![Page 1: BMB 601 MRI - mmrrcc.upenn.edu€¦ · slide 9 Gradients To spatially encode the MRI signal slide 10 Image Contrast Contrast in MRI based on differences in: Relaxation times (T 1,](https://reader034.vdocuments.net/reader034/viewer/2022042916/5f56dac9cc65466fcb103346/html5/thumbnails/1.jpg)
2/3/11
1
A r i B o r t h a k u r, P h D
A s s i s t a n t P r o f e s s o r , D e p a r t m e n t o f R a d i o l o g y A s s o c i a t e D i r e c t o r , C e n t e r f o r M a g n e t i c R e s o n a n c e & O p t i c a l I m a g i n g
U n i v e r s i t y o f P e n n s y l v a n i a S c h o o l o f M e d i c i n e
BMB 601 MRI
slide 2
A brief history…
Isidor Rabi wins Nobel prize in Physics (1944) for for his resonance method for recording the magnetic properties of atomic nuclei.
Felix Bloch and Edward Purcell share Nobel Prize in Physics (1952) for discovery of magnetic resonance phenomenon.
Richard Ernst wins Nobel Prize in Chemistry (1991) for 2D Fourier Transform NMR.
His post-doc, Kurt Wuthrich awarded a Nobel Prize in Chemistry (2002) for 3D structure of macromolecules.
Nobel Prize in Physiology & Medicine awarded to Sir Peter Mansfield and Paul Lauterbur (2003) for MRI.
Who’s next? Seiji Ogawa for BOLD fMRI?
![Page 2: BMB 601 MRI - mmrrcc.upenn.edu€¦ · slide 9 Gradients To spatially encode the MRI signal slide 10 Image Contrast Contrast in MRI based on differences in: Relaxation times (T 1,](https://reader034.vdocuments.net/reader034/viewer/2022042916/5f56dac9cc65466fcb103346/html5/thumbnails/2.jpg)
2/3/11
2
slide 3
Outline Slide
# 3
Hardware: MRI scanner RF coil Gradients
Image contrast Software:
Pulse sequences Fourier Transform
slide 4
How does it work?
http://www.med.harvard.edu/AANLIB/cases/case17/mra.mpg
![Page 3: BMB 601 MRI - mmrrcc.upenn.edu€¦ · slide 9 Gradients To spatially encode the MRI signal slide 10 Image Contrast Contrast in MRI based on differences in: Relaxation times (T 1,](https://reader034.vdocuments.net/reader034/viewer/2022042916/5f56dac9cc65466fcb103346/html5/thumbnails/3.jpg)
2/3/11
3
slide 5
Original Concept*
1. Rotating Gradient 2. Filtered Back-projection
*Lauterbur, Nature (1973)
slide 6
Fourier Imaging*
1. Three orthogonal gradients: Slice Selection Phase Encoding Frequency Encoding
2. k-space Representation of encoded signal
*Kumar, et al. J. Magn. Reson. (1975)
![Page 4: BMB 601 MRI - mmrrcc.upenn.edu€¦ · slide 9 Gradients To spatially encode the MRI signal slide 10 Image Contrast Contrast in MRI based on differences in: Relaxation times (T 1,](https://reader034.vdocuments.net/reader034/viewer/2022042916/5f56dac9cc65466fcb103346/html5/thumbnails/4.jpg)
2/3/11
4
slide 7
MRI scanners
19 Tesla 4.7 Tesla 1.5 Tesla
To generate B0 field and create polarization (M0)
slide 8
MRI coils
Head coil
Mouse MRI platform
Torso coil To transmit RF field (B1) and receive signal
![Page 5: BMB 601 MRI - mmrrcc.upenn.edu€¦ · slide 9 Gradients To spatially encode the MRI signal slide 10 Image Contrast Contrast in MRI based on differences in: Relaxation times (T 1,](https://reader034.vdocuments.net/reader034/viewer/2022042916/5f56dac9cc65466fcb103346/html5/thumbnails/5.jpg)
2/3/11
5
slide 9
Gradients
To spatially encode the MRI signal
slide 10
Image Contrast
Contrast in MRI based on differences in: Relaxation times (T1, T2, T2
*, T1ρ) Local environment
Magnetization = spin density Concentration of water, sodium, phosphorous etc.
Macromolecular interactions Chemical-exchange, dipole-dipole, quadrupolar interactions
Contrast agents Gadolium-based, iron-oxide, manganese
![Page 6: BMB 601 MRI - mmrrcc.upenn.edu€¦ · slide 9 Gradients To spatially encode the MRI signal slide 10 Image Contrast Contrast in MRI based on differences in: Relaxation times (T 1,](https://reader034.vdocuments.net/reader034/viewer/2022042916/5f56dac9cc65466fcb103346/html5/thumbnails/6.jpg)
2/3/11
6
slide 11
Magnetization
Bitar et al. RadioGraphics (2006)
“spin” “spin ensemble” spin-up or
spin-down =
Boltzmann distribution
Net Magnetic Moment
slide 12
Energy levels
Larmor Equation
Energy gap
N+/N- = exp (-ΔE/kBT) Boltzmann distribution
![Page 7: BMB 601 MRI - mmrrcc.upenn.edu€¦ · slide 9 Gradients To spatially encode the MRI signal slide 10 Image Contrast Contrast in MRI based on differences in: Relaxation times (T 1,](https://reader034.vdocuments.net/reader034/viewer/2022042916/5f56dac9cc65466fcb103346/html5/thumbnails/7.jpg)
2/3/11
7
slide 13
MR experiment
M0 aligned along B0 Mz=M0
RF pulse applied in x-y “transverse”
plane
M “nutates” down to x-y plane
Mz=M0cosα and
Mxy=M0sinα
RF off
Detect Mxy signal
in the same RF coil
slide 14
Equation of motion
Bloch Equation (simple form)
![Page 8: BMB 601 MRI - mmrrcc.upenn.edu€¦ · slide 9 Gradients To spatially encode the MRI signal slide 10 Image Contrast Contrast in MRI based on differences in: Relaxation times (T 1,](https://reader034.vdocuments.net/reader034/viewer/2022042916/5f56dac9cc65466fcb103346/html5/thumbnails/8.jpg)
2/3/11
8
slide 15
Effect of RF pulse
The 2nd B field
Choosing a frame of reference rotating at ωrf, makes B1 appear static:
slide 16
Nutation
Lab frame of reference e.g. B1 oscillating in x-y plane
Rotating frame of reference e.g. B1 along y-axis
http://www-mrsrl.stanford.edu/ ~brian/mri-movies/
![Page 9: BMB 601 MRI - mmrrcc.upenn.edu€¦ · slide 9 Gradients To spatially encode the MRI signal slide 10 Image Contrast Contrast in MRI based on differences in: Relaxation times (T 1,](https://reader034.vdocuments.net/reader034/viewer/2022042916/5f56dac9cc65466fcb103346/html5/thumbnails/9.jpg)
2/3/11
9
slide 17
After RF pulse-Relaxation
Spin-Lattice relaxation time=return to thermal equilibrium M0
Spin-spin relaxation with reversible dephasing
Spin-spin relaxation without “reversible” dephasing
T1>T2>T2*
slide 18
Signal detection
http://www-mrsrl.stanford.edu/ ~brian/mri-movies/
![Page 10: BMB 601 MRI - mmrrcc.upenn.edu€¦ · slide 9 Gradients To spatially encode the MRI signal slide 10 Image Contrast Contrast in MRI based on differences in: Relaxation times (T 1,](https://reader034.vdocuments.net/reader034/viewer/2022042916/5f56dac9cc65466fcb103346/html5/thumbnails/10.jpg)
2/3/11
10
slide 19
How does MRI work?
Water Fat 4.7 ppm 1.2 ppm
NMR signal
? =
MR Image
1) Spatial encoding gradients 2) Fourier transform
slide 20
Pulse Sequence (timing diagram)
Less MRI time/low image quality
RF
phase
slice
freq
90°
TE
Echo planar imaging
Less
MRI
tim
e/lo
w im
age
qual
ity
RF
phase slice
freq
90°
TE
Spin-echo TR
180°
RF
phase slice
freq
α (<90°)
TE
Gradient-echo TR
RF
phase slice
freq
90°
Fast spin-echo TR
180° 180° 180°
![Page 11: BMB 601 MRI - mmrrcc.upenn.edu€¦ · slide 9 Gradients To spatially encode the MRI signal slide 10 Image Contrast Contrast in MRI based on differences in: Relaxation times (T 1,](https://reader034.vdocuments.net/reader034/viewer/2022042916/5f56dac9cc65466fcb103346/html5/thumbnails/11.jpg)
2/3/11
11
slide 21
MRI
B0 M0 B1
Gz
Gx
Gy
slide 22
RF
phase
slice
freq
α
TE
Gradient-echo
TR
Slice Selection*
*Mansfield, et al. J. Magn. Reson. (1976) *Hoult, J. Magn. Reson. (1977)
![Page 12: BMB 601 MRI - mmrrcc.upenn.edu€¦ · slide 9 Gradients To spatially encode the MRI signal slide 10 Image Contrast Contrast in MRI based on differences in: Relaxation times (T 1,](https://reader034.vdocuments.net/reader034/viewer/2022042916/5f56dac9cc65466fcb103346/html5/thumbnails/12.jpg)
2/3/11
12
slide 23
Mz
Slice Selection
B0
Mz
Mz
Mxy γGz•z RF
BWRF= γGz•Δz
Δz{
slide 24
Frequency Encoding*
RF
phase
slice
freq
α
TE
Gradient-echo
TR
*Kumar, et al. J. Magn. Reson. (1975)
a.k.a “readout”
![Page 13: BMB 601 MRI - mmrrcc.upenn.edu€¦ · slide 9 Gradients To spatially encode the MRI signal slide 10 Image Contrast Contrast in MRI based on differences in: Relaxation times (T 1,](https://reader034.vdocuments.net/reader034/viewer/2022042916/5f56dac9cc65466fcb103346/html5/thumbnails/13.jpg)
2/3/11
13
slide 25
Frequency Encoding
Mz
γGx•x
BWread= γGx•FOVx
FOVx
slide 26
RF
phase
slice
freq
α
TE
Gradient-echo
TR
Phase Encoding*
*Kumar, et al. J. Magn. Reson. (1975) *Edelstein, et al. Phys. Med. Biol. (1980)
τpe
![Page 14: BMB 601 MRI - mmrrcc.upenn.edu€¦ · slide 9 Gradients To spatially encode the MRI signal slide 10 Image Contrast Contrast in MRI based on differences in: Relaxation times (T 1,](https://reader034.vdocuments.net/reader034/viewer/2022042916/5f56dac9cc65466fcb103346/html5/thumbnails/14.jpg)
2/3/11
14
slide 27
Phase Encoding
γGy2•y
1/τpe= γΔGy•FOVy
FOVy
γGy1•y
γGy0•y
Each PE step imparts a different phase twist to the magnetization along y
slide 28
Traversing k-space
Spin-warp imaging*
RF
phase
slice
freq
α
TE
Gradient-echo
TR
ky
kx
*Edelstein, et al. Phys. Med. Biol. (1980)
![Page 15: BMB 601 MRI - mmrrcc.upenn.edu€¦ · slide 9 Gradients To spatially encode the MRI signal slide 10 Image Contrast Contrast in MRI based on differences in: Relaxation times (T 1,](https://reader034.vdocuments.net/reader034/viewer/2022042916/5f56dac9cc65466fcb103346/html5/thumbnails/15.jpg)
2/3/11
15
slide 29
FT
k-space
freq phase
image
Fourier Transform
slide 30
Spiral Radial Echo-planar
phase
freq
Echo planar freq
freq
Radial
freq
freq Spiral
Traversing k-space
![Page 16: BMB 601 MRI - mmrrcc.upenn.edu€¦ · slide 9 Gradients To spatially encode the MRI signal slide 10 Image Contrast Contrast in MRI based on differences in: Relaxation times (T 1,](https://reader034.vdocuments.net/reader034/viewer/2022042916/5f56dac9cc65466fcb103346/html5/thumbnails/16.jpg)
2/3/11
16
slide 31
Fourier Transform
slide 32
Typical FT pairs
![Page 17: BMB 601 MRI - mmrrcc.upenn.edu€¦ · slide 9 Gradients To spatially encode the MRI signal slide 10 Image Contrast Contrast in MRI based on differences in: Relaxation times (T 1,](https://reader034.vdocuments.net/reader034/viewer/2022042916/5f56dac9cc65466fcb103346/html5/thumbnails/17.jpg)
2/3/11
17
slide 33
K-space
The signal a coil receives is from the whole object:
€
S tx ,ty( ) = ρ x,y( )eiγ Gxtx ⋅x+Gyty ⋅y( )dxdy∫∫
€
kx, y = γGx, ytx, y
€
S kx ,ky( ) = ρ x,y( )eiγ kx ⋅x+ ky ⋅y( )dxdy∫∫
The image is a 2D FT of the k-space signal*:
€
ρ x,y( ) = S kx ,ky( )e−iγ kx ⋅x+ ky ⋅y( )dkxdky∫∫
*Kumar, et al. J. Magn. Reson. (1975)
replace:
K-space signal:
slide 34
K-space weighting
High-frequency data=edges
Low-frequency data=contrast/signal
![Page 18: BMB 601 MRI - mmrrcc.upenn.edu€¦ · slide 9 Gradients To spatially encode the MRI signal slide 10 Image Contrast Contrast in MRI based on differences in: Relaxation times (T 1,](https://reader034.vdocuments.net/reader034/viewer/2022042916/5f56dac9cc65466fcb103346/html5/thumbnails/18.jpg)
2/3/11
18
slide 35
What is wrong?
Original
Freq. de-phaser too large!
*Pauly, http://www.stanford.edu/class/ee369b/tests/mt_sol.pdf
slide 36
What is wrong?
Original
ky step was too large or FOVy was too small!
![Page 19: BMB 601 MRI - mmrrcc.upenn.edu€¦ · slide 9 Gradients To spatially encode the MRI signal slide 10 Image Contrast Contrast in MRI based on differences in: Relaxation times (T 1,](https://reader034.vdocuments.net/reader034/viewer/2022042916/5f56dac9cc65466fcb103346/html5/thumbnails/19.jpg)
2/3/11
19
slide 37
What is wrong?
Original
Freq. gradient amplitude was too low!
slide 38
MRI Examples
![Page 20: BMB 601 MRI - mmrrcc.upenn.edu€¦ · slide 9 Gradients To spatially encode the MRI signal slide 10 Image Contrast Contrast in MRI based on differences in: Relaxation times (T 1,](https://reader034.vdocuments.net/reader034/viewer/2022042916/5f56dac9cc65466fcb103346/html5/thumbnails/20.jpg)
2/3/11
20
slide 39
3D Neuro MRI
slide 40
Susceptibility-Weighted Imaging (SWI)
![Page 21: BMB 601 MRI - mmrrcc.upenn.edu€¦ · slide 9 Gradients To spatially encode the MRI signal slide 10 Image Contrast Contrast in MRI based on differences in: Relaxation times (T 1,](https://reader034.vdocuments.net/reader034/viewer/2022042916/5f56dac9cc65466fcb103346/html5/thumbnails/21.jpg)
2/3/11
21
slide 41
BOLD fMRI
slide 42
Phase Contrast MR Angiography
![Page 22: BMB 601 MRI - mmrrcc.upenn.edu€¦ · slide 9 Gradients To spatially encode the MRI signal slide 10 Image Contrast Contrast in MRI based on differences in: Relaxation times (T 1,](https://reader034.vdocuments.net/reader034/viewer/2022042916/5f56dac9cc65466fcb103346/html5/thumbnails/22.jpg)
2/3/11
22
slide 43
TSE Fat Saturated
TSE TE = 25 ms
Resolution:200x200µm2
slide 44
![Page 23: BMB 601 MRI - mmrrcc.upenn.edu€¦ · slide 9 Gradients To spatially encode the MRI signal slide 10 Image Contrast Contrast in MRI based on differences in: Relaxation times (T 1,](https://reader034.vdocuments.net/reader034/viewer/2022042916/5f56dac9cc65466fcb103346/html5/thumbnails/23.jpg)
2/3/11
23
slide 45
Rationale for Sodium MRI
[PG] decreases with Degeneration
Urban et al Spine 1998
slide 46
Rationale for Sodium MRI
Sodium is a natural biomarker for PG
Urban and Maroudas Bioc. Biop. Acta 1979 Urban and Winlove, J. Magn. Reson. Imag. 2007
![Page 24: BMB 601 MRI - mmrrcc.upenn.edu€¦ · slide 9 Gradients To spatially encode the MRI signal slide 10 Image Contrast Contrast in MRI based on differences in: Relaxation times (T 1,](https://reader034.vdocuments.net/reader034/viewer/2022042916/5f56dac9cc65466fcb103346/html5/thumbnails/24.jpg)
2/3/11
24
slide 47
How is [Na] related to [PG]?
Fixed Charge Density (FCD) Side chains of PG [Na] correlated with [PG] through [FCD]
Maroudas et al., in Adult Articular Cartilage (1979) Lesperance et al., J. Orthop. Res. (1992)
slide 48
Sodium MRI
What do you need?
1. RF coil 2. Transmit/receive switch 3. Broadband capable scanner (all vendors) 4. A short echo-time MRI pulse sequence
![Page 25: BMB 601 MRI - mmrrcc.upenn.edu€¦ · slide 9 Gradients To spatially encode the MRI signal slide 10 Image Contrast Contrast in MRI based on differences in: Relaxation times (T 1,](https://reader034.vdocuments.net/reader034/viewer/2022042916/5f56dac9cc65466fcb103346/html5/thumbnails/25.jpg)
2/3/11
25
slide 49
Sodium MRI Ex Vivo
Wang et al., Spine (2010)
• Sodium maps in bovine discs
slide 50
Sodium MRI Ex Vivo
Wang et al., Spine (2010)
Sodium content vs. PG content
![Page 26: BMB 601 MRI - mmrrcc.upenn.edu€¦ · slide 9 Gradients To spatially encode the MRI signal slide 10 Image Contrast Contrast in MRI based on differences in: Relaxation times (T 1,](https://reader034.vdocuments.net/reader034/viewer/2022042916/5f56dac9cc65466fcb103346/html5/thumbnails/26.jpg)
2/3/11
26
slide 51
Sodium MRI In Vivo
Wang et al., Spine (2010)
• Sodium mapping vs. T2 MRI
slide 52
New 7T MRI!
ultra-short echo pulse sequence
TE/TR=200µs/25ms 2mm isotropic 15 minute acquisition
![Page 27: BMB 601 MRI - mmrrcc.upenn.edu€¦ · slide 9 Gradients To spatially encode the MRI signal slide 10 Image Contrast Contrast in MRI based on differences in: Relaxation times (T 1,](https://reader034.vdocuments.net/reader034/viewer/2022042916/5f56dac9cc65466fcb103346/html5/thumbnails/27.jpg)
2/3/11
27
slide 53
Sodium MRI Movies
Axial Coronal Sagittal
slide 54
Sodium MRI Montage
SNR ~26:1 in cartilage
![Page 28: BMB 601 MRI - mmrrcc.upenn.edu€¦ · slide 9 Gradients To spatially encode the MRI signal slide 10 Image Contrast Contrast in MRI based on differences in: Relaxation times (T 1,](https://reader034.vdocuments.net/reader034/viewer/2022042916/5f56dac9cc65466fcb103346/html5/thumbnails/28.jpg)
2/3/11
28
slide 55
Take home… Slide # 55
Magnet Create B0 Produce M0
RF coil Transmit B1 field Detect Signal
Image contrast Relaxation, concentration, interactions etc.
Gradients Spatial encoding Signal in k-space
Fourier Transform From k-space to image space
Pulse sequences Traverse k-space Image Artifacts