Optimizing MRI Protocols 7/27/2005

Overview
Optimizing MR Imaging • Image contrast in standard clinical
sequences (pulse timing parameters)
Procedures:
The Physicist as a Consultant • Interactions between spatial resolution,
imaging speed and signal-to-noise ratio

Lisa C. Lemen, Radiology Department

• Adapting MR protocols to physiology
University of Cincinnati and system configuration

Substantial number of slides courtesy of Geoff Clarke, UTHSCSA

G. Clarke

Morphology & Physiology

• Tissue parameters (T1, T2, PD, mag transfer)
• Chemical shift (water vs. fat) SNR SPEED
• Blood motion (macroscopic & microscopic)
• Gross motion (peristalsis, respiration)
• Tissue susceptibility
RESOLUTION
• Diffusion of water
• Patient (clinical status, body habitus, prep)

adapted, G. Clarke

G.D. Clarke, UT HSC San Antonio 1

Optimizing MRI Protocols
SNR
SAFETY
COVERAGE
COMFORT/COMPLIANCE
PRICE
RESOLUTION
MR Knee Imaging
AX T1W AX T2W FS Cor T2W FS T2W GRE
Skeletal MR Imaging requires:
• small FOV, high spatial
resolution
• off-center imaging
• avoidance of wrap-around
• elimination of fat signals
G.D. Clarke, UT HSC San Antonio
SPEED
Sag PD PD fat sat
• Soft tissue contrast
• See tendons, ligaments,
bone marrow, cartilage
• arthroscopy or kinematic
evaluation
MR Brain Imaging
AX T1W AX T2W FLAIR
Brain MR Imaging requires:
• Good gray-white matter
contrast
• High spatial resolution
• Excellent timing and gradient
control
MR Liver Imaging
AX T2W AX EPI AX T1W
Body MR Imaging requires:
• Control of respiratory and
other motion artifacts
• Identification and/or
elimination of fat signals
• Avoidance of wrap-around
(aliasing) artifact
7/27/2005
Diffusion Gadolinium MRA
• See inside bony structures
• Depict white matter lesions
• Evaluate cerebral blood
flow (angiogram or
perfusion)
adapted, G. Clarke
Ferumoxide
Advantages:
• Soft tissue contrast
• High degree of contrast
manipulation
• Lesion characterization
• High sensitivity to iron
G. Clarke
2
Optimizing MRI Protocols 7/27/2005

User Selectable Parameters User Selectable Parameters

• Magnetic Field Strength (Bo)
• Magnetic Field Strength (Bo)
• Coil selection
• Coil selection
• RF pulse timing (TR, TE, TI)
• RF pulse amplitude - flip angles (α)
• Receiver bandwidth (BW)
• Gradient amplitude & timing (b-value)
• RF pulse excitation frequency & bandwidth

adapted, G. Clarke adapted, G. Clarke

Image Contrast T1W Images

Spin Echo
• Basic image contrast is effected by the Sequence CSF has weak/no signal
amplitude and timing of the RF pulses used
to excite the spin system. fat emits a strong signal
22 axial slices
• Also manipulated by use of gradient pulses 20 sagittal slices
(to modulate motion) and exogenous
contrast agents (alter tissue properties)

adapted, G. Clarke Bushberg

G.D. Clarke, UT HSC San Antonio 3

Optimizing MRI Protocols 7/27/2005

T2W Images Spin Echo Pulse Sequence

180° 180°
Spin Echo 90° 90°

Sequence TX RF

Gsl

Gpe

Gro

CSF emits a strong signal. Signal

TE TE

fat emits a weak signal. TR

22 axial slices
C. Keener

SE – Effect of TR
TR = 63 ms, NSA = 16 TR =125 ms, NSA = 8 TR = 250 ms, NSA = 4 TR = 500 ms, NSA = 2

Multi-Echo Acquisitions
Image 1

Image 2

Image 3
Bo = 1.5 T
FOV = 230 mm
256 x 256
st = 4 mm
TE = 15 ms

TR = 1 s, NSA = 1 TR = 2 s, NSA = 1 TR = 4 s, NSA = 1

G. Clarke Vlaardingerbroek & den Boer, 1999 G. Clarke

G.D. Clarke, UT HSC San Antonio 4

Optimizing MRI Protocols 7/27/2005

TR (s)
4 Spin Echo - Rules of Thumb
Multiecho 2 I is proportional to M0[1-e-TR/T1]e-TE/T2
Image • TR controls T1 dependence
1.5
Matrix – Scan time
Most T1 Weighted 1.2 – SNR
Most Proton – #slices possible in multi-echo
Density Weighted 0.9 • TE controls T2 dependence
Most T2 Weighted – SNR
0.6
– #slices possible in given TR
G. Clarke TE 30 60 90 120 150 180 ms

T1, T2 and for Various Tissues ~ T1 for Various Bo

Tissue 0.5T 1.5T
Tissue T1(ms) T2(ms)
Fat 215 250
Liver 323 675
Liver 675+142 54+8
Kidney 559
Kidney 559+10 84+8
Muscle 600 1123
Muscle 1123+119 43+4
Gray Matter 656 1136
Gray Matter 1136+91 87+15
White Matter 539 889
White Matter 889+30 86+1.5
(example values from multiple sources)
G. Clarke Akber,
Akber, 1996 (at 63 MHz)

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Optimizing MRI Protocols 7/27/2005

Manipulating Contrast Pulse Sequence Classifications

• The “weighting” of image contrast is related to
delay times, TR (repetition time) & TE (echo time) RF Contrast Application
• Spin Echo – manipulates image contrast with 180o Name Pulses Weighting
refocusing pulses (insensitive to Bo inhomogeneities) Spin Echo Two or T1, PD or Conventional
more T2
• Gradient Echo – manipulates image contrast by
varying the excitation flip angle (fast scans) Gradient One T1 or T2* Fast imaging
Echo (3DFT)
• Inversion Recovery – manipulates image contrast
Inversion Three T1 and T2 Exclude
with 180o inversion pulses
Recovery certain tissues

G. Clarke G. Clarke

MR Sequences T1W Images

RF refocusing Gradient refocusing
Brain or Spine: Liver:
RF & Gradient refocusing Single shot
Single echo
GRASE EPI Spin Echo or FSE Gradient echo or EPI
spoiled
T1 FFE Mag prep
multishot FLASH
RARE SPGR MP_RAGE
FSE single shot TFE
TSE FSPGR
HASTE
Steady state turboFLASH
ssFSE
ssTSE TrueFISP
B-FFE
FIESTA
Manage effect of respiratory motion.

Fig 4.23 Leyendecker images from G. Clarke

G.D. Clarke, UT HSC San Antonio 6

Optimizing MRI Protocols 7/27/2005

Fast Spin Echo

Scan time depends on # TR

Conventional SE: one k-space line per echo per TR

FSE: multiple k-space lines per TR

multiple echoes per TR - echo train length (ETL)
one k-space line per echo

web lecture

K-Space Region vs. Contrast & Resolution

All Data Low Frequencies High Frequencies FSE Pulse Sequence

Phase Encoding Effective TE

SRThomas G. Clarke
ETL = Echo Train Length

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Optimizing MRI Protocols 7/27/2005

FSE Spin Echo vs. Fast Spin Echo

TE = 30 ms TE = 120 ms
Contrast is a mixture
T1-weighted
effective TE (ETE): echo placed in center of k-space
(TR = 500)
echo train spacing (ETS): T2 contribution, #slices

Example: bright fat on T2-weight FSE T2-weighted

Consider time of first and last echoes (TR= 2000)

as well as echo spacing

image from G. Clarke
G. Clarke
Spin Echo Fast Spin Echo (Echo Train Length = 4)

Liver Imaging
Effect of Echo Spacing
AX T2W AX EPI AX T1W Ferumoxide
Very fast (EPI or Gradient
Echo) T1 weighted images
allow effective
management of
respiratory motion.
PD/T1W

PDW
/T1W
SGE
photo
Signal-to-noise decreases for short T2 tissues (gray & white
matter) leading to a decrease in spatial resolution
Vlardengerbrook & den Boer, 1999
G. Clarke G. Clarke

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Optimizing MRI Protocols 7/27/2005

adapted, G. Clarke

Liver Imaging
What is SAR?
AX FSE AX EPI AX T1W Ferumoxide • T2-Weighted
FAST SPIN • The patient is in an RF magnetic field that causes spin
ECHO is often excitation (the B1 field)
used to reduce
• The RF field can induce small currents in the
motion artifact electrically conductive patient which result in energy
& scan time being absorbed.
T2W

• The RF power absorbed by the body is called the

specific absorption rate (SAR)
with Fat sat

• 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.
G. Clarke

Fast Spin Echo - Rules of

Scan Parameters Effecting SAR Thumb
• ETL controls scan time
• Patient size: SAR increases as the patient size
increases – directly related to patient radius – Scan time --- fit with TR
– image blurring
• Resonant frequency: SAR increases with the square
of the Larmor frequency (ωo) – therefore ↑ with Bo2 – SAR
• RF pulse flip angle: SAR increases as the square of • ETE controls contrast
the flip angle (α2)

• Number of RF pulses: SAR increases with the

number of RF pulses in a given time

G. Clarke

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Optimizing MRI Protocols 7/27/2005

SNR and Imaging Bandwidth Conversions

Parameters Values are field dependent
FOVro FOVph NSA • Version A: quoted in kHz, is ± kHz
SNR ∝ ⋅ ∆z ⋅ • Version B: quoted in Hz/pixel
M ro M ph BWrx
• Conversion at 1.5T:
12.8 kHz for a 256 matrix = 25.6 kHz for 512 matrix
FOV = field of view M = matrix size NSA = number of signals averaged = 100 Hz/pixel
BW rx = receiver bandwidth ro = read out (frequency encoding) direction
∆z = slice thickness ph = phase encoding direction
220 Hz chemical shift of fat
=> 2.2 pixel fat-water shift

G. Clarke

FLAIR Images
Inversion Recovery
• Spin Echo
Sequence,
with Inversion
Recovery

G. Clarke

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Optimizing MRI Protocols 7/27/2005

Fluid Attenuated Inversion

Recovery (FLAIR)
• Uses magnitude display.
• Initial 180o pulse applied.
• MZ = 0 is the “bounce point.”
• At TI, 90o pulse applied: longer TI 1800 -2500ms.
• If MZ = 0 at TI, maximum possible echo = 0.
• Allows selective suppression of contrast limiting signals,
e.g., CSF in ventricles.

CSF SUPPRESSION: NEUROLOGICAL

web lecture

FLAIR Multiple Sclerosis

(FLuid Attenuated Inversion Recovery) Proton Density T2-Weighted FLAIR

TR = 2350 TR=2350 TR=2600

TE = 30 TE= 80 TE=145
TI= 1000
Rydberg JN et al. Radiology 1994; 193:173-180
G. Clarke G. Clarke

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Optimizing MRI Protocols 7/27/2005

Inversion Recovery FSE FLAIR Imaging

TR =1400 TR =1400 TR =2000
TI = 100 TI = 280 TI = 280
Modulus Compensated
Phase

T2W-FSE FLAIR-FSE
TE/TR = 98/3500ms, TI/TE/TR = 2200/147/10000ms,
Slice 5/1.5mm, ET:8 (split) Slice 5/1.5mm,
256x224, 1 NEX, 256x160, 1 NEX,
20x20 cm FOV, 3:23 20x20cm FOV, 3:40
G. Clarke Vlaardingerbroek & den Boer, 1999 G. Clarke

Short Tau Inversion Recovery

(STIR)
• Uses magnitude display.
• Initial 180o pulse applied.
• MZ = 0 is the “bounce point.”
• At TI, 90o pulse applied (TI-110-150ms).
• If MZ = 0 at TI, maximum possible echo = 0.
• Allows selective suppression of contrast limiting signals,
e.g., fat around orbitals.

FAT SUPPRESSION: MUSCULOSKELETAL

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Optimizing MRI Protocols 7/27/2005

Spine Imaging
Fat saturation in MSK MRI
Fat is not your friend!
– Chemical shift saturation
• Precession of fat and water are different
Bottom: STIR • Fat peak can be selected for saturation
•Short • Higher field strength required
• TI
•Inversion
•Recovery
– Inversion recovery
• high and low field strength systems
• requires more time
adapted, G. Clarke adapted, Wissman

Chemical Shift in the

Chemical Shift Frequency Encoding Direction
• Chemical shift (fat-water) ~3.5 ppm Actual Lipid signal is shifted
location to a lower
– At 1.5T: frequency.
Produces a signal
42.6 MHz
∆f fat− water = 3.5 ×10 −6 ⋅ ⋅1.5T ≅ 220 Hz Observed
void (dark band)
on the high-
high-
T location frequency side of
– At 0.5T: the lipid and an
increase in signal
42.6 MHz Signal (bright band) on
∆f fat − water = 3.5 ×10 − 6 ⋅ ⋅ 0.5T ≅ 73 Hz intensity the low-
low-frequency
T
• ↓ field strength …. ↓ chemical shift side

Frequency SR Thomas
G. Clarke SRThomas

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Optimizing MRI Protocols 7/27/2005

Chemical Shift – Clinical Presentation

Chemical Shift Artifact
Coronal T1W fast
multiplanar • Occurs in
spoiled – Readout direction
gradient-
gradient-echo • Conventional SE
image
(FMPSPGR) – Phase encode direction
TR(ms)/TE(ms)/α:
TR(ms)/TE(ms)/α • Echo-Planar
103/5.6/800 • Controlled by
Frequency – Fat Pre-Saturation
encode: – STIR sequence
right-
right-to-
to-left – BW choice
Chemical shift artifacts at the lipid-
lipid-water interfaces.
SRThomas adapted, G. Clarke

Liver Imaging
CHESS Chemical Shift
A C

B
A. In phase-spoiled FFE image w/ TE=
4 ms

• This is typically accomplished by preceding a SE or B. Out of phase spoiled FFE images w/

TE = 2 ms
FSE sequence with a 90o pulse that is frequency, not
C. T2 breath-hold FSE with fatsat pulse
spatially, selective.

G. Clarke G. Clarke http://www.users.on.net/~vision/papers/abdomen/abdominal-mri.htm

G.D. Clarke, UT HSC San Antonio 14

Optimizing MRI Protocols 7/27/2005

Magnetization Transfer
Magnetization Transfer Contrast

Multislice
FSE:

Magnetization
Transfer
Contrast
Enhances T2-
Weighted
Appearance
adapted, G. Clarke adapted, G. Clarke

3D Imaging - MTF Post-Contrast T1 Images

• MTF background suppression Images from G. Clarke
–Saturate restricted protons (macromolecules)
–Spin-exchange with more mobile water protons
• Good: reduces background
– doesn’t saturate moving blood, CSF Meningioma
• Bad:
–Orbital fat is more obvious as parenchyma is less
Conventional MRA MRA with MTF
Left – Axial T1W image
of S1 (note nerve root)
Right – Gd-enhanced
image confirms abnormal
Ross Case 5
soft tissue is scar adapted, G. Clarke

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Optimizing MRI Protocols 7/27/2005

Contrast Agents - Gd Contrast Agents

Gadolinium chelate - paramagnetic
– Seven unpaired electrons
– unpaired electrons react with protons in
adjacent water molecules shortening
their relaxation time
& Bo Strength
• Due to increases in tissue T1’s, Gd-
based contrast agents are more
effective at 3T compared to 1.5T
• Use less contrast agent to get same
tissue contrast
or

• reduces T1 relaxation times • Achieve much higher tissue contrast

for the same dose
• enhances T1 signal intensity in
low concentrations
Nobauer-Huhmann IM, Invest Radiol 2002; 37:114-119
adapted, G. Clarke
G. Clarke

MoBI-track MR Angiography SRThomas

3 mask
Contrast-Enhanced MRA images

• T1-weighted sequence for

bright blood
• bolus injection of high dose
(40-60ml) Subtract
3 live images

• acquire central k-space

when contrast is in arteries
in desired region 3D CE MRA: First pass
– may require test bolus or carotid, elliptical-centric
(60 sec acquisition)
automatic detection
image from SR Thomas

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Optimizing MRI Protocols 7/27/2005

Perfusion
Gadolinium
• shortens T2 relaxation of water
– lowers SI on T1 weighted images in high
concentrations

• Nonuniform distribution of Gd-DTPA

increases magnetic susceptibility
differences
– Decreases MR signal on T2*-weighted images

adapted, R. Rojas
adapted, G. Clarke

Perfusion Liver Imaging

Negative Enhancement Integral (NEI)
AX T2W AX EPI AX T1W Ferumoxide Super
“Area below the curve” Paramagnetic Iron
Related to “rCBV” Oxide is the
contrast agent of
choice in liver
imaging
agents
Contrast

Area below the curve related to time T2W Fast Spin Echo T2*W Gradient Echo
R. Rojas G. Clarke

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Optimizing MRI Protocols 7/27/2005

Fast Scanning

• Short - TR Sequences

• Segmented k-space

• Echo Planar Imaging (EPI)

• Parallel Imaging

web lecture

Gradient-Echo Imaging GRE Sequence Advantages

• Fast
– Short TR values allow for fast scanning
(~ 1 sec/image)
• No 1800 pulse
– Decreases by >5X RF power deposition
– Lower minimum TE --> better T1W

• Low flip angle

– Partial (<90o) flip angle keeps all longitudinal
magnetization from being used up

Reference: Wehrli, Fast-Scan Magnetic Resonance. Principles and Applications

– Higher signal intensity for short TR

G. Clarke

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Optimizing MRI Protocols 7/27/2005

Spoiled GRE Spoiled Gradient Echo

• Destroying any residual transverse

magnetization (Mxy)

• Used in steady-state imaging, with very

short TRs
• Short TR, short TE, large flip angle

SPGR and FLASH

Also called spoiled GRASS, fast field echo, FLASH, etc.
G. Clarke G. Clarke

GRE contrast
Flip Angle Magnetic Susceptibility Effects
– <30o, minimizes T1, thus proton density or T2*
– >30o -60o, T1
TR
– Long (200ms), allows full Mxy decay
– Short (<50ms), steady-state precession condition
TE
– Short TE values preserve SNR
– Long TE => T2* contrast, not T2
– Short TE for T1

Sensitive to susceptibility
TR=9.5ms, TE=3.5ms
Flip=28o; 3D we
G. Clarke

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Optimizing MRI Protocols 7/27/2005

TE = 15 ms Effect of Echo Delay on

Susceptibility Induced Gradient-Echo Imaging
Signal Loss.
TE = 10 ms The susceptibility-induced artifacts in GRE
images:
• Increase with TE - limiting the utility of GRE
Signal reduction in T2*-weighted images in many cases.
TE = 5 ms
the region of the • Are worst for tissue/air interfaces, but
nasal and mastoid noticeable at tissue/bone interfaces.
sinuses.
• Are usually a detriment, but are useful in some
Signal loss is less extensive circumstances (e.g., blood-sensitive imaging,
for shorter TE - less T2* BOLD contrast functional imaging, etc.).
effect. SRThomas G. Clarke

Diffusion Imaging : Principles DWI Images bright CSF

Diffusion gradients sensitize MR Image to

motion of extracellular water
More motion = Darker image
S(b) = S(0)exp(-bD)

Large D: mobile water --> low signal

Small D: restricted motion --> high signal

b: larger --> more diffusion weighting

DWI contrast is like an inverse T2 weighting

Watery tissue - mobile molecules - low signal
Freely Diffusing Water = Dark Restricted Diffusion = Bright Solid tissue - stronger signal
dark CSF

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Optimizing MRI Protocols 7/27/2005

Hyper acute CVA 4Hrs. Evol.

DWI Pulse Sequence
- MRI Diffusion

(
b = γ 2 G 2δ 2 ∆ − δ
3
) T2 Echo planar b-value 1000 ADC

Stejskal EO & Tanner JE, 1965. 42: 288-292

adapted, G. Clarke adapted, R. Rojas

Echo Planar Imaging Diffusion Echo-Planar Imaging

(EPI)

ultrafast data acquisition

fill k-space by rapid gradient reversals and echoes
after a SINGLE set of RF pulses

Peter Mansfield, 1980s

•Signal has to be acquired in time ~T2
•Images in less than 100 ms but poor spatial resolution ( ~ 3mm x 3mm pixel)
•Requires very good Bo homogeneity big susceptibility artifacts
G. Clarke

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Optimizing MRI Protocols 7/27/2005

G. Clarke

EPI limits Liver Imaging

AX T2W T2W EPI AX T1W Ferumoxide Increasing the
• Hardware requirements
number of shots
- gradients - bigger, faster increases imaging
- rapid A/D time but decreases
geometric
- memory
distortions
• Artifacts

Echo Planar
- chemical shift • Echo planar is the fastest
imaging sequence and can
- eddy currents be used to minimize 4 Shot
8 Shot
• Acoustic noise motion artifacts
• Sequence flexibility • Long TE Gradient Echoes
• Induced currents in patient produce T2* contrast to
1 Shot
identify tumors 2 Shot
Medhi P-A et al. Radiographics 2001; 21:767

Parallel Imaging Image Acceleration

• Uses spatial information obtained from arrays of Conventional
RF coils breath-hold
cardiac MRI
• Information is used to perform some portion of Requires 14
spatial encoding usually done by gradient fields heartbeats.
and RF pulses
• Multiplies imaging speed SENSE breath-
hold cardiac MRI
– without needing faster-switching gradients
Requires 3
– without additional RF power deposited heartbeats.
http://www.mr.ethz.ch/sense/sense_application.html

adapted, G. Clarke G. Clarke

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Optimizing MRI Protocols 7/27/2005

Summary Pulse Sequence Factors

Resolution Signal-to-Noise Contrast
• Pulse sequence factors have varying
FOV & matrix size FOV & matrix size Relaxation times effects
Slice thickness RF Pulse flip RF Pulse flip – ↑ TR ↑ SNR by allowing more Mz regrowth
angles & timing angles & timing – ↑ TE ↓ SNR by allowing more Mxy dephasing
FSE inter-echo Bo field strength Preparation – 180° refocusing pulses ↑ SNR
spacing pulses
• SE or FSE
Motion artifact Receiver Gradient timing
bandwidth (b-value) – ↑ TI ↓ or ↑ SNR
Chemical shift RF coil sensitivity Magnetization – ↑ α ↓ or ↑ SNR depending on Ernst angle
artifact transfer
C. Keener, MARP
G. Clarke

Suggested Reading Suggested Reading

(In order of increasing complexity)
• MRI: From Picture to Proton McRobbie DW, Moore
EA, Graves MJ & Prince MR. Cambridge Univ.
Press, 2003; ISBN: 0521523192
• Magnetic Resonance Imaging 3rd ed.
Vlaardingerbroek MT, den Boer JA, Luiten A.
Springer 2002; ISBN: 3540436812
• Handbook of MRI Pulse Sequences Bernstein MA,
King KF, Zhou XJ. Elsevier, 2004; ISBN:
0120928612
(practical and specialty references)
• MRI Optimization: A hands-on approach Woodward P, Orrison
Jr WW. McGraw Hill, 1997; ISBN: 0070718016.
• Practical Guide to Abdominal & Pelvic MRI Leyendecker JR,
Brown JJ. Lippincott 2004; ISBN: 0781742951 (sections 1,4)
• T1, T2 relaxation and magnetic transfer at 3T. Stanisz et al.,
MRM 2005 54(3): 507-12.
• MR imaging of the spine at 3T. Shapiro MD, MRI Clin N Am
2006 14(1): 97-108.
• Abdominal MR imaging at 3T. Merkle et al., MRI Clin N Am
2006 14(1): 17-26.

G. Clarke

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