1. MRI Physics: Pulse Sequences
Anna Beaumont
FRCR Part I Physics

2. 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. ˚

3. 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)

4. From Picture to Proton

5. N. B. Application of any gradient introduces alteration in phase
N.B. Application of any gradient introduces alteration in phase. GSS & FE have rephasing/ dephasing lobes to compensate for this
Spin Echo
90°
180° RF Gz
Slice Selection Gy
Phase Encoding
Frequency Encoding Gx
Signal TE
An axial image.. TR

6. Scan Time Frequency encoding done at time of echo
Phase encoding done over many TRs
Scan time is given by
NPE  TR  NEX

7. 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

8. Multiple Spin Echo
180°
90°
180° RF Gz Gy Gx
Signal
TE2
TE1 TR

9. Fast Spin Echo
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

10. 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

11. 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

12. 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.

13. 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.

14. 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.

15. 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

16. 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

17. 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.

18. 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

19. 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

20. FLuid Attenuated Inversion Recovery (FLAIR)
Useful in brain to get rid of CSF signal

21. 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.

22. Gradient Echoes

23. Gradient Echo RF Gz Gy Gx Signal °
For True FISP you balance the Gz and Gx as well and have alternate –alpha RF Gx
Signal

24. 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

25. 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.

26. 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 M0
Mz = M0cos
 M0
Note: for TR>>T1
E = 90° 
Mx,y = M0sin

28. Small α→large amount of Mz left after RF
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

30. 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.

31. 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

32. Gradient Echoes: Types

33. 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.

34. Spoiled Sequences RF RF spoiled: phase () is increased Gz Gy Gx
° ,  RF
RF spoiled:
phase () is increased Gz Gy
For True FISP you balance the Gz and Gx as well and have alternate –alpha RF Gx
Signal

35. Gradient Echoes: Spoiled
Ref: MRI, The Basics by Hashemi, Bradley & Lisanti

36. 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

37. Gradient Echoes: Steady State
Ref: MRI, The Basics by Hashemi, Bradley & Lisanti

38. 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.

39. 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.

40. 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]
..and DWI

41. 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
..and DWI

42. EPI
90°
180° RF Gz Gy Gx
Signal TE TR

43. Examples: Brain
fMRI scans using EPI: 28 slices per 3 s TR

44. 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
..and DWI

45. 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.
..and DWI

46. EPI: Preparation & Contrast
..and DWI

47. Segmented k-Space Single shot Scan time = (TR NAV  NPE)
Scan time = (TR NAV  NPE)/ETL
Scan time = TR

48. Spin Echo Gradient Echo Inversion Recovery Fast SE Spoiled SSFP SS-FID
SS-Echo
STIR
FLAIR
Turbo/Fast
FRFSE
Acronyms all at end
Note ss and SS mean different things
Also non spoiled/ coherent; SSFID aka ‘rewound’, SSecho aka time reversed
Not covered STIR/FLAIR
Not covered Fat/wat sep methods (IDEAL, DIXON)
ssFSE
EPI

49. 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

51. References From Picture to Proton: McRobbie et al.
MRI: The Basics –Hashemi et al.
Slides from presentation of Dr Lothar Schad, University of Heidelberg

52. Next Time…… MRI Techniques Spectroscopy Dynamic Contrast Enhancement
fMRI
Angiography

53. FSPGR (Fast Spoiled Gradient Echo) example in brain
For FSPGR at 1.5T, α =12˚ usually, but does not show on the image!