MRI Pulse Sequences Overview

MRI Pulse Sequences Overview#

Sequence families#

  • Spin-echo family: SE, multi-echo, FSE/TSE

  • Gradient-echo family: GRE, FLASH, bSSFP/FIESTA, EPI

  • Inversion-recovery: STIR, FLAIR, DIR, PSIR

  • Diffusion: DWI, DTI, HARDI, multi-shell

  • Perfusion & flow: ASL, DSC/DCE, TOF-MRA, phase-contrast

  • Quantitative maps: \(T_1\) (MOLLI, VFA), \(T_2/T_2^*\), \(T_{1\rho}\), \(B_1\), \(B_0\)

  • Functional & rapid: BOLD-EPI, multiband/SMS, cine

  • Spectroscopy: PRESS, STEAM, MEGA-PRESS, semi-LASER

  • Magnetization transfer & CEST protocols

  • Accelerated methods: parallel imaging (SENSE/GRAPPA), compressed sensing

Pulse design and contrast#

Combinations of excitation pulses are typically chosen so the measured signal amplitude becomes a function of MR parameters \((\rho, T_1, T_2)\).

Note

Gradient fields are double‑edged swords: - Needed for spatial localization. - Turning them on increases dephasing and destroys some signal.

To recover signal, apply an opposite polarity gradient with the same area (often higher amplitude, shorter time) to rephase.

Why not undo \(G_{\text{phase}}\) and \(G_{\text{freq}}\) afterwards?

  • The phase shift from the phase‑encoding gradient is the spatial encoding. If you undo it, you remove spatial encoding from the image.

  • For the frequency‑encoding gradient (FEG), you cannot simply apply an opposite gradient after readout because the echo and sampling are already finished at \(\mathrm{TE}\). Instead, you compensate in advance with a prephasing gradient (you de‑phase once, then re‑phase during readout).

Why are there multiple \(G_{\text{phase}}\) pulses?

Each repetition uses a different phase‑encoding strength to fill a different row of k‑space. Repeating across many phase encodes fills the full k‑space matrix.

Repetition effects and Ernst angle#

For a single excitation, a \(90^\circ\) pulse yields the most transverse signal. When repeated, TR influences the optimal flip angle because longitudinal magnetization may not fully recover between excitations.

Ernst angle: optimal flip angle depending on \(T_1\) and TR; with short TR, often \(\alpha < 90^\circ\).

Spin‑Echo (SE)#

  1. Apply \(G_{\text{slice}}\) during the RF excitation; otherwise the entire volume is excited.

  2. Apply an opposite‑polarity slice‑selection gradient lobe to: - Rephase dephasing caused by \(G_{\text{slice}}\). - Refocus spins within the selected slice. - Avoid unwanted signal from outside the slice.

  3. Apply a \(180^\circ\) refocusing pulse (with appropriate gradient schemes, e.g., crusher/phase gradients) to control slice cross‑talk and coherence pathways.

  4. Wait after the \(180^\circ\) pulse for dephasing to refocus into the spin echo at \(\mathrm{TE}\).

Gradient‑Echo (GRE)#

  • No \(180^\circ\) refocusing pulse.

  • No post‑\(180^\circ\) waiting period as in SE; echoes formed by gradient polarity/area manipulations.

  • Generally faster and more flexible due to gradient control.

  • Typically \(\alpha \neq 90^\circ\) (small flip angles common).

Inversion‑Recovery (IR)#

Basic form:

\[180^\circ \; \rightarrow \; \text{(wait } TI \text{)} \; \rightarrow \; \text{readout (e.g., SE)}\]

  • :math:`TI`: inversion time between the \(180^\circ\) pulse and the readout that sets which tissue is attenuated or nulled.

STIR (Short TI Inversion Recovery)#

  • Chooses a short \(TI\) to null short :math:`T_1` tissues (e.g., fat).

  • Useful for artifact suppression (implants/metal).

  • Downsides: - Longer TR → longer acquisition time. - Not compatible with T1‑shortening contrast agents (contrast effect is suppressed by fat‑nulling). - Reduced SNR.

FLAIR (Fluid‑Attenuated Inversion Recovery)#

  • Uses a long \(TI\) to null fluid (e.g., CSF).

  • Helps differentiate lesions from ordinary fluids, enhancing lesion conspicuity adjacent to CSF spaces.