overview optimizing mri protocols mri protocols 7/27/2005 g.d. clarke, ut hsc san antonio 4 ax t1w...

Optimizing MRI Protocols 7/27/2005

G.D. Clarke, UT HSC San Antonio 1

Optimizing MRI ProtocolsClinical Practice & Compromises

Geoffrey D. Clarke, Radiology DepartmentUniversity of Texas Health Science Center at San Antonio

Overview• Pulse timing parameters for adjusting

image contrast

• Effects of spatial resolution and imaging speed on signal-to-noise ratio

• Effects of magnetic field strength

• Adapting MRI pulsing protocols to physiology under investigation

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

Morphology & Physiology• Chemical Shift (water vs. fat)

• Blood motion (macroscopic & microscopic)

• Diffusion of water

• Gross motion (peristalsis, respiration)

• Tissue Susceptibility

Tissue Parameters

• Tissue Water Density – Proton Density (PD)

• Longitudinal Relaxation Time (T1)

• Transverse Relaxation Time (T2)

• Magnetization transfer rate constants

User Selectable Parameters• Magnetic Field Strength (Bo)

• RF Pulse timing (TR, TE, TI)

• RF pulse amplitude - flip angles (α)

• Gradient Amplitude & Timing (b-value)

• RF pulse excitation frequency & bandwidth

• Receiver bandwidth (BW)



Contrast-to-Noise Ratio

σ = standard deviation of the signal (the noise)

n = number of signals acquired

Ia,Ib = signal intensities from tissues “a” and “b”

( )σ

ba IInCNR −=

Contrast relationships are determined by the RF pulse timings used and the relaxation properties of tissues under investigation.

Relaxation Times• T1: longitudinal relaxation time defines recovery

of potential for next signal

• T2: transverse relaxation time defines rate of dephasing of MRI signal due to microscopic processes

• T2*: transverse relaxation time with Boinhomogeneity effects added; defines rate of dephasing of MRI signal due to macroscopic and microscopic processes

T1, T2 and for Various Tissues

Tissue T1(ms) T2(ms)

Liver 675+142 54+8 Kidney 559+10 84+8Muscle 1123+119 43+4Gray Matter 1136+91 87+15White Matter 889+30 86+1.5

AkberAkber, 1996 (at 63 MHz), 1996 (at 63 MHz)

Manipulating Contrast• The “weighting” of image contrast is related to

delay times, TR (repetition time) & TE (echo time)

• Spin Echo – manipulates image contrast with 180o

refocusing pulses (insensitive to Bo inhomogeneities)

• Gradient Echo – manipulates image contrast by varying the excitation flip angle (fast scans)

• Inversion Recovery – manipulates image contrast with 180o inversion pulses

Pulse Sequence Classifications ApplicationContrast

WeightingRF PulsesName

Exclude certain tissues

T1 and T2ThreeInversion Recovery

Fast imaging (3DFT)

T1 or T2*OneGradient Echo

ConventionalT1, PD or T2

Two or more

Spin Echo

Spin Echo - Rules of Thumb• TE controls T2 dependence• TR controls T1 dependence• T1 competes with T2 and proton density

“PD Weighted” = long TR, short TE“T1 Weighted” = short TR, short TE“T2 Weighted” = long TR, long TE



Spin-Echo Imaging Sequence

TX

RF1=90o RF2=180o

Spin Echo

time

timeRX

time

time

time

GGslsl

GGroro

Gpe

Multi-Echo AcquisitionsImage 1Image 1

Image 2Image 2

Image 3Image 3

SNR and Imaging Parameters

rxBWNSAzS ⋅∆⋅∝

ph

ph

ro

ro

MFOV

MFOV NR

FOV = field of view M = matrix size NSA = number of signals averagedBWrx = receiver bandwidth ro = read out (frequency encoding) direction∆z = slice thickness ph = phase encoding direction

Matched Bandwidth

Mugler & Brookeman, Magn Reson Imag 1989; 7:487-493.

1 2

Matched Bandwidth• Bandwidth on ADC1 is limited by finite Tmax

& desire to minimize TE1.

• T1 weighting and SNR is sacrificed moreby 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.

Matched Bandwidth = Unmatched Distortion

• Smaller BW on T2W image leads to increased image distortion

T1W T2W



AX T1W AX T2W FLAIR Diffusion Gadolinium

• Gray-white matter contrast

• See inside bony structures

• High spatial resolution

MR Brain Imaging

• Depicts white matter lesions

• Evaluate cerebral blood flow

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

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

Bo = 1.5 T

FOV = 230 mm

256 x 256

st = 4 mm

TE = 15 ms

Vlaardingerbroek & den Boer, 1999

TR (s)4

2

1.5

1.2

0.9

0.6

TE 30 60 90 120 150 180 ms

MultiechoImage Matrix

Most TMost T1 1 WeightedWeighted

Most Proton Most Proton Density WeightedDensity Weighted

Most TMost T2 2 WeightedWeighted

Paramagnetism• Oxygen

• Metal ions with unpaired electrons resulting in positive susceptibility- Fe - Gd - Mg

• Paramagnetism has less than 1/1000th effect of ferromagnetism

• Shortens T1 and T2 times

Gd-DTPA• Typical dose of ~0.1 mM/kg• 550-600 Dalton• seven unpaired electrons

–high magnetic moment

–unpaired electrons react with protons in adjacent water molecules shortening their relaxation time

Gadolinium

• shortens T1 relaxation of water– high SI on T1 weighted images in lower

concentrations

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

concentrations



• Nonuniform distribution of Gd-DTPA increases magnetic susceptibilitydifferences– Decreases MR signal on T2*-weighted

images

Gadolinium Gadolinium Contrast Agents

MeningiomaMeningioma

TT11--weighted Imagesweighted Images

Normal With Gd Contrast

Commercial Contrast Agents Inversion Recovery

FLAIR(FLuid Attenuated Inversion Recovery)

Brain

Lesion

CSF

TI

0 time

Tefftime

Lesion

Brain

Mz

Mxy

Multiple Sclerosis

TR = 2350TE = 30

Proton Density

Rydberg JN et al. Radiology 1994; 193:173-180

T2-Weighted

TR=2350 TE= 80

FLAIR

TR=2600TE=145

TI= 11,000



FSE Pulse Sequence

ETL = Echo Train Length

Effective TE

FSE Point Spread Function Depends on T2

Effect of Echo Spacing

Vlardengerbrook & den Boer, 1999

Signal-to-noise decreases for short T2 tissues (gray & white matter) leading to a decrease in spatial resolution

Spin Echo vs. Fast Spin Echo

TT11--weighted weighted

(TR = 500)(TR = 500)

TT22--weightedweighted

(TR= 2000)(TR= 2000)

Spin Echo Fast Spin Echo (Echo Train Length = 4)Spin Echo Fast Spin Echo (Echo Train Length = 4)

TE = 30 ms

TE = 120 ms

Inversion Recovery FSE

Vlaardingerbroek & den Boer, 1999

Mod

ulus

Phas

e C

ompe

nsat

ed

TR =1400TI = 100

TR =1400TI = 280

TR =2000TI = 280

FLAIR Imaging

T2W-FSE FLAIR-FSETE/TR = 98/3500ms,

Slice 5/1.5mm, ET:8 (split)256x224, 1 NEX,

20x20 cm FOV, 3:23

TI/TE/TR = 2200/147/10000ms, Slice 5/1.5mm, 256x160, 1 NEX,

20x20cm FOV, 3:40



Magnetization Transfer

MultisliceFSE:

Magnetization Transfer Contrast Enhances T2-Weighted Appearance

Magnetization Transfer Contrast

Attenuation Due to Diffusion

)]4

(exp[)0()( 2222 δαδγ −∆−= appDGATEAWhere: α=π/2;G is amplitude of diffusion sensitive gradient

pulse;δ is duration of diffusion sensitive gradient;

∆ is time between diffusion sensitive gradientpulses;

Dapp is the apparent diffusion coefficientHahn E., Phys Rev 1950

Diffusion Weighted Imaging:Prototype Pulse Sequence

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

( )3 b 222 δδγ −∆= G

Diffusion Echo-Planar Imaging

•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

The b-value• Controls amount of diffusion weighting

in image

• The greater the b-value the greater the area under the diffusion-weighted gradient pulses– longer TE

– stronger and faster ramping the gradients



Diffusion Imaging of Infarcts

SE Echo PlanarTE = 80 ms

SE Echo Planarb = 1205 s mm-1

SAG T1W SAG T2W STIR Gadolinium

• See inside bony structures

• Surface coil almost always used

• Evaluate nerve root compression

Left:Coronal

T2W(one slice)

Right:MIP

Spine Imaging

Gradient-Echo Imaging• Partial (<90o) flip angle keeps all

longitudinal magnetization from being used up

• Short TE values preserve SNR• Short TR values allow for fast scanning

(~ 1 sec/image) • Poor T2-weighted contrast• Sensitive to susceptibility

Spoiled Gradient Echo

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

Magnetic Susceptibility Effects Gradient-Echo ImagingThe susceptibility-induced artifacts in GRE

images:• Increase with TE - limiting the utility of GRE

T2*-weighted images in many cases.• Are worst for tissue/air interfaces, but

noticeable at tissue/bone interfaces.• Are usually a detriment, but are useful in some

circumstances (e.g., blood-sensitive imaging, BOLD contrast functional imaging, etc.).



Gradient-Echo Imaging

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

Spatial SaturationSpatial presaturationpulses (slabs) can be

applied in oblique coronal planes and are

used to suppress signal intensities of tissue adjacent to spine and reduce breathing artifacts

Phased Array Surface Coils

www.toshiba-europe.com

www.medical.philips.com

Surface receiver coils are used to maximize signal from regions of interest while minimizing noise from volumes outside of the region of investigation.

STIR(Short TI Inversion Recovery)

Fat

Liver

TI

0 time

Mz

T1-

wei

ghte

dT

1T1 --

wei

ghte

dw

eigh

ted• Right: Saggital T1W

image of T11–L1 demonstrates minimal wedging of the vertebral bodies associated with intravertebral disc herniations (arrows)


Spine Imaging

T2-

wei

ghte

dT

2T2 --

wei

ghte

dw

eigh

ted

• Heavily T2-weighted

images show CSF as bright,

creating myelographic

effect


MRI CT

Spine Imaging



S TI R

S TI R

Top: Sag T1WBottom: STIR

••SShort ••TTI••IInversion••RRecovery


Spine Imaging

Con

tra s

t A

gen t

Con

tra s

t A

gen t

Left – Axial T1W image of S1 (note nerve root)Right – Gd-enhanced image confirms abnormal soft tissue is scar


Spine Imaging

AX T2W AX EPI AX T1W Ferumoxide

Advantages:

• Soft tissue contrast

• High degree of contrast manipulation

• Lesion characterization

• High sensitivity to iron

Liver Imaging

Body MR Imaging requires:

• Control of respiratory an dother motion artiafcts

• Identification and/or elimination of fat signals

• Avoidance of wrap-around (aliasing) artifact

Chemical Shift Artifact• Occurs in

– Readout direction• Conventional SE

– Phase encode direction

• Echo-Planar

• Controlled by– Fat Pre-Saturation– STIR sequence

Chemical shift artifact seen in axial image of kidney

Chemical Shift• Chemical shift (fat-water) ~3.5 ppm

– At 1.5T:

– At 0.5T:

• ↓ field strength …. ↓ chemical shift

HzTTMHzf waterfat 2205.16.42105.3 6 ≅⋅⋅×=∆ −

−

HzTTMHzf waterfat 735.06.42105.3 6 ≅⋅⋅×=∆ −

−

CHESS

• This is typically accomplished by preceding a SE or FSE sequence with a 90o pulse that is frequency, not spatially, selective.



Liver ImagingChemical Shift

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

B. Out of phase spoiled FFE images w/ TE = 2 ms

C. T2 breath-hold FSE with fatsat pulse

A

B

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

C

T2 W

T2 W

T2 W

AX FSE AX EPI AX T1W Ferumoxide • T2-Weighted FAST SPIN ECHO is often used to reduce motion artifact & scan time

Liver Imaging

Echo Planar

Echo Planar

Echo Planar

AX T2W T2W EPI AX T1W Ferumoxide

• Echo planar is the fastest imaging sequence and can be used to minimize motion artifacts

• Long TE Gradient Echoes produce T2* contrast to identify tumors

Increasing the number of shots

increases imaging time but decreases

geometric distortions

8 Shot 4 Shot

1 Shot2 Shot

Medhi P-A et al. Radiographics 2001; 21:767

Liver Imaging

PD/T

1WPD

/T1W

AX T2W AX EPI AX T1W Ferumoxide

PDW /T1WSGE

Very fast (EPI or Gradient Echo) T1 weighted images allow effective management ofrespiratory motion.

photo

Liver Imaging

Co ntra st

ag entsC

o ntra st ag ents

AX T2W AX EPI AX T1W Ferumoxide Super Super Paramagnetic Iron Paramagnetic Iron OxideOxide is the contrast agent of choice in liver imaging

T2W Fast Spin Echo T2*W Gradient Echo

Liver ImagingChanges in MRI with

Bo Field-Strength

Less uniform images

Increases in magnetic

susceptibility

Increased chemical shift?

Increased absorption of

RF power

Poorer T1W contrast due to

longer T1

Increased signal

The UglyThe BadThe Good



Contrast Agents & 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

• Achieve much higher tissue contrast for the same dose

Nobauer-Huhmann IM, Invest Radiol 2002; 37:114-119

What is 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.

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) – therefore ↑ with Bo

2

• RF pulse flip angle: SAR increases as the square of the flip angle (α2)

• Number of RF pulses: SAR increases with the number of RF pulses in a given time

Parallel Imaging• Uses spatial information obtained from arrays of

RF coils

• Information is used to perform some portion of spatial encoding usually done by gradient fields and RF pulses

• Multiplies imaging speed– without needing faster-switching gradients

– without additional RF power deposited

Generalized Projections

X-ray CT Parallel MRI

Parallel imaging can be thought of as being analogous to x-ray CT…

3 RF coils

SENSE Imaging(SENSitivity Encoding)

SENSE

http://www.mr.ethz.ch/sense/

Data acquired from each PA coil element goes into reconstruction of whole image – reduces imaging time, reduces SNR, reduces uniformity.



Image AccelerationConventional breath-hold cardiac MRI Requires 14 heartbeats.

SENSE breath-hold cardiac MRI

Requires 3 heartbeats.

http://www.mr.ethz.ch/sense/sense_application.html

What We Haven’t Covered

http://www.mr.ethz.ch/3t/patient_5.html

•• MR AngiographyMR Angiography

•• InIn--flow enhancement flow enhancement

•• Magnetization transfer Magnetization transfer contrastcontrast

•• MR Perfusion ImagingMR Perfusion Imaging

•• Dynamic contrast uptakeDynamic contrast uptake

•• PresaturatingPresaturating inversion inversion slabs (FAIR)slabs (FAIR)

•• Functional MRIFunctional MRI

•• EchoEcho--planar imagingplanar imaging

•• Blood oxygen level Blood oxygen level dependent contrastdependent contrast

Summary

Magnetization transfer

RF coil sensitivityChemical shift artifact

Gradient timing (b-value)

Receiver bandwidth

Motion artifact

Preparation pulses

Bo field strengthFSE inter-echo spacing

RF Pulse flip angles & timing

RF Pulse flip angles & timing

Slice thickness

Relaxation timesFOV & matrix sizeFOV & matrix size

ContrastSignal-to-NoiseResolutionSuggested 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

overview optimizing mri protocols mri protocols 7/27/2005 g.d. clarke, ut hsc san antonio 4 ax t1w...

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