Section 2 Basic fMRI Physics

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Section 2Basic fMRI Physics
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Other Resources
These slides were condensed from several
excellent online sources. I have tried to give
credit where appropriate. If you would like a
more thorough introductory review of MR physics,
I suggest the following
Robert Coxs slideshow, (f)MRI Physics with
Hardly Any Math, and his book chapters online.
http//afni.nimh.nih.gov/afni/edu/ See
Background Information on MRI section Mark
Cohens intro Basic MR Physics slides http//porkp
ie.loni.ucla.edu/BMD_HTML/SharedCode/MiscShared.ht
ml Douglas Nolls Primer on MRI and Functional
MRI http//www.bme.umich.edu/dnoll/primer2.pdf F
or a more advanced tutorial, see Joseph Hornaks
Web Tutorial, The Basics of MRI http//www.cis.rit
.edu/htbooks/mri/mri-main.htm
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Recipe for MRI

• 1) Put subject in big magnetic field (leave him
  there)
• 2) Transmit radio waves into subject about 3
  ms
• 3) Turn off radio wave transmitter
• 4) Receive radio waves re-transmitted by subject
• Manipulate re-transmission with magnetic fields
  during this readout interval 10-100 ms MRI
  is not a snapshot
• 5) Store measured radio wave data vs. time
• Now go back to 2) to get some more data
• 6) Process raw data to reconstruct images
• 7) Allow subject to leave scanner (this is
  optional)

Source Robert Coxs web slides
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History of NMR
NMR nuclear magnetic resonance Felix Block and
Edward Purcell 1946 atomic nuclei absorb and
re-emit radio frequency energy 1952 Nobel prize
in physics nuclear properties of nuclei of
atoms magnetic magnetic field required resonance
interaction between magnetic field and radio
frequency
Bloch
Purcell
NMR ? MRI Why the name change?
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History of fMRI
MRI -1971 MRI Tumor detection (Damadian) -1973
Lauterbur suggests NMR could be used to form
images -1977 clinical MRI scanner
patented -1977 Mansfield proposes echo-planar
imaging (EPI) to acquire images
faster fMRI -1990 Ogawa observes BOLD effect
with T2 blood vessels became more visible as
blood oxygen decreased -1991 Belliveau observes
first functional images using a contrast
agent -1992 Ogawa et al. and Kwong et al.
publish first functional images using BOLD signal
Ogawa
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Necessary Equipment
4T magnet
RF Coil
gradient coil (inside)
Magnet
Gradient Coil
RF Coil
Source Joe Gati, photos
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The Big Magnet
Very strong
Continuously on
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Magnet Safety
The whopping strength of the magnet makes safety
essential. Things fly Even big things!
Source www.howstuffworks.com
Source http//www.simplyphysics.com/ flying_objec
ts.html
Screen subjects carefully Make sure you and all
your students staff are aware of
hazzards Develop stratetgies for screening
yourself every time you enter the magnet
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Subject Safety

• Anyone going near the magnet subjects, staff
  and visitors must be thoroughly screened
• Subjects must have no metal in their bodies
• pacemaker
• aneurysm clips
• metal implants (e.g., cochlear implants)
• interuterine devices (IUDs)
• some dental work (fillings okay)
• Subjects must remove metal from their bodies
• jewellery, watch, piercings
• coins, etc.
• wallet
• any metal that may distort the field (e.g.,
  underwire bra)
• Subjects must be given ear plugs (acoustic noise
  can reach 120 dB)

This subject was wearing a hair band with a 2 mm
copper clamp. Left with hair band. Right
without. Source Jorge Jovicich
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Protons
Can measure nuclei with odd number of
neutrons 1H, 13C, 19F, 23Na, 31P 1H
(proton) abundant high concentration in human
body high sensitivity yields large signals
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Protons align with field
Outside magnetic field

• randomly oriented

Inside magnetic field

• spins tend to align parallel or anti-parallel to
  B0
• net magnetization (M) along B0
• spins precess with random phase
• no net magnetization in transverse plane
• only 0.0003 of protons/T align with field

M
longitudinal axis
Longitudinal magnetization
transverse plane
Source Mark Cohens web slides
M 0
Source Robert Coxs web slides
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Radio Frequency
Turn your dial to 4T fMRI -- Broadcasting at a
frequency of 170.3 MHz!
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Larmor Frequency
Larmor equation f ?B0 ? 42.58 MHz/T At
1.5T, f 63.76 MHz At 4T, f 170.3 MHz
170.3
Resonance Frequency for 1H
63.8
1.5
4.0
Field Strength (Tesla)
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RF Excitation

• Excite Radio Frequency (RF) field
• transmission coil apply magnetic field along B1
  (perpendicular to B0) for 3 ms
• oscillating field at Larmor frequency
• frequencies in range of radio transmissions
• B1 is small 1/10,000 T
• tips M to transverse plane spirals down
• analogies guitar string (Noll), swing (Cox)
• final angle between B0 and B1 is the flip angle

Transverse magnetization
Source Robert Coxs web slides
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Coxs Swing Analogy
Source Robert Coxs web slides
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Relaxation and Receiving

• Receive Radio Frequency Field
• receiving coil measure net magnetization (M)
• readout interval (10-100 ms)
• relaxation after RF field turned on and off,
  magnetization returns to normal
• longitudinal magnetization? ? T1 signal
  recovers
• transverse magnetization? ? T2 signal decays

Source Robert Coxs web slides
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T1 and TR

• T1 recovery of longitudinal (B0) magnetization
• used in anatomical images
• 500-1000 msec (longer with bigger B0)
• TR (repetition time) time to wait after
  excitation before sampling T1

Source Mark Cohens web slides
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Spatial CodingGradients

• How can we encode spatial position?
• Example axial slice

• Use other tricks to get other two dimensions
• left-right frequency encode
• top-bottom phase encode

Gradient switching thats what makes all the
beeping buzzing noises during imaging!
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Precession In and Out of Phase

• protons precess at slightly different
  frequencies because of
• (1) random fluctuations in the local field at the
  molecular level that affect both T2 and T2 (2)
  larger scale variations in the magnetic field
  (such as the presence of deoxyhemoglobin!) that
  affect T2 only.
• over time, the frequency differences lead to
  different phases between the molecules (think of
  a bunch of clocks running at different rates at
  first they are synchronized, but over time, they
  get more and more out of sync until they are
  random)
• as the protons get out of phase, the transverse
  magnetization decays
• this decay occurs at different rates in
  different tissues

Source Mark Cohens web slides
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T2 and TE
T2 decay of transverse magnetization TE (time
to echo) time to wait to measure T2 or T2
(after refocussing with spin echo or gradient
echo)
Source Mark Cohens web slides
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Echos
pulse sequence series of excitations, gradient
triggers and readouts

• Echos refocussing of signal
• Spin echo
• use a 180 degree pulse to mirror image the
  spins in the transverse plane
• when fast regions get ahead in phase, make them
  go to the back and catch up
• measure T2
• ideally TE average T2
• Gradient echo
• flip the gradient from negative to positive
• make fast regions become slow and vice-versa
• measure T2
• ideally TE average T2

Gradient echo pulse sequence
t TE/2
A gradient reversal (shown) or 180 pulse (not
shown) at this point will lead to a recovery of
transverse magnetization
TE time to wait to measure refocussed spins
Source Mark Cohens web slides
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T1 vs. T2
Source Mark Cohens web slides
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K-Space
Source Travelers Guide to K-space (C.A.
Mistretta)
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A Walk Through K-space
single shot
two shot

• K-space can be sampled in many shots
• (or even in a spiral)
• 2 shot or 4 shot
• less time between samples of slices
• allows temporal interpolation

Note The above is k-space, not slices
vs.
1st volume in 1 sec
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T2

• T2 relaxation
• dephasing of transverse magnetization due to
  both
• - microscopic molecular
  interactions (T2)
• - spatial variations of the
  external main field ?B
• (tissue/air, tissue/bone
  interfaces)
• exponential decay (T2 ? 30 - 100 ms, shorter
  for higher Bo)

Mxy
Mo sin?
T2
T2
time
Source Jorge Jovicich
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Susceptibility
Adding a nonuniform object (like a person) to B0
will make the total magnetic field nonuniform
This is due to susceptibility generation of
extra magnetic fields in materials that are
immersed in an external field For large scale
(10 cm) inhomogeneities, scanner-supplied
nonuniform magnetic fields can be adjusted to
even out the ripples in B this is called
shimming

• Susceptibility Artifact
• -occurs near junctions between air and tissue
• sinuses, ear canals
• -spins become dephased so quickly (quick T2), no
  signal can be measured

sinuses
ear canals
Susceptibility variations can also be seen around
blood vessels where deoxyhemoglobin affects T2
in nearby tissue
Source Robert Coxs web slides
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Hemoglobin
Hemoglogin (Hgb) - four globin chains -
each globin chain contains a heme group - at
center of each heme group is an iron atom (Fe)
- each heme group can attach an oxygen atom
(O2) - oxy-Hgb (four O2) is diamagnetic ? no
?B effects - deoxy-Hgb is paramagnetic ? if
deoxy-Hgb ? ? local ?B ?
Source http//wsrv.clas.virginia.edu/rjh9u/hemog
lob.html, Jorge Jovicich
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BOLD signal
Blood Oxygen Level Dependent signal

• neural activity ? ? blood flow ? ? oxyhemoglobin
  ? ? T2 ? ? MR signal

Mxy Signal
Mo sin?
T2 task
T2 control
Stask
?S
Scontrol
time
TEoptimum
Source fMRIB Brief Introduction to fMRI
Source Jorge Jovicich
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BOLD signal
Source Doug Nolls primer
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First Functional Images
Source Kwong et al., 1992
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Hemodynamic Response Function
signal change (point baseline)/baseline usu
ally 0.5-3 initial dip -more focal and
potentially a better measure -somewhat elusive so
far, not everyone can find it
time to rise signal begins to rise soon after
stimulus begins time to peak signal peaks 4-6
sec after stimulus begins post stimulus
undershoot signal suppressed after stimulation
ends
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Review
Magnetic field
Tissue protons align with magnetic
field (equilibrium state)
RF pulses
Protons absorb RF energy (excited state)
Spatial encoding using magnetic field gradients
Relaxation processes
Relaxation processes
Protons emit RF energy (return to equilibrium
state)
NMR signal detection
Repeat
RAW DATA MATRIX
Fourier transform
IMAGE
Source Jorge Jovicich