Overview
- The four major MRI pulse sequence families, spin echo (SE), fast spin echo (FSE/TSE), gradient echo (GRE), and echo planar imaging (EPI), represent distinct strategies for sampling k-space, with consequent differences in contrast, acquisition speed, SNR, and artefact profile.
- Mastery of their principles, trade-offs, and clinical applications is essential for the RANZCR Part 1 examination.
Spin Echo (SE) Sequences
Mechanism
Each TR interval uses two RF pulses:
- A 90° excitation pulse tips longitudinal magnetisation into the transverse plane.
- A 180° refocusing pulse at TE/2 rephases transverse dephasing, forming a spin echo at TE.
The 180° pulse compensates for static $B_0$ inhomogeneities; signal therefore decays according to true T2 (not the faster T2*). This makes SE inherently robust against susceptibility and field-uniformity artefacts.
Acquisition Time
$$\text{Scan time} = TR \times N_{PE} \times NSA$$
where $N_{PE}$ is the number of phase-encoding steps and $NSA$ (NEX) is the number of signal averages. A typical T2-weighted SE acquisition (TR 2500 ms, 256 phase steps, 1 average) takes ~10-11 minutes, practically prohibitive without multi-slice interleaving. Standard multi-slice SE acquisitions require 10-20 minutes.
Image Contrast
| Weighting | TR | TE | Clinical utility |
|---|---|---|---|
| T1-weighted | Short (300-600 ms) | Short (10-30 ms) | Anatomy, fat, subacute haemorrhage, proteinaceous fluid |
| T2-weighted | Long (2000-3000 ms; longer at 3T) | Long (80-120 ms) | Oedema, pathological lesions, fluid |
| Proton density | Long (2000-3000 ms) | Short (10-30 ms) | Brain, cartilage, menisci |
Advantages and Limitations
Advantages: True T2 contrast unaffected by field inhomogeneity; high SNR; reliable, reproducible tissue contrast; gold standard for contrast comparison.
- Limitations: Long acquisition times; prone to motion artefact over prolonged scanning; unsuitable for breath-hold or dynamic acquisitions.
- Largely replaced in routine practice by FSE for T2-weighted imaging and GRE for T1-weighted body imaging.
Fast Spin Echo (FSE) / Turbo Spin Echo (TSE)
Mechanism
- FSE (synonyms: TSE, RARE, echo-train SE) applies multiple 180° refocusing pulses within a single TR, each with a different phase-encoding gradient, filling multiple k-space lines per excitation.
- The number of echoes per TR is the echo train length (ETL) or turbo factor (TF).
$$\text{Scan time}_{FSE} = \frac{TR \times N_{PE} \times NSA}{ETL}$$
- An ETL of 8 reduces scan time eightfold.
- Combined with half-Fourier (conjugate symmetry) techniques, acquisition time can be halved again.
- The effective TE is determined by the echo filling the centre of k-space, which dominates image contrast.
Image Contrast Compared with Conventional SE
| Feature | Conventional SE | FSE/TSE |
|---|---|---|
| Acquisition time | Long (10-20 min) | Short (2-5 min) |
| Fat signal on T2WI | Intermediate | Brighter (J-coupling suppression) |
| SNR | High | Slightly reduced |
| Image blurring | Minimal | Present; worsens with longer ETL |
| SAR | Moderate | Higher (multiple 180° pulses) |
| Susceptibility artefact | Low | Low (180° pulses compensate $B_0$) |
| Flow void (vessels) | Present | Reduced; flowing blood may appear brighter |
Fat Brightness, Critical Pitfall
- Fat appears paradoxically bright on FSE T2-weighted images relative to conventional SE.
- The rapid train of 180° pulses disrupts J-coupling between adjacent methylene protons in lipid molecules, preventing the normal T2 shortening of fat.
Consequences:
- Vertebral metastases may be obscured in fatty bone marrow on FSE T2 images.
- Perilesional oedema may be masked adjacent to fat.
- Fat suppression (chemical saturation or STIR) must be added when evaluating marrow pathology, soft-tissue lesions, or perilesional oedema.
Image Blurring
- Signal amplitude decays via T2 across the echo train.
- Later echoes, filling peripheral k-space, encoding fine spatial detail, have lower amplitude, producing blurring that worsens with longer ETL and shorter tissue T2.
- This is the fundamental image quality trade-off of FSE: longer ETL = faster scan + more blurring + higher SAR.
FSE Variants
| Variant | Description | Clinical use |
|---|---|---|
| HASTE / SS-FSE | Single excitation; >50% of k-space in one shot | Rapid body T2 imaging; pregnancy; uncooperative patients |
| 3D FSE | 3D k-space with thin isotropic slices | High-resolution spine (nerve roots), MRCP |
| FLAIR | Inversion recovery prepulse + FSE readout | CSF suppression in brain (periventricular lesions) |
| STIR | Short-TI inversion recovery + FSE | Fat suppression; bone marrow oedema; combines T1, T2, PD contrast additively |
STIR suppresses all tissues with short T1 (including fat) and accentuates high-water-content tissues; it more closely resembles a strongly T2-weighted image and is more reliable than spectral fat saturation near metal or at field inhomogeneities.
Gradient Echo (GRE) Sequences
Mechanism
- GRE sequences omit the 180° refocusing pulse.
- Signal formation uses gradient reversal: a dephasing gradient followed by a rephasing (frequency-encoding) gradient reconstitutes the echo.
Consequences:
- $B_0$ inhomogeneities are not compensated → signal decays by T2* (much shorter than T2).
- A partial flip angle ($\alpha < 90°$) allows shorter TR without full saturation of longitudinal magnetisation, enabling very fast acquisitions.
The Ernst angle defines the flip angle giving maximum SNR for a given TR and T1:
$$\cos \alpha_{Ernst} = e^{-TR/T1}$$
- Low flip angles (10-30°) with short TR minimise T1 weighting; higher flip angles (60-90°) increase T1 weighting.
- Image contrast is determined by the combination of flip angle, TR, and TE.
Image Contrast
| Weighting | Flip angle | TR | TE | Key application |
|---|---|---|---|---|
| T1-weighted | High (60-90°) | Short | Short | Dynamic contrast-enhanced imaging, liver |
| T2*-weighted | Low (5-20°) | Short-moderate | Long | Haemorrhage, iron, calcification |
| PD-weighted | Low-moderate | Long | Short | Cartilage, vessels |
T2* contrast is unique to GRE and provides sensitivity to:
- Haemorrhage at all stages (deoxyhemoglobin, methemoglobin, haemosiderin, ferritin shorten T2*)
- Iron deposition (hepatic iron overload, haemochromatosis, transfusional iron)
- Calcification
- Air-tissue interfaces
- Flowing blood appears bright in GRE (flow-related enhancement), basis of time-of-flight MR angiography.
- On conventional SE sequences, flowing blood produces a flow void (low signal); on GRE it is typically bright.
- This distinction is diagnostically important (e.g. differentiating phlebolith from flow void in vascular malformations).
GRE Variants
| Acronym | Full name | Contrast | Application |
|---|---|---|---|
| FLASH / SPGR | Fast low-angle shot / Spoiled GRE | T1 | Dynamic CE, liver, breast |
| GRASS / FISP / FAST | Gradient recalled acquisition in steady state / coherent GRE | T2*/PD | MR angiography, vascular |
| bSSFP / TrueFISP / FIESTA | Balanced steady-state free precession | T2/T1 ratio | Cardiac cine, bowel |
| MPRAGE | Magnetisation-prepared rapid GRE | T1 | Brain volumetric T1 |
| snapshot FLASH / RAGE | Rapid GRE variants | T1 | Breath-hold body |
- Balanced SSFP (bSSFP): Symmetrical gradients in all three directions accumulate both FID and stimulated echo signals, yielding T2/T1 contrast with high SNR and very fast acquisition.
- Particularly useful for cardiac cine and dynamic imaging.
- Uniquely prone to banding artefacts at $B_0$ inhomogeneities (constructive/destructive interference of coherent magnetisation).
Advantages and Limitations
Advantages: Very fast (TR 2-200 ms); enables breath-hold and dynamic acquisitions; bright blood without contrast; T2* sensitivity for haemorrhage, iron, calcification; T1-weighted GRE has replaced SE T1 for body imaging.
Limitations: T2* weighting (not true T2) → exaggerated susceptibility artefact near metal, bone interfaces, air; lower soft-tissue contrast than SE; banding artefacts (bSSFP); chemical shift artefact more prominent at longer TE.
Echo Planar Imaging (EPI)
Mechanism
- EPI is the fastest clinically available MRI technique, acquiring a complete image in 20-100 ms after a single RF excitation (single-shot EPI).
- After excitation, an oscillating readout gradient rapidly alternates polarity, generating a rapid train of gradient echoes; simultaneous small phase-encoding gradient "blips" step through k-space one line at a time in a zigzag pattern until k-space is filled.
The effective TE corresponds to the time when gradient echo amplitude peaks at the centre of k-space (where contrast information resides).
All k-space must be sampled within a time $\lesssim T2^*$ (~50 ms), placing extreme demands on:
- Gradient coils (shielded, low eddy-current coils required)
- Gradient switching speed and linearity
- RF transmitter/receiver hardware
- Analogue-to-digital conversion rate
EPI Implementations
- SE-EPI: 90° excitation → phase/frequency encoding gradients to peripheral k-space → 180° refocusing pulse → oscillating gradient readout train.
- The 180° pulse reduces susceptibility effects and provides T2 weighting at effective TE.
- Longer acquisition time than GRE-EPI; higher SAR; better image quality.
GRE-EPI: Single excitation pulse only (no 180° pulse) → oscillating gradient readout. Faster; T2*-weighted; more susceptible to distortion and signal dropout.
- GRASE (Gradient and Spin Echo): Hybrid sequence combining initial spin echo with a series of gradient echoes per TR, repeated with further 180° RF pulses until k-space is filled.
- Achieves speed of GRE with RF compensation of SE.
- Trade-off: longer acquisition (>100 ms) and greater SAR from multiple 180° pulses.
Image Quality
| Parameter | Typical EPI values |
|---|---|
| Matrix size | $64 \times 64$ or $128 \times 64$ (standard) |
| SNR | Low |
| Spatial resolution | Low relative to SE/GRE |
| Temporal resolution | Very high (real-time capable) |
| Susceptibility sensitivity | Very high (GRE-EPI) |
Clinical Applications
| Application | EPI type | Rationale |
|---|---|---|
| Diffusion-weighted imaging (DWI) | SE-EPI | Speed prevents motion corrupting diffusion encoding gradients; technique of choice |
| fMRI (BOLD) | GRE-EPI | T2* sensitivity to deoxyhemoglobin; high temporal sampling for activation mapping |
| Perfusion imaging (DSC) | GRE-EPI | Dynamic susceptibility contrast tracking |
| Cardiac imaging | SE/GRE-EPI | Freeze cardiac motion |
| EPI-FLAIR | SE-EPI with FLAIR prepulse | Faster FLAIR acquisition than conventional FLAIR |
Artefacts in EPI
| Artefact | Mechanism | Appearance | Mitigation |
|---|---|---|---|
| Geometric distortion | $B_0$ inhomogeneity accumulates across phase-encode direction during slow k-space traversal | Spatial warping; worst at air-tissue interfaces (sinuses, skull base) | SE-EPI (partial); parallel imaging (GRAPPA, SENSE); $B_0$ field map correction |
| Chemical shift / N/2 ghost | Fat resonates ~3.5 ppm offset; during alternating readout polarity, inconsistencies cause half-FOV shifted ghost | Fat-water spatial misregistration; faint duplicate image offset by $N/2$ in phase direction | Fat suppression; increased receiver bandwidth; parallel imaging; phase correction |
| Signal dropout | Susceptibility-induced T2* dephasing at regions of field variation | Signal voids near sinuses, skull base, metal implants | SE-EPI; reduced TE; thinner slices; parallel imaging; $z$-shimming |
| Blurring | T2* decay across readout echo train | Blurring along phase-encode direction | Shorter readout train; multishot EPI |
| Low SNR | Rapid readout, small matrix | Noisy images overall | Signal averaging (at cost of speed) |
Safety Concerns with EPI
- Peripheral nerve stimulation (PNS): Rapidly switching gradients (high $dB/dt$) can stimulate peripheral nerves; IEC limits on gradient switching rates apply.
- Acoustic noise: Loud gradient switching generates noise >100 dB; hearing protection is mandatory.
- SAR: SE-EPI has higher RF energy deposition than GRE-EPI due to the 180° refocusing pulse.
- Eddy currents: Rapid gradient switching induces eddy currents in conductive structures; shielded gradient coils are required to minimise these.
Comparative Summary
| Feature | Conventional SE | FSE/TSE | GRE | EPI |
|---|---|---|---|---|
| Key RF pulses | 90° + 180° | 90° + multiple 180° | Variable flip angle only | 90° ± 180° (SE-EPI) |
| Echo type | Spin echo (true T2) | Spin echo (true T2) | Gradient echo (T2*) | Gradient or spin echo |
| Acquisition speed | Slow (10-20 min) | Moderate (2-5 min) | Fast (seconds) | Very fast (50-100 ms) |
| Susceptibility sensitivity | Low | Low | High | Very high (GRE-EPI) |
| Fat signal on T2WI | Normal | Bright (J-coupling) | Variable | Variable |
| SNR | High | Moderate-high | Moderate | Low |
| Spatial resolution | High | High | Moderate-high | Low |
| Main artefacts | Motion, flow void | Blurring, high SAR, fat brightness | Susceptibility, chemical shift, banding (bSSFP) | Distortion, N/2 ghost, dropout, blurring |
| T2* sensitivity | No | No | Yes | Yes (GRE-EPI) |
| Typical TR | 300-3000 ms | 2000-5000 ms | 2-200 ms | Single shot (~50-100 ms) |
| SAR | Moderate | High | Low-moderate | Low (GRE-EPI); moderate (SE-EPI) |
| Primary clinical role | Historical standard; some brain/spine | Routine brain, spine, MSK, body T2 | Dynamic CE, haemorrhage, MRA, cardiac | DWI, fMRI, perfusion |
RF Energy and Safety Considerations
- MRI uses non-ionising radiofrequency radiation with no ionising radiation dose.
- RF energy deposition is quantified by the Specific Absorption Rate (SAR) in $\text{W kg}^{-1}$.
- IEC and ARPANSA limits typically apply as 2-4 $\text{W kg}^{-1}$ whole-body averaged over 6 minutes.
- FSE/TSE and SE-EPI, with their multiple 180° pulses, generate the highest SAR.
- At 3T, SAR is approximately four times higher than at 1.5T for equivalent sequences, necessitating sequence modifications: reduced ETL, extended TR, or variable-flip-angle refocusing pulses (e.g. hyperecho techniques).
$$\text{Scan time}_{SE} = TR \times N_{PE} \times NSA \qquad \text{Scan time}_{FSE} = \frac{TR \times N_{PE} \times NSA}{ETL}$$
High-Yield Examination Points
- The 180° refocusing pulse in SE/FSE compensates for static $B_0$ inhomogeneity → true T2 contrast and low susceptibility artefact. GRE lacks this → T2* weighting → amplified susceptibility effects.
- FSE fat brightness (T2WI) is a clinically important pitfall due to J-coupling suppression by rapid 180° pulses, always add fat suppression when evaluating bone marrow, perilesional oedema, or soft-tissue pathology adjacent to fat.
- GRE is the sequence of choice for detecting haemorrhage (all stages), iron deposition, and calcification due to T2* sensitivity. Flowing blood is bright on GRE (flow-related enhancement) but produces a flow void on SE.
- EPI enables DWI and fMRI; its characteristic artefacts (geometric distortion, N/2 Nyquist ghost, signal dropout) arise directly from rapid single-shot k-space traversal without RF compensation for field inhomogeneities.
- Increasing ETL in FSE reduces scan time but increases blurring, SAR, and fat signal brightness on T2WI.
- Balanced SSFP (bSSFP/TrueFISP/FIESTA) generates T2/T1 contrast with high SNR; ideal for cardiac cine; uniquely prone to banding artefacts from $B_0$ inhomogeneity.
- GRASE combines gradient echoes with spin echo RF refocusing, offering a speed/image quality compromise between EPI and FSE.
- Susceptibility artefact on GRE is demonstrated dramatically by comparison with FSE: the same dental filling or haemorrhagic lesion appears as a large signal void on GRE-T2* but is substantially suppressed on FSE-T2 due to 180° pulse compensation.