MRI Sequence Physics Explainer

The parameters you turn, the sequence families they build, and how to read a sequence name across scanner vendors. Schematic teaching diagrams, not clinical images.

1 · Core parameters — what each knob physically controls

Every image is a compromise between four things: SNR, spatial resolution, scan time, and contrast. Moving one knob almost always spends one of the others.

Timing

TR — repetition time

ControlsTime between successive excitations of a slice; governs how much longitudinal (T1) recovery occurs before the next pulse. The dominant lever for T1 weighting.

▲ Long TR → more T1 recovery, more slices, higher SNR, less T1 contrast • ▼ Short TR → strong T1 contrast, lower SNR.

Timing

TE — echo time

ControlsTime from excitation to signal sampling; governs how much transverse (T2/T2*) decay is allowed. The dominant lever for T2 weighting.

▲ Long TE → more T2 contrast, lower SNR • ▼ Short TE → higher SNR, minimises T2 effect.

Timing

TI — inversion time

ControlsIn inversion-recovery, the delay after a 180° inversion pulse before excitation. Choosing TI at a tissue’s null point removes its signal — fat (STIR) or CSF (FLAIR).

Short TI (~150–170 ms @1.5T) nulls fat = STIR • Long TI (~2000–2500 ms) nulls CSF = FLAIR.

Flip angle (α)

ControlsHow far the RF pulse tips magnetisation. In spin echo usually 90°; in gradient echo the small flip angle is the key contrast/speed lever.

▲ Large α → more signal & T1 weighting • ▼ Small α → less saturation, faster steady state. The Ernst angle maximises SNR for a given TR/T1.

Readout

Receiver bandwidth (BW)

ControlsRange of frequencies sampled per pixel during readout. Sets readout speed and noise admitted.

▼ Low BW → higher SNR, worse chemical-shift/distortion • ▲ High BW → less chemical shift/susceptibility, shorter min TE, lower SNR (SNR ∝ 1/√BW).

Readout

ETL / turbo factor

ControlsNumber of echoes (phase-encode lines) per TR in FSE/TSE and EPI. The main speed multiplier of fast spin echo.

▲ Long ETL → faster scans, more slices • Cost → T2 blurring, higher SAR, bright fat on FSE.

TR / TE map → image weighting

For conventional spin echo, the TR/TE combination alone predicts the dominant contrast. (Rough 1.5 T guide values.)

	Short TE (~10–20 ms)	Long TE (~80–140 ms)
Short TR (~400–700 ms)	T1-weighted Anatomy; fat bright, fluid dark; post-Gd.	Mixed / rarely used.
Long TR (~2000–4000 ms)	Proton density Cartilage, marrow, menisci.	T2-weighted Fluid/pathology bright — the workhorse.

Rule of thumb: TR drives T1, TE drives T2. Want T1? Both short. Want T2? Both long. Want PD? Long TR, short TE.

2 · Sequence family tree

Three branches by how the echo is formed: a refocusing 180° pulse (Spin Echo), a gradient reversal (Gradient Echo), or one fast blipped readout of k-space (EPI).

Spin Echo branch — 180° refocusing pulse

Spin Echo

Conventional SE

What90° excitation then a 180° refocusing pulse forms the echo, undoing static T2* dephasing.

StrengthImmune to static B0 inhomogeneity → low susceptibility artifact; clean contrast.

WeaknessSlow — one line per TR.

Spin Echo

FSE / TSE

WhatMultiple 180° pulses per TR create an echo train (ETL), filling many k-space lines at once.

StrengthFast; retains SE robustness to susceptibility.

WeaknessT2 blurring with long ETL; bright fat on T2; higher SAR.

Inversion recovery

STIR

WhatIR-prepared FSE with TI set to null fat.

StrengthB0-insensitive fat suppression → works off-isocentre and near metal.

WeaknessLow SNR; don’t combine with gadolinium (may null enhancing tissue).

Inversion recovery

FLAIR

WhatLong-TI IR-FSE nulling CSF while keeping T2 weighting.

StrengthUnmasks periventricular pathology hidden by bright CSF — MS, cortical lesions, SAH.

WeaknessCSF-flow & incomplete-nulling artifacts; long scan.

Single-shot SE

SSFSE / HASTE

WhatHalf-Fourier single-shot FSE — one long echo train captures a whole slice.

StrengthVery fast; motion-insensitive. MRCP, fetal, uncooperative patients.

WeaknessT2 blurring; lower SNR/resolution.

Gradient Echo branch — gradient reversal, no 180°

Gradient echo

Spoiled GRE (FLASH / SPGR / T1-FFE)

WhatSmall flip angle + gradient echo; residual transverse magnetisation spoiled each TR.

StrengthVery fast T1 — breath-hold abdomen, dynamic post-contrast, 3D T1, in/opposed-phase.

WeaknessSusceptibility/T2* sensitive; lower SNR per shot.

Gradient echo

Balanced SSFP (TrueFISP / FIESTA / bFFE)

WhatFully-balanced gradients maintain steady state; contrast ≈ T2/T1 → fluid very bright.

StrengthHigh SNR & speed; bright fluid/blood without gadolinium (cardiac cine, fetal).

WeaknessDark banding from off-resonance/poor shim, worse at 3 T.

Gradient echo

T2*-weighted GRE / SWI

WhatLong-TE gradient echo sensitive to T2* dephasing; SWI adds phase.

StrengthExquisitely sensitive to microhaemorrhage, iron, calcium, cavernomas.

WeaknessDistorts near air/metal; not for clean anatomy.

EPI branch — echo-planar readout

EPI

Diffusion (DWI / DTI)

WhatDiffusion-sensitising gradients on an EPI readout; DTI adds directions for tractography.

StrengthUnique contrast; very fast. Stroke, abscess vs tumour, cellularity.

WeaknessDistortion & N/2 ghosts near air/bone; T2 shine-through — always confirm on ADC.

EPI

fMRI (BOLD)

WhatT2*-weighted single-shot EPI repeated rapidly to detect blood-oxygen-level-dependent change.

StrengthWhole-brain every ~1–3 s; pre-surgical eloquent-cortex mapping.

WeaknessLow CNR (needs statistics); dropout at sinuses; motion-sensitive.

EPI family

Why EPI at all?

TradeEPI reads all of k-space after one excitation — the fastest readout in MRI, which makes diffusion and BOLD practical.

The costLong readout → geometric distortion + Nyquist (N/2) ghost. Mitigate with good shim, higher BW, reduced-FOV / readout-segmented EPI, field-map/reversed-PE correction.

3 · Read a sequence name across vendors

Same physics, different trade names. Match the generic concept to the console label.

Generic concept	Siemens	GE	Philips	Canon
Fast/turbo SE (T2/PD)	TSE	FSE	TSE	FSE / FASE
Single-shot FSE	HASTE	SSFSE	SShTSE	FASE
STIR (fat-null IR)	STIR / TIRM	STIR	STIR	STIR
FLAIR (CSF-null IR)	FLAIR	FLAIR	FLAIR	FLAIR
Spoiled (T1) GRE	FLASH	SPGR / FSPGR	T1-FFE	Fast FE
3D volumetric T1 (IR-prep GRE)	MPRAGE	BRAVO / IR-FSPGR	3D T1 TFE	3D Fast FE
Balanced SSFP	TrueFISP	FIESTA	bFFE (bTFE)	True SSFP
GRE T2* / SWI	GRE · SWI	MERGE · SWAN	T2-FFE · SWIp	Field Echo · SWI
Diffusion EPI	DWI / RESOLVE	DWI / eDWI	DWI	DWI

⚠ Names drift between software releases; treat this as a decoder, not gospel. When unsure, check the sequence’s parameters — the physics is the source of truth.

Quick decision guide — which family for which job?

Clean T1/T2 anatomy or near metal? Spin echo (SE/FSE/TSE).

Robust fat or CSF suppression? STIR (fat) or FLAIR (CSF); STIR near metal.

Speed / breath-hold T1 / dynamic / 3D? Spoiled GRE; MPRAGE/BRAVO/TFE for 3D T1.

Bright fluid without gadolinium? Balanced SSFP — watch banding.

Microbleeds/iron/calcium? T2*-GRE / SWI.

Stroke/function? EPI — DWI/ADC, BOLD.

The four-way trade-off, restated

You can’t maximise SNR, resolution, scan time and contrast at once — pick three, pay in the fourth. Bigger voxels/lower BW/more averages → SNR at cost of resolution/time. Smaller voxels → resolution at cost of SNR/time. Long ETL/parallel imaging → speed at cost of blurring/g-factor noise. TR/TE/TI/flip set contrast — each with its own SNR & time cost.

Diagrams are schematic teaching aids. Representative timing values are 1.5 T approximations and vary with field strength, vendor and protocol.

Key references: Westbrook & Talbot, MRI in Practice, 5th ed (Wiley, 2018). Elster, Questions and Answers in MRI (mriquestions.com). Bitar R et al., “MR Pulse Sequences: What Every Radiologist Wants to Know but Is Afraid to Ask,” RadioGraphics 2006;26:513–537. Cross-vendor terminology per Siemens MRI Acronyms card and MRImaster.