1. MR Sequences and Techniques
BME595 MR Physics Lectures 2/3
Chen Lin, Ph.D.
Rev. 2/2007

2. The Anatomy of Basic MR Pulse Sequences
Magnetization Preparation Section
Chemical Shift Selective Saturation
Spatial Selective Saturation
Inversion Recovery (IR)
Magnetization Transfer (MT), CHESS water suppression
Data Acquisition Section
Excitation
Phase Encoding
Echo Generation
Spin Echo (SE), Fast SE, Single-shot FSE (HASTE)
Gradient Recalled Echo (GRE), Fast GRE, Single-shot GRE (EPI)
Diffusion Weighting (DWI/DTI) and Gradient Moment Nulling (GMN)
Frequency Encoding and Digital sampling
Increment Phase Encoding
Magnetization Recovery Section
Spoiling
Driven Equilibrium

3. Slice/Slab Selective Excitation
a SINC RF Pulse RF
Trapezoid Gradient Pulse Gz

4. Phase Encoding Trapezoid Gradient Pulses Gy
Gradient Performance: Rise Time, Max. Amplitude and FOV

5. Echo
The directions of magnetic moments in the transverse plane are re-aligned to generate a detectable signal.
The time integral of gradient pulses from excitation to echo, i.e. the accumulated phase shift (q ~ y Gy t), is zero.
No necessary for all three axis at the same time.

6. Spin Echo B1
a: the magnetization is in the transverse plane immediately after a 90 deg excitation pulse
b: because of B0 inhomogeneity and chemical shift, the precession rates are slightly different. (They are labeled as Fast and Slow.) The magnetization begin to fan out
With a 180 pulse, they are flipped along y axis (can be along x axis too).
C: After reversing the direction, the fast ones will catch up with the slow one and line up at the TE to form an echo.
Please not the T1 and T2 relaxation are neglected.
Add a chinese fan picture
TE/2

7. The “Spin Echo Race”
Start and Finish
1800 Refocusing RF Pulse

8. Slice/Slab Selective Refocusing
1800 SINC RF Pulse RF
Trapezoid Gradient Pulse Gz

9. Frequency Encoding
Trapezoid Gradient Pulse Gx
Echo
Signal

10. Spin Echo (SE) Sequence
Excitation
Refocusing
Phase Encoding
Frequency Encoding
A pair of RF pulses produces a single echo. This echo is always detected in the presence of a readout gradient of constant amplitude. The excitation-detection process is repeated many times, each time with a different amplitude of the phase-encoding gradient applied prior to signal detection. ADC = analog-to-digital conversion.
Slice selective 90 and 180 deg pulses
Phase encoding gradient pulse is incremented or decremented one step per TR
TE/2
TE/2
Next
Excitation TR

11. PD Weighted Imaging
Short TE, Long TR

12. Short TE (<<T1), Intermediate TR (~T1)
T1 Weighted Imaging
Short TE (<<T1), Intermediate TR (~T1)

13. Axial T1w SE TR = 500 msec TE = 15 msec Dark CSF
Figure 4. Transverse T1-weighted spin-echo image (500/15 [TR msec/TE msec]) shows that the cerebrospinal fluid in the lateral ventricles has low signal intensity (arrow).
Dark CSF

14. Intermediate TE ( ~T2), Long TR ( >> T1)
T2 Weighted Imaging
Intermediate TE ( ~T2), Long TR ( >> T1)

15. Axial T2w SE
TR = 2000 msec
TE = 90 msec
Bright CSF

16. Gradient Recalled Echo (GRE)
Excitation
Phase Encoding
Frequency Encoding
Figure 11. Gradient-echo pulse sequence timing diagram. This class of sequences is characterized by the absence of a 180° refocusing pulse. Echo formation is accomplished by application of gradient pulses of opposite polarity (readout direction). ADC = analog-to-digital conversion. TE

17. SE versus GRE Reverse de-phasing in the transverse plane due to:
Chemical shift
Local field inhomogeneity
T2 weighted instead of T2* weighted
Less artifacts.
Longer TR and higher RF energy deposition due to refocusing RF pulse.

18. Multi-contrast Sequence
Additional SE
TE2
Figure 5. Multiple-echo spin-echo pulse sequence timing diagram, two echoes illustrated. Multiple refocusing RF pulses are used to produce multiple echoes. Each echo is detected in the presence of a constant amplitude readout gradient, following a common amplitude of the variable phase-encoding gradient. ADC = analog-to-digital conversion. k1 k2
Image 1
Image 2

19. Fast/Turbo SE (RARE) Rewind Rewind Rewind TE = ? ETL/Turbo Factor = ?
Figure 7. Echo train spin-echo pulse sequence timing diagram. Illustrated is an echo train length of three. Multiple refocusing RF pulses are used to produce multiple echoes. Each echo is detected in the presence of a constant amplitude readout gradient, following a unique amplitude of the variable phase-encoding gradient. Arrows indicate the stepping direction of the phase-encoding tables. ADC = analog-to-digital conversion. k
TE = ?
ETL/Turbo Factor = ?

20. 3D Sequence Slab Excitation Phase Encoding in Z Phase Encoding in Y
Figure 2. A 3D pulse sequence timing diagram. Volume excitation and signal detection are repeated in amplitude, duration, and relative timing each time. Two phase-encoding tables are present, one in the phase-encoding direction and one in the section (slice) direction, which are independently incremented in amplitude each time the sequence is executed. The compensation gradient in the section direction is incorporated into the gradient table.
Frequency
Encoding in X Y k X

21. Ultra-fast Sequences Single-shot FSE / TSE (HASTE)
Echo Planar Imaging (EPI)
Interleave of SE and GRE (TGSE, GRASE)

22. SS-FSE Sequence k

23. EPI Sequence k

24. GRASE/TGSE Sequence
GRE
GRE
GRE
GRE SE SE

25. Chemical Shift
The electron density around each nucleus varies according to the types of nuclei and chemical bonds in the molecule, producing different opposing field. Therefore, the effective field at each nucleus will vary.
n-CH, n-CH2, n-CH3, n-OH, n-NH
Sources of frequency difference: 1. Chemical shift
-CH 1
-CH2 1331
-CH3 methyl 121
-OH hydroxyl 1

26. MR Signal Frequencies at 1.5T
MNS
13C 23Na P F 1H
MHz
Frequency
1H MRS
Nuclei other than 1H also produce MR signal but at different frequencies
1H in different chemical compounds also has different resonance frequencies. (click animation)
Note the chemical shift unit, ppm, used by spectroscopist
Water MI Cho Cr Glu NAA Lac/Lipid
ppm
Chemical Shift 1ppm = 63Hz

27. Saturation
Saturation = Selective excitation + De-phrasing (with gradient)
Chemical Shift Selective Saturation:
Suppress signal within certain resonance frequency range. i.e. Fat Sat.
Narrow bandwidth excitation with no gradient applied.
Improve contrast and conspicuity.
Spatial Selective Saturation:
Suppress signal within certain spatial range. i.e. Sat. Band.
Slab selective excitation + de-phasing to create signal void.
Reduce flow/motion/phase-warp artifacts.

28. Fat Saturation T1w T1w + FS
This is a nice example of the use of spatial spectral
excitation to reduce fat – particularly within the orbits
T1w
T1w + FS

29. Inversion Recovery (IR)? TI
Figure 8. Inversion-recovery pulse sequence timing diagram. A 180° inversion pulse is applied prior to a 90° excitation pulse of a spin-echo acquisition. ADC = analog-to-digital conversion.

30. Contrast vs Inversion Time
Tissue 1
Figure 9. T1 recovery curves following 180° inversion pulse. a, Tissue with a short T1 value (dashed arrow) and that with a long T1 value (solid arrow) have negative longitudinal magnetization and are assigned different pixel values. b, Tissue with a short T1 value (dashed arrow) has positive longitudinal magnetization, and tissue with a long T1 value (solid arrow) has negative longitudinal magnetization. Phase sensitive image reconstruction assigns different pixel values. Magnitude image reconstruction assigns equal pixel values. c, Tissue with a short T1 value (dashed arrow) has positive longitudinal magnetization, and tissue with a long T1 value has zero longitudinal magnetization and contributes no signal intensity to the image.
Null Points
Tissue 2

31. Applications of IR Improve T1 contrast IR-SPGR/MP-RAGE
Selective nulling based on T1 difference:
STIR with TI = 150ms to suppress fat signal.
FLAIR with TI = 2000ms to suppress CSF.
More accurate T1 measurement.
Phase sensitive IR
Figure 10. Sagittal echo train inversion-recovery, STIR image (5,000/30/150 [TR msec/TE msec/TI msec]) shows that fat has low signal intensity, such as that for bone marrow, and fluid has high signal intensity, such as that for suprapatellar effusion (arrow).
STIR

32. Spoiler Prevent magnetization build up in the transverse plane.
Through variable crusher gradient or RF phase cycling.
Suppress artifacts due to remaining transverse magnetization from previous TR.
Reduce T2 weighting in GRE sequences.
Spoiled GRE: FLASH/SPGR
Un-spoiled/Coherent GRE: FISP/GRASS, PSIF/SSFP, TrueFISP/FIESTA

33. Driven Equilibrium (Fast Recovery, Restore)
A 1800y + a 900-x RF pulses to focus and flip the transverse magnetization to Z axis.
Allow shorter TR for the recovery of magnetization.
Increase T2 weighting.

34. Thank you !