Allen W. Song, PhD Brain Imaging and Analysis Center Duke University

Allen W. Song, PhDBrain Imaging and Analysis CenterDuke University

MRI: Contrast Mechanismsand Pulse Sequences

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

Two Types of Contrast

Static Contrast: Image contrast is generated from the static properties of biological systems (e.g. density).

Motion Contrast: Image contrast is generated from movement (e.g. blood flow, water diffusion).

T2 Decaytransverse

MRSignal

T1 Recoverylongitudinal

MRSignal

50 ms50 ms 1 s1 s

Static Contrast Imaging Methods

timetime timetime

1. Weighted by the Proton Density

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

3. Weighted by the Longitudinal Relaxation Time (T1)

Most Common Static Contrasts

Proton Density Contrast

Contrast solely dependent on proton density,without influence from relaxation times.

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

TR TE

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 Image

T2 and T2* Contrasts

Contrast dominated by the difference inT2 and T2* (transverse relaxation times).

T2Cars on the same track

T2*Cars on different tracks

Transverse Relaxation Times

To get pure T2 contrast, we need perfectlyhomogeneous magnetic field. Thisis difficult to achieve, as sometimeeven if the actual field is uniform,the presence of biological tissue will still change the homogeneity.

So how do we then remove the influenceof the magnetic field inhomogeneity?

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

Time Reversal Using 180o RF Pulse

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

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

0.3

0.4

0.5

0.6

0.7

0.8

0.9

1

T2 Decay

MR

Sig

nal

MR

Sig

nal T1 Recovery

TR TE

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 Image

T2* Weighted Image

PD ImagesPD Images

T2* ImagesT2* Images

T1 Contrast

Contrast dominated by the T1 (longitudinal relaxation time) differences.

The Effect of TR and TE on T1 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

0.3

0.4

0.5

0.6

0.7

0.8

0.9

1

T1 contrast T2 contrast

T2 Decay

MR

Sig

nal

MR

Sig

nal

T1 Recovery

TR TE

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 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 Contrast

IR-Prepped T1 Contrast

In summary, TR controls T1 weighting and TE controls T2 weighting. Short T2 tissues are dark on T2 images, but short T1 tissues 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 (water molecule random motion) Perfusion weighting (blood flow into capillaries)

Flow Weighting: MR Angiogram

• Time-of-Flight Contrast

• Phase 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 Angiogram

Random Motion: Water Diffusion

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

Large Lobes

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. The absolute magnitude of the diffusion coefficient (ADC) can help determine proton pools with different mobility

2. The diffusion direction can indicate fiber tracks

ADCADC AnisotropyAnisotropy

Fiber Tractography

DTI and fMRI

AB

C

D

Perfusion

The injection of fluid into a blood vessel in order to reachan organ or tissue, usually to supply nutrients and oxygen.

In practice, we often mean capillary perfusion as most delivery/exchanges happen in the capillary beds.

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. It is non-invasive2. Combined with proper diffusion weighting

to eliminate flow signal first, it can be used to assess capillary perfusion

Perfusion Contrast

PerfusionPerfusionDiffusionDiffusion

Perfusion Map

Some fundamental acquisition methods commonly used to generate

static and motion contrasts,and their k-space views

k-Space Recap

Kx = /20tGx(t) dt

Ky = /20tGx(t) dt

Equations that govern k-space trajectory:

These equations mean that the k-space coordinatesare 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 field

Signal 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”?

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

For fMRI, we need to have temporal resolution on the order of a few tens of ms to be considered “fast”. Echo-planar imaging, 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

Echo Planar Imaging (EPI)

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

Gradient-Recalled EPI Images Under Homogeneous Field

Distorted EPI Images with Imperfect Field

x imperfectionx imperfection

y imperfectiony imperfection

z imperfectionz imperfection

Spiral Imaging

t = TERFRF

GxGx

GyGy

GzGz

t = 0

K-Space Representation of Spiral Image Acquisition

Why Spiral?

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

Gradient Recalled Spiral Images Under Homogeneous Field

Distorted Spiral Images with Imperfect Field

x imperfectionx imperfection

y imperfectiony imperfection

z imperfectionz imperfection