Spin-echo pulse sequences

Spin-echo pulse sequences

After reading this chapter, you will be able to:

  • Explain the purpose of pulse sequences.
  • Describe how spin-echoes are created.
  • Understand the mechanisms of common spin-echo pulse sequences.
  • Apply what you have learned to understand how images of different weighting are created using spin-echo pulse sequences.


Pulse sequences enable control of the way in which the system applies RF pulses and gradients. They are used to determine image weighting. Dephasing, caused by magnetic field inhomogeneities, produces a rapid loss of coherent transverse magnetization (and therefore signal) so that it reaches zero before most tissues have had time to attain their T1 or T2 relaxation times. As we explored in Chapter 2, the FID decays within about 10 ms, which is too fast to measure any significant relaxation. Pulse sequences are methods used by the MR system to rephase the magnetic moments of hydrogen nuclei at a later point in time. This rephasing produces a signal called an echo. As data are collected from the echo later in the sequence, image contrast relies on the differences in the T1 recovery times, T2 decay times, or proton density between tissues.

There are two ways of rephasing the magnetic moments of hydrogen nuclei to produce an echo – by using an additional 180° RF pulse or by using gradients. Sequences that use a 180° RF rephasing pulse to generate an echo are called spin-echo pulse sequences; those that use a gradient are called gradient-echo pulse sequences (see Chapter 4).

There are many different pulse sequences, and each is designed for a specific purpose. This chapter discusses the mechanisms, uses, and parameters for each of the common spin-echo pulse sequences and their advantages and disadvantages. Each manufacturer uses different acronyms to distinguish between individual pulse sequences. A table is included that compares the common acronyms for spin-echo pulse sequences for the main manufacturers (Table 3.1). A more comprehensive table is also provided at the beginning of the book. These tables are only a guide; they are not meant to compare the performance or specification of each system. The parameters included in this chapter depend on field strength and the nuances of individual systems. However, they should be suitable for most field strengths used in clinical imaging.

Table 3.1 Spin-echo pulse sequences and their common acronyms.

Generic GE Philips Siemens Toshiba Hitachi
Conventional spin-echo SE SE SE SE SE
Fast or turbo spin-echo FSE TSE TSE FSE FSE
Inversion recovery IR IR IR IR IR

Abbreviations used in Table 3.1

SE spin-echo STIR short tau inversion recovery
FSE fast spin-echo FLAIR fluid attenuated inversion recovery
TSE turbo spin-echo DRIVE driven equilibrium
IR inversion recovery


All spin-echo pulse sequences are characterized by RF rephasing. The spin-echo pulse sequence commonly uses a 90° RF excitation pulse to flip the NMV fully into the transverse plane. The NMV precesses in the transverse plane inducing a voltage in the receiver coil. A FID occurs when the 90° RF excitation pulse switches off (see Chapter 1). T2* dephasing from inhomogeneities in the B0 field occurs almost immediately, and signal decays to zero. After a time called tau, another RF pulse is used to compensate for this dephasing and refocus or rephase the magnetic moments of hydrogen nuclei (Figure 3.1). It commonly has a magnitude of 180° and is called the 180° RF rephasing pulse.

Diagram shows four arrows on top which point upward where three of them are labeled dephrasing and diagram below it shows graph labeled free induction decay (FID).

Figure 3.1 T2* dephasing.

T2* dephasing causes the magnetic moments of hydrogen nuclei to dephase or “fan out” in the transverse plane. The magnetic moments are now out of phase with each other on the transverse plane, i.e. they are at different positions on the precessional path at any given time. The magnetic moments that slow down form the trailing edge of the fan (shown in blue in Figures 3.2 and 3.3). The magnetic moments that speed up form the leading edge of the fan (shown in red in Figures 3.2 and 3.3). The 180° RF rephasing pulse is then applied. It has sufficient energy to move the NMV through 180°. As the NMV is still in the transverse plane, it remains in this plane but at a physically opposite position to that before the RF rephasing pulse is applied. The 180° RF rephasing pulse flips the individual magnetic moments through 180° (rather like flipping a pancake). They are still in the transverse plane, but magnetic moments that formed the trailing edge before the 180° RF rephasing pulse now form the leading edge. Conversely, magnetic moments that formed the leading edge before the 180° RF rephasing pulse now form the trailing edge (as shown in the bottom half of Figure 3.2).

Graphs show x-, y, and z-axes with labels for 90 degrees pulse vectors in phase in eight different forms, vectors begin to dephase, high-frequency vectors (red) take lead, et cetera.

Figure 3.2 180° RF rephasing.

Diagram shows basic spin-echo pulse sequence with six arrows which point upward labeled T2* dephasing, vectors flipped 180 degrees, and rephasing.

Figure 3.3 A basic spin-echo pulse sequence.

The direction of precession remains the same, and so the trailing edge begins to catch up with the leading edge because, due to magnetic field inhomogeneities, these magnetic moments precess faster than the trailing edge. At a specific time (TE), the two edges are superimposed. The magnetic moments of hydrogen nuclei are momentarily in phase because they are all at the same place on the precessional path. At this instant, there is in-phase transverse magnetization, and so maximum signal is induced in the receiver coil. This signal is called a spin-echo.

In spin-echo pulse sequences, T2* dephasing is eliminated by the 180° RF rephasing pulse because magnetic field inhomogeneities are largely predictable. T2 decay is not affected by the 180° RF rephasing pulse because this is caused by spin–spin interactions, which randomly fluctuate [1]. In addition, by rephasing the spin-echo at a later point in time in the pulse sequence, time is allowed for tissues to reach their T1 and T2 relaxation times, and therefore a different image weighting is obtained (Figure 3.3).

imagesRefer to animation 3.1 on the supporting companion website for this book: www.wiley.com/go/westbrook/mriinpractice

Diagram shows three cars labeled old tractor, family saloon, and sports car. Four sets of four concentric circles are drawn labeled race begins, race end, et cetera.

Figure 3.4 The Larmor Grand Prix.

imagesRefer to animation 3.2 on the supporting companion website for this book: www.wiley.com/go/mriinpractice

The TR is the time between each 90° RF excitation pulse for each slice. The TE is the time between the 90° RF excitation pulse and the peak of the spin-echo (Figure 3.5). The time taken to rephase after the 180° RF rephasing pulse equals the time to dephase when the 90° RF excitation pulse is withdrawn. This time is called tau. The TE is therefore twice tau and the system times the 180° RF rephasing pulse by halving the TE selected in the scan protocol.

Diagram shows pulse sequence where two sets of pulses are displayed with dimensions of tau, TE, and tau.

Figure 3.5 Tau.

Look at Figure 3.5 and note the symmetry of the spin-echo. As the magnetic moments of hydrogen nuclei gradually come into phase, signal gradually builds, reaching a peak at the TE when all magnetic moments are in phase. However, the magnetic moments that are precessing rapidly soon overtake those that are precessing slowly, and dephasing occurs again. This results in a gradual loss of signal, which mirrors the gradual growth before the peak of the echo. This accounts for the symmetry of the spin-echo.

Having described the fundamental principles of rephasing, it is time to explore the variety of pulse sequences in the spin-echo family. These are generically called;

  • conventional spin-echo
  • fast or turbo spin-echo (FSE/TSE)
  • inversion recovery, which includes STIR and FLAIR.

The mechanisms of pulse sequences and their appropriate timing parameters are important. In the following section, scan tips link the theory of spin-echo pulse sequences to practice. Theory is related to what is going on “behind the scenes” when we select a timing parameter in the scan protocol.



Conventional spin-echo uses a 90° RF excitation pulse followed by one or more 180° RF rephasing pulses to generate one or more spin-echoes. Each 180° RF rephasing pulse generates a separate spin-echo that is received by a coil and used to create an image. Although any number of echoes may be created, spin-echo sequences typically generate either one or two echoes.

Contrast is mainly determined by the spin-echo, but there is also a contribution from the fact that the magnetic moments of hydrogen nuclei are rephased by negative polarity applications of the slice select and frequency-encoding gradients [2]. In addition, spoiler gradients are applied at the end of each TR period to ensure that there is no coherent transverse magnetization at the beginning of the next repetition (see Chapter 4).

Spin-echo using one echo

This pulse sequence is used to produce T1-weighted images by selecting a short TR and a short TE. One 180° RF rephasing pulse is applied after the 90° RF excitation pulse. The single 180° RF rephasing pulse generates a single spin-echo. T iming parameters are usually selected to produce a single T1-weighted image. A short TE ensures that the 180° RF rephasing pulse and subsequent spin-echo occur early so that only a little T2 decay occurs. Differences in T2 decay times of the tissues are minimized and do not, therefore, dominate the spin-echo and its contrast. A short TR, however, ensures that fat and water vectors do not fully recover, and so the differences in their T1 recovery times dominate the spin-echo and its contrast (Figure 3.6). A single T1-weighted image is therefore obtained for every slice location.

Diagram shows pulse sequence of spin-echo where three sets of pulses are displayed with dimensions of short TR and short TE.

Figure 3.6 Spin-echo with one echo.

Spin-echo using two echoes

This is used to produce both a proton density and a T2-weighted image in the TR period. The first spin-echo is generated early by selecting a short TE. Only a little T2 decay occurs, and so T2 decay time differences between the tissues are minimized in this echo. The second spin-echo is generated much later by selecting a long TE. A significant amount of T2 decay occurs, and so differences in the T2 decay times of the tissues are maximized in this echo. The TR is long so that T1 recovery differences between the tissues are minimized in each spin-echo. The first spin-echo therefore has a short TE and a long TR, and is PD-weighted. The second spin-echo has a long TE and a long TR, and is T2-weighted (Figure 3.7). Two images are therefore produced for every slice location. One is PD-weighted, and the other is T2-weighted.

Diagram shows pulse sequence of spin-echo where four sets of pulses are displayed with dimensions of long TR and second TE (long).

Figure 3.7 Spin-echo with two echoes.


Spin-echo pulse sequences are considered the gold standard in that the contrast they produce is understood and predictable. They produce T1-, T2-, and PD-weighted images of good quality and in most parts of the body (Table 3.2). However, due to relatively long scan times, PD- and T2-weighted images are often acquired using FSE/TSE (see next section).

Table 3.2 Advantages and disadvantages of spin-echo.

Advantages Disadvantage
Good image quality Long scan times
Very versatile
True T2 weighting
Available on all systems
Gold standard for image contrast and weighting

Suggested parameters

Single echo (for T1 weighting):

• TR 300–700 ms
• TE 10–30 ms.

Dual echo (for PD/T2 weighting):

• TR 2000 m s+
• TE1 20 ms
• TE2 80 ms.

Table 3.3 Things to remember – conventional spin-echo.

Spin-echo sequences are characterized by 180° RF rephasing pulses that refocus the magnetic moments of spins to produce an echo
T1, T2, and PD weighting are all achievable using conventional spin-echo
Conventional spin-echo is traditionally used to acquire one or two echoes to achieve T1, T2, or proton density weighting
Although they are old sequences, they are still considered the gold standard and can be used to image anatomy and pathology in all body areas



As the name suggests, FSE or TSE is a spin-echo pulse sequence but with scan times that are much shorter than conventional spin-echo. It is also known as RARE (Rapid Acquisition with Relaxation Enhancement) [3].

The scan time is a function of the TR, the number of signal averages (NSA) and the phase matrix (see Chapter 7 and Equation (6.7)). The scan time is reduced by decreasing one or more of these parameters. In TSE, the scan time is decreased by modifying the phase matrix component of this equation. The number of phase-encoding steps is maintained so that the phase matrix is unchanged; however, in TSE, the number of phase-encoding steps per TR is increased. As a result, k-space is filled more efficiently, and the scan time decreases.

In conventional spin-echo, one phase-encoding step is applied per TR on each slice, and therefore only one line of k-space is filled per TR (Figure 3.8). In TSE, the scan time is reduced by performing more than one phase-encoding step and subsequently filling more than one line of k-space per TR. This is achieved by using several 180° RF rephasing pulses to produce several spin-echoes to form an echo train (Figure 3.9). Each rephasing produces a spin-echo, and a different phase-encoding step is performed on this echo. In conventional spin-echo, raw image data from each spin-echo are stored in k-space, and each spin-echo is used to produce a separate image (usually PD- and T2-weighted; see earlier in this chapter). In TSE, data from each spin-echo are placed into one image. The number of 180° RF rephasing pulses performed every TR corresponds to the number of spin-echoes produced in the echo train and the number of lines of k-space filled with data from these echoes. This number is called the turbo factor or the echo train length (ETL). The higher the turbo factor, the shorter the scan time, as more phase-encoding steps are performed per TR. For example:

  • In conventional spin-echo, if a 256 phase matrix is selected, 256 phase encodings are performed. Assuming 1 NSA is also selected, 256 TR periods must elapse to complete the scan.
  • In TSE, using the same parameters but selecting a turbo factor of 16, 16 phase-encoding steps are performed every TR. Therefore 256 ÷ 16 (i.e. 16) TR periods must elapse to complete the scan. The scan time is therefore reduced to 1/16 of the original (Equation (3.1)).
Diagram shows spatial encoding in conventional spin-echo where five blocks are placed with labels for slice-select, phase encoding, and frequency encoding.

Figure 3.8 Spatial encoding in conventional spin-echo.

Diagram shows echo train where set of blocks are placed along horizontal line labeled phase encoding different amplitude.

Figure 3.9 The echo train.

Equation 3.1

ST is the scan time (s)

TR is the repetition time (ms)

M(p) is the phase matrixp) could be replaced by M(p) as per the nomenclature.”?>

NSA is the number of signal averages

ETL is the echo train length or turbo factor

This equation enables the scanner to calculate the scan time in TSE. The longer the echo train, the shorter the scan time, but this may result in fewer slices per TR

At each 180° RF pulse/phase encoding combination, a different amplitude of phase-encoding gradient slope is applied to fill a different line of k-space. In TSE, several lines corresponding to the turbo factor are filled every TR (Figure 3.9). Therefore, k-space is filled more rapidly, and the scan time decreases.

Mar 9, 2019 | Posted by in MAGNETIC RESONANCE IMAGING | Comments Off on Spin-echo pulse sequences
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