ECSE6963 Biological Image Analysis

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ECSE-6963Biological Image Analysis

• Lecture 5
• Common Medical Imaging Instrument
• MRI PET Scanner
• Badri Roysam
• Rensselaer Polytechnic Institute, Troy, New York
  12180.

Center for Sub-Surface Imaging Sensing
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Recap

• Probes, media, and objects
• Basic types of microscopes
• The Radon Transform, back projection algorithm,
  the X-Ray CT Scanner

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Magnetic Resonance Imaging (MRI)

• Biggest advance since X-Rays X-Ray CT
• Was called Nuclear Magnetic Resonance in the
  early days
• The word Nuclear made people uncomfortable
  during the 70s, was not needed.
• MRI has advanced to a point of becoming the
  method of choice for most parts of the body

1952 Nobel Prize Felix Bloch and Edward
Purcell 1991 Nobel Prize Richard R. Ernst
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Basic Principle

• Use radio waves instead of X-Rays to probe
• Problem Wavelength is too long!
• Get around this limitation by producing images
  based on spatial variations in the phase and
  frequency of the radio frequency energy being
  absorbed and emitted by the imaged object.
• Exploit magnetic properties of abundant particles
  such as protons in tissue
• When protons are placed in a magnetic field, they
  become capable of receiving and then transmitting
  electromagnetic energy.
• The strength of the transmitted energy is
  proportional to the number of protons in the
  tissue.
• Signal strength is modified by properties of each
  proton's microenvironment, such as its mobility
  and the local homogeneity of the magnetic field.
• MR signal can be "weighted" to accentuate some
  properties over others.

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Physics Background - Spin

• All physical particles (electrons, protons,
  neutrons.) possess a fundamental property known
  as spin
• Spin is always a multiple of /- ½ .
• Think of spin as a tiny spinning magnet with a
  north pole and a south pole
• When an external magnetic field B is applied
  along the z axis, the tiny magnets line up along
  the same axis
• It can absorb/emit energy at a characteristic
  frequency
• These frequencies are in the radio frequency
  range

Nuclei with highest biological abundance
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Behavior when a field is applied

• Each mini-magnet has two states
• Lined up along B, and against
• There is an energy difference between these two
  states
• Change in stage implies absorbing or emitting
  radio-frequency energy

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Behavior when radio excitation is applied

• At equilibrium, net magnetization vector is along
  B (z axis)
• When we apply radio frequency energy at frequency
  ?, the magnetization can turn slowly away from
  the equilibrium angle
• The change in angle depends on how long the RF
  energy is applied
• A 90o turn can make the z component of the
  magnetization Mz zero (takes several
  milliseconds)
• If we apply a long enough RF pulse, the
  magnetization can even turn by 180o

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Behavior when radio excitation is stopped

• If we stop this RF excitation, it returns to
  equilibrium

T1 spin-lattice relaxation time
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Behavior when radio excitation is stopped

• Excitation in the x-y plane makes the
  magnetization precess (wobble, like a spinning
  top) around the z axis.
• Rate of precession is called the Larmor
  frequency
• The transverse magnetization Mxy returns to
  equilibrium according to

T2 spin-spin relaxation time
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T1 and T2

• T1 is applicable along the magnetic field
  (axial/longitudinal)
• Cant be detected directly
• Measures how quickly equilibrium is achieved with
  external field
• T2 is applicable in a transverse direction to the
  magnetic field
• Can be detected directly
• Measures how long the precession persists after
  excitation is turned off
• Useful to know T1 and T2 because they are
  characteristically different for each kind of
  tissue
• These equations are for one proton

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The FID signal

• A rotating magnetization will induce a current in
  a coil perpendicular to the z axis (say, along x
  axis)
• This signal decays as T2
• This signal is called the free induction decay
  or FID.

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The 90o FID

• The RF pulse is long enough to flip the net
  magnetization by 90o
• The magnetization vectors decay can be measured
  with a coil.
• To get a strong signal
• Increase B0
• Reduce temperature T
• Material with high ?
• Material with more protons
• In general, more spins
• More abundant material

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The Overall MRI Signal

• Theres not enough time to establish full
  equilibrium in practice. If TR is the time
  available for recovery after the previous pulse,
  the longitudinal magnetization actually available
  is

• ? proton density
• This magnetization produces the transverse
  magnetization in response to a 90o pulse. We
  measure this at time TE

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Weighted Signals

• By choosing TR and TE suitably, we can make one
  of the factors T1, T2, or ? dominate

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Imaging Process Basic Idea

• If the external field is constant, B, then for
  the 3 points in the brain, the resonance
  frequency is the same, so they cant be
  distinguished
• We just see the sum of 3 signals

• One way to distinguish the points is to change B,
  i.e., a small gradient field (about 0.01 T/m).
• Only the points whose resonant frequency matches
  will respond

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Selecting a Slice thru the Patient

• Apply a linear magnetic field gradient Gz during
  the time that the RF pulse is applied
• Only the small window of z values for which the
  resonance frequency is matched will resonate

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Back-Projection Imaging

• Apply 1-D field gradient at multiple angles in
  the x-y plane
• Record MR spectra at multiple angles and use back
  projection algorithm
• Gx, Gy, and Gz are components of a 3-D field
  gradient

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Pulse Sequence for Back-Projection Imaging

• Apply a linear magnetic field gradient Gz during
  the time that the RF pulse is applied to excite a
  slice through the patient
• Use Gx, Gy, to set the angle while recording the
  signal

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More Current Technology

• Briefly,
• GS selects the slice along the z axis
• G? sets the phase encoding w.r.t the y axis
  within the plane at the selected z value
• Gf sets the frequency encoding w.r.t the x axis
  within the plane at the selected z value

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The Instrument

• The magnets are extremely strong (1 3 Tesla)
• Enough to hurl a trashcan across a room!
• Extremely noisy claustrophobic inside the
  machine
• Optimal design of coils, pulse sequences, and
  reconstruction algorithms is big business
• Current instruments have progressed way beyond
  the back-projection scheme outlined here

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MRI Images
T1
T2
Proton Density

• Pixel sizes approx. 3 mm3
• By collecting a series of images, it is possible
  to calculate 3 values at each pixel T1, T2 ,
  Proton density ?
• Different tissues show up differently on each of
  these channels
• Basis of image segmentation!

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MRI Images
Axial (trans-axial, horizontal)
Coronal
Sagittal
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CT vs. MRI

• CT
• Cheap Fast
• Good resolution with bone
• Hard to distinguish soft tissues without contrast
  agent
• Cant distinguish atoms beyond their X-Ray
  cross-section
• X-Rays harmful to body

• MRI
• Expensive Slow
• Can distinguish bone and various soft tissues
• Can distinguish specific atoms
• No known health hazards to MR imaging

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Main advantages of MRI

• Structural Functional Imaging Possible
• Differentiation between various kinds of soft
  tissue.
• X-rays pass through soft tissue without much
  absorption
• High sensitivity to early pathological changes
  makes early detection possible.
• Studies of blood vessels and flow without use of
  contrast
• just oxygen level of blood gives contrast
• 3-D, allowing Multi-planar display
• i.e. axial, sagittal, coronal, and oblique.
• Multi-channel output
• Enables better segmentation
• No known biological hazards
• Magnetic fields dont ionize, unlike X-rays
• Exceptions people with pacemakers and/or
  implanted metallic objects cant be imaged safely

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Recent Developments

• Faster imaging (about 5 images/sec)
• Echo Planar MR can image the brain in seconds
  instead of minutes
• Of late, the importance of MRI in diagnosis is
  also greatly enhanced by its ability to do
• Functional mapping of the brain
• Exploit the fact that oxygen level differences in
  blood lead show up on MRIs.
• Spectroscopy and molecular imaging

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Nuclear Medicine

• Basic Idea
• Inject patient with radio-isotope labeled
  substance (tracer)
• Chemically the same, but physically different
• Detect the radioactive emissions (gamma rays)
• Super-short wavelength
• But, cant achieve the implied high resolution
• Detection technology limitations
• Not enough photons!
• Use filtered back-projection to reconstruct the
  3-D image
• Like fluorescence microscopy, except we dont
  need excitation

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SPECT PET
PET image Showing a tumor

• Major Functional imaging tools
• SPECT Single-photon Emission Computed Tomography
• cheap and low-resolution
• Tells us where blood is flowing
• PET Positron Emission Tomography
• expensive and higher-resolution

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SPECT Instrument

• The gamma camera is a 2-D array of detectors
• One or more gamma cameras are used to capture 2-D
  projections at multiple angles
• Use filtered back-projection to reconstruct 3-D
  image!
• Actual sinograms appear noisy due to the fact
  that we dont have enough photons
• Quantum-limited imaging

3-camera SPECT instrument
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PET Idea
Gamma Photon 1
Nucleus (protonsneutrons)

• Basic Idea
• Nucleus emits a positron
• A short-lived particle
• Same mass as electron, but opposite charge
• Positron collides with a nearby electron and
  annihilates
• Two 511 keV gamma rays are produced
• They fly in opposite directions (to conserve
  momentum)

BANG
electrons
Gamma Photon 2
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Emission Detection
Ring of detectors

• If detectors A B receive gamma rays at the
  approx. same time, we have a detection
• Hard sensor and electronics design problem,
  expensive

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Image Reconstruction

• We can organize our set of detections as a set of
  angular views
• Use filtered back-projection algorithm!

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PET Images

• Single-channel images
• Noisy, and blurry
• Not ideal for segmentation
• Segment MRI/CT for defining anatomy
• Register the images
• Measure activity

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Better Algorithms

• Filtered back-projection algorithm
• produces a background artifact, discussed earlier
• Noisy reconstruction
• The Maximum Likelihood algorithm produces a
  better reconstruction for the same data

Filtered Back-Projection
Maximum Likelihood
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References on MRI

• Main MRI Reference
• http//www.cis.rit.edu/htbooks/mri/inside.htm
• Other MRI References
• http//www.spincore.com/nmrinfo/mri_s.html
• http//dmoz.org/Science/Chemistry/Nuclear_Magnetic
  _Resonance/Theory_of_NMR_and_MRI/Basic_NMR_and_MRI
  _Theory/

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References on SPECT PET

• PET
• http//www.crump.ucla.edu/lpp/lpphome.html
• SPECT Imaging
• http//www.physics.ubc.ca/mirg/intro.html
• SPECT Image Atlas
• http//brighamrad.harvard.edu/education/online/Bra
  inSPECT/BrSPECT.html

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Summary

• Discussion of major medical instruments
• Structure imaging
• Function imaging
• Next Class
• Image Pre-processing methods

Image Acquisition
Image Reconstruction Pre-processing
Image Segmentation
Morphometry Higher-Level Analysis
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Instructor Contact Information

• Badri Roysam
• Professor of Electrical, Computer, Systems
  Engineering
• Office JEC 6046
• Rensselaer Polytechnic Institute
• 110, 8th Street, Troy, New York 12180
• Phone [phone]
• Fax [phone]
• Email roysam_at_ecse.rpi.edu
• Website http//www.rpi.edu/roysab
• NetMeeting ID (for off-campus students)
  128.113.61.80
• Secretary Jeanne Denue, JEC 6049, (518) 276
  6313, denuej_at_ecse.rpi.edu