Chapter 17: Pulse Sequences & Contrast

Chapter 15 covered magnetization and relaxation, Chapter 16 covered encoding position. What remains is which tissue difference ends up in the image. Imaging the same body, MRI can produce completely different contrast just by changing how the pulses are played and how long we wait. Unlike changing the window on a CT image after the fact, the contrast itself is designed at acquisition time — and at its center are the spin echo and two timing parameters, TR and TE.

The spin echo

As Chapter 15 showed, the FID after a 90° pulse decays with T2*, faster than the true T2, because of static dephasing from $B_0$ inhomogeneity. Static means reversible.

Apply a 180° pulse a time $\tau$ after the 90° pulse and every spin's phase is inverted. Spins that were running ahead are set back by exactly their lead; slow spins move to the front. Wait another $\tau$ and all phases realign, so the signal returns as an echo. The time at which the echo peaks is the echo time TE (= $2\tau$).

Only the static inhomogeneity ($T_2'$) is rewound. The true T2 decay from random spin–spin interactions cannot be recovered, so the echo height is set by $e^{-\mathrm{TE}/T_2}$. The spin echo is thus a device that removes the fast T2* decay and isolates the true T2.

Simulation: spin-echo refocusing

The magnetization tipped by the 90° pulse fans out and the signal drops; at TE/2 a 180° pulse fires automatically. Watch the fan fold back and the signal return as an echo at TE. A longer TE makes the echo peak later, and since more true T2 decay has occurred, the echo is lower. Shortening T2 lowers it too.

TR, TE, and contrast

The interval at which the spin echo is repeated is the repetition time TR. Together, TR and TE decide whether T1 or T2 differences appear in the image. The spin-echo signal is approximated by:

$$S = \rho \left(1 - e^{-\mathrm{TR}/T_1}\right) e^{-\mathrm{TE}/T_2}$$

where $\rho$ is proton density. The factor $(1 - e^{-\mathrm{TR}/T_1})$ carries the T1 effect (shorter TR emphasizes T1 differences), and $e^{-\mathrm{TE}/T_2}$ carries the T2 effect (longer TE emphasizes T2 differences). Combining them gives three practical contrasts:

• T1-weighted (short TR, short TE): short-T1 fat is bright, long-T1 CSF is dark. Used for anatomy.
• T2-weighted (long TR, long TE): long-T2 CSF, edema, and lesions are bright. Strong for detecting pathology.
• Proton-density (long TR, short TE): both T1 and T2 effects are suppressed, showing $\rho$ differences.

Inversion recovery and GRE

Placing a 180° pulse first, inverting the magnetization before imaging, is inversion recovery (IR). By choosing the inversion time TI, you can null the signal of a tissue whose $M_z$ is crossing zero. For sufficiently long TR the null occurs at $\mathrm{TI} = T_1 \ln 2$. FLAIR (nulling CSF) and STIR (nulling fat) are applications that suppress an overly bright tissue to make lesions stand out.

Making the echo with gradients alone, without a 180° pulse, is the gradient echo (GRE). Without the 180° it is faster, but the T2* dephasing cannot be rewound, so the contrast depends on T2* rather than T2. With small flip angles and short TR it enables fast imaging — a thread that continues into the next chapter.

Simulation: TR/TE contrast simulator

The signal equation is applied to the brain phantom; moving TR and TE swaps the contrast. Try the four presets, then move the sliders yourself to explore the space in between. Switch to inversion-recovery mode and set TI near the CSF null, and the lateral ventricles alone go black — a FLAIR image. Same phantom, same anatomy, yet the parameters alone change the appearance this much.

Key points

The spin echo rewinds the static dephasing (T2*) with a 180° pulse at TE/2 and isolates the true T2. Choosing the repetition time TR and echo time TE lets you design T1-, T2-, or proton-density contrast from the same body. Inversion recovery nulls a chosen tissue, and GRE drops the 180° pulse for speed at the cost of T2* contrast. We now have the tools to create signal, encode position, and design contrast. The next chapter asks how fast this imaging can be made — its limits and the reconstruction tricks that push them.

References

• Hahn EL. Spin Echoes. Physical Review 80, 580–594 (1950).
• Carr HY, Purcell EM. Effects of Diffusion on Free Precession in Nuclear Magnetic Resonance Experiments. Physical Review 94, 630–638 (1954).
• Bernstein MA, King KF, Zhou XJ. Handbook of MRI Pulse Sequences. Elsevier (2004).
• Nishimura DG. Principles of Magnetic Resonance Imaging. Stanford University (2010).