MRI Physics 2: Contrasts and Protocols

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MRI Physics 2 Contrasts and Protocols

• Chris Rorden, Paul Morgan
• Types of contrast Protocols
• Static T1, T2, PD
• Endogenous T2 BOLD (fMRI), DW
• Exogenous Gadolinium Perfusion
• Motion ASL

www.fmrib.ox.ac.uk/karla/ www.hull.ac.uk/mri/lect
ures/gpl_page.html www.cis.rit.edu/htbooks/mri/cha
p-8/chap-8.htm www.e-mri.org/cours/Module_7_Sequen
ces/gre6_en.html
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MR Contrast a definition

• We use different MRI protocols that are dominated
  by different contrasts.
• Contrasts influence the brightness of a voxel.
• For example, water (CSF) is relatively dark in a
  T1-weighted scan, but relatively bright in a T2
  scan.

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MR Contrast

• Four types of MR contrasts
• Static Contrast Sensitive to relaxation
  properties of the spins (T1, T2)
• Endogenous Contrast Contrast that depends on
  intrinsic property of tissue (e.g. fMRI BOLD)
• Exogenous contrast Contrast that requires a
  foreign substance (e.g. Gadolinium)
• Motion contrast Sensitive to movement of spins
  through space (e.g. perfusion).

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Anatomy of an MRI scan

• Place object in strong static magnetic field,
  then.
• Transmit Radio frequency pulse atoms absorb
  energy
• Wait
• Listen to Radio Frequency emission due to
  relaxation
• Wait, Goto 1
• Time between set 1 and 3 is our Echo Time (TE)
• Time between step 1 being repeated is our
  Repetition Time (TR).
• TR and TE influence image contrast.

TR
TE
Time
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T1 and T2 definitions

• T1-Relaxation Recovery
• Recovery of longitudinal orientation.
• T1 time refers to interval where 63 of
  longitudinal magnetization is recovered.
• T2-Relaxation Dephasing
• Loss of transverse magnetization.
• T2 time refers to interval where only 37 of
  original transverse magnetization is present.

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Contrast T1 and T2 Effects

• T1 effects measure recovery of longitudinal
  magnetization.
• T2 refers to decay of transverse magnetization.
• T1 and T2 vary for different tissues. For
  example, fat has very different T1/T2 than CSF.
  This difference causes these tissue to have
  different image contrast.
• T1 is primarily influenced by TR, T2 by TE.

Fat Short T1
1
1
CSF Long T2
Magnetization
Signal
CSF Long T1
Fat Short T2
0
0
0.2
0
0
3
TR (s)
TE (s)
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T1 Effects get them while their down

• Consider very short TR
• Fat has rapid recovery, each RF pulse will
  generate strong signal.
• Water has slow recovery, little net magnetization
  to tip.

T1 effects explain why we discard the first few
fMRI scans the signal has not saturated, so
these scans show more T1 than subsequent images.
Before first pulse1H in all tissue strongly
magnetized.
After several rapid pulses CSF has little net
magnetization, so these tissue will not generate
much signal.
Fat
CSF
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Signal Decay Analogy

• After RF transmission, we can detect RF emission
• Emission at Larmor frequency.
• Emissions amplitude decays over time.
• Analogous to tuning fork frequency constant,
  amplitude decays

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Relaxation

• After RF absorption ends, protons begin to
  release energy
• Emission at Larmor frequency.
• Emissions amplitude decays over time.
• Different tissues show different rates of decay.
• Free Induction Decay (FID).
• Strongest signal immediately after transmission.
• Most signal with short TE.
• Why not always use short TE?

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TE and T2 contrast

1. Signals from all tissue decays with time.
2. Signal decays faster in some tissues than others.
3. Optimal contrast between tissue when they emit
   relatively different signals.

White Matter Fast Decay
Optimal GM/WM contrast
Gray Matter Slow Decay
Contrast difference between GM and WM signal
Signal
Signal
0
.2
0
.2
TE (s)
TE (s)
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Optimal contrast

• Optimal TE will depend on which tissues you wish
  to contrast
• Gray matter vs White matter
• CSF vs Gray matter

Signal
0
.2
TE (s)
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T2 Dephasing

• RF pulse sets phase.
• Initially, everything in phase maximum signal.
• Signals gradually dephase signal is reduced.
• Some tissue shows more rapid dephasing than other
  tissue.

Fat

CSF
Time
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T1 and T2 contrasts

• Every scan is influenced by both T1 and T2.
• However, by adjusting TE and TR we can determine
  which effect dominates
• T1-weighted images use short TE and short TR.
• Fat bright (fast recovery), water dark (slow
  recovery)
• T2-weighted images use long TE and long TR they
  are dominated by the T2
• Fat dark (rapid dephasing), water bright (slow
  dephasing).
• Proton density images use short TE and long TR
  reflect hydrogen concentration. A mixture of T1
  and T2

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T2 vs T2

• T2 only one reason for dephasing
• Pure T2 dephasing is intrinsic to sample (e.g.
  different T2 of CSF and fat).
• T2 dephasing includes true T2 as well as field
  inhomogeneity (T2m) and tissue susceptibility
  (T2ms).
• Due to these artifacts, Larmor frequency varies
  between locations.
• T2 leads to rapid loss of signal images with
  long TE with have little coherent signal.

1
T2
Signal
T2
0
0
0.2
TE (s)
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Susceptibility artifacts

• Magnet fields interact with material.
• Ferromagnetic (iron, nickel, cobalt)
• Strongly attracted dramatically increases
  magnetic field.
• all steel has Iron (FE), but not all steel is
  ferromagnetic (try putting a magnet on a
  austenitic stainless steel fridge).
• Paramagnetic (Gd)
• Weakly attracted slightly increases field.
• Diamagnetic (H2O)
• Weakly repelled slightly decreases field.

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Tissue Susceptibility

• Due to spin-spin interactions, hydrogens
  resonance frequency differs between materials.
• E.G. hydrogen in water and fat resonate at
  slightly different frequencies (220 Hz 1.5T).
• Macroscopically These effects can lead spatial
  distortion (e.g. fat shift relative to water)
  and signal dropout.
• Microscopically field gradients at boundaries of
  different tissues causes dephasing and signal
  loss.

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Field Inhomogeneity Artifacts

• When we put an object (like someones head)
  inside a magnet, the field becomes non-uniform.
• When the field is inhomogeneous, we will get
  artifacts resonance frequency will vary across
  image.
• Prior to our first scans, the scanner is
  shimmed to make the field as uniform as
  possible.
• Shimming is difficult near air-tissue boundaries
  (e.g., sinuses).
• Shimming artifacts more intense at higher fields.

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Spin Echo Sequence

• Spin echo sequences apply a 180º refocusing pulse
  half way between initial 90º pulse and
  measurement.
• This pulse eliminates phase differences due to
  artifacts, allowing measurement of pure T2.
• Spin echo dramatically increases signal.

Actual Signal
1
T2
Signal
T2
0
0.5 TE
0.5 TE
Time
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Spin Echo Sequences

• The refocusing pulse allows us to recover true
  T2.
• Image from
• www.e-mri.org/cours/Module_4_Signal/contraste1_en.
  html
• Web site includes interactive adjustment of T1/T2

T2
T2
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Analogy for Spin Echo

• Consider two clocks.
• Clock 1 minute hand takes 70 minutes to make a
  revolution.
• Clock 2 minute hand takes 55 minutes to make a
  revolution.
• Simultaneously,set both clocks to read 1200. (
  send in 90º RF pulse).
• Wait precisely one hour
• Minute hands now differ out of phase.
• Reverse direction of each clock ( send in 180º
  RF pulse).
• Wait precisely one hour
• Minute hands now identical both read noon.
• They are briefly back in phase

420º
Minute hand rotation
0
1 hour
1 hour
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T2 fMRI Signal is an artifact

• fMRI is Blood Oxygenation Level Dependent
  measure (BOLD).
• Brain regions become oxygen rich after activity
  ratio of Hbr/HbrO2 decreases

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BOLD effect

• Deoxyhemoglobin (Hbr) acts as contrast agent
• Frequency spread causes signal loss over time
• Effect increases with delay (TE echo time)

• But, overall signal reduces with TE.
• Optimal BOLD TE 60ms for 1.5T, 30ms at 3T.
• Fera et al. (2004) J MRI 19, 19-26

www.fmrib.ox.ac.uk/karla/
0.2
0
TE (s)
Low High
Frequency
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BOLD artifacts

• fMRI is a T2 image we will have all the
  artifacts that a spin-echo sequence attempts to
  remove.
• Dephasing near air-tissue boundaries (e.g.,
  sinuses) results in signal dropout.

BOLD
www.fmrib.ox.ac.uk/karla/
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Optimal fMRI scans

• More observations with shorter TR, but slightly
  less signal per observation (due to T1 effects
  and temporal autocorrelation).
• When you have a single anatomical region of
  interest use the fewest slices required for a
  very short TR.
• For exploratory group study, use a scan that
  covers whole brain with minimal spatial
  distortion (for good normalization).
• Typical 3T 3x3x3mm 64x64 matrix, 36 slices,
  SENSE r2, TE35ms, TR 2100ms
• Typical 1.5T 3x3x3mm 64x64 matrix, 36 slcies,
  TE60ms, TR 3500ms.

• Shorter TR yields better SNR
• Diminishing returns
• G.H. Glover (1999) On Signal to Noise Ratio
  Tradeoffs in fMRI

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Diffusion Imaging

• Diffusion imaging is an endogenous contrast.
• Apply two gradients sequentially with opposite
  polarity.
• Stationary tissue will be both dephased and
  rephased, while spins that have moved will be
  dephased.
• Sensitive to acute stroke (DWI, see lesion
  lecture)
• Multiple directions can measure white matter
  integrity (diffusion tensor imaging, see DTI
  lecture)

water diffuses faster in unconstrained ventricles
than in white matter
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Gadolinium Enhancement

• Gd Perfusion scans are an example of an exogenous
  contrast.
• intravenously-injected.
• Gd not detected by MRI (1H).
• Gd has an effect on surrounding 1H.
• Gd shortens T1, T2, T2 of surrounding tissue.
• makes vessels, highly vascular tissues, and areas
  of blood leakage appear brighter.
• Very rare side effect allergic reaction.
• Gd can help measure perfusion.
• Useful for clinical studies how much blood is
  getting to a region, how long does it take to get
  there?

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Time of Flight

• ToF is a motion contrast.
• In T1 scans, motion of blood between slices can
  cause artifacts.
• ToF intentionally magnifies flow artifacts.
• Several Protocols of ToF, E.G
• Use very short TR, so signal in slice is
  saturated. External spins flowing into slice have
  full magnetization.
• Conduct a Spin Echo Scan 90º and 180º inversion
  pulses applied to different slices. Only nuclei
  that travel between slices show coherent signal.

Saturated Spins
Flow
Unsaturated Spins
SLICE
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Arterial Spin Labelling
www.fmrib.ox.ac.uk/karla/
z (B0)
excitation
blood
y
x
inversion
white matter low perfusion Gray matter high
perfusion

• ASL is an example of a motion contrast
• IMAGEperfusion IMAGEuninverted IMAGEinverted
• Perfusion is useful for clinical studies how
  much blood is getting to a region, how long does
  it take to get there?

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Common Neuroimaging Protocols

• T1 scans high resolution, good gray-white matter
  contrast VBM lecture.
• T2/DW scans permanent brain injury lesion
  lecture.
• Gd scans acute brain dysfunction lesion
  lecture.
• DTI scans white matter fiber tracking DTI
  lecture.
• T2/ASL scans scans for brain activity most of
  this course.

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Advanced Physics Notes

• We described 2D images using a 90º flip angle and
  spin echo for refocusing.
• The very short TR of our T1 3D sequences use
  smaller flip angle with gradient echo refocusing.
  
• Optimal flip angle Ernst angle. It is
  calculated from the TR value and the T1 of
  tissue.

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Advanced Physics Notes

• Field strength influences T1 and T2.
• Optimal TR/TE for contrast will depend on field
  strength.
• Higher Field Faster T2 decay Typically, TE
  decreases as field increases faster imaging.
• Higher Field Slower T1 recovery TR must
  increase with field strength. Influences T1
  contrast e.g. time of flight improves improves
  with field strength.

1
3.0T Scanner
1.5T Scanner
Magnetization
Signal
0
0
.2
0
3
TE (s)
TR (s)