Optimizing MRI Protocols
7/27/2004
Overview
• Parameters Affecting Image Quality
Optimizing MRI Protocols
(SNR, CNR, Spatial Accuracy)
Geoffrey D. Clarke, Ph.D.
University of TX Health Science Center
San Antonio, TX
• Manipulating Image Contrast (Standard)
• Classifications of Pulse Sequences
• Relationships Between Resolution & SNR
• MR Image Speed
• Manipulating Image Contrast (Advanced)
Image Quality
• Image Contrast
• Image Resolution
• Signal-to-Noise Ratio
• Imaging Speed
Intrinsic (Tissue) Parameters
Image Contrast
• Basic image contrast is effected by the
amplitude and timing of the RF pulses
used to excite the spin system.
• More advanced methods may use gradient
pulses (to modulate motion) and alter
tissue properties with exogenous contrast
agents
Extrinsic (Selectable) Parameters
• Tissue Water Density (Proton Density)
• Magnetic Field Strength
• Longitudinal Relaxation Time (T1)
• RF Pulse timing
– Magnetization transfer rate coefficients
• Transverse Relaxation Time (T2)
– Excitation pulse repetition time (TR)
– Time to echo (TE) & inter-echo spacing (Tie)
– Inversion time (TI)
• Chemical Shift (water vs. fat)
• RF pulse amplitude (flip angles)
• Tissue Motion
• Gradient Amplitude & Timing
– Macroscopic (flowing blood)
– Microscopic (apparent diffusion coefficient)
• Tissue Susceptibility (air, fat, bone, blood)
G.D. Clarke, AAPM 2004
– b-value
• RF pulse excitation frequency & bandwidth
• Receiver bandwidth
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Optimizing MRI Protocols
7/27/2004
Spin (Proton) Density
Tissue
% Water
Tissue
Spin Echo Pulse Sequence
% Water
Liver
70 %
Spleen
78%
Kidney
75%
Brain (GM)
85%
Muscle
73%
Brain (WM)
75%
Heart
78%
Tendon
60%
RF2
RF1
(rephasing)
rephasing)
(excitation)
TX
time
Spin
Echo
FID
RX
time
TE
From Akber SF, Physiol Chem Phys & Med 1996; 28: 205-238.
Out of Phase Spins
(Transverse Magnetization)
Spins in Phase
Out of Phase
Precessing
Off-resonance by 17,040 Hz
17, 040 Hz = 17, 040 cycles per second = 360 × 17, 040 degrees/sec
180o ÷ (360o × 17, 040 degrees/sec) = 3 × 10-5 s = 30µs
τ
τ
Dephasing of MR Signal
(Transverse Magnetization)
Coherent Signal
Less Signal
No Signal
Signal decays exponentially:
Mxy = Mo exp [- TE / T2* ]
where
(Magnetic field
1/T2* = 1/T2 + (γ/2π) * ∆Bo
(after 90o rf pulse)
inhomogeneity)
Rephasing of the MR Signal
(Spin Echoes)
4
3
2
1
Signal Dephasing
2
3
Longitudinal (T1) Relaxation
Longitudinal relaxation is a recovery process:
4
1
180o pulse
180o
Rephased Signal
A rephasing
radio frequency pulse, changes the
phase of the net magnetization vectors by 180o. Thus
spins precessing in the same direction come together
of moving apart. This forms a SPIN ECHO.
G.D. Clarke, AAPM 2004
After 90o
pulse - all
spin energy
is kinetic
After 5*T1,
Spins lose energy
full
potential
to their
of net
environment, signal
magnetization
decreases
is
reestablished
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Comparison of T1, T2 and for
Various Tissues
Liver
675+142
Kidney
559+10
Muscle
1123+119
Gray Matter 1136+91
White Matter 889+30
T2(ms)
54+8
84+8
43+4
87+15
86+1.5
Longitudinal
Magnetization
T1(ms)
Mo
1- exp (-TR / T1)
100’s of ms
Transverse
Magnetization
Tissue
Time Scale of MR
Relaxation Processes
exp (-TE/T2*)
Akber, 1996 (at 63 MHz)
10’s of ms
Manipulating Contrast
• The “weighting” of image contrast
• Gradient Echo – manipulating image
contrast by varying the flip angle
Rules of Thumb
• TE controls T2 dependence
• TR controls T1 dependence
• T1 competes with T2 and proton density
• Spin Echo – manipulating image contrast
with 180o refocusing pulses
“PD Weighted” = long TR, short TE
• Inversion Recovery – manipulating image
contrast with 180o inversion pulses
“T2 Weighted” = long TR, long TE
Pulse Sequence Classifications
“T1 Weighted” = short TR, short TE
Spin-Echo Imaging Sequence
rf1
Name
Gradient
Echo
Spin Echo
Inversion
Recovery
RF
Pulses
Contrast
Weighting
Application
One
T1 or T2*
Fast imaging
(3DFT)
Two or
more
T1, PD or
T2
conventional
Three
T1 and T2
Excludes
certain
tissues
RX
G.D. Clarke, AAPM 2004
rf2
TX
Gsl
Gro
Gpe
Spin
Echo
time
time
time
time
time
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Multi-Echo Acquisitions
Spin Echo Imaging – Effect of TR
TR = 63 ms, NSA = 16
TR =125 ms, NSA = 8
TR = 250 ms, NSA = 4
TR = 500 ms, NSA = 2
Signal
Strength
Mo exp(-TE/T2)
Mo exp (-TE/T2*)
90o
180o
180o
SE1
2*TE
TE
Bo = 1.5 T
o
SE2 180
time
SE3
3*TE
Gslice
FOV = 230 mm
256 x 256
st = 4 mm
Gread
TE = 15 ms
TR = 1 s, NSA = 1
TR = 2 s, NSA = 1
Gphase
TR = 4 s, NSA = 1
Vlaardingerbroek & den Boer, 1999
TR (s)
4
Multiecho
Image
Matrix
Sensitivity Plots
(pulse sequence optimization)
2
Proton Density
104
1.5
Most T1 Weighted
1.2
Most Proton
Density
Weighted
0.9
Most T2
Weighted
0.6
60
90
T2
0.9
Mo
103
TR
(ms)
0.1 Mo
102
10
102
10
TE 30
T1
120 150 180 ms
10310
TE (ms)
102
103 10
102
TE (ms)
103
TE (ms)
Inversion Recovery
Multi-Slice
Imaging
90o
180o
180o
180o
Spin Echo
TI
TE
TR
Inversion
Excitation Refocusing
+Mo
• Increased efficiency by scanning multiple
planes during TR interval
M = Mo (1 – 2 exp[-TI/T1])
TI
(Crooks L, Arakawa M, Hoenninger J et al. Radiology 1982; 143: 169-174.)
-Mo
G.D. Clarke, AAPM 2004
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STIR
(Short TI Inversion Recovery)
Mz
Inversion Recovery FSE
TR =1400
TI = 100
0
TR =2000
TI = 280
Phase
Compensated
Fat
TR =1400
TI = 280
time
Modulus
Liver
TI
Vlaardingerbroek & den Boer, 1999
FLAIR
Multiple Sclerosis
(FLuid Attenuated Inversion Recovery)
Proton Density
Mz
Brain
T2-Weighted
FLAIR
Mxy
Lesion
Lesion
0
time
CSF
Brain
Teff
TI
TR = 2350
TE = 30
time
TR=2350
TE= 80
TR=2600
TE=145
TI= 11,000
Rydberg JN et al. Radiology 1994; 193:173-180
Steady-State Free Precession
(SSFP or True FISP)
Relative Sensitivity of
Gradient Echo Sequences
TX
Field
Echo
rf
RX
Slice Select
0.40
Digitizer On
Gsl
Gpe
T2=30 ms
FISP
0.20
0.20
Dephasing
Phase
Encode
Phase
Rewinder
SSFP
My/Mo
Read Out
My/Mo
Rephasing
Gro
0.40
T2 =200 ms
SSFP
FISP
FLASH
0
0
0
30o
60o
90o
Flip Angle
120o
150o
180o
FLASH
0
30o
60o
90o
120o
150o
180o
Flip Angle
Also called FAST, ROAST
G.D. Clarke, AAPM 2004
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Cystic Mass
Gradient-Echo Imaging
Spin Echo
TR/TE
= 2500/90
NSA =1
5 mm
FISP
TR/TE = 22/10
NSA =8
8 mm
True FISP
TR/TE = 16/6
flip = 40o
NSA =8
5 mm
True FISP
TR/TE = 16/6
flip = 70o
NSA =8
5 mm
Reference: Wehrli, Fast-Scan Magnetic Resonance. Principles and Applications
Signal-to-Noise Ratio
SNR and Imaging Parameters
• Signal-to-noise in an RF coil:
S
N
∝
v
ω o M o ∫ B1 (r ) dV
SNR ∝
4kT BW Rt
FOVro FOVph
NSA
⋅ ∆z ⋅
M ro M ph
BWrx
S = signal
dV = elemental volume of tissue
N = noise
k = Boltzman’s constant
FOV = field of view
ωo = resonant frequency
T = patient temperature
BW rx = receiver bandwidth ro = read out (frequency encoding) direction
Mo = net magnetization
BW = receiver bandwidth
B1(r) = RF field distribution
Rt = total resistance (coil + patient)
M = matrix size
∆z = slice thickness
n = number of signals averaged
ph = phase encoding direction
Matched Bandwidth
Matched Bandwidth
• Bandwidth on ADC1 is limited by finite
Tmax & desire to minimize TE1.
• T1 weighting and SNR is sacrificed
more by T2 decay than by BW
• T2-weighted image - lots of time for
ADC2, poorer SNR. It would be nice to
decrease BW (increase Tmax)
Mugler & Brookeman, Magn Reson Imag 1989; 7:487-493.
G.D. Clarke, AAPM 2004
ADC
90o
ADC
t
180o
TE1 ≈ 20 ms
TE2 ≈ 60-80 ms
Mugler & Brookeman, Magn Reson Imag 1989; 7:487-493.
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Matched Bandwidth =
Unmatched Distortion
T1W
Chemical Shift
• Chemical shift (fat-water) ~3.5 ppm
T2W
– At 1.5T:
∆f fat − water = 3.5 × 10 −6 ⋅
42.6 MHz
⋅1.5T ≅ 220 Hz
T
– At 0.5T:
∆f fat − water = 3.5 ×10 −6 ⋅
42.6 MHz
⋅ 0.5T ≅ 73 Hz
T
• ↓ field strength …. ↓ chemical shift
• Smaller BW on T2W image leads to increased
image distortion
Chemical Shift Artifact
• Occurs in
• Conventional SE
– Phase encode
direction
σ
σ = standard deviation of the background signal
(the noise)
• Echo-Planar
– Fat Pre
- Saturation
– STIR sequence
(I a − I b )
CNR = n
– Readout direction
• Controlled by
Contrast-to-Noise Ratio
Chemical shift artifact
seen in axial image of
kidney
Steady state free precession
(SSFP)
Signal is produced by rapidly applying balanced gradients and RF
pulses. Use to maximize the overall signal.
ƒ
FIESTA (fast imaging
employing steady
state acquisition)
ƒ
Balanced FFE (fast
field echo)
ƒ
True FISP (fast
imaging with steady
precession)
n = number of signals acquired
Ia,Ib = signal intensities from tissues “a” and “b”
IR Turbo-FLASH
180o
α
α
α
α
α
α
α
FID Train (one for each image line)
TI
TR
Hinton et al. Invest
Radiol 2003; 38:436
G.D. Clarke, AAPM 2004
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Optimizing MRI Protocols
7/27/2004
FSE Pulse Sequence
3D FLASH vs. 3D Turbo FLASH
RF
Gro
Gpe
Overall
Signal
Tie
Echo
IR Turbo FLASH
TI = 500 ms, TR/TE = 10/4.5
NSA =1, flip = 10o
Things That have “Blurry” point
spread functions are “Sharp” in the
Image
K-space
Center of
K-space
FLASH
TR/TE = 12/4.5
NSA = 1, flip = 8o
ETL = Echo Train Length
FSE Point Spread Function
Depends on T2
FT
Image
Space
Effect of Echo Spacing
SE
FSE
FSE
Fat
Sat
Multi-Shot EPI Pulse Sequences
Echo 2
Echo 1
Echo 3
Echo 4
Spoiler
ES = 60 ms, TF =3
FSE
FSE
Slice
Select
ES = 30 ms, TF =7
Blip 2
Blip 3
Blip 4
FSE
Start
Blip
Spoiler
Rewind
ES = 15 ms, TF =15
ES = 13 ms, TF =20
ES = 10 ms, TF =27
Signal-to-noise decreases for short T2 tissues (gray & white
matter) leading to a decrease in spatial resolution
Vlardengerbrook & den Boer, 1999
G.D. Clarke, AAPM 2004
Preparatory
(Fat Sat)
RF
Dephase/
Excitation Rephase
TR
ts
Tie
Ttot
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Comparison of EPI and SE
Magnetization Transfer
PROTON SPECTRUM
0
Frequency (Hertz)
“Free” Water
Lipids
Single shot EPI
TE =80
128x128; 120 ms
Nine-shot EPI
TR 3000, TE 21
252x256; 1:06
Gradient Echo with MTC Pulse
0
T2-weighted SE
TR 2400, TE 80
192x256; 7:44
“Bound” Water
217 Hz
Frequency (Hertz)
1500 Hz
Magnetization Transfer Contrast
Off-resonance rf pulse
RF excitation
Multislice
FSE:
TX
Digitizer On
Field
Echo
RX
Slice Select
Gsl
Rephasing
Spoilers
Read Out
Crushers
or
Spoilers
Dephasing
Gro
Phase
Encode
Gpe
Slice thickness - RF bandwidth
Magnetization
Transfer
Contrast
Enhances T-2
Weighted
Appearance
Crafted RF Pulses
sin x
A sinc function ( x ) envelope on the r.f.
pulse produces a nearly square excitation
profile of the phantom…..
– thinner
slices
require
longer RF
pulses
FT
– ↓ ∆z ↓ ∆ω
Bandwidth =
1
period
G.D. Clarke, AAPM 2004
time
FT
FT
BW
frequency
tp
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Cranial Nerves
MRI Slice Thickness
• Signal ramps have a slope of 10:1
• Signal from ramp is 10 x slice thickness
• Two ramps are used to compensate for inplane rotation of the phantom
• Phantom does not compensate for tilting
backwards or swaying left-right
10 mm slice
Frequency Encoding & FOV
Phase Encode Gradient
– The field of view (FOVx) is determined by
the range of frequencies in the x- axis which
are sampled
Bandwidth
FOVx =
The maximum phasephase-encoding gradient is :
G
γ ⋅ Gx
– The receiver bandwidth is not the same as
the RF bandwidth
ph − max
=
2π
γ
BW π
N
= ⋅
FOV γ FOV ⋅ Ty
The phasephase-encoding gradient increment is :
∆G
↑ FOVx
– FOV must be sufficient to cover all tissue in
the slice to avoid aliasing
ph
=
π
1
⋅
γ FOV ⋅ Ty
• Note that a factor of two is gone from Gph-max
because Gph runs from- Gph=max to Gph=max
CHESS
Sampling the Signal
900sat
– Each signal is digitally sampled to produce
one line in the k- space matrix
900
1800
RF
∆k x = γ ⋅ Gx ∆t x
MHz mT
⋅
⋅ msec
T
m
cycles
=
m
1
∆k x =
FOVx
⋅
where FOV is the desired field of view
• ↑ BW ↑ FOVx
• ↓ Gx
3 mm slice
Gspoiler
∆k x =
G.D. Clarke, AAPM 2004
Signal
•
This is typically accomplished by preceding a SE or
FSE sequence with a 90o pulse that is frequency, not
spatially, selective.
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Spatial Saturation
Fat Suppression
Blood Flow
90o Sat
Pulse
90o-180o
SE Pulses
T1W images without (left) and with (right) fat suppression.
Spatial Saturation
Gadolinium Contrast Agents
• GD-DTPA, Gd-DOTA, Gd-HP-DO3A:
a. No Sat Pulse
b. Inferior Sat Pulse
c. Superior Sat
Pulse
d. Inferior and
Superior
Sat Pulses
the old standards, generally diffusable but not in
brain due to Blood Brain Barrier
– In low doses decrease T1
– In higher doses decrease T1 and T2*
NEW INTRAVASCULAR AGENTS • Blood pool agents
– Magnetic iron oxide particles
– Bind serum albumin, have higher relaxivity
GE Signa Applications Guide, Vol 1
Gadolinium Contrast Agents
Normal
T-1
Dynamic Contrast Studies
weighted Images
With Gd Contrast
Meningioma
• Dynamic study of breast tumor
• Curves denote difference between uptake of normal
glandular tissue & lesion
Vlaardingerbroek & den Boer, 1999
G.D. Clarke, AAPM 2004
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Optimizing MRI Protocols
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Diffusion Weighted Imaging:
Prototype Pulse Sequence
Attenuation Due to Diffusion
δ
A(TE ) = A(0) exp[−γ 2G 2 Dappδ 2α 2 (∆ − )]
4
Where: α=π/2;
G is amplitude of diffusion sensitive gradient
pulse;
δ is duration of diffusion sensitive gradient;
∆ is time between diffusion sensitive gradient
pulses;
Dapp is the apparent diffusion coefficient
The b-value
90o
180o
time
G
G
δ
δ
(
b = γ 2G 2δ 2 ∆ − δ
∆
3
)
Stejskal EO & Tanner JE, 1965. 42: 288-292
Diffusion EPI Pulse Sequence
• Controls amount of diffusion weighting
in image
RF 90o
• The greater the b-value the greater the
area under the diffusion-weighted
gradient pulses
FE
180o
SS
Gx
Gx
PE
– longer TE
– stronger and faster ramping the gradients
MR
signal
~100 ms
Diffusion Imaging of Infarcts
SE Echo Planar
TE = 80 ms
Biorelaxometry
SE Echo Planar
b = 1205 s mm-1
Koenig, et. al, 1983
G.D. Clarke, AAPM 2004
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Optimizing MRI Protocols
Specific Absorption Rate (SAR)
• The patient is in an RF magnetic field that causes spin
excitation (the B1 field)
• The RF field can induce small currents in the
electrically conductive patient which result in energy
being absorbed.
• The RF power absorbed by the body is called the
specific absorption rate (SAR)
• SAR has units of watts absorbed per kg of patient
• If the SAR exceeds the thermal regulation capacity
the patient’s body temperature will rise.
SAR Effects on Pulse
Sequences
7/27/2004
Scan Parameters Effecting SAR
• Patient size: SAR increases as the patient size
increases – directly related to patient radius
• Resonant frequency: SAR increases with the square
of the Larmor frequency (ωo)
• RF pulse flip angle: SAR increases as the square of
the flip angle (α
• Number of RF pulses: SAR increases with the
number of RF pulses in a given time
Uniformity at 3 Tesla
1.5T
• Decrease number of slices per study
• Requires decreased flip angles, even
in gradient echo sequences
3T
• Forces increases in TR
• Limits use of Fast Spin Echo imaging
• B1 field maps in a conductive saline phantom
(18 cm diameter)
RL Greenman et al. JMRI 2003, 17(6): 648648-655
Summary
• RF pulses can be crafted to select slices
• RF pulse timing (TE, TR & TI) is used to
manipulate soft tissue contrast in MR images
• Gradient echo imaging with partial flip angles is
faster than spin echo imaging
• Spin Echoes correct for poor magnetic fields
• Inversion recovery can be used to get rid of fat or
CSF from images
• Contrast agents are used to manipulate tissue T1
G.D. Clarke, AAPM 2004
Summary
• Presaturation schemes can effect flow,
chemical shift and T1-weighted contrast
• Fast imaging methods are often applied to
imaging physiology as well as anatomy
• Typically, SNR is reduced with increases
in resolution, contrast and imaging speed
• Various image parameters will have to be
adjusted for each magnetic field strength
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