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MRI Physics 2: Contrasts and Protocols

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Title: MRI Physics 2: Contrasts and Protocols


1
MRI Physics 2 Contrasts and Protocols
  • Chris Rorden
  • 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/lectures/gpl_page.html
  • www.cis.rit.edu/htbooks/mri/chap-8/chap-8.htm
  • www.e-mri.org/cours/Module_7_Sequences/gre6_en.htm
    l

2
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.

3
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).

4
Anatomy of an MRI scan
  • Place object in strong magnetic field atoms
    align to field.
  • Transmit Radio frequency pulse atoms absorb
    energy
  • Wait
  • Listen to Radio Frequency emission due to
    relaxation
  • Wait, Goto 2
  • Time between set 2 and 4 is our Echo Time (TE)
  • Time between step 2 being repeated is our
    Repetition Time (TR).
  • TR and TE influence image contrast.

TR
TE
Time
5
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.

6
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)
7
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
8
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

9
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.
  • Therefore, do we always want a short TE?

10
TE and T2 contrast
  • Signals from all tissue decays with time.
  • Signal decays faster in some tissues than others.
  • 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)
11
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)
12
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
13
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.

14
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)
15
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.

16
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.

17
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.

18
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
19
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
20
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
21
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

22
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
23
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/
24
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

25
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
26
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?

27
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. Except, 90º and 180º
    inversion pulses applied to different slices.
    Only nuclei that travel between slices show
    coherent signal.

Saturated Spins
Flow
Unsaturated Spins
SLICE
28
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?

29
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.

30
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.

31
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)
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