G16.4427 Practical MRI 1 – 5 th March 2015 G16.4427 Practical MRI 1 Advanced pulse sequences.

G16.4427 Practical MRI 1 – 5th March 2015

G16.4427 Practical MRI 1

Advanced pulse sequences


Signal Formula for SE

Mxy negligible (TR >> T2, or spoiler gradient)

= 90° = 180°

MzA

short pulse (no T1 relaxationbetween A and B, or C and D)

Bernstein et al. (2004) Handbook of MRI Pulse Sequences


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?


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


Example of Dual-Echo SE Acquisition

Proton density-weightedTE/TR = 17/2200 ms

T2-weightedTE/TR = 80/2200 ms


Dual-Echo SE



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


Paper Discussion


Advanced pulse sequences


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


Ghosting Artifacts

• 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

Phase errors may resultfrom the multiple positiveand negative passes through k-spaceGhost artifacts in the phase direction


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


GRE and EPI

Netl = echo train length = number of echoes following RF excitation

tesp = echo spacing (typically echoes are evenly spaced)

A series of echoesis produced beforeMxy decays away dueto T2* relaxation



EPI Readout Gradient

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?



EPI Readout Gradient

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.

The second half of each lobe serves as prephasing for thefollowing gradient(that is why the polaritymust alternate)



EPI Phase-Encoding Gradient

a) Constant phase-encoding gradient throughout the entire readout echo train (ky varies linearly with time)

• Gridding is needed before reconstructionb) A series of blips with the same polarity and identical area,

each played before the acquisition of an echo



Gradient-Echo EPI



Spin-Echo EPI

What is different compared to GRE-EPI?


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?


Typical PC Pulse Sequence

Typically a bipolar gradient is added to only one of the three logical axes at a time

Toggling of the bipolar gradient (dotted lines) varies the gradient first moment and introduces flow sensitivity along that axisBernstein et al.

(2004) Handbook of MRI Pulse Sequences


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


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


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?


Diffusion Weighting in GRE and SE

Spin Echo Gradient Echo



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?


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


Diffusion-Weighted Single-Shot SE



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)


Example: White Matter Infarct


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

…


DW Image vs. ADC Map


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?


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


Two-Point Dixon Pulse SequenceIn conventional spin echo Δ = 0

Question: what happens if Δ ≠ 0



Two-Point Dixon Pulse SequenceIn 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:1. Δ = 0 and normal acquisition

• Fat and water in-phase at kx = 0 (in-phase image)2. 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)3.

ϕ = 2πfcsΔ at kx = 0


Two-Point Dixon TechniqueBecause 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


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?


Example: Healthy Liver

AJR April 2010, vol. 194(4), p. 964-971


Example: Fatty Liver

AJR April 2010, vol. 194(4), p. 964-971


Any questions?


See you next Thursday!

G16.4427 Practical MRI 1 – 5 th March 2015 G16.4427 Practical MRI 1 Advanced pulse sequences.

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