calculation of procession frequency
The idea of using 90 and 180 RF pulses
How to get spatial information
Purposes of using 3 magnetic field gradients in x, y, and z directions
Advantages of MRI scan over CT scan
Advantages of CT scan over MRI scan

5.10 Tutorial : MRI Image Formation
T5a: For a 22 MRI imaging area, if The phase coding along y-direction is
p=[0, 90],
the frequency coding along x-direction is
f=(0.8+0.2x) [T] where x=[1, 2],
form the MRI image by filling the 22 pixel imaging area with the color map in
Figure 1 based on the received signal strength data in the Table below

Frequency (MHz) 0 receiver 90 receiver

42.580 0.82 0.57
51.096 0.42 0.16
Color Map
(1,1) (1,2) 0.7 ~ 1.00
Figure 1 y
0.3 ~ 0.69
(2,1) (2,2) 0.0 ~ 0.29
Tutorial : MRI Image Formation
T5b: Figure 1 shows the coordinates of an MRI imaging area.
The magnetic field gradients used for the MRI imaging are
Bx = 0.8 + 0.2x [T] in the x-direction,
Bz = 0.7 + 0.3z [T] in the z-direction,
the received signals for a MRI scan after Fourier transform are
shown in Figure 2. Form the MRI image by filling the 33 pixel
imaging area with the colour map in Figure 3.

Figure 3
Figure 2 EE8094/EE0001/5-50