7  Basic Pulse Sequences 47

7 Basic Pulse Sequences

Let us once again go through the different steps that make up an MR pulse
sequence.
– Excitation of the target area
– Switching on the slice-selection gradient,
– Delivering the excitation pulse (RF pulse),
– Switching off the slice-selection gradient.
– Phase encoding
– Switching on the phase-encoding gradient repeatedly, each time with a
different strength, to create the desired number of phase shifts across
the image.
– Formation of the echo or MR signal
– Generating an echo, which can be done in two ways (discussed
below).
– Collection of the signal
– Switching on the frequency-encoding or readout gradient,
– Recording the echo.
These steps are repeated many times, depending on the desired image
quality. A wide variety of sequences are used in medical MR imaging. The
most important ones are the spin echo (SE) sequence, the inversion recov-
ery (IR) sequence, and the gradient echo (GRE) sequence, which are the
basic MR pulse sequences.
We have already briefly mentioned echoes (▶ Chapter 3) and said that
some time must elapse before an MR signal forms after the hydrogen pro-
tons have been excited. Now we can explain why this is so:
– Before an MR signal can be collected, the phase-encoding gradient
must be switched on for spatial encoding of the signal.
– Some time is also needed to switch off the slice-selection gradient and
switch on the frequency-encoding gradient.
48  

– Finally, formation of the echo itself also takes time, which varies with
the pulse sequence used.

7.1 Spin Echo (SE) Sequences

Spin echo sequences use a slice-selective 90° RF pulse for excitation, after
which transverse magnetization decays with T2*, as discussed in ▶ Chap-
ter 2. Dephasing occurs because some spins precess faster than others as a
result of the static magnetic field inhomogeneities that are always present.
This is why after half of the echo time (TE) has elapsed, a 180° RF pulse is
delivered to reverse or refocus the spins: those spins that were ahead before
are now behind and vice versa. However, the spins that are now behind will
catch up as they are still exposed to the same field inhomogeneities that
caused the phase differences in the first place. Thus, after the second half
of the TE interval has passed, all spins meet once again in phase. This is the
moment at which the echo forms (▶ Fig. 28). The role of the 180° refocus-
ing pulse in generating the spin echoes can be illustrated by considering a
race in which a number of runners start together and, after some time, are
given a signal to go back. At the time the signal is given, the fastest runners
will have covered the longest distance but also have the longest way back.
Assuming that everyone is still running at their initial speed, they will all
arrive at the starting line together. (The analogy is not quite correct since
it is not the direction of precession that is reversed but merely the position
of the spins on the precessional path relative to each other. Applied to the
example of the race, a magician would have to reverse the order of the run-
ners without their noticing!)
The 180° refocusing pulse then serves to eliminate the effects of static
magnetic field inhomogeneities (T2*) but cannot compensate for variable
field inhomogeneities that underlie spin-spin interaction (T2). Therefore,
the magnetization decay that occurs after excitation is slower as it is a func-
tion of T2 rather than T2*. Because of this decay, the transverse magnetiza-
tion component is smaller at the time the echo is collected than immedi-
ately after excitation though the decrease in signal is less pronounced than
it would be without application of the 180° refocusing pulse. Again, in our
analogy, this means that not all runners arrive at the starting line together
because they do not always run at a constant speed.
Spin echo sequences are characterized by an excellent image quality pre-
cisely because the effects of static field inhomogeneities are eliminated by
7  Basic Pulse Sequences 49

Fig. 28.  SE sequence. The excitation pulse always has a flip angle of 90°; the dephased
spins are refocused into the spin echo by the 180° pulse. The dashed lines indicate the
phase-encoding steps

application of the 180° refocusing pulse. The tradeoff is a fairly long scan
time, which makes the sequence highly sensitive to motion artifacts. SE se-
quences are still used as the standard sequences for acquiring T1-weighted
or PD-weighted images. They are preferred for PD imaging because they are
less susceptible to motion artifacts compared with FSE sequences.

7.2 Black Blood Effect

The black blood effect, or outflow effect, refers to a natural high contrast be-
tween flowing blood and tissue. It is a specific feature of SE sequences due to
the long echo time. Flowing blood appears black because it does not give a
signal. This has two reasons:
50  

– All or most of the blood leaves the imaging slice during the long TE and
thus the spins are not affected by the 180° refocusing pulse.
– In case of turbulent blood flow, there is additional signal loss due to
phase dispersion.
Based on the fact that normal flowing blood is black, we can explain those
cases where the outflow effect does not occur:
– If there is slow blood flow, excited blood stays in the slice and produces a
signal.
– Excited blood may also remain within a slice and become visible if a
long segment of a blood vessel lies within the imaging slice.
– In case of thrombosis, a fresh thrombus will yield a bright signal while
an older, organized thrombus appears somewhat darker.

7.3 Multislice Imaging

Conventional imaging with inactive repetition times (TR) between two

successive excitation pulses is highly inefficient, especially when using se-
quences with long scan times and long TRs (e.g. scan time of almost 3 min
for acquisition of a T1-weighted SE image with 256 excitations and a TR
of 500 msec). The “wait times” or “dead times” can be put to good use by
exciting and recording signals from other slices during this period. In this
way, 12 slices instead of only one can be acquired in the same time (or even
up to 30 slices for T2-weighted sequences with TRs of 2000–4000 msec;
▶ Fig. 29).
A disadvantage of multislice imaging is that, due to imperfect slice pro-
files or RF pulses, protons outside the selected slice will also be excited. As
a result, there will be less longitudinal magnetization and a weaker MR
signal.

7.4 Inversion Recovery (IR) Sequences

Inversion recovery (IR) sequences are typically used for T1-weighted or fat-
suppressed imaging but they can also be used to acquire T2-weighted im-
ages.
An IR sequence is an SE sequence with an additional 180° inversion pulse
that precedes the usual 90° excitation pulse and 180° rephasing pulse of a
conventional SE sequence. The inversion pulse flips longitudinal magnetiza-
7  Basic Pulse Sequences 51

Fig. 29.  Multislice imaging (interleaved acquisition). The inactive repetition time, TR,
for the first slice is used productively to acquire data from other slices. In the example
shown, we thus obtain four slices instead of only one in the same time. (The rectangles
represent the different slices)

Fig. 30a–c.  Inversion recovery sequence with T1 relaxation. Following the 180° inver-
sion pulse (a), the longitudinal magnetization vector points in the opposite direction (b).
T1 relaxation takes place from –z to +z (c, d). No signal forms as long as there is no vec-
tor component in the transverse plane (the null point of a tissue)

tion from the positive z-direction into the negative z-direction (▶ Fig. 30),
which is indicated by the longitudinal magnetization vector now pointing
in the opposite direction. As no component of the magnetization vector is
in the transverse plane, no signal forms after delivery of the 180° RF pulse.
Instead, the inverted longitudinal magnetization vector moves through the
transverse plane to return to its original orientation. After some relaxation
has occurred, the 90° pulse of the SE sequence is applied. The time between
the 180° pulse and the 90° RF pulse is the inversion time (TI).
Image contrast can be manipulated by changing the inversion time. With
a short TI and delivery of the 90° excitation pulse immediately after the 180°
inversion pulse, all negative longitudinal magnetization is flipped into the
52  

transverse plane. With a longer interval, less longitudinal magnetization is

tilted into the transverse plane and a weaker signal is generated. If, however,
inversion time is long enough to allow full relaxation, the signal again be-
comes stronger.
Two IR techniques are widely used in routine clinical applications: the
short TI inversion recovery (STIR) sequence and the fluid-attenuated inver-
sion recovery (FLAIR) sequence.

7.5 STIR Sequences

STIR (short TI inversion recovery) sequences are widely used for fat sup-
pression because they reliably eliminate the signal from fat at all magnetic
field strengths. A standard STIR sequence inverts the longitudinal magneti-
zation of both fat and water by delivery of the 180° pulse, which is followed
by a TI of some hundred milliseconds. To suppress the fat signal, the TI is
adjusted such that the 90° RF pulse is emitted exactly at the moment when
fat passes through zero. The TI for fat suppression is about 150 msec at a
field strength of 1.5 T and about 100 msec at 0.5 T.

7.6 FLAIR Sequences

FLAIR (fluid-attenuated inversion recovery) is an inversion recovery tech-

nique that differs from STIR in that very long TI values (typically about
2000 msec) are used. Another difference is that FLAIR sequences are FSE
sequences. With such long inversion times, there is nearly complete sup-
pression of the signal from cerebrospinal fluid (CSF) while there is excel-
lent detection of signals from brain tissue, tumors, edema, and fat. FLAIR
sequences a very useful for detecting lesions with a poor contrast to sur-
rounding brain tissue.

7.7 Gradient Echo (GRE) Sequences

Gradient echo sequences are also known as gradient-recalled echo or fast-

field echo (FFE) sequences. As suggested by the name, GRE sequences em-
ploy the gradient coils for producing an echo rather than pairs of RF pulses.
This is done by first applying a frequency-encoding gradient with negative
7  Basic Pulse Sequences 53

polarity to destroy the phase coherence of the precessing spins (dephasing).

Subsequently, the gradient is reversed and the spins rephase to form a gradi-
ent echo (▶ Fig. 31).

Fig. 31.  Gradient echo sequence. For the sake of simplicity, a flip angle α of 90° is as-
sumed here as well

Since no 180° refocusing pulse is needed to generate gradient echoes,

very short repetition times (TR) can be achieved. As TR is a major deter-
minant of the overall scan time of a GRE sequence – and of most other
sequences – much faster imaging is possible compared with SE and IR se-
quences, which is the most important advantage of GRE imaging. As a re-
sult, GRE sequences are less frequently troubled by motion artifacts and are
thus preferred whenever a short scan time is desirable. A disadvantage of
a short TR is that the time available for T1 relaxation is also short. This
may lead to saturation and reduce the SNR when a large flip angle is used.
Because no 180° RF pulse is delivered, static field inhomogeneities are not
compensated for and the signal decays with T2*. The image contrast result-
ing from differences in the T2* decay of various tissues is called T2* con-
trast. The T2* contrast of GRE images is affected by TE, which should be as
short as possible to achieve optimal T1 weighting (to minimize T2* contrast
54  

and to reduce susceptibility effects). Conversely, a longer TE is selected to

accentuate T2* contrast. T1 effects are minimized by simultaneously using a
long TR. T2*-weighted images are useful to detect calcifications or deposits
of blood products in tissues with a very short T2 such as connective tissues.
GRE sequences are also used in conjunction with the administration of iron
oxide-based contrast media (▶ Chapter 12).
One problem, however, needs to be briefly mentioned. Since some GRE
sequences are very fast and use very short repetition times, it is highly likely
that part of the signal will be “left over” from cycle to cycle. This signal must
be destroyed when T1-weighted images are acquired. The purposeful de-
struction of the residual MR signal is called spoiling and is accomplished by
turning on the slice-select gradient an additional time to dephase the spins
before the next RF pulse is applied. Spoiled GRE sequences are widely used
in the clinical setting and are available from all manufacturers of MR scan-
ners.
Popular spoiled GRE sequences are SPGR (spoiled gradient echo) and
FLASH (fast low angle shot). The contrast in spoiled GRE sequences can be
manipulated as follows:
– T1 weighting increases as TR decreases;
– T1 weighting increases with the flip angle;
– T2* weighting increases with TE.
Proton density-weighted images are generated with a fairly long TR
(100–400 msec), a low flip angle (≤ 20°), and a short TE (5–10 msec).
T2*-weighted images result when a long TR (20–500 msec) and long TE
(2–50 msec) are used. T1 weighting is achieved by a short TR (20–80 ms),
short TE (5–10 msec), and a flip angle of 30–50°.
Spoiled GRE sequences can be acquired in the 2D or 3D mode. The 3D
spoiled GRE technique enables volumetric thin-slice imaging without inter-
slice gaps and allows for multiplanar reformatting.
A special type of GRE sequence used for routine MR imaging is the
steady-state free precession (SSFP) sequence. SSFP is an unspoiled sequence
in that part of the phase coherence of transverse magnetization is preserved
from one TR interval to the next. This means that the transverse magne-
tization generated with a single RF pulse contributes to the formation of
several echoes. Various acronyms are used by different manufacturers to
designate SSFP sequences such as GRASS (gradient-recalled acquisition in
the steady state) or FISP (fast imaging with steady-state precession). Further
developments of the SSFP technique are FIESTA (fast imaging employing
steady-state acquisition), balanced FFE (fast-field echo), and true FISP. FI-
ESTA and true FISP are T2-weighted GRE sequences whose image contrast
7  Basic Pulse Sequences 55

is determined by the T2/T1 ratio. Blood has a high T2/T1 ratio and there-
fore appears bright on SSFP images. Another advantage of SSFP is that it is
not very prone to flowing blood. SSFP sequences are characterized by very
short scan times and are thus well suited for vascular imaging and real-time
imaging of moving organs such as the heart (▶ Chapter 11.6).

7.8 Multiecho Sequences

Several echoes can be generated in a single cycle with both SE and GRE
sequences: additional spin echoes are produced by applying extra 180° re-
focusing RF pulses while multiple gradient echoes are generated by repeat
reversal of the frequency-encoding gradient. Multiecho techniques are em-
ployed for two reasons:
– The generation of multiple echoes enables acquisition of a sequence
with several measurements that differ in their echo times and T2
weightings. For instance, a repetition time of 2000 msec with echo times
of 20 msec for the first and 80 msec for the second echo allows acquisi-
tion of a proton density-weighted image (20 msec) and a T2-weighted
image (80 msec) with a single measurement. The multiecho technique is
routinely used in the clinical setting (▶ Fig. 32).
– The multiecho technique accelerates data acquisition and can be used for
ultrafast imaging (▶ Chapter 8).

Fig. 32.  Multiecho SE sequence. A second 180° refocusing RF pulse (4) is applied to
generate a second echo (5), resulting in an image with heavier T2 weighting due to the
longer TE. The second 180° pulse is delivered exactly midway between the first (3) and
the second (5) echo
56  

References

1. Mitchell DG, Cohen MS (2004) MRI principles, 2nd ed. Saunders, Philadelphia
2. Elster AD (1993) Gradient-echo MR imaging: Techniques and acronyms. Radiol-
ogy 186:1
3. Haacke EM, Frahm J (1991) A guide to understanding key aspects of fast gradient
echo imaging. J Magn Reson Imaging 1:621