MRI Physics: Pulse Sequences

Anna Beaumont

FRCR Part I Physics

Characteristics of an MRI Sequence

• Essential components of any sequence– RF excitation pulse– Gradients for spatial encoding– Signal reading (combining one or a number of echo

types) determining type of contrast (T1, T2, T2*)• Options consist of other RF pulses, gradients or

variable reconstruction methods to– Modify contrast– Accelerate the sequence– Reduce artefacts

• User must choose sequence parameters (TR, TE, flip angle, Field of View (FOV)

• Compromise between contrast, resolution and speed.

˚

Main Types of Pulse Sequence

• Spin Echo– Multi-Spin Echo– Fast Spin Echo (FSE) or Turbo Spin Echo– Single shot FSE– Inversion Recovery

• STIR• FLAIR

• Gradient Echo– Spoiled Gradient Echo

• Ultrafast Gradient Echo– Steady State Gradient Echo– Contrast Enhanced Steady State– Echo Planar Imaging (EPI)

• From Picture to Proton

RF

Gz

Gy

Gx

Signal

TE

90° 180°

Slice Selection

Phase Encoding

Frequency Encoding

An axial image..

Spin Echo

TR

• N.B. Application of any gradient introduces alteration in phase. GSS & FE have rephasing/ dephasing lobes to compensate for this

Scan Time

• Frequency encoding done at time of echo• Phase encoding done over many TRs• Scan time is given by

NPE TR NEX

Multi-Echo Sequences

• Allow several images of the same slice position without increasing overall acquisition time

• Images obtained with different contrast

• After first echo is obtained, free interval until next TR.

• By applying a new 180° pulse a new echo is received (but with the *same* phase encoding).

• The echo time of the 2 images differs and the second image will be more T2 weighted than the first.

• Typically used to obtain simultaneously PD & T2-weighted images

Multiple Spin Echo

RF

Gz

Gy

Gx

Signal

TE1

TR

90° 180° 180°

TE2

• Before we can acquire the second echo, we have to “rewind” the phase encoding to undo the dephasing of the spins. To do this, a phase encoding step of equal strength but opposite in sign is applied after the completion of the data acquisition.

• From Picture to Proton

Fast Spin Echo

Fast Spin Echo

• Interval time after the first echo used to retrieve echo train and fill other k-space lines.

• Done by applying new 180° pulses to obtain a spin echo “train”.

• After each echo, the phase encoding is cancelled and a different phase encoding applied to the following echo

• Number of echoes received in the same repetition (TR) time is called the Turbo factor or Echo Train Length (ETL)

• Because of the reduced number of repetitions (TR), k-space is filled faster and slice acquisition time reduced.

• Time of scan = (NPE TR NEX )/ ETL

FSE: Contrast, resolution & Scan Time

• Contrast is modified compared to a standard SE sequence.

• As echoes received at different echo time, echoes corresponding to central k-space are the ones determining image contrast

• Time at which these echoes are acquired is called effective TE

• TEeff is arranged to coincide with the central parts of k space.

• FSE can be PD, T1 or T2 weighted– In T1 weighted sequences need to choose short TR: limits echo train length.

• More commonly used in T2 weighting, e.g. pelvic imaging

Fast Spin Echo

• The manner in which k-space is filled is illustrated here. Each echo is responsible for a portion or segment of k-space. So different lines of k-space will have different T2 weighting. The echo that contributes the central segment determines the effective echo time.

• We could assign any of the echoes to acquire the centre of k-space, thus changing the effective TE, The order in which phase encoding is applied therefore affects the contrast.

FSE: Image compromises

• Multi-slice acquisitions now limited – more of time within TR used up by echo train, so reduces possibility of acquiring large number of interleaved slices.

• To compensate for this, a longer TR can be used with increased scan time for T2 or PD-weighted images, but not T1.

• FSE images, with their many large RF pulses, may exceed the SAR limit.– To reduce this, need to reduce no. of slices, increase TR or reduce ETL.

• Higher k-space data: – if the higher spatial frequencies are acquired for longer actual TE they will be attenuated by

T2 relaxation and some spatial resolution will be lost. – If they are acquired at a shorter TE than the effective TE they will be emphasised, which

may lead to excessive ringing or Gibbs’ artefact. – For this reason additional filtering may be applied for FSE sequences.

FSE: Fat signal

• Within lipid molecules a spin-spin coupling (J coupling) occurs between atomic nuclei– Shortens T2– Fast repetition of 180° pulses perturbs J coupling and

causes fat T2 to lengthen

• Fat has higher T2 in FSE than SE• DIET (Delayed Interval Echo Train) sequence is fast SE where

delays between 180° pulses will not affect J coupling as much– Fat appearance will be closer to that observed in standard

SE.

UltraFast SE (Single Shot Technique)

• Echo Train Technique can be pushed to fill entire Fourier plane with a single 90° pulse (so TR is infinite)

• Requires successive application of as many 180° pulses as there are k-space lines to fill.

• Partial k-space acquisition can be

used– Just over half k-space lines acquired– Missing lines calculated using k-space

symmetry properties– Reduces acquisition time, but to detriment of

SNR

UltraFast SE (Single Shot Technique)

• Images are highly T2 weighted as majority of k-space lines are filled with long TE echoes.

• Duration = TE * NPE

• Well adapted to imaging non-circulating liquid structures appearing as highly T2 weighted signal: Cholangio MRI (gallbladder, biliary system and pancreas: MRCP); Uro-MRI

• Low sensitivity to movement

• Cons– Decay in SNR– Low spatial resolution and blurring in PE direction

Short TI Inversion Recovery (STIR)

• Instead of an initial 90° pulse, use 180°

• Spins flipped in longitudinal plane

• Start to recover• Fat & Water

recover at different rates

• Apply 90° pulse when fat passing through zero

• Only water is flipped into transverse plane to give a signal.

Short TI Inversion Recovery (STIR)

• Time between initial 180 and 90 pulse is known as the inversion time TI

• Method of fat/ water suppression imaging

• TI of ~140ms will suppress fat

FLAIR: Fluid Attenuated Inversion Recovery

• Aim is to suppress liquid signals by IR

• Nulling of water signal at TI~ 2000ms

• Imaging sequence of FSE preferable to compensate long acquisition time linked to long TR

• Routinely used in cerebral MRI for oedema imaging

FLuid Attenuated Inversion Recovery (FLAIR)

• Useful in brain to get rid of CSF signal

Gradient Echoes• Gradient echo differs from Spin Echo Sequence

– Flip angle usually below 90˚.– Absence of a 180˚ RF rephasing pulse

• Lower flip angle decreases amount of magnetisation tipped to transverse plane– Consequence is faster recovery of longitudinal

magnetisation– Allows shorter TR/TE – decreases scan time– Allows new contrasts between tissues and a stronger MR

signal in case of short TR.

Gradient Echoes

Gradient Echo

RF

Gz

Gy

Gx

Signal

°

Gradient Echoes• Production of Echoes

– As no 180 pulse need a bipolar readout gradient (same as FE gradient).

– Echo forms from applying a dephasing gradient before the FE or readout gradient.

• Dephasing stage is inverse and half effect of readout gradient

• During signal acquisition readout FE gradient will rephase spins in first half of readout, and they will then dephase in second half.

• Gradient only reverses dephasing caused by itself so inhomo-geneities are not corrected

Gradient Echoes• Reminder: decay of transverse magnetisation due to several

factors: – Spin-spin relaxation which is tissue specific → T2

weighting– B0 field inhomogeneities & magnetic susceptibility

• (Susceptibility is a property of matter: determines how easily it becomes magnetised when placed in an external field. Susceptibility artefacts are signal voids present due to differences in susceptibility between objects and tissue or air/tissue interface)

• As there is no 180° rephasing pulse images are therefore T2* (not T2) weighted

• These sequences are thus more sensitive to magnetic susceptibility artefacts than SE.

Partial flip-angle

• For a given flip angle and relaxation time T1, there is an optimal TR to obtain the maximum signal after a series of excitation pulses. Optimum flip is given by Ernst angle

)/exp(cos 10 TTRE

Note: for TR>>T1 E = 90°

Mz = M0cos M0

Mx,y = M0sin

M0

• Small α→large amount of Mz left after RF. Recovery for Mz will take less time than SE→ little differentiation in T1 values :

– Small α→ reduced T1 weighting

– Large α (with large TR)→ increased T1 weighting

• TE: similar to SE– Short TE reduces T2* weighting and increases PD (or T1 weighting)

– Long TE enhances T2* weighting.

• TR: A short TR (with small α) → incomplete decay of Mxy . Residual Mxy will contribute to next signal (Steady state):– Short TR enhances T2* weighting.

• A Long TR (remember we’re talking relative here – long in GE is short in SE!) allows more recovery of T1 curves and better differentiation of T1 values. Also causes more T2* decay, reducing steady state component and thus reducing T2* weighting

Gradient Echoes: Types• In GE, TR reduction may cause permanent residual

transverse magnetisation, in TR < T2:– Transverse magnetisation will not have completely

disappeared at the onset of the next repetition & will be submitted to flip caused by excitation pulse.

Gradient Echoes: Types• Three main classes of GE sequence can be distinguished,

depending on how residual transverse magnetisation is managed– Spoiled or incoherent GE (SPGR/FLASH)

• Mss eliminated by use of RF/ gradient spoiling.

– Rewound or coherent GE (GRASS/FISP)• Mss conserved. Rewinder gradient applied to PE direction at end of

cycle to reverse effects.• By maintaining residual transverse magnetisation excitation pulses

will produce new echoes (Hahn echoes, stimulated echoes) in addition to the GE that depends on the FID.

– Time reversed GE (SSFP/PSIF)• Very complicated to explain!• Only uses the Hahn type echoes

Gradient Echoes: Types

Gradient Echoes: Spoiled• The steady state can be detrimental, namely for T1

weighted sequences. To resolve this problem, gradients and/or RF pulses (spoilers) are used to eliminate this residual transverse magnetisation

• Spoiling gradients and RF Pulses: • The spoiling RF pulse consists in randomly varying

the excitation pulse phase (α) at each repetition (best method)

• A spoiling gradient has two components:– A constant component, consisting of prolonging the

readout gradient– A variable component, changing randomly at each

repetition, in the direction of the slice selection gradient.

Spoiled Sequences

RF

Gz

Gy

Gx

Signal

° ,

RF spoiled:phase () is increased

Gradient Echoes: Spoiled

• Ref: MRI, The Basics by Hashemi, Bradley & Lisanti

Gradient Echoes: Spoiled• In this type of echo gradient sequence image weighting will

depend on:– The flip angle for T1 weighting (the greater the angle, the more T1

weighting)– The TE for T2* weighting (the shorter the TE, the more reduced T2*

weighting)– If flip angle is small, → PD weighting

Gradient Echoes: Steady State

• Ref: MRI, The Basics by Hashemi, Bradley & Lisanti

Gradient Echoes: Steady State

• In Steady state GE sequences residual transverse magnetisation is conserved.

• This will participate in the signal and contrast and vary according to the type of sequence.

• By maintaining residual transverse magnetisation excitation pulses will produce new echoes (Hahn echoes, stimulated echoes) in addition to the GE that depends on the FID.– 90˚-180˚ pulse combination generates spin echo.– Any pair of RF pulses, of any flip angle, can form a Hahn or partial

echo. Smaller in magnitude than spin echoes and have T2 dependence.

Gradient Echoes: Steady State

• GRASS/FISP– Gives more signal than spoiled GE, but more complicated weighting.– At long TR (>100ms) and small α little difference between spoiled and no spoiled

as Mss had time to decay.

– Rewound sequences produce good myelographic effect images.– Since signal is relatively independent of TR, rewound sequences are excellent for

high contrast between fluid and solid structures in rapid imaging.– However; because of combination of refocused and fresh transverse

magnetisation, sensitive to motion anf flow which can destroy the steady state transverse coherence.

• SSFP/PSIF– Strictly speaking not a GE as signal is of Hahn echo origin.– Images give a T2 weighted appearance but with advantage of faster acquisition

than spin echo.– Disadvantages are sensitivity to motion and relatively low SNR– Clinical applications are few, but one is as an alternative to EPI for Diffusion

Weighted Imaging.

Echo Planar Imaging (EPI)

• EPI is the fastest acquisition method in MRI (100ms/ slice), but with limited spatial resolution.

• Excitation pulse, (sometimes preceded by magnetisation preparation, e.g Inversion Recovery, Fat Suppression)

• Continuous signal acquisition in the form of a gradient echo train to acquire total or partial k-space (single shot or segmented acquisition).

• Readout & PE gradients adapted to spatial image encoding, with several trajectories to fill k-space [constant (non-blipped) or intermittent (blipped) PE gradient, spiral acqusition]

Echo Planar Imaging (EPI)

• Single-shot (can be run multi-shot)– Scan time = TR

• Inherently noisy

• Prone to distortions and ghosting

• Limited resolution (64 or 128)

• Can be SE or GE based

• Widespread use in fMRI and real time cardiac imaging

EPI

RF

Gz

Gy

Gx

Signal

TE TR

90° 180°

Examples: Brain

• fMRI scans using EPI: 28 slices per 3 s TR

EPI: Preparation & Contrast

• Requires high performance gradients: need to allow rapid on-off switching of gradients.– Limits on how large this can be are determined by

peripheral nerve stimulation

• Contrast determined by excitation pulse & possible magnetisation preparation

• Options– GE-EPI: single RF pulse, with no preparation → T2*

weighting– SE-EPI: pair of 90°-180° pulses (SE type) → T2 weighting– IR-EPI: 180° inversion pulse then RF excitation pulse

→ T1 weighting– DW-EPI: preparatory pattern for diffusion weighting

EPI: Preparation & Contrast

• For GE train a readout gradient is continuously applied, with positive & negative alternations.

• With alternating gradient k-space scanned from left to right and back with each echo.

• At same time PE gradient may be permanent & constant (non-blipped) giving a zigzag trajectory or intermittent (blipped).

• Spiral filling of k-space needs PE & FE gradients with a growing sine wave shape.

EPI: Preparation & Contrast

• T

Segmented k-Space

Scan time = (TR NAV NPE)/ETL

Scan time = (TR NAV NPE)

Scan time = TR

Scan time = TR

Single shot

Spin Echo Gradient Echo

Inversion Recovery

STIR

ssFSE

EPI

SSFPSpoiled

SS-EchoSS-FID

Turbo/FastFRFSE

FLAIR

Fast SE

Some Terminology

• Multi or single-shot– Related to number of TRs required to acquire FULL k-

space• Partial k-space

– speed up image sequence by NOT acquiring complete k-space

• Partial and Reduced Flip– Less than 90 flip angles and less than 180 refocusing

pulses respectively• Echo Train

– Closely spaced signal echoes (with a certain echo spacing) within one TR

• Parallel Imaging– Use of multi-coil sensitivities to speed up image

acquisition• Inversion Pulse

– Use of 180 excitation pulse to invert magnetisation

References• From Picture to Proton: McRobbie et al.• MRI: The Basics –Hashemi et al.• www.imaios.com• Slides from presentation of Dr Lothar Schad,

University of Heidelberg

Next Time……

• MRI Techniques– Spectroscopy– Dynamic Contrast Enhancement– fMRI– Angiography

FSPGR (Fast Spoiled Gradient Echo) example in brain

• For FSPGR at 1.5T, α =12˚ usually, but does not show on the image!