Transcript Temporal Aspects of Visual Extinction

MRI Physics 2: Contrasts and Protocols
 Chris Rorden, Paul Morgan
 Types of contrast: Protocols
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–
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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.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 T1weighted scan, but relatively
bright in a T2 scan.
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MR Contrast
 Four types of MR contrasts:
1. Static Contrast: Sensitive to relaxation properties
of the spins (T1, T2)
2. Endogenous Contrast: Contrast that depends on
intrinsic property of tissue (e.g. fMRI BOLD)
3. Exogenous contrast: Contrast that requires a
foreign substance (e.g. Gadolinium)
4. 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.
1.
2.
3.
4.



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.
TE
Time
TR
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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
Fat: Short T1
1
1
CSF: Long T1
0
0
0
TR (s)
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CSF: Long T2
Signal

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.
Magnetization



Fat: Short T2
0
TE (s)
0.2 6
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.
Before first pulse:
1H in all tissue
strongly magnetized.
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.
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.
Optimal
GM/WM
contrast
White Matter: Fast Decay
Signal
Signal
Gray Matter: Slow Decay
0
TE (s)
.2
0
Contrast: difference
between GM and
WM signal
TE (s)
.2
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Optimal contrast
 Optimal TE will depend on which tissues you wish to
contrast
Signal
– Gray matter
vs White matter
– CSF
vs Gray matter
0
TE (s)
.2
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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).
 T2* leads to rapid loss of signal:
images with long TE with have little
coherent signal.
1
T2
Signal
 Due to these artifacts, Larmor frequency
varies between locations.
1
1
1
1



*
T 2 T 2 T 2 M T 2 MS
T2*
0
0
TE (s)
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0.2
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, hydrogen’s
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 someone’s 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
Actual Signal
1
T2
Signal
 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.
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.
– Minute hands now differ: out of phase.
 Reverse direction of each clock (~ send in
180º RF pulse).
 Wait precisely one hour
420º
Minute hand rotation
 Simultaneously,set both clocks to read
12:00. (~ send in 90º RF pulse).
 Wait precisely one hour
0
– Minute hands now identical: both read noon.
– They are briefly back in phase
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
www.fmrib.ox.ac.uk/~karla/
reduces with TE.
Optimal BOLD TE
~60ms for 1.5T,
0
~30ms at 3T.
TE (s)
0.2
Fera et al. (2004) J MRI 19, 19-26
Low
Frequency
High
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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.
Non-BOLD
BOLD
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www.fmrib.ox.ac.uk/~karla/
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 r=2, TE=35ms, TR=
2100ms
– Typical 1.5T: 3x3x3mm 64x64 matrix, 36
slcies, TE=60ms, 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:
SLICE
1. Use very short TR, so signal in slice is
saturated. External spins flowing into slice Flow
have full magnetization.
2. Conduct a Spin Echo Scan: 90º and 180º
inversion pulses applied to different
Unsaturated
slices. Only nuclei that travel between
Spins
slices show coherent signal.
Saturated
Spins
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Arterial Spin Labelling
z (=B0)
excitation
y
www.fmrib.ox.ac.uk/~karla/
inversion
slab
blood
x
inversion
imaging
plane
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.
3.0T Scanner
Signal
1.5T Scanner
Magnetization
1
0
0
TE (s)
.2
0
TR (s)
3
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