1. Principles of nuclear magnetic resonance and MRI Review
Chapter 3
Principles of nuclear magnetic resonance and MRI
Review

2. Basic Physics of MRI
Nuclei line up with magnetic moments either in a parallel or anti-parallel configuration.
In body tissues more line up in parallel creating a small additional magnetization M in the direction of B0.
Nuclei spin axis not parallel to B0 field direction.
Nuclear magnetic moments precess about B0.

3. Larmor frequencies of RICs MRIs
Basic Physics of MRI
Frequency of precession of magnetic moments given by Larmor relationship
f = g x B0
f = Larmor frequency (mHz)
g = Gyromagnetic ratio (mHz/Tesla)
B0 = Magnetic field strength (Tesla)
g ~ 43 mHz/Tesla
Larmor frequencies of RICs MRIs
3T ~ 130 mHZ
7T ~ 300 mHz
11.7T ~ 500 mHz

4. Basic Physics of MRI NMRable Nuclei
Body 1H content is high due to water (>67%)
Hydrogen protons in mobile water are primary source of signals in fMRI and aMRI

5. Basic Physics of MRI
M is parallel to B0 since transverse components of magnetic moments are randomly oriented.
The difference between the numbers of protons in the parallel (up here) and anti-parallel states leads to the net magnetization (M).
Proton density relates to the number of parallel states per unit volume.
Signal producing capability depends on proton density. B0

6. RF pulse duration and strength determine flip angle
Basic Physics of MRI
Frequency of rotation of M about B1 determined by the magnitude (strength) of B1.
RF pulse duration and strength determine flip angle
Basic RF Pulse Concepts
RF Pulse
strength
duration

7. Basic Physics of MRI
FID = Free Induction Decay
90° RF pulse rotates M into transverse (x-y) plane
Rotation of M within transverse plane induces signal in receiver coil at Larmor frequency.
Magnitude signal dependent on proton density and Mxy.
FID magnitude decays in an exponential manner with a time constant T2. Decay due to spin-spin relaxation.

8. Need for 180° Pulse - Spin Echo
FID also diminishes due to local static magnetic field inhomogeneity
Some spins precess faster and some slower than those due to B0
90°
Blue one is fast precessing spins.
Question: What is the time between 90 and 180 pulse?
Note: to use vector concept to explain a common question concerning the180 flipping of both blue and red spins.
180°
time
TE/2-
TE/2+
180 ° RF pulse reverses dephasing at TE (echo time)
Residual decay due to T2
Spin Echo Signal TE

9. Nuclear Magnetic Resonance (NMR) Signal: Spin Echo (SE)
TR (repetition time) = time between RF excitation pulses
90o
180o
90o
FID
Spin Echo
90 itself is capable of generate a FID signal
pair used to obtain a spin-echo (SE) signal.
Definition of TR TE.
TE/2
TE/2
TE = time from 90o pulse to center of spin echo

10. Developing Contrast Using Weighting
Contrast = difference in image values between different tissues
T1 weighted example: gray-white contrast is possible because T1 differs between these two types of tissue

11. T1 and T2 T1-Relaxation: Recovery
Recovery of longitudinal orientation of M along z-axis.
‘T1 time’ refers to time interval for 63% recovery of longitudinal magnetization.
Spin-Lattice interactions.
T2-Relaxation: Dephasing
Loss of transverse magnetization Mxy.
‘T2 time’ refers to time interval for 37% loss of original transverse magnetization.
Spin-spin interactions,and more.

12. Properties of Body Tissues
T1 (ms)
T2 (ms)
Grey Matter (GM)
950
100
White Matter (WM)
600 80
Muscle
900 50
Cerebrospinal Fluid (CSF)
4500
2200
Fat
250 60
Blood
1200
T1 values for B0 ~ 1Tesla.
T2 ~ 1/10th T1 for soft tissues

13. Basic Physics of MRI: T1 and T2
T1 is shorter in fat (large molecules) and longer in CSF (small molecules). T1 contrast is higher for lower TRs.
T2 is shorter in fat and longer in CSF. Signal contrast increased with TE.
TR determines T1 contrast
TE determines T2 contrast.

14. Contrast, Imaging Parameters
T1W
T2W
r - proton density
SE – spin echo imaging
GRE – gradient echo imaging
Short TEs reduce T2W
Long TRs reduce T1W

15. Making an Image k-space (frequency domain) A k-space domain image is formed using frequency and phase encoding

16. Two Spaces k-space Image space ky y FT-1 x kx FT Final Image
Acquired Data
Image space x y
Final Image
FT-1 FT
MRI task is to acquire k-space image then transform to a spatial-domain image. kx is sampled (read out) in real time to give N samples. ky is adjusted before each readout.
MR image is the magnitude of the Fourier transform of the k-space image

17. The k-space Trajectory
Equations that govern 2D k-space trajectory
kx = g 0t Gx(t) dt
if Gx is constant kx = gGxt
ky = g 0t’ Gy(t) dt
if Gy is constant ky = gGyt’
The kx, ky frequency coordinates are established by durations (t) and strength of gradients (G).

18. Simple MRI Frequency Encoding:
RF Excitation
Slice
Selection (Gz)
Frequency
Encoding (Gx)
digitizer on
Readout
Exercise drawing k-space manipulation

19. Frequency Encoding Gradient (Gx)
The k-space Trajectory
Frequency Encoding Gradient (Gx)
Move to left side of k-space.
(0,0) ky
Digitizer records N samples along kx where ky = 0 kx

20. Simple MRI Frequency Encoding: Spin Echo
Excitation
Slice
Selection
Frequency
Encoding (Gx)
digitizer on
Readout
Exercise drawing k-space representation

21. The K-space Trajectory
180 pulse
Digitizer records N samples of kx where ky = 0

22. Frequency and Phase Encoding for 2D Spin Echo Imaging
digitizer on
Excite
Slice
Select
Frequency
Encode
Phase
Readout 90
180 kx ky

23. The 2D K-space Trajectory
180 pulse
Digitizer records N samples of kx and N samples of ky

24. Gradient Echo Imaging
Signal is generated by magnetic field refocusing mechanism only (the use of negative and positive gradient)
Signal intensity is governed by
S = So e-TE/T2*
Can be used to measure T2* value of the tissue
R2* = R2 + R2ih +R2ph (R2=1/T2)
Used in 3D and BOLD fMRI

25. MRI Pulse Sequence for Gradient Echo Imaging
Excitation
Slice
Selection
Frequency
Encoding
Phase
Encoding
digitizer on
Readout
Ernst angle (E) for optimum SNR .

26. FLASH Pulse Sequence TR1 TR2 TRN crusher crusher TRN/2 TRN/2 TRNB1
TR1
TR2
refocus Gz
TRN Gy
crusher
crusher Gx
acquire
TRN/2 B1
TRN/2
TRN Gz Gy
crusher
crusher
TR2 Gx
TR1
2D Gradient Echo
RF (10-15 degrees)
Short TR (10-50 msec)
N= 256 ( sec per slice)
Fig Courtesy of Peter Jezzard.

27. 3D Sequence (Gradient Echo)
acq kz Gx
read Gy
phase
Select
& phase Gz ky B1 kx RF
Scan time = NyNzTR
Good for high resolution T1W images of brain

28. 3D T1W brain image
0.8mm spacing
Time = 25 min

29. 2D Echo Planar Imaging (EPI)b) B1
refocus Gz Gy Gx
acquire
2d Gradient Echo
Entire 2D slice within one TR
64x64 or 128x128
Time per slice (30-50 msec)
Whole volume (2-4 sec)
Good for fMRI studies
Fig Courtesy of Peter Jezzard.

30. FLASH Image T2* Weighted
TE = 30 msec
CSF is bright
Signal loss and distortions due to local differences in magnetic field
Sources of Contrast in Brain
- Endogenous - BOLD
- Exogenous - could be contrast agent (Gd based)
- Other - Susceptibility
R2* = net T2 relaxation rate = 1/T2*
R2* = R2tis + R2ih + R2BOLD + R2suc
Fig courtesy of Peter Jezzard.

31. Quantitative Measurements Using fMRI Review
Chapter 8
Quantitative Measurements Using fMRI
Review

32. T2* fMRI Signal

33. From Neural Activity to fMRI Signal
Signalling
Vascular response
Vascular tone (reactivity)
Autoregulation
Metabolic signalling
BOLD signal
glia
arteriole
venule
B0 field
Synaptic signalling
Blood flow,
oxygenation
and volume
End bouton
dendrite
Complex relationship between change in neural activity and change in blood flow (CBF), oxygen consumption (CMRO2) and volume (CBV).

34. fMRI Bold Response Model
time
BOLD response, %
initial
dip
positive
BOLD response
post stimulus
undershoot
overshoot 1 2 3
stimulus
Initial dip 0.5-1sec
Overshoot peak 5-8 sec
+ BOLD response 2-3%
Final undershoot variable
Deoxyhemoglobin
BOLD signal
Figure 8.1. from textbook.

35. Graded BOLD Response
Graded change in signal for a) BOLD and b) perfusion (CBF).
3 minute visual pattern stimulation with different luminance levels.
Note max BOLD change of 2-3 % and max CBF change of %.
Figure 8.2. from textbook. N=12 subjects.

36. Perfusion vs. Volume Change
30 second stimulation
3-second intervals
DCBF rapid
DCBV slow
BOLD volume assessed using exogenous tracer that remains in blood.
In rat experiments TC for DCBV similar to that for BOLD overshoot.
Figure 8.4. from textbook.
Mandeville et al., 1999

37. Measurement of Cerebral Blood Flow with PET or MRI (Arterial Spin Labeling - ASL)+
511 keV
PET
Method
O-15 H20
Uses magnetically labeled arterial blood water as an endogenous flow tracer
Potentially provide quantifiable CBF in classical units (mL/min per 100 gm of tissue)
Detre et al., 1992

38. Arterial Spin Labelling
z (=B0)
inversion
slab
imaging
plane
excitation
blood y x
inversion
white matter = low perfusion
Gray matter = high perfusion
ASL is an example of a motion contrast
IMAGEperfusion = IMAGEuninverted – IMAGEinverted
Perfusion is useful for clinical studies: how much blood is getting to a region, how long does it take to get there?

39. Hardware for MRI Review
Chapter 5
Hardware for MRI
Review

40. 3T Siemens Trio 60 cm patient bore
40 mT/m max gradient amplitude per axis
200 T/m/sec slew rate
2nd order active shimming
~0.30 ppm B0 homogeneity over 40 cm sphere
self shielded
Shielding
Shims
Field Strength

41. A helium-cooled superconducting magnet generates the static field.
Always on: only quench field in emergency.
niobium titanium wire.
Coils allow us to
Make static field homogenous (shims: solenoid coils)
Briefly adjust magnetic field (gradients: solenoid coils)
Transmit, record RF signal (RF coils: antennas)
MRI Scanner Anatomy

42. Superconductor Magnet

43. Necessary Equipment Magnet Gradient Coils RF Coil 3T magnet RF Coil
(inside)
Magnet
Gradient Coils
RF Coil

44. Magnet Shielding and Shimming
Iron Shielding
Magnet
Shim coil
Gradient coil
RF coil
Subject
Shims
superconducting
static
room temperature
Figure 5.2 from textbook.

45. Gradient Coils
Sounds generated during imaging due to mechanical stress within gradient coils.

46. Current and Gradient Pulse Shapeb
a. gradient current supplied (short rise time induces eddy currents)
b. eddy currents oppose changing field w/o compensation
c. gradient current supplied with eddy current compensation
d. potential field vs time with eddy current compensation
Jerry Allison.

47. dB/dt Effect (more eddy currents) Peripheral Nerve Stimulation
dB/dt -- dE/dt
dt is gradient ramp time
dB/dt largest near ends of gradient coils
spatial gradient of dE/dt also important dB dt

48. dB/dt / E-Field Characteristics of Stimulation
Not dependent on B0
Gradients - 40mT/m (larger Bmax for longer coil)
Gradient Coil Differences - strength (increases dB) and length (head vs. body determines site)
Rise Time - shorter rise time means larger shorter dt and therefore larger dB/dt
Other
Disruption of nearby medical electronic devices
Subject Instructions
Don’t clasp hands - closed circuit, lower threshold
Report tingling, muscle twitching, painful sensations

49. MRI Scanner Components

50. Same or different transmit and receive coil.
Schematic of MRI System
Exciter
Synthesizer
XMTR
T/R
switch RF
Coil
Preamp
RCVR
A/P
RAM
Host
Pulse
programmer
Synthesizer, A/P
XMTR, RCVR, T/R
Shim
driver
coils
Gradient
Amps
Gx, Gy, Gz
Network
Same or different transmit and receive coil.
A/P - Array Processor
RF, Shim, Gradient Coils inside magnet
All but Host, RAM, and A/P in equipment room
Figure 5.1b from textbook.

51. RF Coil
RF Coils can transmit and receive RF signals (i.e. apply B1 and monitor Mxy)
A typical coil is a tuned LC circuit and may be considered a near-field antenna

52. Comprehensive Receiving coils
7 standard configuration：
QD head coil
QD Neck Coil
QD Body Coil
NSM-P035 Permanent Magnet MRI
QD Extremity Coil
Flat Spine Coil
Breast Coil

53. Surface Coils

54. RF Coil Uniformity and SNR50
100
150
200
250
400
600
800
1000
1200
1400
Surface coil/head coil comparison 1 2 3 4
17 cm spherical phantom
distance, mm b
(1)
(2)
(3)
(4)
B1 directions indicated by color arrows.
(1) two surface coils on opposite sides in phase.
(2) two surface coils out of phase.
(3) single surface coil on right side. (largest SNR)
(4) head coil. (most uniform SNR)
Figure 5.7 from textbook.

55. Stimulus Presentation / Monitoring

56. Additional Equipment Software Time-Line Control Stimulus
E-Prime
Software
Time-Line
Control Stimulus
Monitor Response
Synchronize timing with MRI

57. fMRI Study Time New Design Scanning Preprocessing Statistical Analysis
4+ hr (one instance)
New Design
Scanning
Setup
Scans
Take down
Preprocessing
Statistical Analysis
1-1.5 hr/subject
15-20 min
45 min to 1 hr
15 min
<2 hr/ subject 
variable

58. fMRI Study – All Data Total Data per subject can be 0.5-1.0 gBytes
Raw Data ~200 mBytes
Motion Correction ~180 mBytes
Other Corrections ~180 mBytes each possibly
Spatial Normalization ~ 30 mBytes
Statistical Analysis
Statistical Parametric Image (128x128x20) < 1 MByte
Statistical Parametric Map (2x SPI) > 1 MByte
Total Data per subject can be gBytes

59. Spatial and temporal resolution in fMRI Review
Chapter 7
Spatial and temporal resolution in fMRI
Review

60. Typical Paradigm Instruction Presentation stimulation timing
fMRI responses
time (s)
Trial #1
Trial #2
Presentation
Response
Behaviour 5
Instruction
Presentation
stimulation
timing
Processing
sensing
decision
Response
plan
motor
Task
Behavior
BOLD signal time course
presentation (black)
processing (light grey)
response (dark grey)
Onset and Width of BOLD response as temporal measures.
---- Not time to peak ----
Figure 7.4 from textbook.

61. Estimating Neural Processing Time From BOLD Response Onset
350
300
250
200
150
-50 50
100  
kinematic RT (ms)
BOLD onset difference (ms)
(b) V1
SMA M1
time
fMRI response ampitude  
(a)
Figure 7.5 from textbook.
Task – use joystick to move cursor from start box to target box as rapidly and accurately as possible (10 trials in multiple subjects).
BOLD response – V1 (primary visual cortex), SMA (supplementary motor area), M1 (primary motor area)
Analysis – D but not t increases with increasing reaction time (RT).
Conclusion – Delay in reaction time from planning rather than execution of movement.

62. Estimating Neural Processing Time From from BOLD Response Width
fMRI signal change from SPL
Time after presentation (s) . 9 8 1 2 3
fMRI
(b) 5
Trial A
Trial B
RT(A) RT(B)
Task
(a)
Task – determine if one object could be rotated to match a second. Rotation angle varied by design. Press button yes or no.
BOLD response – Superior Parietal Lobule (SPL)
Analysis – Normalized width of BOLD response correlated with reaction time (RT).
Conclusion – SPL intimately involved in mental rotation of object.
(c) 1 6 2 8 4
Normalized width of BOLD response (s) R e a c t i o n T m ( s )
Figure 7.6 from textbook.

63. Selection of optimal pulse sequences for fMRI Review
Chapter 6
Selection of optimal pulse sequences for fMRI
Review

64. Advantages
Disadvantages
BOLD
Highest activation contrast 2x-4x over perfusion
complicated non-quantitative signal
easiest to implement
no baseline information
multislice trivial
susceptibility artifacts
can use very short TR
Perfusion
unique and quantitative information
low activation contrast
baseline information
longer TR required
easy control over observed vasculature
multislice is difficult
non-invasive
slow mapping of baseline information
no susceptibility artifacts
Table 6.1a. Summary of practical advantages and disadvantages of pulse sequences (derived from textbook)

65. Time/secs 1 2 4 3 Perfusion TI ASL3
Perfusion
Venous outflow
Venous outflow No
Velocity
Nulling
Velocity
Nulling
Arteries
Arterioles
Capillaries
Venules
Veins TI
ASL
Figure 6.1a Signal is detected from water spins in the arterial-capillary region of the vasculature and from water in tissues surrounding the capillaries. Relative sensitivity controlled by adjusting TI and by incorporating velocity nulling gradients (also known as diffusion weighting). Nulling and TI~1 sec makes ASL sensitive to capillaries and surrounds.

66. Time/secs 1 2 4 3
Arterial inflow
(BOLD TR < 500 ms)
GE-BOLD No
Velocity
Nulling
Velocity
Nulling
Arteries
Arterioles
Capillaries
Venules
Veins
Figure 6.1b Gradient Echo BOLD is sensitive to susceptibility perturbers of all sizes, and are therefore sensitive to all intravasculature and extravascular effects in the capillary-venous portions of the vasculature. If a very short TR is used may show signal from arterial inflow, which can be removed by using a longer TR and/or outer volume saturation.

67. Time/secs 1 2 4 3
Arterial inflow
(BOLD TR < 500 ms)
SE-BOLD No
Velocity
Nulling
Velocity
Nulling
Arteries
Arterioles
Capillaries
Venules
Veins
Figure 6.1c Spin Echo BOLD is sensitive to susceptibility perturbers about the size of a red blood cell or capillary, making it predominantly sensitive to intravascular water spins in vessels of all sizes and to extravascular (tissue) water surrounding capillaries. Velocity nulling reduces the signals from larger vessesl.

68. Gradient-echo RF Gx Gz Gy
90° TE
ASL
pulse TI
Spin-echo
180° TE RF Gx Gz Gy
ASL
pulse TI
90°
spin-echo
180° TE RF Gx Gz Gy
90° t
t/2
Figure 6.2 Pulse sequence diagrams of (a) gradient echo, (b) spin echo, and (c) asymmetric spin echo EPI. The TE is shown at the center of 9-line k-space (typically 64 or more lines).  is the offset from center of k-space to echo. Additional pulses needed for ASL are indicated schematically.

69. Chapter 4
Ultrafast fMRI
Review

70. Effects of Field Homogeneity
R2* = R2 + R2mi +R2ma
R2 = transverse relaxation rate due to spin-spin interactions and diffusion through microscopic gradients
R2mi = transverse relaxation rate due to microscopic changes, i.e. deoxyhemoglobin
R2ma = transverse relaxation rate due to macroscopic field inhomogeneity
R2*a is relaxation rate during activation
R2*r is relaxation rate at rest

71. 4x4x4 mm3
2x2x2 mm3
Spin Echo
Gradient Echo EPI
Fig. 4.3 EPI obtained with TE= 60 and TR=3000 msec and 63 and 95 ky lines. Note recovery of signal loss in d vs c and ghosting in c.

72. For EPI where is the readout signal largest?
gradient
echo
readout window
r.f.
read gradient TE
dephase
rephase
Fig. 4.5 Gradient echo (GE) echo forms at center of readout window where area under rephasing gradient = area of dephasing gradient. Unlike spin echo dephasing is due to spatial difference in Larmor frequencies during application of gradients. First half of readout window is rephasing and second half is dephasing again. This process repeats at the center of readout window for each ky line in k-space for EPI.
For EPI where is the readout signal largest?

73. RF
Slice
Read
Phase a)
Read
Phase b) n
n-1 1
n-1 2 n 2 1
Fig GE EPI pulse sequence and k-space organization of samples.
What flip angle is used for EPI?

74. Effect of system parameters on EPI images for fixed field of view.
Echo Spacing
Resolution
SNR
Geometric distortion
Increase gradient slew rate
Reduced
---
Increase sampling bandwidth (kx)
Increase number of shots (interleaving ky)
Increased
Use of ramp sampling (similar to slew rate effect)
Increase read matrix (kx)
Increase phase matrix (ky)
Increased*
Increase field strength
Table 4.1 from text.
* actual resolution increase less than expected due to smoothing effect of signal decay.

75. fMRI methods for reduced k-space coverage
Keyhole
acquire full k-space as reference
acquire reduced low-frequency k-space fMRI study
fill in missing k-space from reference
Half-Fourier
acquire 50-60% of k-space starting at highest ky
theoretical symmetry used to fill in missing ky

76. fMRI methods for reduced k-space coverage
Sensitivity encoding (SENSE)
Multiple RF coils with independent signal for each (parallel imaging)
Calibration maps from full k-space
each coil part of k-space
2X improvement EPI, 4X for GE
UNFOLD
Acquire k-space in sequential time segments
time 1 acquire lines 1, 5, 9,
time 2 acquire lines 2, 6, 10,
time 3 acquire lines 3, 7, 11,
time 4 acquire lines 4, 8, 12,
reorder into k-space
4x faster per segment reduces inter echo distortions