MRI Contrast Mechanisms and Pulse Sequences Allen W

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MRI: Contrast Mechanisms and Pulse Sequences Allen W. Song, Ph. D Brain Imaging and

MRI: Contrast Mechanisms and Pulse Sequences Allen W. Song, Ph. D Brain Imaging and Analysis Center Duke University

Image Contrasts

Image Contrasts

The Concept of Contrast = difference in signals emitted by water protons between different

The Concept of Contrast = difference in signals emitted by water protons between different tissues For example, gray-white contrast is possible because T 1 is different between these two types of tissue

Two Types of Contrast Static Contrast: Image contrast is generated from the static properties

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).

Static Contrast Imaging Methods MR Signal T 2 Decay transverse T 1 Recovery longitudinal

Static Contrast Imaging Methods MR Signal T 2 Decay transverse T 1 Recovery longitudinal 50 ms time 1 s time

Most Common Static Contrasts 1. Weighted by the Proton Density 2. Weighted by the

Most Common Static Contrasts 1. Weighted by the Proton Density 2. Weighted by the Transverse Relaxation Times (T 2 and T 2*) 3. Weighted by the Longitudinal Relaxation Time (T 1)

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

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

The Effect of TR and TE on Proton Density Contrast TE MR Signal TR

The Effect of TR and TE on Proton Density Contrast TE MR Signal TR T 1 Recovery t (s) T 2 Decay t (ms)

Optimal Proton Density Contrast · Technique: use very long time between RF shots (large

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 256 128 volume · ~1 mm resolution

Proton Density Weighted Image

Proton Density Weighted Image

T 2 and T 2* Contrasts Contrast dominated by the difference in T 2

T 2 and T 2* Contrasts Contrast dominated by the difference in T 2 and T 2* (transverse relaxation times).

Transverse Relaxation Times T 2 Cars on the same track T 2* Cars on

Transverse Relaxation Times T 2 Cars on the same track T 2* Cars on different tracks

To get pure T 2 contrast, we need perfectly homogeneous magnetic field. This is

To get pure T 2 contrast, we need perfectly homogeneous magnetic field. This is difficult to achieve, as sometime even if the actual field is uniform, the presence of biological tissue will still change the homogeneity. So how do we then remove the influence of the magnetic field inhomogeneity?

Time Reversal Using 180 o RF Pulse Fast Spin TE/2 t=0 Fast Spin TE/2

Time Reversal Using 180 o RF Pulse Fast Spin TE/2 t=0 Fast Spin TE/2 t=TE Slow Spin TE/2 t=0 Slow Spin t=TE TE/2 Slow Spin 180 o turn t = TE/2

The Effect of TR and TE on T 2* and T 2 Contrast T

The Effect of TR and TE on T 2* and T 2 Contrast T 1 Recovery T 1 Contrast TE MR Signal TR T 2 Decay T 2 Contrast

Optimal T 2* and T 2 Contrast · Technique: use large TR and intermediate

Optimal T 2* and T 2 Contrast · Technique: use large TR and intermediate TE · Useful for functional (T 2* contrast) and anatomical (T 2 contrast to enhance fluid contrast) studies · Several minutes for 256 128 volumes, or second to acquire 64 20 volume · 1 mm resolution for anatomical scans or 4 mm resolution [better is possible with better gradient system, and a little longer time per volume]

T 2 Weighted Image

T 2 Weighted Image

T 2* Weighted Image T 2* Images PD Images

T 2* Weighted Image T 2* Images PD Images

T 1 Contrast dominated by the T 1 (longitudinal relaxation time) differences.

T 1 Contrast dominated by the T 1 (longitudinal relaxation time) differences.

The Effect of TR and TE on T 1 Contrast TE T 1 Recovery

The Effect of TR and TE on T 1 Contrast TE T 1 Recovery T 1 contrast MR Signal TR T 2 Decay T 2 contrast

Optimal T 1 Contrast · Technique: use intermediate timing between RF shots (intermediate TR)

Optimal T 1 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 256 128 volume · ~1 mm resolution

T 1 Weighted Image

T 1 Weighted Image

Inversion Recovery to Boost T 1 Contrast So S = So * (1 –

Inversion Recovery to Boost T 1 Contrast So S = So * (1 – 2 e –t/T 1) S = So * (1 – 2 e –t/T 1’) -So

IR-Prepped T 1 Contrast

IR-Prepped T 1 Contrast

In summary, TR controls T 1 weighting and TE controls T 2 weighting. Short

In summary, TR controls T 1 weighting and TE controls T 2 weighting. Short T 2 tissues are dark on T 2 images, but short T 1 tissues are bright on T 1 images.

Motion Contrast Imaging Methods Prepare magnetization to make signal sensitive to different motion properties

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

Flow Weighting: MR Angiogram • Time-of-Flight Contrast • Phase Contrast

Time-of-Flight Contrast Saturation Acquisition Excitation No Flow No Signal Medium Flow Medium Signal High

Time-of-Flight Contrast Saturation Acquisition Excitation No Flow No Signal Medium Flow Medium Signal High Flow High Signal Vessel

Pulse Sequence: Time-of-Flight Contrast RF 90 o Time to allow fresh flow enter the

Pulse Sequence: Time-of-Flight Contrast RF 90 o Time to allow fresh flow enter the slice 90 o Excitation Gx Saturation Gy Gz Image Acquisition

Phase Contrast (Velocity Encoding) Blood Flow v Externally Applied Spatial Gradient -G Externally Applied

Phase Contrast (Velocity Encoding) Blood Flow v Externally Applied Spatial Gradient -G Externally Applied Spatial Gradient G T 0 2 T Time

Pulse Sequence: Phase Contrast 90 o RF Excitation G Gx -G Gy Phase Image

Pulse Sequence: Phase Contrast 90 o RF Excitation G Gx -G Gy Phase Image Acquisition Gz

MR Angiogram

MR Angiogram

Random Motion: Water Diffusion

Random Motion: Water Diffusion

Diffusion Weighting Externally Applied Spatial Gradient -G Externally Applied Spatial Gradient G 0 T

Diffusion Weighting Externally Applied Spatial Gradient -G Externally Applied Spatial Gradient G 0 T 2 T Time

Pulse Sequence: Gradient-Echo Diffusion Weighting Excitation RF 90 o G Gx G - Image

Pulse Sequence: Gradient-Echo Diffusion Weighting Excitation RF 90 o G Gx G - Image Gy Acquisition Gz Large Lobes

Pulse Sequence: Spin-Echo Diffusion Weighting 180 o RF 90 o Excitation G G Gx

Pulse Sequence: Spin-Echo Diffusion Weighting 180 o RF 90 o Excitation G G Gx Image Gy Gz Acquisition

Diffusion Anisotropy

Diffusion Anisotropy

Determination of f. MRI Using the Directionality of Diffusion Tensor

Determination of f. MRI Using the Directionality of Diffusion Tensor

Advantages of DWI 1. The absolute magnitude of the diffusion coefficient (ADC) can help

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 ADC Anisotropy

Fiber Tractography

Fiber Tractography

DTI and f. MRI D A B C

DTI and f. MRI D A B C

Perfusion The injection of fluid into a blood vessel in order to reach an

Perfusion The injection of fluid into a blood vessel in order to reach an 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 Imaging Plane Labeling Coil Transmission

Perfusion Weighting: Arterial Spin Labeling Imaging Plane Labeling Coil Transmission

Arterial Spin Labeling Can Also Be Achieved Without Additional Coils Pulsed Labeling Imaging Plane

Arterial Spin Labeling Can Also Be Achieved Without Additional Coils Pulsed Labeling Imaging Plane Alternating Inversion FAIR EPISTAR Flow-sensitive Alternating IR EPI Signal Targeting with Alternating Radiofrequency

Pulse Sequence: Perfusion Imaging 90 o 180 o EPISTAR RF Gx Image Gy Gz

Pulse Sequence: Perfusion Imaging 90 o 180 o EPISTAR RF Gx Image Gy Gz Odd Scan Alternating opposite Distal Inversion Even Scan 180 o 90 o 180 o FAIR RF Gx Image Gy Gz Alternating Proximal Inversion Odd Scan Even Scan

Advantages of ASL Perfusion Imaging 1. It is non-invasive 2. Combined with proper diffusion

Advantages of ASL Perfusion Imaging 1. It is non-invasive 2. Combined with proper diffusion weighting to eliminate flow signal first, it can be used to assess capillary perfusion

Perfusion Contrast

Perfusion Contrast

Perfusion Map Diffusion Perfusion

Perfusion Map Diffusion Perfusion

Some fundamental acquisition methods commonly used to generate static and motion contrasts, and their

Some fundamental acquisition methods commonly used to generate static and motion contrasts, and their k-space views

k-Space Recap Equations that govern k-space trajectory: Kx = g/2 p 0 t Gx(t)

k-Space Recap Equations that govern k-space trajectory: Kx = g/2 p 0 t Gx(t) dt Ky = g/2 p 0 t Gx(t) dt These equations mean that the k-space coordinates are determined by the area under the gradient waveform

Gradient Echo Imaging ¨Signal is generated by magnetic field refocusing mechanism only (the use

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/T 2* where TE is the echo time (time from excitation to the center of k-space) ¨Can be used to measure T 2* value of the tissue

MRI Pulse Sequence for Gradient Echo Imaging Excitation Slice Selection Frequency Encoding Phase Encoding

MRI Pulse Sequence for Gradient Echo Imaging Excitation Slice Selection Frequency Encoding Phase Encoding digitizer on Readout

K-space view of the gradient echo imaging Ky 1 2 3. . . .

K-space view of the gradient echo imaging Ky 1 2 3. . . . n Kx

Multi-slice acquisition Total acquisition time = Number of views * Number of excitations *

Multi-slice acquisition Total acquisition time = Number of views * Number of excitations * TR Is this the best we can do? Interleaved excitation method

TR …… Excitation …… Slice Selection …… Frequency Encoding …… Phase Encoding readout Readout

TR …… Excitation …… Slice Selection …… Frequency Encoding …… Phase Encoding readout Readout readout

Spin Echo Imaging ¨Signal is generated by radiofrequency pulse refocusing mechanism (the use of

Spin Echo Imaging ¨Signal is generated by radiofrequency pulse refocusing mechanism (the use of 180 o pulse ) ¨It doesn’t reflect the uniformity of the magnetic field ¨Signal intensity is governed by S = So e-TE/T 2 where TE is the echo time (time from excitation to the center of k-space) ¨Can be used to measure T 2 value of the tissue

MRI Pulse Sequence for Spin Echo Imaging Excitation 90 180 Slice Selection Frequency Encoding

MRI Pulse Sequence for Spin Echo Imaging Excitation 90 180 Slice Selection Frequency Encoding Phase Encoding digitizer on Readout

K-space view of the spin echo imaging Ky 1 2 3. . . .

K-space view of the spin echo imaging Ky 1 2 3. . . . n Kx

Fast Imaging Sequences How fast is “fast imaging”? In principle, any technique that can

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 f. MRI, we need to have temporal resolution on the order of a few tens of ms to be considered “fast”. Echoplanar imaging, spiral imaging can be both achieve such speed.

Echo Planar Imaging (EPI) ¨ Methods shown earlier take multiple RF shots to readout

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 2 T 2* [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 2 D images per second

Echo Planar Imaging (EPI) Pulse Sequence . . . K-space View . . .

Echo Planar Imaging (EPI) Pulse Sequence . . . K-space View . . .

Why EPI? ¨ Allows highest speed for dynamic contrast ¨ Highly sensitive to the

Why EPI? ¨ Allows highest speed for dynamic contrast ¨ Highly sensitive to the susceptibility-induced field changes --- important for f. MRI ¨ Efficient and regular k-space coverage and good signal-to-noise ratio ¨ Applicable to most gradient hardware

Gradient-Recalled EPI Images Under Homogeneous Field

Gradient-Recalled EPI Images Under Homogeneous Field

Distorted EPI Images with Imperfect Field x imperfection y imperfection z imperfection

Distorted EPI Images with Imperfect Field x imperfection y imperfection z imperfection

Spiral Imaging RF t = TE t=0 Gx Gy Gz

Spiral Imaging RF t = TE t=0 Gx Gy Gz

K-Space Representation of Spiral Image Acquisition

K-Space Representation of Spiral Image Acquisition

Why Spiral? • More efficient k-space trajectory to improve throughput. • Better immunity to

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

Gradient Recalled Spiral Images Under Homogeneous Field

Distorted Spiral Images with Imperfect Field x imperfection y imperfection z imperfection

Distorted Spiral Images with Imperfect Field x imperfection y imperfection z imperfection