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The Basics of MRIIves Levesque
BIC Seminar Series, October 5th, 2009
McConnell Brain Imaging CentreMontreal Neurological InstituteMcGill University
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Acknowledgments for material
Prof. Bruce PikeIlana LeppertDr. Jennifer CampbellMichael FerreiraChristine TardifDr. Luis Concha
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MRI: a simple overview
somethinghappens
put subjectin scanner
knock!buzz! knoc
k!
bang!
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MRI: behind the scenes
Fourier transform
B0
NMRGx
z
y
encoding
x
z
y
M
B1
excitation
detection
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Outline
• NMR physics• Spatial encoding and reconstruction• Basic MRI sequences: GE, SE• Special contrast: DWI, BOLD• Trade-offs and limitations• Image artefacts• SafetyN
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NMR Physics
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NMR: Nuclear spin• “odd-numbered” nuclei have net angular
momentum• magnetic moment, or spin, designated by
vector µ
• In biological tissue: 1H, 23Na, and 31P
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NMR: spins in magnetic field• magnetic moments (spins) align to external magnetic• net excess of spins in parallel state (lower energy)
state of net magnetization, vector M
B0
external field B0
M
∑=i
inet µMNO
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Spins in a magnetic field experience a torque:
Static field produces precession about at Larmor frequency
γ/2π = 42.58 MHz/T for 1H, f ~ 64 MHz at 1.5 T
This is the resonance frequency
NMR - Free precession & resonance
0Bf γ=
BMM γ×=dt
dB0
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• Superconducting solenoid magnet
• Liquid helium cooling
• Many km’s of wire• 1.0 – 9.4 tesla
The main magnet
B0NOT
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Manipulating magnetization
• Apply magnetic field B1– Perpendicular to B0– Amplitude ~ 20µT– Alternating with frequency f1
• Rotate M from z-axis to transverse (xy) plane
– Most efficient on resonance (f1 = f0)
y
xz
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Excitation (stationary frame of reference)
B1 field in yellow, magnetization vector in red
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The rotating frame of reference
f0 = γ B0
y
x
z
B0y’
x’
z
M M
Mxy
Mz
• “laboratory” frame of reference
• vector M precesses at resonant frequency
• rotating frame of reference (at f0)
• “ignore” precession of M
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Excitation (rotating frame of reference)
B1 field in yellow, magnetization vector in red
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Relaxation
• M returns to equilibrium
• Recovery of Mz• Decay of Mxy• Each appens at
a different rate
y’
x’
z
B0 Recovery of Mz
Decay of Mxy
*rotating frame of reference!
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T1 Relaxation: Recovery of Mz
• Energy exchange with surrounding medium
0 1 2 3 40
0.2
0.4
0.6
0.8
1Mz recovery: T1
ρ(1- e-t/T1)
Mz
y’
x’
z
B0 T1 relaxation
Time (s)
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T2 Relaxation: Decay of Mxy
• Effect of spin-spin interaction
0 0.1 0.2 0.3 0.40
0.2
0.4
0.6
0.8
1Mxy decay: T2
ρe-t/T2
Mxy
y’
x’
z
B0
T2 relaxationTime (s)
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T2* Relaxation: Faster decay of Mxy
• Additional effect of B0 inhomogeneity
• Reversible
y’
x’
z
B0
T2* relaxation > T2 relaxation
0 0.1 0.2 0.3 0.40
0.2
0.4
0.6
0.8
1
Time (s)
Mxy decay: T2, T2*
Mxy
ρe-t/T2*
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Relaxation in the lab frame
Individual spins in blue, Mxy in yellow, Mz in red
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Image contrast• Signal depends on:
– sequence parameters (TR, TE, α)– NMR parameters in tissue: PD, T1, T2, T2*– diffusion, MT, iron, contrast agents, etc.
• Each pulse sequence has its own behavior
T1W T2W PD or “Intermediate”
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T1 & T2 relaxation in CNS at 3 T
0 0.6 0.80
0.1
0.2
0.3
0.4
0.5
0.6
0.7
0.8
0.9
1
Time (s)
T2 relaxation
0 1 2 3 40
0.1
0.2
0.3
0.4
0.5
0.6
0.7
0.8
0.9
1
Time (s)
T1 relaxation
WM
GM
GM
WM
CSF
CSF
0.2 0.4
Mz Mxy
GM: T1 = 1300 ms T2 = 100 ms ρ = 0.8WM: T1 = 800 ms T2 = 80 ms ρ = 0.7
CSF: T1 = 5500 ms T2 = 2200 ms ρ = 1.0NO
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NMR signal detection
f0x
y
z
B0
stationary (lab) frame of reference0 0.2 0.4 0.6 0.8 1
-1
0
1
Time (ms)
Sig
nal
“FID”
f0
T2* decay
NMR signal received in RF coil (Faraday’s Law)
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• excitation– apply magnetic field B1, perpendicular to B0 , at
resonant frequency f0, to rotate M0 into x-y plane• evolution
– M0 precesses freely, relaxing to equilibrium on z-axis– energy released in relaxation process at frequency f0
• detection– detect signal: changing magnetic flux in x-y plane
produces a voltage in receive coil
• waiting (for TE) and spatial encoding
• repetition (after TR)
Beyond exploiting the resonance
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Spatial Encoding and Reconstruction
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Magnetic field gradients
• Linear variations in magnetic field (millitesla / meter)
• Manipulate frequency of precession• Encode spatial information in signal
– frequency (readout)– phase (prior to readout)NO
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Gradients modify the amplitude of B0
B0
Gz= dB0/dz
B0 Gy= dB0/dy
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B0
frequency (Hz)
MRI: localization in 1-D
Paul Lauterbur
FT
f0time (ms)
sign
al
f0 = γ B0Gx f > f0f < f0
N samples N points
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kx
ky
x
y
2D FT
magnitude k-space data magnitude reconstructed image
2D-FT imaging
N1 samples per TR
N2 repetitions of TR N2 voxels
N1 voxels
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3D-FT imaging
3D FT
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3D-FT imaging
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Echo-planar imaging (EPI)
• Acquire entire 2D space in one shotky
kx
RF
Gy
Gx NOT F
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Example of alternate k-space trajectory
• interleaved spirals
kx
ky
RF
Gx
Gy NOT F
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Basic MRI sequences
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Breakdown of MRI experiment: the “sequence”
acquisition
TETR
preparation
- inversion preparation- MT saturation
relaxation
- acquire other slices- spoil or rewind
excitation
- RF pulses
- refocusing pulses - selective or non-selective
encoding
- gradients
- diffusion encoding
acquisition
- gradients- signal detectionNO
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The gradient echo sequence
acquisition
TETR
preparation
- inversion preparation (MP-RAGE)
- MT saturation
relaxation
2D: acquire other slices
3D: spoil or rewind
excitation
- excitation pulse
2D: slice-selective3D: non- or slab-selective
encoding
- phase encoding gradients
acquisition
- read-out gradients- data acquisition
- single-line or EPI
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GE images depend on T1 and T2*
T1w FLASH
Localizer (“scout”) Post-gadolinium T1w
GE EPINO
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Spin echo
• T2* decay caused by spin dephasing
• Any pair of RF pulses can reverse (or refocus) T2’ to some extent
• 90°-180° combination is most effective• SE signal decays with time T2
22*
2
111TTT ′
+=
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The spin echo sequence
acquisition
TRTE/2TE/2
relaxation
2D: acquire other slices
excitation
- excitation pulse- refocusing pulse
2D: slice-selective
encoding
- phase encoding gradients
read-out
- read-out gradients- data acquisition
- single-line or “turbo”
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Turbo spin echo
acq. acq. acq.
2D FT
N2 / 3 repetitions of TR N2 voxels
3 × N1 samples per TR N1 voxels
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Turbo spin echo images
TR/TE = 2.7s/12ms, ETL 3, 256x256, 60 slices
TR/TE = 5.4s/83ms, ETL 7, 256x256, 60 slicesNO
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Diffusion contrast in MRI
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Gradients and phaseGy
timeB0 B0 + Gy
Gy
B0
Total:Total:
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Gradient dephasing and rephasingG
time
B0
Total:
B0 - G B0
Total:
B0 + G
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Gradients, phase, and motionG
time
B0B0 + G B0 B0 - G
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Diffusion MRI SE sequence
EPI
diffusion encoding gradients
×NO
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Diffusion indices
FA: anisotropy
index
RGB plot: principal direction,
scaled by FA
trace of diffusion tensor ~ Dav
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BOLD MRI
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O2
at rest
O2
ACTIVATED
BOLD contrast
∆T2*
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Hemoglobin and T2*
deoxy-Hbχ ~ 1.6
oxy-Hbχ ~ -0.3
longer T2, T2*
↑ BOLD upon↑ activation
shorter T2,T2*
baseline BOLD
oxy-RBCdeoxy-RBC
B0
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fMRI acquisition
• series of stimulus conditions–activation and baseline
off
on
stimulus
rapid image acquisition NO
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fMRI example: finger tapping task
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GE-BOLD vs SE-BOLD
Vessel Radius [µm]
∆R2*
[s-1
]
GE BOLD (TE = 40ms)
Vessel Radius [µm]
∆R2
[s-1
]
SE BOLD (TE = 100ms)
• GE-BOLD offers greater sensitivity• SE-BOLD more specific to small vessels
Buxton, 2002NO
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Choices, trade-offs and limitations
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Voxel-size, FoV, and scan time are linked
N2 voxelsN2 repetitions of TR
2D FT
N1 samples per TR N1 voxels
scan duration = TR × N2 × NslicesNO
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Voxel size & scan time: link to SNR
( )21,, TTfTVSSNR readvoxel
S
ρσ
∝≡
Basic T1w
1×1×1 mm3
256×256×160
1
1
15.7 minutes
Voxel size
Matrix size
# averages
rel. SNR
Acq. time
High-res
0.5×0.5×1 mm3
512×512×160
1
0.25
31.4 minutes
Thick slice
1×1×2 mm3
256×256×80
1
2
7.9 minutes
High-res + SNR
0.5×0.5×1 mm3
512×512×160
16
1
8.4 hours!
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+ Better SNR (up to 2×)+ Higher BOLD sensitivity
• Longer T1
- Higher energy deposition- B1 less homogeneous- More B0 artefacts
Impact of field strength
MP-RAGE, C. Tardif
1.5 T 3 T
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Artefacts:what’s wrong with my image?
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Subject motion affects images
phase encoding
• Motion during scan corrupts phase encoding• Solutions: subject co-operation, immobilization, fast
imagingNO
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Flow artefacts
2D SETR 3s
TE 50ms
3D slab-selective FLASHNO
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Ghost sightings in EPI imagesphase encoding
signal × 10• Imperfect gradient behaviour results in ghosting• Solutions: select phase encode direction to avoid
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Magnetic susceptibility artefacts
• Changes in susceptibility affect B0 homogeneity– Image distortion and signal pile-up
• Solutions: parallel imaging, shorter TE, angulation
GR
EE
PI
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MRI Safety
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MRI safety: the main magnetic fieldThe magnet is always on, and will “perturb” instruments
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MRI safety: Peripheral nerve stimulation• Magnetic field variations in time (dB/dt) induce
currents– Gradient coils switch on/off in less than 1 millisecond
• Currents induced in the subject can produce nerve stimulus
• Effect is greatest at the ends of the coils, because gradient amplitude is greater there
B0
Gz=dB0/dz
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MRI safety: Energy deposition
• B1 field deposits energy into the body, results in heating
• SAR = specific absorption rate– power per unit (subject) mass, W/kg
• Heat is dissipated by the body’s own cooling, with the help of ventilation
• Monitored by the scanner
TRPSAR RFRFτ∝
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Summary
Fourier transform
B0
NMR Gy
z
x
encoding
y
z
x
M
B1
excitation
detection
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Useful referencesMRI From Proton to Picture
DW McRobbie, EA Moore, MJ Graves, Cambridge Press, 2002 (preview on Googlebooks)
Introduction to Functional Magnetic Resonance Imaging: Principles and TechniquesRB Buxton, Cambridge Press, 2002 (preview on Googlebooks)
Principles of magnetic resonance imagingDwight Nishimura, 1996 (out-of-print )
Magnetic Resonance Imaging: Physical Principles and Sequence DesignEM Haacke, Wiley, 1999
FMRIB MRI physics lectureshttp://www.fmrib.ox.ac.uk/education/graduate-training-course/program/lectures/mri-physics/mri-physics-course
The Basics of MRI (Joseph Hornak)http://www.cis.rit.edu/htbooks/mri/
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The Basics of MRIAcknowledgments for materialMRI: a simple overviewMRI: behind the scenesOutlineNMR PhysicsNMR: Nuclear spinNMR: spins in magnetic fieldNMR - Free precession & resonanceThe main magnetManipulating magnetizationExcitation (stationary frame of reference)The rotating frame of referenceExcitation (rotating frame of reference)RelaxationT1 Relaxation: Recovery of MzT2 Relaxation: Decay of MxyT2* Relaxation: Faster decay of MxyRelaxation in the lab frameImage contrastT1 & T2 relaxation in CNS at 3 TNMR signal detectionSpatial Encoding and ReconstructionMagnetic field gradientsGradients modify the amplitude of B0Basic MRI sequencesBreakdown of MRI experiment: the “sequence”The gradient echo sequenceGE images depend on T1 and T2*Spin echoThe spin echo sequenceTurbo spin echoTurbo spin echo imagesDiffusion contrast in MRIDiffusion MRI SE sequenceDiffusion indicesBOLD MRIBOLD contrastHemoglobin and T2*Choices, trade-offs and limitationsVoxel-size, FoV, and scan time are linkedVoxel size & scan time: link to SNRArtefacts:what’s wrong with my image?Subject motion affects imagesFlow artefactsGhost sightings in EPI imagesMagnetic susceptibility artefactsMRI SafetyMRI safety: the main magnetic fieldMRI safety: Peripheral nerve stimulationMRI safety: Energy depositionSummaryUseful references
Recommended