G16.4427 Practical MRI 1 – 3 rd March 2015 G16.4427 Practical MRI 1 Basic pulse sequences.

G16.4427 Practical MRI 1 – 3rd March 2015

G16.4427 Practical MRI 1

Basic pulse sequences


Gradient Echo (GRE)• A class of pulse sequences that is primarily used for

fast scanning– 3D volume imaging– Cardiac imaging

• Gradient reversal on the frequency-encoded axis forms the echo– A readout prephasing gradient lobe dephases the spins,

then they are rephased with a readout gradient with opposite polarity

• Can be fast because the flip angle is less than 90°– Why does that allows GRE to be fast?


Gradient Echo (GRE)• A class of pulse sequences that is primarily used for

fast scanning– 3D volume imaging– Cardiac imaging

• Gradient reversal on the frequency-encoded axis forms the echo– A readout prephasing gradient lobe dephases the spins,

then they are rephased with a readout gradient with opposite polarity

• Can be fast because the flip angle is less than 90°– Fast T1 recovery short TR can be used (e.g. 2-50 ms)


Small Flip-Angle RF Pulse

What property of the small flip angle RF pulse is evident from this illustration?

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


Example of a GRE Pulse SequenceThe peak of the GRE occurs when the area under the two gradient lobes is equal.



T2 and T2* Dephasing• T2 dephasing:– Inherent to tissue type– Molecular environment– Magnetic fields constantly changing in time

• T2* dephasing– Imperfect static magnetic field– Air pockets (e.g. lungs) in body– Metal parts in body (e.g. stents, clips)– Magnetic fields that are constant in time– All of this PLUS T2 dephasing


Transverse Relaxation

T2* is always shorter than T2



Response to a Series of RF Excitations• The excitation pulse is the only RF pulse in

each TR (unless preparation pulses are used)• With a sufficient number of excitation pulses,

Mz reaches a steady state• GRE sequences can be classified by the

response of the transverse magnetization Mxy

– Spoiled: if ~0 just before each excitation– Steady-state free precession (SSFP): if reaches a

nonzero steady state


Spoiling• Spoiling can be accomplished in different ways– The simplest method is to use TR ~ 5T2

• Practical only with interleaved multi-slice acquisitions

– End-of-sequence gradient spoiler• Not effective at spoiling the transverse steady state• Spatially non uniform because gradients produce

spatially varying fields

– RF spoiling• Phase-cycle the RF excitation pulses according to a

predetermined schedule (i.e. flip the magnetization down in a different direction each time)


RF SpoilingStripe pattern artifact due to the spatially varying field produced by the gradients. (e.g. when the phase-encoding gradient is used as a spoiler, so no phase rewinding lobe is used)

(Bright stripes are unspoiled regions)



RF SpoilingStripe pattern artifact due to the spatially varying field produced by the gradients. (e.g. when the phase-encoding gradient is used as a spoiler, so no phase rewinding lobe is used)

RF spoiling: phase of the B1 field for the jth RF pulse in the rotating frame:

(equivalent to the phase twist imparted by the phase-encoding gradient)

• The recommended value for the starting phase increment is ϕ0 = 117°

• During each TR the received MR signal must be shifted by the same phase, so that k-space data are consistent

(Bright stripes are unspoiled regions)



Steady State Mz for Spoiled GRE

• If the longitudinal magnetization at point A is MzA, after the excitation pulse MzB = MzAcosθ

• In the TR between points B and C, T1 relaxation occurs, so:

• When a steady state is reached MzA = MzC



The signal Sspoil is caused by the gradient rephasing the FID at an echo time TE, so it is given by:

Which is equal to:

Ernst Angle

Richard Ernst

August 14, 1933

1991 Nobel Prize in Chemistry

“Ernst angle”

The flip angle that maximize the signal is:


SSFP-FID (FISP) And SSFP-Echo• Standard GRE with greater signal than spoiled pulse

sequences– Often at the cost of less contrast

• SSFP-Echo less usedConditions for SSFP:• phase coherent (RF pulses have the same phase, or sign alternation, in the rotating frame)• TR < T2

• Accumulated phase is the same in each TR ( same gradient area)

If met, than steady states for both Mz and Mxy will be established

(A FID-like signal just after the RF and atime-reversed just before each pulse) Bernstein et al. (2004) Handbook of MRI Pulse Sequences


SSFP-FID (FISP) And SSFP-Echo

Chavhan GB et al. (2008) Radiographics vol. 28(4)

• Phase-coherent RF pulses with same flip-angle and constant TR < T2 steady state– Post-excitation signal (S+), FID arising from most recent RF pulse– Echo reformation signal (S-) when residual echo is refocused at the time

of the subsequent RF pulse


SSFP-FID And SSFP-Echo Signals

If TR >> T2


SSFP-FID And SSFP-Echo Signals

If TR >> T2

If θ << 1 (PD-weighting at low flip angles)


Balanced SSFP (True FISP)• For SSFP the gradient area on any axis must not vary among TR intervals

• For Balanced SSFP the gradient area on any axis is zero during each TR– Peaks of SSFP-FID and SSFP-Echo combine at TE (coherent sum of two signals

– The magnitude of the signal changes for sign alternated pulses

If the balanced SSFP signal is rephased in the center of the TR interval (i.e. TE = TR/2), the decay is governed by T2 rather than T2*• decreasing TE can increase susceptibility weighting in balanced SSFP (the contrary happens for spoiled GRE and SSFP-FID)

Used in practice because of greater signal


Balanced SSFP

Scheffler K and Lehnhardt S (2003) Eur Radiol vol. 13


Artifacts of Balanced SSFP• In regions where a phase shift removes the sign

alternation there is a signal loss– Banding artifact

Unwanted phase shifts are always present– Short TR (e.g. less than 7 ms) are needed– Question: are balanced SSFP easier or more difficult to

implement at higher field strength?


Banding Artifacts in Balanced SSFP

Scheffler K and Lehnhardt S (2003) Eur Radiol vol. 13


Examples of Banding Artifacts


Artifacts of Balanced SSFP• In regions where a phase shift removes the sign

alternation there is a signal loss– Banding artifact– Question: for example what could cause a phase

shift?• Unwanted phase shifts are always present– Short TR (e.g. less than 7 ms) are needed– Question: are balanced SSFP easier or more difficult

to implement at higher field strength?


Artifacts of Balanced SSFP

• In regions where a phase shift removes the sign alternation there is a signal loss– Banding artifact

• Unwanted phase shifts are always present– Short TR (e.g. less than 7 ms) are needed– Question: are balanced SSFP easier or more

difficult to implement at higher field strength?


Artifacts of Balanced SSFP

• In regions where a phase shift removes the sign alternation there is a signal loss– Banding artifact

• Unwanted phase shifts are always present– Short TR (e.g. less than 7 ms) are needed– More difficult to implement at high field • Increased susceptibility variations • SAR associated with very short TR


Particular Cases of Balanced SSFP• For short TR (TR << T2 < T1) the signal formula becomes:

Question: what does the formula tells you about the signal from fluids in balanced SSFP images?


Particular Cases of Balanced SSFP• For short TR (TR << T2 < T1) the signal formula becomes:

– The signal is maximized for:

• At flip angles ~ 90° becomes more highly T2 / T1 weighted:

Max of nearly M0/2 when T2 = T1 extremely strong signal for a short TR pulse sequence


ExampleSSFP-FID and Spoiled GRE:TR = 14 msTE = 6 ms

Balanced SSFP:TR = 6 msTE = 3 ms


Inversion Recovery (IR)• Pulse sequences with an inversion pulse followed by a time delay

prior to an RF excitation– Produce images with T1-weighted contrast. Why?


Inversion Recovery (IR)• Pulse sequences with an inversion pulse followed by a time

delay prior to an RF excitation– Produce images with T1-weighted contrast. – Time delay is know as the inversion time (TI)

• Consists of two parts:– Inversion pulse, spoiler gradient (optional), slice selection

gradient (if selective inversion pulse)– A self-contained pulse sequence (e.g. GRE) after TI

• Require long TR (2-11 s) to preserve the contrast– 2D IR sequences more frequently used

• Benefits from real rather than magnitude reconstruction– Why?


Inversion Recovery (IR)• Pulse sequences with an inversion pulse followed by a time

delay prior to an RF excitation– Produce images with T1-weighted contrast. Why?– Time delay is know as the inversion time (TI)

• Consists of two parts:– Inversion pulse, spoiler gradient (optional), slice selection gradient

(if selective inversion pulse)– A self-contained pulse sequence (e.g. GRE) after TI

• Require long TR (2-11 s) to preserve the contrast– 2D IR sequences more frequently used

• Benefits from real rather than magnitude reconstruction– Mz ranges from –M0 and +M0 increased tissue contrast


Diagram of IR Pulse Sequence

Besides T1-weighted images, what is another application of IR pulse sequences that we mentioned during a previous lecture?



Principles of IR• Immediately after the inversion pulse:

• During the time interval TI

(for long TR)

If θinv = 180°: If θinv = 90°:

Saturation Recovery(SR)


IR and SR Curves

The TI value that nulls the longitudinal magnetization is called the “nulling time” or “zero-crossing point”

SRIR

nulling time



Examples of IR Applications• T1 mapping– A series of IR images are acquired from the same location

with different TI (everything else the same)– Long TR used to avoid signal saturation– Non-linear fitting (for magnitude IR, first need to obtain

the zero-crossing and negate signals before it)• Lipid suppression (STIR)– Improves contrast for lesions embedded in fat (e.g. edema

in bone marrow), as lipids appear bright like many lesions in post-contrast

– Water signal loss (any tissue with T1 similar to fat)– Long acquisition time


Radiofrequency Spin Echo (SE)• Formed by an excitation pulse and one or more

refocusing pulse– Usually a 90° pulse followed by 180° pulse

• Typically 2D mode using interleaved multislice• Allows to obtain a specific contrast weighting• Greater immunity to off-resonance artifacts – Why?


Radiofrequency Spin Echo (SE)• Formed by an excitation pulse and one (or more in

multi-echo SE) refocusing pulse– Usually a 90° pulse followed by 180° pulse

• Typically 2D mode using interleaved multislice• Allows to obtain a specific contrast weighting• Greater immunity to off-resonance artifacts because

of the 180° refocusing pulse• As T2 > T2* heavily T2-weighted images possible with

long TE without much signal loss (dephasing)• Only a single phase-encoding step in any TR interval


Single-Echo SE



Determination of TE

The gradient area on the frequency-encoding axis determines the temporal location of the peak of the echo (when the area under readout gradient balances the area of the prephasing gradient lobe)

Sometimes Δ is nonzero due to systems imperfections (e.g. eddy currents that shift gradient lobes)What is the effect?



Determination of TE

The gradient area on the frequency-encoding axis determines the temporal location of the peak of the echo (when the area under readout gradient balances the area of the prephasing gradient lobe)

Sometimes Δ is nonzero due to systems imperfections (e.g. eddy currents that shift gradient lobes) The signal will have some T2* weighting

Note: some specialized sequences usenonzero Δ intentionally



Partial-Echo SE

What differences do you notice?



Partial-Echo SE

The peak of the echo (not the center of the readout) occurs when the RF spin would have refocused in the absence of imaging gradients- Used to avoid T2* weighting of the signal and reduce minimum TE- Achieved by reducing the area of the prephasing lobe- Image reconstruction with partial Fourier methods



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)



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


Any questions?


See you on Thursday!

G16.4427 Practical MRI 1 – 3 rd March 2015 G16.4427 Practical MRI 1 Basic pulse sequences.

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