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MRI: Contrast Mechanisms and Pulse Sequences
Allen W. Song, PhD Brain Imaging and Analysis Center Duke University
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Image Contrasts
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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
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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).
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Static Contrast Imaging Methods
T2 Decay transverse MR Signal T1 Recovery longitudinal MR Signal time 1 s time 50 ms
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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)
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Proton Density Contrast
Contrast solely dependent on proton density, without influence from relaxation times.
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The Effect of TR and TE on Proton Density Contrast
MR Signal MR Signal T1 Recovery T2 Decay t (s) t (ms)
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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
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Proton Density Weighted Image
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T2 and T2* Contrasts Contrast dominated by the difference in
T2 and T2* (transverse relaxation times).
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Transverse Relaxation Times
Cars on the same track T2* Cars on different tracks
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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?
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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
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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
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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]
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T2 Weighted Image
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T2* Weighted Image T2* Images PD Images
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T1 Contrast Contrast dominated by the T1 (longitudinal relaxation time) differences.
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The Effect of TR and TE on T1 Contrast TR TE T2 Decay MR Signal
T1 Recovery TR TE
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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
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T1 Weighted Image
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Inversion Recovery to Boost T1 Contrast
S = So * (1 – 2 e –t/T1) So S = So * (1 – 2 e –t/T1’) -So
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IR-Prepped T1 Contrast
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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.
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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)
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Flow Weighting: MR Angiogram
Time-of-Flight Contrast Phase Contrast
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Time-of-Flight Contrast
No Flow Medium Flow High Flow No Signal Medium Signal High Vessel Acquisition Saturation Excitation
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Pulse Sequence: Time-of-Flight Contrast
Excitation Image Acquisition RF Gx Gy Gz Saturation Time to allow fresh flow enter the slice
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Phase Contrast (Velocity Encoding)
Externally Applied Spatial Gradient G Spatial Gradient -G Blood Flow v Time T 2T
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Pulse Sequence: Phase Contrast
RF Excitation G Gx Phase Image Acquisition -G Gy Gz
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MR Angiogram
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Random Motion: Water Diffusion
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Diffusion Weighting T 2T Externally Applied Externally Applied
Spatial Gradient G Externally Applied Spatial Gradient -G T 2T Time
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Pulse Sequence: Gradient-Echo Diffusion Weighting
Excitation Image Acquisition RF Gx Gy Gz G -G Large Lobes
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Pulse Sequence: Spin-Echo Diffusion Weighting
RF Excitation G G Gx Image Acquisition Gy Gz
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Diffusion Anisotropy
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Determination of fMRI Using the Directionality of Diffusion Tensor
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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
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Fiber Tractography
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DTI and fMRI A B C D
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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.
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Perfusion Weighting: Arterial Spin Labeling
Imaging Plane Labeling Coil Transmission
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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
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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
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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
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Perfusion Contrast
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Perfusion Map Diffusion Perfusion
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Some fundamental acquisition methods commonly used to generate
static and motion contrasts, and their k-space views
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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
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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
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MRI Pulse Sequence for Gradient Echo Imaging
Excitation Slice Selection Frequency Encoding Phase Encoding digitizer on Readout
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K-space view of the gradient echo imaging
Ky 1 2 3 . n Kx
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Multi-slice acquisition
Total acquisition time = Number of views * Number of excitations * TR Is this the best we can do? Interleaved excitation method
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readout Excitation Slice Selection Frequency Encoding Phase Readout …… TR
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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
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MRI Pulse Sequence for Spin Echo Imaging
180 90 Excitation Slice Selection Frequency Encoding Phase Encoding digitizer on Readout
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K-space view of the spin echo imaging
Ky 1 2 3 . n Kx
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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.
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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 low resolution 2D images per second
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Echo Planar Imaging (EPI)
... Pulse Sequence K-space View
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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
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Gradient-Recalled EPI Images Under Homogeneous Field
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Distorted EPI Images with Imperfect Field
x imperfection y imperfection z imperfection
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Spiral Imaging t = TE RF Gx Gy Gz t = 0
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K-Space Representation of Spiral Image Acquisition
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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.
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Gradient Recalled Spiral Images Under Homogeneous Field
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Distorted Spiral Images with Imperfect Field
x imperfection y imperfection z imperfection
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