1. Advanced pulse sequences
G Practical MRI 1
Advanced pulse sequences

2. Signal Formula for SE = 90° = 180° short pulse (no T1 relaxation
Bernstein et al. (2004) Handbook of MRI Pulse Sequences
= 90°
= 180°
Mxy negligible
(TR >> T2, or
spoiler gradient)
MzA
short pulse (no T1 relaxation
between A and B, or C and D)

3. Multi-Echo SE
The transverse magnetization can be repeatedly refocused into subsequent SEs by playing additional RF refocusing pulse
The series of echoes is called an echo train
Each echo number fits its own independent k-space
The length of the echo train is limited by T2 decay
In most cases we are interested in 2 echoes (an early and a late one). Question: if TR is long, what contrast will have the 2 resulting images?

4. Multi-Echo SE
The transverse magnetization can be repeatedly refocused into subsequent SEs by playing additional RF refocusing pulse
The series of echoes is called an echo train
Each echo number fits its own independent k-space
The length of the echo train is limited by T2 decay
In most cases we are interested in 2 echoes (an early and a late one).  if TR is long, the two images will be PD- and T2-weighted, respectively

5. Example of Dual-Echo SE Acquisition
Proton density-weighted
TE/TR = 17/2200 ms
T2-weighted
TE/TR = 80/2200 ms

6. Dual-Echo SE
Bernstein et al. (2004) Handbook of MRI Pulse Sequences

7. T2-Mapping
It is a common application of acquiring longer echo trains (otherwise more than two echoes per TR are rarely acquired in MRI)
In theory we can acquire long echo train of SEs and fit the signal intensity at each pixel to calculate T2
In practice there are systematic errors that make it difficult to fit a monoexponential decay curve
Variable flip angle across slice profile
Stimulated echoes can introduce unwanted T1-weighting variations into the echo-train signals
If magnitude reconstruction is used, the noise floor has nonzero mean leading to incorrectly larger T2 values

8. Paper Discussion

9. Advanced pulse sequences

10. Echo Planar Imaging (EPI)
EPI is one of the fastest MRI pulse sequences
2D image in few tens of milliseconds
Allowed developing challenging MR applications
Diffusion, perfusion, cardiac imaging, etc.
EPI uses a gradient-echo train
Typical to produce ~100 gradient echoes to produce a low-resolution image from a single RF excitation
More prone to a variety of artifacts
Ghosting along phase-encoded direction

11. Ghosting Artifacts
Phase errors may result
from the multiple positive
and negative passes through k-space
Ghost artifacts in the
phase direction
Not caused by motion, but by eddy currents, imperfect gradients, field non-uniformities, or a mismatch between the timing of the even and odd echoes
Which results in mis-registration of alternating lines of k-space

12. GRE vs. EPI
In a simple GRE pulse sequence the transverse magnetization decays as Mxy(t) = Mxy(0)e-t/T2*
Half lifetime of Mxy is T2*ln2
A very small fraction of the lifetime is actually used for data acquisition in GRE
EPI maximally uses the transverse magnetization without additional RF excitations
Bipolar oscillating readout gradient produces a series of echoes, each individually phase-encoded

13. GRE and EPI
Bernstein et al. (2004) Handbook of MRI Pulse Sequences
A series of echoes
is produced before
Mxy decays away due
to T2* relaxation
Netl = echo train length = number of echoes following RF excitation
tesp = echo spacing (typically echoes are evenly spaced)

14. EPI Readout Gradient
Bernstein et al. (2004) Handbook of MRI Pulse Sequences
Starts with a prephasing gradient that position the k-space trajectory to kx,min followed by a series of readout gradient lobes with alternating polarity. Question: what is the area of the prephasing gradient lobe Gx,p?

15. EPI Readout Gradient
The second half of
each lobe serves as
prephasing for the
following gradient
(that is why the polarity
must alternate)
Bernstein et al. (2004) Handbook of MRI Pulse Sequences
Starts with a prephasing gradient that position the k-space trajectory to kx,min followed by a series of readout gradient lobes with alternating polarity. Answer: Half the area of the first readout gradient area.

16. EPI Phase-Encoding Gradient
Bernstein et al. (2004) Handbook of MRI Pulse Sequences
Constant phase-encoding gradient throughout the entire readout echo train (ky varies linearly with time)
Gridding is needed before reconstruction
A series of blips with the same polarity and identical area, each played before the acquisition of an echo

17. Gradient-Echo EPI
Bernstein et al. (2004) Handbook of MRI Pulse Sequences

18. Spin-Echo EPI
What is different compared to GRE-EPI?

19. Phase Contrast (PC) Imaging
A method to image moving magnetization by applying flow-encoding gradients
Image flow in blood vessels and CSF, track motion
The flow-encoding gradients translates velocity into the phase of the image
Bipolar gradient, as it produces linear proportionality
The axis of the gradient determines the direction of flow sensitivity
Normally applied to only one axis at a time
Typically performed with GRE pulse sequences, adding phase-encoding gradients. Why?

20. Typical PC Pulse Sequence
Toggling of the bipolar gradient (dotted lines) varies the gradient first moment and introduces flow sensitivity along that axis
Bernstein et al. (2004) Handbook of MRI Pulse Sequences
Typically a bipolar gradient is added to only one of the three logical axes at a time

21. PC Acquisition and Reconstruction
Two complete sets of image are acquired varying only the 1st moment of the bipolar gradient
The amount of such operator-selected variation determines the amount of velocity encoding
The phases of the two images are subtracted on a pixel-by-pixel basis in image domain
Allows to quantify flow direction, flow velocity and volume flow rate
Phase-difference or complex-difference reconstruction methods are in common use

22. Diffusion Imaging
In the presence of a magnetic field gradient, diffusion of water molecules causes a phase dispersion of the transverse magnetization
The degree of signal loss depends on tissue type, structure, physical and physiological state
Diffusion imaging is a family of techniques
E.g. DWI, DTI, DKI
All diffusion pulse sequences contain diffusion-weighting gradients
DWI typically employs a single b-value, other quantitative mapping methods at least 2 b-values

23. Diffusion-Weighting Gradients
Typically consist of two lobes with equal area
Amplitude is the maximum allowed
Pulse width is larger than most imaging gradients
When used, water diffusion can cause an attenuation in proton MRI signals
Degree of attenuation depends on the product between the diffusion coefficient D and the b-value
b-value is analogous to TE in T2-weighted sequences
Increasing gradient amplitude, separation of its lobes, or pulse width of each lobe results in a higher b-value. How does diffusion-weighting change consequently?

24. Diffusion Weighting in GRE and SE
Spin Echo
Gradient Echo
Bernstein et al. (2004) Handbook of MRI Pulse Sequences

25. Single-Shot Spin-Echo EPI
The most prevalent sequence due to high acquisition speed (e.g. < 100 ms per image)
A pair of identical gradient lobes on either side of the refocusing pulse
Gradient direction can be controlled by varying its vector components along the 3 axes
To minimize TE the max amplitude is used to achieve the desired b-value
What is another way to minimize TE?

26. Single-Shot Spin-Echo EPI
The most prevalent sequence due to high acquisition speed (e.g. < 100 ms per image)
A pair of identical gradient lobes on either side of the refocusing pulse
Gradient direction can be controlled by varying its vector components along the 3 axes
To minimize TE the max amplitude is used to achieve the desired b-value
Maximizing SR also reduces TE, but can cause peripheral nerve stimulation

27. Diffusion-Weighted Single-Shot SE
Bernstein et al. (2004) Handbook of MRI Pulse Sequences

28. Diffusion-Weighted (DW) Imaging
In the presence of a gradient, molecular diffusion attenuates the MRI signal exponentially:
Tissue with fast diffusion experiences more signal loss  low intensity in the DW image
To remove the patient-orientation dependence, 3 DW images can be obtained with a DW gradient applied along the three orthogonal directions
If same b-value then isotropic DW image
(S and S0 are the voxel signal intensity with and without diffusion)

29. Example: White Matter Infarct

30. Quantitative Apparent Diffusion Coefficient (ADC) Mapping
A series of DW images are acquired with multiple b-values:
A linear fit between ln(S0/Si) and bi is performed on a pixel-by-pixel basis to find D
The contrast of the ADC map is inverted compared to a DW image
To keep a constant TE in all DW images, b-values are typically changed by varying the diffusion-gradient amplitude instead of its duration
Contribution from imaging gradients should be included in b-value calculation to avoid overestimating ADC …

31. DW Image vs. ADC Map

32. Fat Suppression
Because of its short T1, the bright appearance of fat is a problem for T1-weighted images with short TR and short TE
Fat is a main contributor to chemical shift artifacts
There are several methods for fat suppression
Spectrally selective RF pulses
What are the drawbacks?

33. Fat Suppression
Because of its short T1, the bright appearance of fat is a problem for T1-weighted images with short TR and short TE
Fat is a main contributor to chemical shift artifacts
There are several methods for fat suppression
Spectrally selective RF pulses
B1 and B0 inhomogeneities, not good at low field strengths
Short TI recovery (STIR)
B1 inhomogeneities, long scan, signal from other tissues

34. Two-Point Dixon Pulse Sequence
In conventional spin echo Δ = 0
Question: what happens if Δ ≠ 0
Bernstein et al. (2004) Handbook of MRI Pulse Sequences

35. Two-Point Dixon Pulse Sequence
In conventional spin echo Δ = 0
If Δ ≠ 0, spins with different chemical shifts will be out of phase at kx = 0 (unless phase shift happens to be a multiple of 2π)
If the 180° pulse is delayed or advanced by Δ/2, the RF spin echo is delayed or advanced by Δ relative to where kx = 0
Consider a voxel with a water and a fat spin having a frequency difference fcs and assume there are no B0 inhomogeneities
In the 2-point Dixon technique, we acquire two SE images:
Δ = 0 and normal acquisition
Fat and water in-phase at kx = 0 (in-phase image)
Δ = 1/(2fcs) and RF pulse advanced or delayed by Δ/2 = 1/(4fcs)
Fat and water 180° out-of-phase at kx = 0 (out-of-phase image)
ϕ = 2πfcsΔ
at kx = 0

36. Two-Point Dixon Technique
Because image contrast is heavily determined by the peak signal amplitude that occurs at kx = 0, the resulting complex images are approximately given by:
I0 = W + F I1 = W – F
Separate images of the water and fat magnetization can be reconstructed from:
W = (1/2) (I0 + I1) F = (1/2) (I0 - I1)
The water image W can be used as a fat suppressed image, whereas W and F separately provide information about the relative water and fat content of tissues

37. Limits of Two-Point Dixon
The 2-point Dixon technique assumes perfect B0 homogeneity which is almost never true
Due to ΔB0 fat and water have accumulated an additional phase shift Δϕ = γ(ΔB0)Δ at kx = 0 in I1
Although fat and water spins in any given voxel are still anti-parallel in the opposed-phase image, they might no longer be parallel or anti-parallel to the fat and water spins in the in-phase image
(example of 90° phase shift caused by B0 inhomogeneities)
Question:
what is wrong with the combined images?

38. Example: Healthy Liver
AJR April 2010, vol. 194(4), p

39. Example: Fatty Liver
AJR April 2010, vol. 194(4), p

40. Any questions?

41. See you next Thursday!