Medical Image Analysis

1
Medical Image Analysis

• Medical Imaging Modalities Magnetic Resonance
  Imaging

Figures come from the textbook Medical Image
Analysis, Second Edition, by Atam P. Dhawan, IEEE
Press, 2011.
2
Magnetic Resonance Imaging

• Nuclear magnetic resonance
• The selected nuclei of the matter of the object
• Blood flow and oxygenation
• Different parameters weighted,
  weighted, Spin-density
• Advance MR Spectroscopy and Functional MRI
• Fast signal acquisition of the order of a
  fraction of a second

Figures come from the textbook Medical Image
Analysis, Second Edition, by Atam P. Dhawan, IEEE
Press, 2011.
3
Figure comes from the Wikipedia,
www.wikipedia.org.
Figures come from the textbook Medical Image
Analysis, Second Edition, by Atam P. Dhawan, IEEE
Press, 2011.
4
Figure 4.12. MR images of a selected
cross-section that are obtained simultaneously
using a specific imaging technique. The images
show (from left to right), respectively, the
T1-weighted, T-2 weighted and the Spin-Density
property of the hydrogen protons present in the
brain.
Figures come from the textbook Medical Image
Analysis, Second Edition, by Atam P. Dhawan, IEEE
Press, 2011.
5
Magnetic Resonance Imaging

• 1H high sensitivity and vast occurrence in
  organic compounds
• 13C the key component of all organic
• 15N a key component of proteins and DNA
• 19F high relative sensitivity
• 31P frequent occurrence in organic compounds
  and moderate relative sensitivity

Adapted from the Wikipedia, www.wikipedia.org.
6
MR Spectroscopy
Figure comes from the Wikipedia,
www.wikipedia.org.
Figures come from the textbook Medical Image
Analysis, Second Edition, by Atam P. Dhawan, IEEE
Press, 2011.
7
MR Spectroscopy
Figure comes from the Wikipedia,
www.wikipedia.org.
Figures come from the textbook Medical Image
Analysis, Second Edition, by Atam P. Dhawan, IEEE
Press, 2011.
8
Functional MRI
Figure comes from the Wikipedia,
www.wikipedia.org.
Figures come from the textbook Medical Image
Analysis, Second Edition, by Atam P. Dhawan, IEEE
Press, 2011.
9
MRI Principles

• spin-lattice relaxation time
• spin-spin relaxation time
• the spin density

Figures come from the textbook Medical Image
Analysis, Second Edition, by Atam P. Dhawan, IEEE
Press, 2011.
10
MRI Principles

• Great web sites
• Simulations from BIGS - Lernhilfe für Physik und
  Technik
• http//www.cis.rit.edu/class/schp730/bmri/bmri.htm
  

Figures come from the textbook Medical Image
Analysis, Second Edition, by Atam P. Dhawan, IEEE
Press, 2011.
11
MRI Principles

• Spin
• A fundamental property of nuclei with odd atomic
  weight and/or odd atomic numbers is the
  possession of angular moment
• Magnetic moment
• The charged protons create a magnetic field
  around them and thus act like tiny magnets

Figures come from the textbook Medical Image
Analysis, Second Edition, by Atam P. Dhawan, IEEE
Press, 2011.
12
MRI Principles

• the spin angular moment
• the magnetic moment
• a gyromagnetic ratio, MHz/T
• A hydrogen atom
• 42.58 MHz/T

Figures come from the textbook Medical Image
Analysis, Second Edition, by Atam P. Dhawan, IEEE
Press, 2011.
13
Figure 4.13. Left A tiny magnet representation
of a charged proton with angular moment, J.
Right A symbolic representation of a charged
proton with angular moment, J and a magnetic
moment, µ.
Figures come from the textbook Medical Image
Analysis, Second Edition, by Atam P. Dhawan, IEEE
Press, 2011.
14
MRI Principles

• Precession of a spinning proton
• The interaction between the magnetic moment of
  nuclei with the external magnetic field
• Spin quantum number of a spinning proton ½
• The energy level of nuclei aligning themselves
  along the external magnetic field is lower than
  the energy level of nuclei aligned against the
  external magnetic field

Figures come from the textbook Medical Image
Analysis, Second Edition, by Atam P. Dhawan, IEEE
Press, 2011.
15
Figure 4.14 (a) A symbolic representation of a
proton with precession that is experienced by the
spinning proton when it is subjected to an
external magnetic field. (b) The random
orientation of protons in matter with the net
zero vector in both longitudinal and transverse
directions.
Figures come from the textbook Medical Image
Analysis, Second Edition, by Atam P. Dhawan, IEEE
Press, 2011.
16
MRI Principles

• Equation of motion for isolated spin
• Solution

Figures come from the textbook Medical Image
Analysis, Second Edition, by Atam P. Dhawan, IEEE
Press, 2011.
17
Longitudinal Vector OX at the transverse
position X
Figures come from the textbook Medical Image
Analysis, Second Edition, by Atam P. Dhawan, IEEE
Press, 2011.
18
Figure 4.15 (a). Nuclei aligned under thermal
equilibrium in the presence of an external
magnetic field. (b). A non-zero net longitudinal
vector and a zero transverse vector provided by
the nuclei precessing in the presence of an
external magnetic field.
Figures come from the textbook Medical Image
Analysis, Second Edition, by Atam P. Dhawan, IEEE
Press, 2011.
19
Figures come from the textbook Medical Image
Analysis, Second Edition, by Atam P. Dhawan, IEEE
Press, 2011.
20
MRI Principles

• The precession frequency
• Depends on the type of nuclei with a specific
  gyromagnetic ratio and the intensity of the
  external magnetic field
• This is the frequency on which the nuclei can
  receive the Radio Frequency (RF) energy to change
  their states for exhibiting nuclear magnetic
  resonance
• The excited nuclei return to the thermal
  equilibrium through a process of relaxation
  emitting energy at the same precession frequency

21
MRI Principles

• 90-degree pulse
• Upon receiving the energy at the Larmor
  frequency, the transverse vector also changes as
  nuclei start to precess in phase
• Form a net non-zero transverse vector that
  rotates in the x-y plane perpendicular to the
  direction of the external magnetic field

Figures come from the textbook Medical Image
Analysis, Second Edition, by Atam P. Dhawan, IEEE
Press, 2011.
22
Figure 4.16. The 90-degree pulse causing nuclei
to precess in phase with the longitudinal vector
shifted clockwise by 90-degrees as a result of
the absorption of RF energy at the Larmor
frequency.
Figures come from the textbook Medical Image
Analysis, Second Edition, by Atam P. Dhawan, IEEE
Press, 2011.
23
MRI Principles

• 180-degree pulse
• If enough energy is supplied, the longitudinal
  vector can be completely flipped over with a
  180-degree clockwise shidf in the direction
  against the external magnetic field

Figures come from the textbook Medical Image
Analysis, Second Edition, by Atam P. Dhawan, IEEE
Press, 2011.
24
Figure 4.17. The 180-degree pulse causing nuclei
to precess in phase with the longitudinal vector
shifted clockwise by 180-degrees as a result of
the absorption of RF energy at the Larmor
frequency.
Figures come from the textbook Medical Image
Analysis, Second Edition, by Atam P. Dhawan, IEEE
Press, 2011.
25
MRI Principles

• Relaxation
• The energy emitted during the relaxation process
  induces an electrical signal in a RF coil tuned
  at the Larmor frequency
• The free induction decay of the electromagnetic
  signal in the PF coil is the basic signal that is
  used to create MR images
• The nuclear excitation forces the net
  longitudinal and transverse magnetization vectors
  to move

Figures come from the textbook Medical Image
Analysis, Second Edition, by Atam P. Dhawan, IEEE
Press, 2011.
26
MRI Principles

• A stationary magnetization vector
• The total response of the spin system

Figures come from the textbook Medical Image
Analysis, Second Edition, by Atam P. Dhawan, IEEE
Press, 2011.
27
Figure 4.18. The transverse relaxation process of
spinning nuclei.
Figures come from the textbook Medical Image
Analysis, Second Edition, by Atam P. Dhawan, IEEE
Press, 2011.
28
MRI Principles

• The longitudinal and transverse magnetization
  vectors with respect to the relaxation times
• where

Figures come from the textbook Medical Image
Analysis, Second Edition, by Atam P. Dhawan, IEEE
Press, 2011.
29
Figure 4.19. (a) Transverse and (b) longitudinal
magnetization relaxation after the RF pulse.
Figures come from the textbook Medical Image
Analysis, Second Edition, by Atam P. Dhawan, IEEE
Press, 2011.
30
MRI Principles

• The RF pulse causes nuclear excitation changing
  the longitudinal and transverse magnetization
  vectors
• After the RF pulse is turned off, the excited
  nuclei go through the relaxation phase emitting
  the absorbed energy at the same Larmor frequency
  that can be detected as an electrical signal,
  called the Free Induction Decay (FID)

Figures come from the textbook Medical Image
Analysis, Second Edition, by Atam P. Dhawan, IEEE
Press, 2011.
31
MRI Principles

• The NMR spin-echo signal (FID signal)

Figures come from the textbook Medical Image
Analysis, Second Edition, by Atam P. Dhawan, IEEE
Press, 2011.
32
MR Instrumentation

• The stationary external magnetic field
• Provided by a large superconducting magnet with a
  typical strength of 0.5 T to 1.5 T
• Housing of gradient coils
• Good field homogeneity, typically on the order of
  10-50 parts per million
• A set of shim coils to compensate for the field
  inhomogeneity

Figures come from the textbook Medical Image
Analysis, Second Edition, by Atam P. Dhawan, IEEE
Press, 2011.
33
Figure 4.20. A general schematic diagram of a MR
imaging system.
Figures come from the textbook Medical Image
Analysis, Second Edition, by Atam P. Dhawan, IEEE
Press, 2011.
34
Figure comes from the Wikipedia,
www.wikipedia.org.
Figures come from the textbook Medical Image
Analysis, Second Edition, by Atam P. Dhawan, IEEE
Press, 2011.
35
Figure comes from the Wikipedia,
www.wikipedia.org.
Figures come from the textbook Medical Image
Analysis, Second Edition, by Atam P. Dhawan, IEEE
Press, 2011.
36
MR Instrumentation

• An RF coil
• To transmit time-varying RF pulses
• To receive the radio frequency emissions during
  the nuclear relaxation phase
• Free Induction Decay (FID) in the RF coil

Figures come from the textbook Medical Image
Analysis, Second Edition, by Atam P. Dhawan, IEEE
Press, 2011.
37
MR Pulse Sequences

• NMR signal
• The frequency and the phase
• Spatial encoding in MR imaging
• Frequency encoding and phase encoding

Figures come from the textbook Medical Image
Analysis, Second Edition, by Atam P. Dhawan, IEEE
Press, 2011.
38
Figure 4.21 (a). Three-dimensional object
coordinate system with axial, sagittal and
coronal image views. (b) From top left to
bottom right Axial, coronal and sagittal MR
images of a human brain.
Figures come from the textbook Medical Image
Analysis, Second Edition, by Atam P. Dhawan, IEEE
Press, 2011.
39
Figures come from the textbook Medical Image
Analysis, Second Edition, by Atam P. Dhawan, IEEE
Press, 2011.
40
MR Pulse Sequences
Figure 4.22. (a) Three-dimensional spatial
encoding for spin-echo MR pulse sequence. (b) A
linear gradient field for frequency encoding.
(c). A step function based gradient field for
phase encoding.
Figures come from the textbook Medical Image
Analysis, Second Edition, by Atam P. Dhawan, IEEE
Press, 2011.
41
Figures come from the textbook Medical Image
Analysis, Second Edition, by Atam P. Dhawan, IEEE
Press, 2011.
42
MR Pulse Sequences

• Frequency encoding
• A linear gradient is applied throughout the
  imaging space a long a selected direction
• The effective Larmor frequency of spinning nuclei
  is also spatially encloded along the direction of
  the gradient
• Slice selection for axial imaging

Figures come from the textbook Medical Image
Analysis, Second Edition, by Atam P. Dhawan, IEEE
Press, 2011.
43
MR Pulse Sequences

• The phase-encoding gradient
• Applied in steps with repeated cycles
• If 256 steps are to be applied in the
  phase-encoding gradient, the readout cycle is
  repeated 256 times, each time with a specific
  amount of phase-encoding gradient

Figures come from the textbook Medical Image
Analysis, Second Edition, by Atam P. Dhawan, IEEE
Press, 2011.
44
Spin Echo Imaging

• Between the application of the 90 degree pulse
  and the formation of echo (rephasing of nuclei
• Between the 90 degree pulse and 180 degree pulse

Figures come from the textbook Medical Image
Analysis, Second Edition, by Atam P. Dhawan, IEEE
Press, 2011.
45
Figure 4.23. The transverse relaxation and echo
formation of the spin echo MR pulse sequence.
Figures come from the textbook Medical Image
Analysis, Second Edition, by Atam P. Dhawan, IEEE
Press, 2011.
46
Spin Echo Imaging

• K-space
• The placement of raw frequency data collected
  through the pulse sequences in a
  multi-dimensional space
• By taking the inverse Fourier transform of the
  k-space data, an image about the object can be
  reconstructed in the spatial domain
• The NMR signals collected as frequency-encoded
  echoes can be placed as horizontal lines in the
  corresponding 2-D k-space

Figures come from the textbook Medical Image
Analysis, Second Edition, by Atam P. Dhawan, IEEE
Press, 2011.
47
Spin Echo Imaging

• K-space
• As multiple frequency encoded echoes are
  collected with different phase-encoding
  gradients, they are placed as horizontal lines in
  the corresponding k-space with the vertical
  direction representing the phase-encoding
  gradient values

Figures come from the textbook Medical Image
Analysis, Second Edition, by Atam P. Dhawan, IEEE
Press, 2011.
48
Figure comes from the Wikipedia,
www.wikipedia.org.
Figures come from the textbook Medical Image
Analysis, Second Edition, by Atam P. Dhawan, IEEE
Press, 2011.
49
Spin Echo Imaging

• the cycle repetition time
• weighted
• A long and a long
• weighted
• A short and a short
• Spin-density
• A long and a short

Figures come from the textbook Medical Image
Analysis, Second Edition, by Atam P. Dhawan, IEEE
Press, 2011.
50
Figure 4.24. A spin echo pulse sequence for MR
imaging.
Figures come from the textbook Medical Image
Analysis, Second Edition, by Atam P. Dhawan, IEEE
Press, 2011.
51
Spin Echo Imaging

• The effective transverse relaxation time from the
  field inhomogeneities

Figures come from the textbook Medical Image
Analysis, Second Edition, by Atam P. Dhawan, IEEE
Press, 2011.
52
Spin Echo Imaging

• The effective transverse relaxation time from a
  spatial encoding gradient

Figures come from the textbook Medical Image
Analysis, Second Edition, by Atam P. Dhawan, IEEE
Press, 2011.
53
Inversion Recovery Imaging

• IR imaging
• IR imaging pulse sequence allows relaxation of
  some or all of before spins are rephased
  through 90-degree pulse and therefore emphasizes
  the effect of longitudinal magnetization
• 180-degree pulse is first applied along with the
  slice selection frequency encoding gradient

Figures come from the textbook Medical Image
Analysis, Second Edition, by Atam P. Dhawan, IEEE
Press, 2011.
54
Echo Planar Imaging

• A single-shot fast-scanning method
• Spiral Echo Planar Imaging (SEPI)
• where

55
Figure 4.25. A single shot EPI pulse sequence.
Figures come from the textbook Medical Image
Analysis, Second Edition, by Atam P. Dhawan, IEEE
Press, 2011.
56
Figure 4.26. The k-space representation of the
EPI scan trajectory.
Figures come from the textbook Medical Image
Analysis, Second Edition, by Atam P. Dhawan, IEEE
Press, 2011.
57
Figure 4.27. The spiral scan trajectory of SEPI
pulse sequence in the k-space.
Figures come from the textbook Medical Image
Analysis, Second Edition, by Atam P. Dhawan, IEEE
Press, 2011.
58
Figure 4.28. The SEPI pulse sequence
Figures come from the textbook Medical Image
Analysis, Second Edition, by Atam P. Dhawan, IEEE
Press, 2011.
59
Figure 4.29. MR images of a human brain acquired
through SEPI pulse sequence.
Figures come from the textbook Medical Image
Analysis, Second Edition, by Atam P. Dhawan, IEEE
Press, 2011.
60
Gradient Echo Imaging

• Fast low angle shot (FLASH) imaging
• Utilize low-flip angle RF pulses to create
  multiple echoes in repeated cycles to collect the
  data required for image reconstruction
• A low-flip angle (as low as 20 degrees)
• The readout gradient is inverted to re-phase
  nuclei leading to the gradient echo during the
  data acquisition
• The entire pulse sequence time is much shorter
  than the spin echo pulse sequence

Figures come from the textbook Medical Image
Analysis, Second Edition, by Atam P. Dhawan, IEEE
Press, 2011.
61
Figure 4.30. The FLASH pulse sequence for fast MR
imaging.
Figures come from the textbook Medical Image
Analysis, Second Edition, by Atam P. Dhawan, IEEE
Press, 2011.
62
Flow Imaging

• Tracking flow
• Diffusion (incoherent flow) and perfusion
  (partially coherent flow)
• The FID signal generated in the RF receiver coil
  by the moving nuclei and velocity-dependent
  factors
• MR angiography

Figures come from the textbook Medical Image
Analysis, Second Edition, by Atam P. Dhawan, IEEE
Press, 2011.
63
Figure 4.31. A flow imaging pulse sequence with
spin echo.
Figures come from the textbook Medical Image
Analysis, Second Edition, by Atam P. Dhawan, IEEE
Press, 2011.
64
Figure 4.32 Left A proton density image of a
human brain. Right The corresponding perfusion
image.
Figures come from the textbook Medical Image
Analysis, Second Edition, by Atam P. Dhawan, IEEE
Press, 2011.
65
Figure 4.33. Gradient echo based MR pulse
sequence for 3-D MR volume angiography.
Figures come from the textbook Medical Image
Analysis, Second Edition, by Atam P. Dhawan, IEEE
Press, 2011.
66
Figure 4.34. An MR angiography image.
Figures come from the textbook Medical Image
Analysis, Second Edition, by Atam P. Dhawan, IEEE
Press, 2011.
67
Flow Imaging
angiography image
Figure comes from the Wikipedia,
www.wikipedia.org.
68
FMRI

• fMRI imaging
• Measure blood oxygen level during sensory
  stimulation or any task that causes a specific
  neural activity
• Visual or auditory stimulation, finger movement,
  or a cognitive task
• Blood oxygenated level dependence (BOLD)
• Oxygenated hemoglobin ( ) is
  diamagnetic, while deoxygenated hemoglobin (
  ) is paramagnetic

69
Figure comes from the Wikipedia,
www.wikipedia.org.
70
FMRI

• fMRI imaging
• A reduction of the relative deoxy-hemoglobin
  concentration due to an increase of blood flow
  and hence increased supply of fresh
  oxy-hemoglobin during neural activity is measured
  as an increase in or weighted MR
  signals

71
Diffusion Imaging

• Diffusion process
• Water molecules spread out over time that is
  represented by Brownian motion
• An anisotropic Gaussian distribution along a
  given spatial axis such that the spread of the
  position of molecules after a time along a
  spatial axis can be represented with a
  variance of
• where is diffusion coefficient in the tissue
  

72
DTI color image
Figure comes from the Wikipedia,
www.wikipedia.org.
73
Diffusion Imaging

• Diffusion process
• Anisotropic diffusion in the white matter
• Isotropic diffusion in the gray matter
• Motion probing gradients (MPG) to examine the
  motion of water molecules in the diffusion
  process in a specific direction
• The MR FID signal is decreased for healthy
  tissue, and increased with trapped-in water
  molecules

74
Diffusion Imaging

• Diffusion process
• where is the gyromagnetic ratio, is
  diffusion coefficient, and is the strength
  of two MPG gradients each with duration
  separated by applied in spatial
  directions

75
Diffusion Imaging

• Diffusion process

76
Diffusion Imaging

• Diffusion process
• Fractional anisotropy (FA)
• Multiple sclerosis, strokes, tumors, Parkinsons
  and Alzheimers disease
• Attention deficit hyperactivity disorder (ADHS)

77
Contrast, Spatial Resolution, and SNR

• Spin-echo imaging pulse sequence
• Inversion recovery (180-90-180) imaging pulse
  sequence

78
Contrast, Spatial Resolution, and SNR

• Gradient echo imaging pulse sequence

79
Contrast, Spatial Resolution, and SNR

• Paramagnetic contrast agent
• gadolinium (Gd) to change the susceptibility of
  the net magnetization vector
• Reduces relaxation time and increases the
  signal intensity of -weighted images
• Noise and field inhomogeneities
• RF noise, field inhomogeneities, motion,
  chemical shift

80
Contrast, Spatial Resolution, and SNR

• Chemical shift
• The deviation of its effective resonance
  frequency in the presence of other nuclei from a
  standard reference without any other nuclei with
  their local magnetic fields present
• ppm

81
Contrast, Spatial Resolution, and SNR

• Induced magnetic field in alkenes
• Induced magnetic field in alkynes

Figure comes from the Wikipedia,
www.wikipedia.org.