G16.4427 Practical MRI 1
Basic pulse sequences
G16.4427 Practical MRI 1 – 3rd March 2015
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?
G16.4427 Practical MRI 1 – 3rd March 2015
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)
G16.4427 Practical MRI 1 – 3rd March 2015
Small Flip-Angle RF Pulse
Bernstein et al. (2004)
Handbook of MRI Pulse
Sequences
What property of the small flip angle RF pulse
is evident from this illustration?
G16.4427 Practical MRI 1 – 3rd March 2015
Example of a GRE Pulse Sequence
The peak of the GRE occurs when
the area under the two gradient
lobes is equal.
Bernstein et al.
(2004) Handbook
of MRI Pulse
Sequences
G16.4427 Practical MRI 1 – 3rd March 2015
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
G16.4427 Practical MRI 1 – 3rd March 2015
Transverse Relaxation
Bernstein et al. (2004) Handbook of MRI Pulse Sequences
T2* is always shorter than T2
G16.4427 Practical MRI 1 – 3rd March 2015
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
G16.4427 Practical MRI 1 – 3rd March 2015
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)
G16.4427 Practical MRI 1 – 3rd March 2015
RF Spoiling
(Bright stripes are unspoiled regions)
Stripe 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)
Bernstein et al. (2004) Handbook of MRI Pulse Sequences
G16.4427 Practical MRI 1 – 3rd March 2015
RF Spoiling
(Bright stripes are unspoiled regions)
Stripe 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:
f j = f j-1 + jf0
(equivalent to the phase twist imparted by
the phase-encoding gradient)
Bernstein et al. (2004) Handbook of MRI Pulse Sequences
• 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
G16.4427 Practical MRI 1 – 3rd March 2015
Steady State Mz for Spoiled GRE
Bernstein et al. (2004) Handbook
of MRI Pulse Sequences
• 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:
M zC = M zB e
-TR/T1
+ M 0 (1- e
-TR/T1
) = M zA cosq e
-TR/T1
+ M 0 (1- e
• When a steady state is reached MzA = MzC
G16.4427 Practical MRI 1 – 3rd March 2015
-TR/T1
)
Ernst Angle
The signal Sspoil is caused by the gradient rephasing the
FID at an echo time TE, so it is given by:
Sspoil = M zA sin q e
-TE/T2 *
Which is equal to:
Sspoil =
Richard Ernst
August 14, 1933
M 0 sin q (1- e
(1- cos q e
-TR/T1
-TR/T1
)
)
e
-TE/T2 *
The flip angle that maximize the signal is:
q E = arccos(e-TR/T )
1
1991
Nobel Prize in Chemistry
G16.4427 Practical MRI 1 – 3rd March 2015
“Ernst angle”
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 used
Conditions 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)
(A FID-like signal just after the RF and a
time-reversed just before each pulse)
If met, than steady states for both Mz
and Mxy will be established
Bernstein et al. (2004) Handbook of MRI Pulse Sequences
G16.4427 Practical MRI 1 – 3rd March 2015
SSFP-FID (FISP) And SSFP-Echo
• 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
Chavhan GB et al. (2008) Radiographics vol. 28(4)
G16.4427 Practical MRI 1 – 3rd March 2015
SSFP-FID And SSFP-Echo Signals
SSFPFID
æ q ö æ ( E1 - cos q )(1- E22 ) ö
= M 0 tan ç ÷ ç 1÷
2
2
ç
÷ø
è 2ø è
p -q
SSFPECHO
æ q ö æ (1- E1 cos q )(1- E22 ) ö
= M 0 tan ç ÷ ç 1÷
2
2
ç
÷ø
è 2ø è
p -q
If TR >> T2  SSFPFID = M 0 sin q
1- E1
1- E1 cos q
G16.4427 Practical MRI 1 – 3rd March 2015
E1 = e
-TR/T1
E2 = e
-TR/T2
p = 1- E1 cos q - E22 (E1 - cos q )
q = E2 (1- E1 )(1+ cos q )
SSFP-FID And SSFP-Echo Signals
SSFPFID
æ q ö æ ( E1 - cos q )(1- E22 ) ö
= M 0 tan ç ÷ ç 1÷
2
2
ç
÷ø
è 2ø è
p -q
SSFPECHO
æ q ö æ (1- E1 cos q )(1- E22 ) ö
= M 0 tan ç ÷ ç 1÷
2
2
ç
÷ø
è 2ø è
p -q
If TR >> T2  SSFPFID = M 0 sin q
If θ << 1  SSFPFID
E1 = e
-TR/T1
E2 = e
-TR/T2
p = 1- E1 cos q - E22 (E1 - cos q )
q = E2 (1- E1 )(1+ cos q )
1- E1
1- E1 cos q
æqö
= 2 M 0 tan ç ÷ » M 0 sin q (PD-weighting at low flip angles)
è 2ø
G16.4427 Practical MRI 1 – 3rd March 2015
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
SSFPbal ,alt
(1- E1 )
-TE/T2
= M 0 sin q
e
1- ( E1 - E2 )cos q - E1 E2
SSFPbal ,noalt
Used in practice
because of
greater signal
(1- E1 )
-TE/T2
= M 0 sin q
e
1- ( E1 + E2 )cos q + E1 E2
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)
G16.4427 Practical MRI 1 – 3rd March 2015
Balanced SSFP
Scheffler K and Lehnhardt S (2003) Eur Radiol vol. 13
G16.4427 Practical MRI 1 – 3rd March 2015
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?
G16.4427 Practical MRI 1 – 3rd March 2015
Banding Artifacts in Balanced SSFP
Scheffler K and Lehnhardt S (2003) Eur Radiol vol. 13
G16.4427 Practical MRI 1 – 3rd March 2015
Examples of Banding Artifacts
G16.4427 Practical MRI 1 – 3rd March 2015
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?
G16.4427 Practical MRI 1 – 3rd March 2015
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?
G16.4427 Practical MRI 1 – 3rd March 2015
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
G16.4427 Practical MRI 1 – 3rd March 2015
Particular Cases of Balanced SSFP
• For short TR (TR << T2 < T1) the signal formula becomes:
SSFPbal ,alt
M 0 sin q
-TE/T2
»
e
(T1 / T2 )(1- cos q ) + (1+ cos q )
Question: what does the formula tells you about the signal from fluids in
balanced SSFP images?
G16.4427 Practical MRI 1 – 3rd March 2015
Particular Cases of Balanced SSFP
• For short TR (TR << T2 < T1) the signal formula becomes:
SSFPbal ,alt
M 0 sin q
-TE/T2
»
e
(T1 / T2 )(1- cos q ) + (1+ cos q )
– The signal is maximized for:
qmax = arccos ( (T1 - T2 ) (T1 + T2 ))
• At flip angles ~ 90° becomes more highly T2 / T1 weighted:
SSFPbal ,alt|q =90°
M 0T2 -TE/T2
»
e
T1 + T2
Max of nearly M0/2 when T2 = T1
 extremely strong signal for a short TR
pulse sequence
G16.4427 Practical MRI 1 – 3rd March 2015
Example
SSFP-FID
and Spoiled
GRE:
TR = 14 ms
TE = 6 ms
Balanced SSFP:
TR = 6 ms
TE = 3 ms
G16.4427 Practical MRI 1 – 3rd March 2015
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?
G16.4427 Practical MRI 1 – 3rd March 2015
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?
G16.4427 Practical MRI 1 – 3rd March 2015
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
G16.4427 Practical MRI 1 – 3rd March 2015
Diagram of IR Pulse Sequence
Bernstein et al. (2004) Handbook of MRI Pulse Sequences
Besides T1-weighted images, what is another application of IR
pulse sequences that we mentioned during a previous lecture?
G16.4427 Practical MRI 1 – 3rd March 2015
Principles of IR
• Immediately after the inversion pulse:
M xy = M 0 sin q inv
M z = M 0 cosq inv
• During the time interval TI
dM z M 0 - M z
=
dt
T1
-t/T
M z = M 0 éë1- (1- cos q inv )e 1 ùû
If θinv = 180°:
(
M z = M 0 1- 2e
-t/T1
(for long TR)
If θinv = 90°:
)
(
M z = M 0 1- e
-t/T1
)
Saturation Recovery
(SR)
G16.4427 Practical MRI 1 – 3rd March 2015
IR and SR Curves
SR
IR
nulling time
Bernstein et al. (2004) Handbook of MRI Pulse Sequences
The TI value that nulls the longitudinal magnetization
is called the “nulling time” or “zero-crossing point”
G16.4427 Practical MRI 1 – 3rd March 2015
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
G16.4427 Practical MRI 1 – 3rd March 2015
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?
G16.4427 Practical MRI 1 – 3rd March 2015
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
G16.4427 Practical MRI 1 – 3rd March 2015
Single-Echo SE
Bernstein et al. (2004) Handbook of MRI Pulse Sequences
G16.4427 Practical MRI 1 – 3rd March 2015
Determination of TE
The gradient area on the frequencyencoding 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?
Bernstein et al. (2004) Handbook of MRI Pulse Sequences
G16.4427 Practical MRI 1 – 3rd March 2015
Determination of TE
The gradient area on the frequencyencoding 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 use
nonzero Δ intentionally
Bernstein et al. (2004) Handbook of MRI Pulse Sequences
G16.4427 Practical MRI 1 – 3rd March 2015
Partial-Echo SE
Bernstein et al. (2004) Handbook
of MRI Pulse Sequences
What differences do you notice?
G16.4427 Practical MRI 1 – 3rd March 2015
Partial-Echo SE
Bernstein et al. (2004) Handbook
of MRI Pulse Sequences
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
G16.4427 Practical MRI 1 – 3rd March 2015
Signal Formula for SE
= 90°
Bernstein et al. (2004)
Handbook of MRI Pulse
Sequences
= 180°
Mxy negligible
(TR >> T2, or
spoiler gradient)
MzA
short pulse (no T1 relaxation
between A and B, or C and D)
(
M zB = M zA cos90° = 0
(
M zD = M zC cos180° = - M 0 1- e
-TE/2T1
)
M zE = M zD e
M zC = M 0 1- e
-(TR-TE/2)/T1
(
(
+ M 0 1- e
)
æ 180° ö -TE/T2
-(TR-TE/2)/T1
-TR/T1
-TE/T2
S SE = M zE sin 90°sin 2 ç
e
=
M
12e
+
e
e
0
è 2 ÷ø
G16.4427 Practical MRI 1 – 3rd March 2015
-(TE/2) T1
)
)
-(TR-TE/2)/T1
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?
G16.4427 Practical MRI 1 – 3rd March 2015
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
G16.4427 Practical MRI 1 – 3rd March 2015
Example of Dual-Echo SE Acquisition
Proton density-weighted
TE/TR = 17/2200 ms
T2-weighted
TE/TR = 80/2200 ms
G16.4427 Practical MRI 1 – 3rd March 2015
Dual-Echo SE
Bernstein et al. (2004) Handbook of MRI Pulse Sequences
G16.4427 Practical MRI 1 – 3rd March 2015
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
G16.4427 Practical MRI 1 – 3rd March 2015
Any questions?
G16.4427 Practical MRI 1 – 3rd March 2015
See you on Thursday!
G16.4427 Practical MRI 1 – 3rd March 2015