Contrast Mechanism and Contrast Mechanism and Pulse SequencesPulse Sequences

Contrast Mechanism and Contrast Mechanism and Pulse SequencesPulse Sequences

Allen W. Song Allen W. Song

Brain Imaging and Analysis CenterBrain Imaging and Analysis Center

Duke UniversityDuke University

III.1 Image ContrastsIII.1 Image Contrasts

The Concept of ContrastContrast = difference in signals emitted by water protons

between different tissuesFor example, gray-white contrast is possible because T1 is

different between these two types of tissue

T2 Decay

MRSignal

T1 Recovery

MRSignal

50 ms50 ms 1 s1 s

Static Contrast Imaging Methods

1.1. Weighted by the Proton DensityWeighted by the Proton Density

2.2. Weighted by the Transverse Relaxation Times (T2 and T2*)Weighted by the Transverse Relaxation Times (T2 and T2*)

3.3. Weighted by the Longitudinal Relaxation Time (T1)Weighted by the Longitudinal Relaxation Time (T1)

Most Common Static Contrasts

The Effect of TR and TE onProton Density Contrast

0 10 20 30 40 50 60 70 80 90 1000

0.5

1

1.5

2

2.5

0 0.2 0.4 0.6 0.8 1 1.2 1.4 1.6 1.8 20

0.5

1

1.5

2

2.5

T2 Decay

MR

Sig

nal

t (ms)t (s)

MR

Sig

nal

TRTR TETE

T1 Recovery

Optimal Proton Density Contrast

Technique: use very long time between RF shots (large TR) and very short delay between excitation and readout window (short TE)

Useful for anatomical reference scans Several minutes to acquire 256256128 volume ~1 mm resolution

Proton Density Weighted ImageProton Density Weighted Image

T2T2T2*T2*

Cars on different tracksCars on different tracks

Transverse Relaxation Times

180o turnt = TE/2

180o turnt = TE/2

TE/2

TE/2

t=0

t=TE

t=0

t=TE

Fast Spin Fast Spin

Fast Spin Fast Spin

Slow Spin Slow Spin

Slow SpinSlow Spin

Since the Magnetic Field Factor is always present, Since the Magnetic Field Factor is always present, how can we isolate it to achieve a singular T2 Contrast?how can we isolate it to achieve a singular T2 Contrast?

TE/2

TE/2

The Effect of TR and TE onT2* and T2 Contrast

0 0.2 0.4 0.6 0.8 1 1.2 1.4 1.6 1.8 20

0.1

0.2

0.3

0.4

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0.9

1

0 10 20 30 40 50 60 70 80 90 1000

0.1

0.2

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T2 Decay

MR

Sig

nal

MR

Sig

nal T1 Recovery

TRTR TETE

T1 ContrastT1 Contrast T2 ContrastT2 Contrast

Optimal T2* and T2 Contrast

Technique: use large TR and intermediate TE

Useful for functional (T2* contrast) and anatomical (T2 contrast to enhance fluid contrast) studies

Several minutes for 256 256 128 volumes, or second to acquire 64 64 20 volume

1mm resolution for anatomical scans or 4 mm resolution [better is possible with better gradient system, and a little longer time per volume]

T2 Weighted ImageT2 Weighted Image

T2* Weighted ImageT2* Weighted Image

PD ImagesPD Images

T2* ImagesT2* Images

The Effect of TR and TE onT1 Contrast

0 0.2 0.4 0.6 0.8 1 1.2 1.4 1.6 1.8 20

0.1

0.2

0.3

0.4

0.5

0.6

0.7

0.8

0.9

1

0 10 20 30 40 50 60 70 80 90 1000

0.1

0.2

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1

T1 contrast T2 contrast

T2 Decay

MR

Sig

nal

MR

Sig

nal

T1 Recovery

TRTR TETE

Optimal T1 Contrast

Technique: use intermediate timing between RF shots (intermediate TR) and very short TE, also use large flip angles

Useful for creating gray/white matter contrast for anatomical reference

Several minutes to acquire 256256128 volume ~1 mm resolution

T1 Weighted ImageT1 Weighted Image

-S-So

SSo

S = SS = Soo * (1 – 2 e * (1 – 2 e –t/T1–t/T1))

S = SS = Soo * (1 – 2 e * (1 – 2 e –t/T1’–t/T1’))

Inversion Recovery to Boost T1 ContrastInversion Recovery to Boost T1 Contrast

IR-Prepped T1 Contrast

In summary, TR controls T1 weighting and In summary, TR controls T1 weighting and TE controls T2 weighting. Short T2 tissues TE controls T2 weighting. Short T2 tissues are dark on T2 images, but short T1 tissues are dark on T2 images, but short T1 tissues are bright on T1 images.are bright on T1 images.

Motion Contrast Imaging Methods

Prepare magnetization to make signal sensitive to different motion properties

Flow weighting (bulk movement of blood) Diffusion weighting (scalar or tensor) Perfusion weighting (blood flow into capillaries)

Flow Weighting: MR Angiogram

•Time-of-Flight ContrastTime-of-Flight Contrast

•Phase ContrastPhase Contrast

Time-of-Flight Contrast

No Flow

Medium Flow

High Flow

No Signal

Medium Signal

High Signal

Vessel

AcquisitionSaturation Excitation

Vessel Vessel

90o

Excitation

ImageAcquisition

RF

Gx

Gy

Gz

90o

Saturation

Time to allow fresh flow enter the slice

Pulse Sequence: Time-of-Flight Contrast

Phase Contrast (Velocity Encoding)

Externally AppliedSpatial Gradient G

Externally AppliedSpatial Gradient -G

Blood Flow v

2

0

2)()(

GvT

dtvtxGdtvtxGT T

T

Time

T2T0

90o

Excitation

Phase

Image

Acquisition

RF

Gx

Gy

Gz

G

-G

Pulse Sequence: Phase Contrast

MR AngiogramMR Angiogram

Diffusion Weighting

Dtl 2

Externally AppliedExternally AppliedSpatial Gradient Spatial Gradient GG

Externally AppliedExternally AppliedSpatial Gradient -Spatial Gradient -GG

TimeTime

TT2T2T00

322

3

2TGD

oeSS

Pulse Sequence: Gradient-Echo Diffusion Weighting

90o

Excitation

Image

Acquisition

RF

Gx

Gy

Gz

G

-G

90o

Excitation

Image

Acquisition

RF

Gx

Gy

Gz

G

180o

G

Pulse Sequence: Spin-Echo Diffusion Weighting

Diffusion Anisotropy

Determination of fMRI Using the Directionality of Diffusion Tensor

Advantages of DWI

1.1. The absolute magnitude of the diffusion The absolute magnitude of the diffusion coefficient can help determine proton pools coefficient can help determine proton pools with different mobilitywith different mobility

2. The diffusion direction can indicate fiber tracks2. The diffusion direction can indicate fiber tracks

ADCADC AnisotropyAnisotropy

Fiber Tractography

DTI and fMRI

AB

C

D

Perfusion Weighting: Arterial Spin Labeling

TransmissionTransmission

Imaging PlaneImaging Plane

Labeling CoilLabeling Coil

AlternatingAlternatingInversionInversion

Pulsed LabelingPulsed Labeling

AlternatingAlternatingInversionInversion

Imaging PlaneImaging Plane

FAIRFAIRFlow-sensitive Alternating IRFlow-sensitive Alternating IR

EPISTAREPISTAREPI Signal Targeting with Alternating RadiofrequencyEPI Signal Targeting with Alternating Radiofrequency

Arterial Spin Labeling Can Also Be Achieved Without Additional Coils

RF

Gx

Gy

Gz

Image

90o 180o

Alternating oppositeDistal Inversion

OddScan

EvenScan

180o

RF

Gx

Gy

Gz

Image

90o180o180o

AlternatingProximal Inversion Odd Scan

Even Scan

Pulse Sequence: Perfusion Imaging

FA

IRF

AIR

EP

IST

AR

EP

IST

AR

Advantages of ASL Perfusion Imaging

1.1. It can non-invasively image and quantifyIt can non-invasively image and quantify blood deliveryblood delivery2.2. Combined with proper diffusion weighting, Combined with proper diffusion weighting, it can assess capillary perfusionit can assess capillary perfusion

Perfusion ContrastPerfusion Contrast

PerfusionPerfusionDiffusionDiffusion

Diffusion and Perfusion ContrastDiffusion and Perfusion Contrast

III.2 III.2 Some of the fundamental acquisition Some of the fundamental acquisition methods and their k-space viewmethods and their k-space view

k-Space Recap

Kx = Kx = /2/200ttGx(t) dtGx(t) dt

Ky = Ky = /2/200ttGx(t) dtGx(t) dt

Equations that govern k-space trajectory:Equations that govern k-space trajectory:

These equations mean that the k-space coordinatesThese equations mean that the k-space coordinatesare determined by the area under the gradient waveformare determined by the area under the gradient waveform

dxdyeyxIkkS ykxkiyx

yx )(2),(),(

Gradient Echo Imaging

Signal is generated by magnetic field refocusing mechanism only (the use of negative and positive gradient)

It reflects the uniformity of the magnetic fieldSignal intensity is governed by S = So e-TE/T2*

where TE is the echo time (time from excitation to the center of k-space)Can be used to measure T2* value of the tissue

MRI Pulse Sequence for Gradient Echo Imaging

digitizer ondigitizer on

ExcitationExcitation

SliceSliceSelectioSelectionnFrequencyFrequency EncodingEncoding

PhasePhase EncodingEncoding

ReadoutReadout

K-space view of the gradient echo imaging

Kx

Ky

123.......n

Multi-slice acquisition

Total acquisition time =Total acquisition time = Number of views * Number of excitations * TRNumber of views * Number of excitations * TR

Is this the best we can do?Is this the best we can do?

Interleaved excitation methodInterleaved excitation method

readoutreadout

ExcitationExcitation

SliceSliceSelectioSelectionnFrequencyFrequency EncodingEncoding

PhasePhase EncodingEncoding

ReadoutReadout

readoutreadout readoutreadout

…………

…………

…………

TRTR

Spin Echo Imaging

Signal is generated by radiofrequency pulse refocusing mechanism (the use of 180o pulse )

It doesn’t reflect the uniformity of the magnetic fieldSignal intensity is governed by S = So e-TE/T2

where TE is the echo time (time from excitation to

the center of k-space)Can be used to measure T2 value of the tissue

MRI Pulse Sequence for Spin Echo Imaging

digitizer ondigitizer on

ExcitationExcitation

SliceSliceSelectioSelectionnFrequencyFrequency EncodingEncoding

PhasePhase EncodingEncoding

ReadoutReadout

9090 180180

K-space view of the spin echo imaging

Kx

Ky

123.......n

Fast Imaging Sequences

How fast is “fast imaging”?How fast is “fast imaging”?

In principle, any technique that can generate an entire image In principle, any technique that can generate an entire image with sub-second temporal resolution can be called fast imaging.with sub-second temporal resolution can be called fast imaging.

For fMRI, we need to have temporal resolution on the order of For fMRI, we need to have temporal resolution on the order of a few tens of a few tens of msms to be considered “fast”. Echo-planar imaging, to be considered “fast”. Echo-planar imaging, spiral imaging can be both achieve such speed.spiral imaging can be both achieve such speed.

Echo Planar Imaging (EPI)

Methods shown earlier take multiple RF shots to readout enough data to reconstruct a single image Each RF shot gets data with one value of phase encoding

If gradient system (power supplies and gradient coil) are good enough, can read out all data required for one image after one RF shot Total time signal is available is about 2T2* [80 ms]

Must make gradients sweep back and forth, doing all frequency and phase encoding steps in quick succession

Can acquire 10-20 low resolution 2D images per second

......

...

Pulse Sequence K-space View

Why EPI?

Allows highest speed for dynamic contrast

Highly sensitive to the susceptibility-induced field

changes --- important for fMRI

Efficient and regular k-space coverage and good

signal-to-noise ratio

Applicable to most gradient hardware

Spiral ImagingSpiral Imaging

t = TERFRF

GxGx

GyGy

GzGz

t = 0

K-Space Representation of Spiral Image Acquisition

Why Spiral?

• More efficient More efficient kk-space trajectory to improve-space trajectory to improve throughput.throughput.• Better immunity to flow artifacts (no gradient atBetter immunity to flow artifacts (no gradient at the center of k-space)the center of k-space)• Allows more room for magnetization preparation,Allows more room for magnetization preparation, such as diffusion weighting.such as diffusion weighting.

Under very homogeneous magnetic field, images look good …

Gradient-Recalled EPI Images Under Homogeneous Field

Gradient Recalled Spiral Images Under Homogeneous Field

However, if we don’t have a homogeneous field …(That is why shimming is VERY important in fast imaging)

Distorted EPI Images with Imperfect x-Shim

Distorted Spiral Images with Imperfect x-Shim