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

Image Contrasts

The Concept of Contrast Contrast = difference in signals emitted by water protons between different tissues For 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).

Static Contrast Imaging Methods T2 Decay transverse MR Signal T1 Recovery longitudinal MR Signal time 1 s time 50 ms

Most Common Static Contrasts Weighted by the Proton Density Weighted by the Transverse Relaxation Times (T2 and T2*) Weighted by the Longitudinal Relaxation Time (T1)

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

The Effect of TR and TE on Proton Density Contrast MR Signal MR Signal T1 Recovery T2 Decay t (s) t (ms)

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256128 volume ~1 mm resolution

Proton Density Weighted Image

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

Transverse Relaxation Times Cars on the same track T2* Cars on different tracks

To get pure T2 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 180o RF Pulse Fast Spin Fast Spin TE/2 t=0 180o turn t = TE/2 Fast Spin Fast Spin TE/2 t=TE Slow Spin Slow Spin TE/2 t=0 180o turn t = TE/2 Slow Spin TE/2 Slow Spin t=TE

The Effect of TR and TE on T2* and T2 Contrast TR TE T1 Recovery MR Signal MR Signal T2 Decay T1 Contrast T2 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 T2* Images PD Images

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

The Effect of TR and TE on T1 Contrast TR TE T2 Decay MR Signal 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 256256128 volume ~1 mm resolution

T1 Weighted Image

Inversion Recovery to Boost T1 Contrast S = So * (1 – 2 e –t/T1) So S = So * (1 – 2 e –t/T1’) -So

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 Vessel Acquisition Saturation Excitation

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

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

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

MR Angiogram

Random Motion: Water Diffusion

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

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

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

Diffusion Anisotropy

Determination of fMRI Using the Directionality of Diffusion Tensor

Advantages of DWI 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

DTI and fMRI A B C D

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

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

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

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

Perfusion Contrast

Perfusion Map Diffusion Perfusion

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

k-Space Recap Kx = g/2p 0t Gx(t) dt Ky = g/2p 0t Gx(t) dt Equations that govern k-space trajectory: Kx = g/2p 0t Gx(t) dt Ky = g/2p 0t 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 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 Excitation Slice Selection Frequency Encoding Phase Encoding digitizer on Readout

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 * TR Is this the best we can do? Interleaved excitation method

readout Excitation Slice Selection Frequency Encoding Phase Readout …… TR

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 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 Spin Echo Imaging 180 90 Excitation Slice Selection Frequency Encoding Phase Encoding digitizer on Readout

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 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 2T2* [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

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

Allows highest speed for dynamic contrast 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 imperfection y imperfection z imperfection

Spiral Imaging t = TE RF Gx Gy Gz 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 imperfection y imperfection z imperfection