introduction to mri physics - fsl.fmrib.ox.ac.ukapps/2018/fsl_intromri.pdf · mri scans: carefully...
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Introduction to MRI Physics
Slides originally by Karla Miller, FMRIB Centre
Slides available at:http://users.fmrib.ox.ac.uk/~mchiew/teaching/
Modified by Mark Chiew ([email protected])
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MRI PhysicsMonday:★ Basics of magnetic resonance★ Image formation★ Signal statistics (SNR)★ Functional MRI
Wednesday:★ Image contrast (T2 and T2*)★ Spin vs. gradient echo★ Fast imaging★ Diffusion MRI
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What are we trying to achieve?Informed decision making: You need to take responsibility for the design, implementation & execution of your study
• Protocols need to be tailored to the problem
• Learning some physics will make this less daunting
A common language: You need to be able to talk to experts
• Communicate your needs to physicists/radiographers/techs
• Build an MR vocabulary (terminology/jargon)
• Gain some intuition behind imaging concepts
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MRI Physics
★ Basics of magnetic resonance★ Image formation★ Signal statistics (SNR)★ Functional MRI
spin
1H
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“Spin”spin N
S
Almost all sub-atomic particles have “spin”• All nuclei with odd numbers of protons/neutrons
will have non-zero net spin
1H
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1H, 13C, 23Na, 31P
The abundance of water in the human body makes this very powerful!
All hydrogen protons will act like little magnets
HH
O
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1H, 13C, 23Na, 31P
ATP
Can also do this with phosphorous nuclei
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Spins, or magnetization (when referred to in bulk) behave similarly to classic physical systems
In many ways analogous to simple oscillators, like swings or pendulums
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1. ExcitationMagnetization can be moved or rotated by applying “excitation” magnetic fields (RF)
2. ResonanceMagnetization will “resonate” at a frequency proportional to magnetic field strength
3. RelaxationThe oscillations die out, i.e. magnetisation “relaxes” back to equilibrium – speed of relaxation is tissue-dependent!
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The External Magnetic Field (B0)
External field: protons align slightly ⇒ net magnetization (M)
Only a few parts-per-million!
spinN
S
Normally: protons randomly oriented ⇒ no net magnetism
N
S(no magnetic field)
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Magnetic resonance
Magnetic: external field (B0) magnetizes sample
Resonance: magnetization has characteristic (resonant) frequency proportional to external field B0
ω0 = γB0This “Larmor Equation” defines the resonant frequency
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Coordinate system
Direction of main field (B0) defines coordinate systemLongitudinal axis: parallel to B0 (typically z)Longitudinal magnetisation: Portion of M aligned with B0
M
B0
xy
z
B0
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Coordinate system
Direction of main field (B0) defines coordinate systemTransverse plane: perpendicular to B0 (typically x,y)Transverse magnetisation: Portion of M perpendicular to B0
M
B0
xy
z
B0
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Excitation pulse (yellow) tips magnetisation away from B0
Excitation must occur at the resonant frequency ω0
courtesy of William Overall
B0
ω0 = γB0
The Basic MRI Experiment: 1. Excitation
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B0
courtesy of William Overall
In a frame that rotates with B1, magnetisation is simply “flipped” or “tipped” out of alignment with B0
Hence the term “flip angle” or “tip angle”
The Basic MRI Experiment: 1. Excitation
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Once excited, magnetisation precesses/oscillates/rotates at resonance frequency
B0
courtesy of William Overall
ω0 = γB0
The Basic MRI Experiment: 2. Resonant Precession
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As it precesses, it also “relaxes” back into alignment with B0
Speed of relaxation has time constants: T1, T2, T2*, which relate to the image contrast
B0
courtesy of William Overall
The Basic MRI Experiment: 3. Relaxation
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T1 : describes speed of recovery along longitudinal (z) axisT2, T2* : describe speed of signal decay in transverse (x-y) plane
B0
courtesy of William Overall
The Basic MRI Experiment: 3. Relaxation
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As the magnetization precesses and relaxesThe precession induces a voltage in the receive coilsCoils only detect rotating, transverse magnetisation
B0
courtesy of William Overall
The Basic MRI Experiment: 4. Signal Detection
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Magnetic field gradients (G): pulsed on & off, “static”
Magnetic fields everywhere…
Main magnetic field (B0): always on, staticExcitation RF field (B1): pulsed on & off, 60-300 MHz
B0 Gx,GyB1
MRI scans: carefully timed RF and gradient “pulse sequences”
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MRI Physics
★ Basics of magnetic resonance★ Image formation★ Signal statistics (SNR)★ Functional MRI
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Add a spatially varying magnetic field gradient (G)• Field varies linearly along one direction• Gradient field adds to or subtracts from B0
Magnetic Field Gradients
B0G
Differentiate between signal from different locations
magnet
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No Gradient
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x-Gradient
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y-Gradient
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Resonance frequency is proportional to total field:Static B0 + applied gradients
B0
Precession
courtesy of William Overall
ω0 = γ(B0+G(x,y,z))
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Distinguish different spatial locations by assigning different resonant frequencies to different positions
Gradients and Resonance
Higherfrequency
Lowerfrequency
Higher field
Lower field
B0
ω0 = γ(B0+G(x,y,z))
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Imagine differentiating between instruments based on their frequency content!
Lowest frequency
Highest frequency
Middle frequencies
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Frequency decomposition
Violins
Cellos(playing the loudest)
Bass
Other instruments(playing quietly)
Am
plitu
de
FourierTransform
Am
plitu
de
time (s)
frequency (Hz=s-1)InverseFourierTransform
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Simple “imaging” experiment (1D)
increasingfield x
y
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Simple “imaging” experiment (1D)
Fourier Transform: Gives us the “frequency content” of our signals
timeSignal
Fourier transform
“Image”position
frequency/
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Simple “imaging” experiment (1D)
This is “frequency encoding”
timeSignal
Fourier transform
“Image”position
frequency/
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It’s a bit more complex in more than 1 dimensionHave 3 gradient fields (along x, y, z)Manipulate the strength & timing independently
Magnetic gradients
Gx,Gy
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Gradients in multiple dimensions
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Magnetic field gradients
B0
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Gradients in multiple dimensions
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B0
Combined field gradients
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Spatial frequencies or patterns
At any instant in time, signal is across space is defined by a specific “pattern” of the magnetisation phase (orientation), i.e., its spatial frequency that depends on the applied gradients
Spatial frequencies:• sinusoidal pattern over
space instead of time• extend to multiple
dimensions
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Gradients and Spatial FrequencyStrong, positivegradient
Strong, negativegradient
zerogradient
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zerogradient
Gradients and Spatial Frequencyhigher
resonancefrequency
faster precession
stronger gradientmagnetic field
lower resonancefrequency
slower precession
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This is one spatial frequency...
signal
xsign
aly
2 cyclesalong y:
ky=2
0 cycles along x:kx=0
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y
signal
xsign
alThis is another one...
0 cyclesalong y:
ky=0
2 cycles along x:kx=2
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signal
xsign
aly
This is another one...
2 cyclesalong y:
ky=2
2 cycles along x:kx=2
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(4,0) (0,4)
Each of these represents one 2D pattern or frequency: denote (kx,ky)
(2,0)
(2,1)
(0,2)
(1,2)
(2,2)
(4,4)
(8,1)
“k” values are the number of cycles in each direction
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2D “k-space” describes contribution of each spatial frequency
Patterns determine the “where” in k-space
ky=0
kx=0
x
x
(2,1)
(0,4)
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ky=0
kx=0
(0,4)
2D “k-space” describes contribution of each spatial frequency
Sum total signal after application of these patterns determines the “value” of each k-space location
(2,1)
x
x
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Imagex
y“k-space”kx
ky
Signal from RF coil
Fouriertransform
Fillingk-space
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(4,0) (0,4)
Think of each pattern (k-space location) as a filter on a camera
(2,0)
(2,1)
(0,2)
(1,2)
(2,2)
(4,4)
(8,1)
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Imagine our “camera” can only see one colour at a time
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Imagine our “camera” can only see one colour at a time (blue filter)
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Imagine our “camera” can only see one colour at a time (red filter)
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Imagine our “camera” can only see one colour at a time (green filter)
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Combine the filtered images to form the final image
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Scanner takes a series of measurements with each k-space “spatial filter” (as many filters as voxels)
Measurements are then combined using the Fourier Transform to form image
The “spatial filters” are applied using gradients
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Scanner takes a series of measurements with each k-space “spatial filter” (as many filters as voxels)
More spatial resolution → more voxels andfilters needed → longer acquisition time
Higher resolution means “finer” features, which require “finer” filters
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If gradient is on, spatial frequencies change over time
Visualize as gradients “move us” through k-space!
ky
kx
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If gradient is on, spatial frequencies change over time
Visualize as gradients “move us” through k-space!
ky
kx
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Imagex
y“k-space”
Signal from RF coil
Fouriertransform
k-spacetrajectory
The trajectory is the ordering of k-space data acquisition
Trajectory = Path through k-spaceor the sequence of spatial filters
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Linescan (2DFT) Acquisition
Acquire one line after each excitation
kx
ky
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Linescan (2DFT) Acquisition
Acquire one line after each excitationUseful for structural images (minimal artifacts)
kx
ky
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Echo-planar Imaging (EPI) Acquisition
Acquire all of k-space in a “single shot”Used for FMRI, diffusion imaging
kx
ky
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Slice Selection
ω0frequency
gradient
excited slice
Transmit all frequencies corresponding to desired slice
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2D Multi-slice Imaging
excited slice
Slices excited and acquired sequentially (separately) Most scans acquired this way (including FMRI, DTI)
t1t2
t3t4
t5t6
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t1
}
z=1+4
t2
z=2+5
t3
z=3+6
Simultaneous Multi-slice Imaging
“Multi-Band” Factor 2
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MRI Physics
★ Basics of magnetic resonance★ Image formation★ Signal statistics (SNR)★ Functional MRI
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SNR =
Signal
σnoise
Signal-to-noise ratio (SNR)
Signal-to-noise ratio: describes signal “robustness”All else being equal, we want to maximize SNR!!
low SNRhigh SNR
(magnitude)(standard deviation)
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Signal-to-noise ratio (SNR)
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Protocol choices affecting SNR...
• RF receive coil & field strength• Timing: bandwidth, TE & TR• Voxel volume• Scan duration (imaging time)• Anything affecting signal!!!
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SNR and acquisition time or averages
scan time
σnoise
Longer acquisition ⇒ less noise ⇒ higher SNR
SNR improves with the square root of scan timei.e., to double SNR you need to scan 4x longer
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Larger voxels have signal from more tissue!– Signal proportional to voxel volume– 2x2x2mm has 8x higher SNR than 1x1x1mm!
? 8xSNR
SNR and voxel volume
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Averaging to achieve high resolution
? 8xSNR
Can we recover lost SNR by averaging?Yes! But requires a 64-fold increase in scan time (because you only get square root benefit)
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Contrast-to-noise ratio (CNR)
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MRI Physics
★ Basics of magnetic resonance★ Image formation★ Signal statistics (SNR)★ Functional MRI
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A source of signal loss: dephasing
When spins are “in-phase”, they are all oriented the same wayOver time, the spins within a voxel lose alignment (“dephase”)
B0
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Apparent increase in T2 = T2*
timesi
gnal
Dephasing causes magnetization vectors to partially “cancel” each other out
Dephasing results in a lower net signal magnitudeApparent decrease in T2: called T2* (more on Wednesday)
Perfect field(T2 decay)
Imperfect fieldwith inhomogeneity
(T2* decay)
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Deoxyhaemoglobin is the source of FMRI signal
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Deoxyhaemoglobin is the source of FMRI signal
When oxygen is bound to the haemoglobin, it shields the magnetic effects of iron atoms in the heme groups
Fe
Fe
Fe
Fe
O2 O2
O2 O2
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Deoxyhaemoglobin is the source of FMRI signal
Without oxygen, the iron (Fe) is exposed, causing magnetic field inhomogeneities due to its strong magnetic properties
Fe
Fe
Fe
Fe
Field inhomogeneity leads to T2* change (FMRI signals)
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The BOLD Effect [ Ogawa et al, 1990 ]
Blood Oxygenation Level Dependent (BOLD) effect
imaging voxel
Vessels, depending on orientation and blood oxygen content will alter their local magnetic fields
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BOLD Effect – vessel orientation
0ºVessel parallel
45º 90ºVessel perpendicular
Water
Vessel
Water
Vessel
Water
Vessel
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radius = 50 μm radius = 100 μm radius = 150 μm
Water
Vessel
Water
Vessel
Water
Vessel
B0 direction Strength of MagneticField Inhomogeneity
BOLD Effect – vessel size
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Oxygenation = 60% Oxygenation = 30% Oxygenation = 0%
Water
Vessel
Water
Vessel
Water
Vessel
B0 direction Strength of MagneticField Inhomogeneity
BOLD Effect – blood oxygenation level
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Oxygenation: Y=60%More Oxygenated HbLow inhomogeneityLonger T2*Higher signal
Oxygenation: Y=0%More de-oxygenated HbHigh inhomogeneityShorter T2*Lower signal
BOLD Contrast
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HbO2
HbO2
HbO2
HbO2
Vascular Response to Activation
O2 metabolism
dHb
dHb
HbO2
HbO2dHb
HbO2HbO2
dHbdHb
HbO2
blood flow
HbO2
HbO2
HbO2
HbO2
HbO2HbO2
HbO2 HbO2
HbO2
HbO2HbO2
HbO2
HbO2
HbO2
[dHb]
dHb = deoxyhemoglobinHbO2 = oxyhemoglobin
capillary
blood volume
HbO2
HbO2HbO2
neuron
dHb
HbO2
HbO2
dHb
dHb
dHb
dHb
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20 40 60 80
0.2
0.4
0.6
0.8
1.0
active
Echo time (TE, ms)
BO
LD
sig
na
l
rest
20 40 60 80
0.2
0.4
0.6
0.8
1.0
active
Echo time (TE, ms)
BO
LD
sig
na
l
rest
difference
(contrast)
20 40 60 80
0.2
0.4
0.6
0.8
1.0
active
Echo time (TE, ms)
BO
LD
sig
na
l
rest
difference
(contrast)
optimal
range
BOLD Contrast
Typically, 1–5% signal change
Signal increases during activation (less decay)Signal change for longer delay (TE)
[dHb]
[dHb]
O2 use
bloodflow [dHb]
bloodvolume
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BOLD signal and field strength (B0)
But image artefacts get worse at higher field strength
3T is currently a good tradeoff of signal vs artefacts
SNR and BOLD effects can increase with field strength
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Sources of BOLD Signal
Neuronal activity Metabolism
Blood flow
Blood volume
[dHb] BOLDsignal
Indirect measure of activity (via metabolism!)Subject’s physiological state & pathology can change
neurovascular coupling, muddying interpretation
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Hemodynamic response function (HRF)
Vascular response to activity is delayed & blurredDescribed by “hemodynamic response function”
Stimulustiming
BOLDresponse
on
off
Limits achievable temporal resolutionMust be included in signal model
time
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What is required of the scanner?
Typical stimulus lasts 1–30 sRapid imaging: an image every few secondsAnatomical images take minutes to acquire!Acquire “single-shot” images (e.g., EPI)
1 2 3 …image TR
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Typical* FMRI Parameters
Parameter Value Relevant points
TE(echo time)
1.5T: 60 ms3.0T: 30-40 ms7.0T: 15-25 ms
Determines functional contrast, set ≈T2*
TR(repeat time)
1–4 s HRF blurring < 1s;Poor resolution > 4s
Matrix size / Resolution
64x64 – 96x96 2–3 mm
Limited by distortion, SNR, FOV
Scan duration
2-15 mins Lower limit: sensitivity Upper limit: compliance
* Typical, not fixed!!
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Confounds: Noise
Noise: signal fluctuations leading to less robust detection with respect to statistical measures
Purely random noise(example: “thermal”)
Structured noise(example: “physiological”)
time
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Confounds: Artefacts
Dropout Distortion
Artefacts: systematic errors that interfere with interpretability of data/images
“Ghosting”
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Source of signal dropout
BOLD contrast is based on signal dephasingBOLD imaging requires longish delay (TE) for contrast
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Dephasing also occurs near air-tissue boundaries Sensitivity to BOLD means signal loss near air-tissue boundaries
Dropout is just extreme dephasing
sinus
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BOLD Signal Dropout
Long TEShort TEDephasing near air-tissue boundaries (e.g., sinuses)BOLD contrast coupled to signal loss (“black holes”)Air-tissue effect is often larger than BOLD effectDropout is not correctable post-acquisition!
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Image distortion
We think frequency maps to spatial location...So errors in frequency cause spatial mis-localization!More on Wednesday...
Field map
field offset local warping
EPI
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Final thoughts
Understand how different experimental parameters affect SNR and image artefacts
Tradeoffs: you can’t get something for nothing, but you do have options
Get to know an engineer/physicist/radiographer: get help setting up study protocols, show them your artefacts
Quality assurance: always look at your data, even if you are running a well-tested protocol