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Unit II. Image formation and acquisition
principles.
Part II Major imaging modalities
Dr. Felipe Orihuela-Espina
Outline




Fundamental models of image formation
 Kinds of radiation and imaged properties
The imaging system
 Point spread function
 Imaging filters: Monochromatic, colour, multi-spectral and hyperspectral images
 Resolution (pixel, spatial, radiometric/magnitude,spectral, temporal, superresolution)
Image quality and uncertainties in image formation (digitization, quantum efficiency,
metamerism, calibration, CNR, SNR)
Major imaging modalities
 Magnetic Resonance Imaging
 Optical Imaging
 X-Ray
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
(X-Ray) CT
(X-Ray) Fluoroscopy
 Coherent Tomography (OCT)
 Diffuse Optical Imaging (NIRS)
 Microscopy
 Confocal imaging
 One and two-photon imaging
Electrical and magnetic imaging
 EEG/MEG
 EMG
 ECG
Ultrasound
© 2015. Dr. Felipe Orihuela-Espina
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Some references
 Very nice slides on image acquisition
systems including CT, MRI, Ultrasound,
PET, SPECT
 http://webpages.uncc.edu/krs/courses/6010/m
edvis/imaq1a.pdf
 You may find some good MRI examples
at:
 http://www.mrtip.com/serv1.php?type=db1&dbs=t2%20weig
hted%20image
© 2015. Dr. Felipe Orihuela-Espina
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MAJOR IMAGING MODALITIES
© 2015. Dr. Felipe Orihuela-Espina
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MAGNETIC RESONANCE
IMAGING
© 2015. Dr. Felipe Orihuela-Espina
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System Overview
MR system components. a)
Diagram showing the
relative locations of the
main magnet coils, x, y, and
z gradient coils, integral rf
transmitter body coil and rf
receiver coils. b) Typical
arrangement for a
cylindrical bore MR system
showing the magnet bore
and the reference
coordinate axes with the
static Bo field direction
along the horizontal z axis.
Figure from [Ridgway JP
(2010) JCMR 12:71]
© 2015. Dr. Felipe Orihuela-Espina
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Momentum
 The momentum of an object is the
product of its mass m and velocity v.
 Of course…
© 2015. Dr. Felipe Orihuela-Espina
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Angular momentum
 The angular momentum
L of a particle about a
given origin is defined as
the cross product:
 where r is the position
vector of the particle
relative to the origin, p is
the linear momentum of the
particle
 A related physical
concept is torque; τ=r xF
Relationship between force (F), torque (τ),
momentum (p), and angular momentum (L)
vectors in a rotating system.
Figure from [Wikipedia:Angular_momentum]
© 2015. Dr. Felipe Orihuela-Espina
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Spin
 Spin of a particle is an intrinsic form of
angular momentum carried by elementary
particles*
 ...the other being orbital angular momentum
 The spin is also known as: nuclear spin or
intrinsic spin.
 For you, the spin is the rotation of a
particle around some axis.
*Elementary particles are those whose substructre is unknown. It include
among ohters electrons and photons, as well as the more fanciful muons,
Higgs boson, etc
© 2015. Dr. Felipe Orihuela-Espina
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Spin
 Orbital momentum vs spin
Figure from: [nitt.edu in
http://laser.physics.sunysb.edu/~casey/journal/]
"Vector cones" of total angular momentum J
(purple), orbital L (blue), and spin S (green)
Figure from
[Wikipedia:Angular_momentum_operator]
The orbital momentum is also denoted L
as a generic angular momentum a few
slides ago, but remembar that spin is ALSO
an angular momentum
© 2015. Dr. Felipe Orihuela-Espina
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Spin
 Why do particles spin?
 “Spin is derived from some very deep interaction
with spacetime at the quantum level (for which we
currently have no physical theory). By the time
this interaction is transmitted all the way back up
to our macroscopic version of spacetime (for
which we do have a physical theory) we see an
effect we call “spin”.” [User abbottsys]
 Reference
https://www.physicsforums.com/threads/why-do-allelementary-particles-spin.288954/
 ☞ In other words; we have no clue! [Felipe’s
dixit!]
© 2015. Dr. Felipe Orihuela-Espina
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Spin and magnetism
 A spinning charged
object carries charge in
circles,...
 ...which is just another
way of describing a
current loop.
 Current loops create
“dipole” magnetic fields.
Figure from:
[http://www.askamathematician.com/201
1/10/q-what-is-spin-in-particle-physicswhy-is-it-different-from-just-ordinaryrotation/]
BTW, this is a nice intro to spin!
© 2015. Dr. Felipe Orihuela-Espina
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Magnetic moment
 The characteristics of the current loop are
summarized in its magnetic moment:
 Where A [m2] is the area of the loop and I
[Amperes] is the intensity of the current*
Figure from: [http://hyperphysics.phyastr.gsu.edu/hbase/magnetic/magmom.html]
*Current are moving charges.
© 2015. Dr. Felipe Orihuela-Espina
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Magnetic moment
 The magnetic moment is:
 a measure of the object's tendency to align with a
magnetic field.
 There are two sources for a magnetic moment: the
motion of electric charge and spin angular momentum.
 a quantity that determines the torque τ [Joules J]
that the particle (magnet) will experience in an
external magnetic field B [Teslas T]
© 2015. Dr. Felipe Orihuela-Espina
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Magnetic moment
 The direction of the spin determines whether the
magnetic moment points “upwards” (north;
anticlockwise) or downwards (south; clockwise)
 If many particles are spinning together
microscopically; and they are not aligned e.g.
some oriented north and some oriented south,
they may cancel each other at macroscopic level.
 If not all cancel each other, the collection of particles
(e.g. atom or molecule) is said to have a net spin*.
The sign of the net spin indicates the direction.
*Elementary particles also have a net spin; e.g. proton, neutron, electron,
neutrino, and quarks all have a spin ½.
© 2015. Dr. Felipe Orihuela-Espina
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Magnetism
 So in summary…
 Magnetism is a property of
matter that is a result of the
orbiting electrons in atoms.
 The magnetic field B is the
vector field (it has direction
and magnitude) that
characterises the areas
where an object exhibits a
magnetic influence.
 Magnetic forces are NOT
related to gravity.
Figure from: [cronodon.com in
http://laser.physics.sunysb.edu/~casey/journal/]
© 2015. Dr. Felipe Orihuela-Espina
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Resonance
 The natural frequency is the frequency at
which an object oscillates when it is not
disturbed by an outside force.
 All objects have a natural frequency or set of
frequencies at which they vibrate.
 Natural frequencies depends on the object’s
mass and stiffness (flexibility)
© 2015. Dr. Felipe Orihuela-Espina
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Resonance
 Resonance is the tendency of a system to
oscillate with greater amplitude at some
frequencies than at others. [Wikipedia:Resonance]
 Frequencies at which the response amplitude is a
relative maximum are known as the system's
resonant frequencies, or resonance frequencies.
 Resonance are free vibrations (those occurring
without the need of an external force) of elastic
bodies
 Resonance occurs for both, mechanical and
electromagnetic waves.
© 2015. Dr. Felipe Orihuela-Espina
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Resonance
 Resonance implies that a system is in tune
with its natural frequencies [Cho, Jones
and Singh (1993) Foundations of Medical
Imaging, John Wiley & Sons]
 Note that some particles e.g. electrons, have
its own magnetic field caused by the spin, and
it “resists” being pushed at a faster or slower
rate.
© 2015. Dr. Felipe Orihuela-Espina
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Nuclear Magnetic Resonance
 In nuclear magnetic resonance the nuclei
of atoms exposed to an external magnetic
field absorb and re-emit electromagnetic
radiation.
 Atoms have a nucleus composed of protons:
 In the case of hydrogen; the nucleus has 1 single
proton.
 The proton (like the electron) spins, which of
course generates a small magnetic field.
© 2015. Dr. Felipe Orihuela-Espina
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Nuclear Magnetic Resonance
 A spin packet is a
N
group of spins
experiencing the same
magnetic field strength.
 At any instant in time,
the magnetic field due
to the spins in a spin
packet can be
represented by a
magnetization vector.
S
Each “square” represents a spin packet, and the vector
represent the net magnetization of each spin packet
Figure from: [http://www.cis.rit.edu/htbooks/mri/chap3/chap-3.htm#3.9]
© 2015. Dr. Felipe Orihuela-Espina
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Nuclear Magnetic Resonance
 The vector sum of the
N
magnetization vectors
from all of the spin
packets, divided by
the number of spin
packets, is the net
magnetization.
S
Figure from:
[http://www.cis.rit.edu/htbooks/mri/chap3/chap-3.htm#3.9]
© 2015. Dr. Felipe Orihuela-Espina
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Nuclear Magnetic Resonance
 When a particle with a spin is placed in an external
magnetic field B0, it magnetically “aligns” itself with
the field*.
 [https://www.imt.liu.se/edu/courses/TBMT02/mri/physi
cs_1_notes.pdf]
 Specifically, at thermal equilibrium (i.e. no heat
transfer between spin packets), the net
magnetization vector lies along the direction of the
applied magnetic field B0 and is called the
equilibrium magnetization M0.
*Well, this is just a coarse approximation of what is really going on. In the magnetic field of an MRI scanner at room
temperature, there is approximately the same number of proton nuclei aligned with the main magnetic field Bo as
counter aligned. The aligned position is slightly favoured, as the nucleus is at a lower energy in this position. For every
one-million nuclei, there is about one extra aligned with the B0 field as opposed to the field [Ballinger 1994]. Whatever;
This results in a net or macroscopic magnetization pointing in the direction of the main magnetic field.
© 2015. Dr. Felipe Orihuela-Espina
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Nuclear Magnetic Resonance
 By convention, the
N
external magnetic
field B0 and the net
magnetization vector
at equilibrium both lie
along the Z axis.
S
Figure from:
[http://www.cis.rit.edu/htbooks/mri/chap3/chap-3.htm#3.9]
© 2015. Dr. Felipe Orihuela-Espina
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Nuclear Magnetic Resonance
 In other words; at thermal
N
equlibrium, the Z
component of
magnetization MZ:
 …this is called longitudinal
magnetization.
 In the absence of any other
perturbation, there is no
transverse magnetization:
 MY=MX=0
S
Figure from:
[http://www.cis.rit.edu/htbooks/mri/chap3/chap-3.htm#3.9]
© 2015. Dr. Felipe Orihuela-Espina
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Nuclear Magnetic Resonance
 Remember the energy of a photon E is
related to its frequency f by Planck’s
constant h:
© 2015. Dr. Felipe Orihuela-Espina
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Nuclear Magnetic Resonance
 When placed in a magnetic field of strength B0, a
particle with a net spin can absorb a photon of
frequency f such that:
 with μ being its magnetic moment, and g being a constant.
 The frequency f is called the resonance frequency.
Note that it depends on the strength of the magnetic
field.
© 2015. Dr. Felipe Orihuela-Espina
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Relaxation
 If enough electromagnetic energy is pumped into the system,
it is possible to saturate the spin system and make MZ = 0.
 The equilibrium magnetization can be disrupted (excited) by
absorbing energy from properly tuned frequency pulses.
 This new radiation is referred to as B1 field.
 This takes spin packets to a higher energy state.
 The frequency of these frequency pulses lie in the radio
spectrum i.e. the photons frequency.
 The frequency of a photon is in the radio frequency (RF)
range;
 In NMR spectroscopy, between 60 and 800 MHz for hydrogen
nuclei.
 In clinical MR, for hydrogen imaging, between 15 and 80 MHz
© 2015. Dr. Felipe Orihuela-Espina
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Relaxation
 Relaxation describes how quickly spins "forget"
the direction in which they are oriented.
[Wikipedia:Relaxation_(NMR)]
 After the excitation with the frequency pulse is
stop, the spin packets slowly go back to its original
equilibrium magnetization state through relaxation
processes.
 …that is MZ goes back to being equal to M0.
 …This (re-)magnetization does no occur
instantaneously…giving rise to the so called T1
relaxation process.
 Note that spin packets are returning from the high energy
state (excited by the frequency pulse) to the low energy or
ground state (where they are at equilibrium).
© 2015. Dr. Felipe Orihuela-Espina
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T1 Processes
 The time constant which
describes how MZ returns to its
equilibrium value is called the
spin lattice relaxation time
(T1)
 T1 is the decay constant for the
recovery of the longitudinal Z
component of the nuclear spin
magnetization.
 The T1 relaxation time is the
time for the magnetization to
return to 63% of its original
length.
 For certain MR images, the
image is just a grayscale map
of the T1 for the tissue,
Figure from:
[http://www.cis.rit.edu/htbooks/mri/chap3/chap-3.htm#3.9]
© 2015. Dr. Felipe Orihuela-Espina
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T1 Processes
T1 relaxation process.
Diagram showing the
process of T1 relaxation
after a 90° RF pulse is
applied at equilibrium. The z
component of the net
magnetisation, Mz is
reduced to zero, but then
recovers gradually back to
its equilibrium value if no
further rf pulses are applied.
The recovery of Mz is an
exponential process with a
time constant T1. This is the
time at which the
magnetization has
recovered to 63% of its
value at equilibrium.
Figure from [Ridgway JP
(2010) JCMR 12:71]
© 2015. Dr. Felipe Orihuela-Espina
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Precesion
 Precession is a change in the orientation of the rotational
axis of a rotating body [Wikipedia:Precession]
 Larmor precession (named after Joseph Larmor) is the
precession of the magnetic moments of electrons, muons, all
leptons with magnetic moments, which are quantum effects of
particle spin.
 Exposure of individual nuclei to RF radiation (B1 field) at the
Larmor frequency causes nuclei in the lower energy state to
jump into the higher energy state. [Ballinger 1994]
 On a macroscopic level, exposure of an object or person to RF
radiation at the Larmor frequency, causes the net magnetization
to spiral away from the B0 field. [Ballinger 1994]; that is it
generates a transversal magnetization.
 After a certain length of time, the net magnetization vector rotates 90
degrees and lies in the transverse or x-y plane. It is in this position that
the net magnetization can be detected on MRI.
© 2015. Dr. Felipe Orihuela-Espina
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T2 Process
 The time constant which describes
the return to equilibrium of the
transverse magnetization, MXY, is
called the spin-spin relaxation
time, T2
 T2 relaxation or spin-spin
relaxation occurs when spins in
the high and low energy state
exchange energy but do not loose
energy to the surrounding lattice.
This results macroscopically in
loss of the transverse
magnetization. [Ballinger 1994]
 T2 is always less than or equal to
T1. In biological materials, the T2
time is considerably shorter than
the T1 time.
Figure from:
[http://www.cis.rit.edu/htbooks/mri/chap3/chap-3.htm#3.9]
© 2015. Dr. Felipe Orihuela-Espina
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T1 and T2 processes
 A video showing the spin of a proton
under a constant magnetic field B0.
Visualization of the T1 and T2 relaxation
times.
 http://upload.wikimedia.org/wikipedia/common
s/transcoded/1/11/Proton_spin_MRI.webm/Pr
oton_spin_MRI.webm.720p.webm
© 2015. Dr. Felipe Orihuela-Espina
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T2* Relaxation
 ☞ In addition to T1 and
T2 there is also a T2*
relaxation which is the
loss of signal seen with
dephasing of individual
magnetizations.
 We won’t get into further
detail, but if you want to
know more:
 Ridgway (2010) Journal of
Cardiovascular Magnetic
Resonance, 12(1):71
 Excellent article!
Figure from: [Ridgway (2010) Journal of
Cardiovascular Magnetic Resonance, 12(1):71 ]
© 2015. Dr. Felipe Orihuela-Espina
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Types of materials
(with respect to their magnetic properties)
 Materials may be:
 Ferromagnetic
 Paramegnetic
 Superparamagnetic
 Diamagnetic
© 2015. Dr. Felipe Orihuela-Espina
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Ferromagnetism
 Ferromagnetic materials have a
large positive magnetic susceptibility,
i.e., when placed in a magnet field,
the field strength is much stronger
inside the material than outside.
 They remain magnetized when
thexternal magnetic field is removed.
 This is different from paramagnetic,
superparamagnetic, and diamagnetic
materials.
 Ferromagnetic materials: iron, nickel,
Effect of a ferromagnetic
material on the magnetic
field flux lines.
Figure from
[BallingerR1994]
cobalt, etc
© 2015. Dr. Felipe Orihuela-Espina
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Superparamagnetism
 Superparamagnetic materials have a
large positive magnetic susceptibility.
 But unlike ferromagnetic materials; they do
not maintain magnetization after removal of
the external magnetic field
 On MRI they increase T1 and T2
relaxation rates (decrease in the T1 and
T2 times)
 Superparamagnetic materials: contrast
agents containing iron* for bowel, liver,
and lymph node imaging, ferritin and
hemosiderin (two breakdown products of
hemoglobin), etc
Effect of a
superparamagnetic material
on the magnetic field flux
lines.
Figure from
[BallingerR1994]
*Iron itself is ferromagnetic, but in combination with other atoms may give
the molecule superparamagnetic properties.
© 2015. Dr. Felipe Orihuela-Espina
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Paramagnetism
 Paramagnetic materials have a
(small) positive magnetic
susceptibility.
 Susceptibility is less than one-
thousand of that of ferromagnetic
materials.
 On MRI they increase T1 and T2
relaxation rates (decrease in the
T1 and T2 times)
 Paramagnetic materials: Oxygen
and ions of various metals like Fe,
Mg, and Gd, Myoglobin,
© 2015. Dr. Felipe Orihuela-Espina
Effect of a paramagnetic
material on the magnetic
field flux lines.
Figure from
[BallingerR1994]
39
Diamagnetism
 Diamagnetic materials have no
intrinsic atomic magnetic moment,
but when placed in a magnetic field
weakly repel the field, resulting in a
small negative magnetic susceptibility
 On MRI they increase T1 and T2
relaxation rates (decrease in the T1
and T2 times)
 Diamagnetic materials: water, copper,
nitrogen, [most] biological tissues.
© 2015. Dr. Felipe Orihuela-Espina
Effect of a diamagnetic
material on the magnetic
field flux lines.
Figure from
[BallingerR1994]
40
Pulse sequence
 The contrast on the MR image can be manipulated
by changing the pulse sequence parameters.
 A pulse sequence sets the specific number,
strength, and timing of the RF and gradient pulses.
 The pulse sequence is responsible for the MRI
modality.
 The two most important parameters are the
repetition time (TR) and the echo time (TE).
© 2015. Dr. Felipe Orihuela-Espina
41
Pulse sequence

Repetition Time (TR) is the amount of time that between successive pulse sequences
applied to the same slice.

Echo time (TE) represents the time in milliseconds between the application of the 90°
pulse and the peak of the echo signal in Spin Echo and Inversion Recovery pulse
sequences;
 in other words: the time from the center of the RF-pulse to the center of the echo in which signals
are measured after RF excitation.
Figure from: [http://mri-q.com/tr-and-te.html]

To know more:
 Buxton (2002) “Introduction to Functional Magnetic Resonance Imaging: Principles and Techniques”

Cambridge University Press. 523 pgs
[https://www.cis.rit.edu/htbooks/mri/chap-4/chap-4.htm]
© 2015. Dr. Felipe Orihuela-Espina
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Pulse sequence
 Some common pulse
sequences:
 T1-weighted: short TR and short
TE (TR < 1000msec, TE <
30msec).
 T2-weighted: long TR and long
TE (TR > 2000msec, TE >
80msec).
 Other sequences:
 Fast Spin Echo (FSE)
 Gradient Echo (GRE
 Fluid Attenuated Inversion Recove




(FLAIR)
STIR sequence (Short TI
Inversion Recovery)
SPIR sequence (Spectral Presaturation with InversionRecovery)
SPAIR (Spectral Adiabatic
Inversion Recovery)
…and many others…
Figures from [http://spinwarp.ucsd.edu/neuroweb/Text/br-100.htm]
© 2015. Dr. Felipe Orihuela-Espina
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Pulse Sequence
An example of Fast Spin Echo. Also this is an example of how a pulse sequence
Is often represented in MRI.
Figure from [http://www.mr-tip.com/serv1.php?type=db1&dbs=t2%20weighted%20image]
© 2015. Dr. Felipe Orihuela-Espina
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Pulse sequence
Table from: [Nazir et al (2010) JPMA 60:470-473]
© 2015. Dr. Felipe Orihuela-Espina
45
T1 and T2 weighted
MRI at the time of shunt dysfunction showing panventriculomegaly with
holocord syrinx (a) Sagittal T1 weighted, (b) Sagittal T2 weighted
Figure from [Muthukumar N (2012) J. Craniovertebral Junction and Spine
© 2015. Dr. Felipe Orihuela-Espina
3(1)26:110125]
46
T1 and T2 weighted
T1 and T2 weighted images; TR and TE are indicated
Figure from: [Figure 8.3 Buxton (2002) “Introduction to Functional
Magnetic Resonance Imaging: Principles and Techniques” Cambridge
University Press. 523 pgs]
© 2015. Dr. Felipe Orihuela-Espina
47
Diffusion-Weighted Imaging (DWI)
Figure from [BammerR2005]
© 2015. Dr. Felipe Orihuela-Espina
48
Diffusion-Weighted Imaging (DWI)
Figure from [BammerR2005]
© 2015. Dr. Felipe Orihuela-Espina
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Diffusion-Weighted Imaging (DWI)
Figure from [BammerR2005]
© 2015. Dr. Felipe Orihuela-Espina
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Diffusion-Weighted Imaging (DWI)
Figure from [BammerR2005]
© 2015. Dr. Felipe Orihuela-Espina
51
Diffusion Tensor Imaging (DTI)
Figure from [BammerR2005]
© 2015. Dr. Felipe Orihuela-Espina
52
Echo Planar Imaging (EPI)
Figure from [BammerR2005]
© 2015. Dr. Felipe Orihuela-Espina
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Echo Planar Imaging (EPI)
Figure from [BammerR2005]
© 2015. Dr. Felipe Orihuela-Espina
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Diffusion Tensor Imaging (DTI)
Figure from [BammerR2005]
© 2015. Dr. Felipe Orihuela-Espina
55
Diffusion Tensor Imaging (DTI)
Figure from [BammerR2005]
© 2015. Dr. Felipe Orihuela-Espina
56
Final remarks
 Magnetic resonance imaging has become
one of the most important forms of medical
imaging.
 This short intro is of course insufficient to
show the richness and complexity of this
imaging modality.
 You are encouraged to read more about
MRI!
© 2015. Dr. Felipe Orihuela-Espina
57
THANKS, QUESTIONS?
© 2015. Dr. Felipe Orihuela-Espina
58
BACK UP
© 2015. Dr. Felipe Orihuela-Espina
59
Electric energy
 Remeber; matter has two basic
properties; mass and energy.
 Energy has two basic forms:
 Kinetic - energy of motion
(whether spin or longitudinal)
and
 Potential - energy of position or
state in a force field (e.g.
altitude)
 This is turn can be gravitational,
electric or elastic.
 Many physical processes
cause energy to be converted
from potential to kinetic or the
reverse, and from energy to
mass or the reverse.
Figure from: [http://arachnoid.com/gravity/]
© 2015. Dr. Felipe Orihuela-Espina
60
Electric charge
 Electric charge q is the physical property of
matter that determines their electromagnetic
interaction.
 The basic unit is Coulomb.
 Electric charge is quantized; it always comes in
integer multiples of e=1.602x10-19 [Coulombs]
which is called the elementary charge.
 Protons have a charge of q=+e and electrons
have a charge of q=-e.
© 2015. Dr. Felipe Orihuela-Espina
61
Electric charge and spin
 ☞NOTE: Despite spin generating a magnetic force, the
electric charge is a distinct intrinsic property from spin;
Electric charge is responsible for potential energy, whereas
spin is responsible for kinetic energy, yet of course they are
related:
 The spin value qs can take on only values proportional to the
electric charge qe through the constant of proportionality S:
 To know more:
 Sasso D () “On Primary Physical Transformations of Elementary

Particles: the Origin of Electric Charge”
Mahdi JN (2014) “On the nature of electric charge” nternational
Journal of Physical Sciences, 9(4):54-60]
© 2015. Dr. Felipe Orihuela-Espina
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Coulomb’s law
 Electric charge is responsible for the force
experienced by particles when placed in an
electromagnetic field.
 Particles with electric charge of different sign
do attract each other, whereas those of the
same sign repel each other as described by
Coulomb’s law:
 Where q1 and q2 are the electric charges of the
particles, r is the distance separating those
particles and ke=8.987…x109 is a constant.
 ☞ The force is along the straight line joining them. If
the two charges have the same sign, the
electrostatic force between them is repulsive; if they
have different sign, the force between them is
attractive.
© 2015. Dr. Felipe Orihuela-Espina
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