I t d tiI t d tiIntroduction Introduction to to
M ti R I i (MRI) Ph iM ti R I i (MRI) Ph i
David C. Zhu, Ph.D.
Magnetic Resonance Imaging (MRI) PhysicsMagnetic Resonance Imaging (MRI) Physics
Cognitive Imaging Research CenterAssociate Professor of Radiology, Psychology
and (adjunct) Electrical & Computer Engineeringand (adjunct) Electrical & Computer Engineering
Text Book Suggestiongg
Functional Magnetic Resonance Imaging, Third Edition (August 2014) by Scott A Huettel Allen WEdition (August, 2014) by Scott A. Huettel Allen W. Song Gregory McCarthy, Sinauer Associates, Inc.
Traditional Imaging
TT1weighted
T2weighted
T2 FLAIR T2* weighted
Blood flow Cerebral blood flow (perfusion)(perfusion)
Ventricle movement
Cerebrospinal fluid dynamics
Zhu DC, Xenos M, Linninger AA and Penn RD. D i f l t l t i l d b i l fl id iDynamics of lateral ventricle and cerebrospinal fluid in normal and hydrocephalic brains. J Magn Reson Imaging. 2006;24:756-770.
Carotid Plaque Hemorrhage Detection and Characterizationwith 3D SHINE
≥ 28 ms T2*
14 ms
21 ms
3D SHINE & T2* map 3D SHINE & T2* map
14 ms
7 ms
0 ms
Type II
(b) (c)(a)
Type I
( ) ( )
Zhu DC, Vu AT, Ota H, DeMarco JK. Magn Reson Med. 2010;64:1341-1351.
A happy volunteer after surviving an fMRI session
MMeNo hair Brain only
RED regions: Activated when seeing scenes.
Orange regions: Activated more to indoor thanindoor than outdoor scenes.
BLUE regions:Activated when
Henderson JM, Larson CL, Zhu DC. 2007 & 2008.
Activated when seeing faces.
Diffusion Tensor Imaging
The brain functional network called default-mode network (in RED), which can be identified with 7 minutes
f MRI iof MRI scanning.
Normal brains of Brains with older adults Alzheimer’s disease
Green regions: functional connection.
OOrange regions: Structural connection
Zhu DC, Majumdar S, Korolev IO, Berger KL, Bozoki AC. Journal of Alzheimer's Disease. 2013.
connection.
Data acquisitionPulse sequence development
Types of Research
- Pulse sequence development- Image reconstruction technique development- Coil development
Data analysis- Statistical method
D i i- Data mining- Resting state
Vi li iVisualization- Pattern recognition- Human-computer interfacesp
Applications- Normal aging, Resting state, Alzheimer.g g g-Visual, Language, Executive processing, Memory- …………
GoalsGoalsGoalsGoals
1. Basic concepts of MRI2. Basic meanings of TE, TR, T1, T2, T2*, k space, EPI
An atom
Nucleusp+
e- p+
n
C l t d i MRICommon elements used in MRI:
1H, 13C, 23Na, 31P
Hydrogen
Nucleus
e- p+
( we have a lot of H2O)!
Spin Physics1H ( t ) classically:1H (proton)
Angular Momentum (spinspin)N
classically:
Magnetic dipole
Magnetic field B
S
Magnetic field B
Quantized to lower and higher energy states with a Boltzmann distribution: ~ 3 ppm/T excess in lower energy.
dM M B= ×γ
Bloch Equation:
ω γ= Bdt
M B= ×γ
M = magnetization = net magnetic moment for all spins in a sample
ω = Larmor frequencyγ= 42.58 MHz/T for protonγ
ω ≅ 128 MHz at 3 TE = h ω, h = 6.626 x 10-34 J S
JT Bushberg, JA Seibert, EW Leidholdt Jr., and JM Boone. The Essential Physics of Medical Imaging
A happy volunteer after surviving a fMRI session
Magnet
Superconducting electromagnets
Magnet
Gradient coils -261°C
RF coilsZero i t
Subject body
resistance
Coil for the static magnetic field
Gradient Coil
RF coils (Transmit and Receive)
surface coil volume coil phased-array coil
Magnetic Resonance Imaging Hardware Interface in Control RoomInterface in Control Room
fMRI stimulusfMRI stimulus presentation system
3T magnet Room
Equipment Room:Equipment Room:Gradient amplifiers
RF amplifierP l tPulse sequence generator
Image reconstruction
Spin-Lattice (T1) and Spin-Spin (T2) Relaxation Processes
(T2 becomes T2* if local field is inhomogeneous)
Z
M S i f t (dephasing)Z
M
Y
B0
Spins fan out (dephasing)
T2 decay
Longitudinal magnetization YInitial 90°
XT1 recovery
re-growth
X
T deca and
T2 decay andT1 recovery
RF excitation
vector summation
Z
T2 decay andT1 recoverycontinueBack to
equilibrium state
1 ycontinue
TE = time of echo
TR = time of repetition
YRF
TE time of echo
X
T2* Decay and T1 Recovery Movie 1
http://www.stanford.edu/class/ee369b/Site/Movies.html
T2* Decay and T1 Recovery Movie 2
*2|)0(M||)(M| xyxyT
t
et −=
)1(M)(M 10z
Tt
et −−=
*21 )1(0TTE
TTR
eekMS −−−=
Courtesy of Brian Hargreaves. http://www-mrsrl.stanford.edu/~brian/mri-movies/
TR = 3sGradient Echo
TR = 3s
TE = 6.9 ms TE = 45 ms
Z
Y
X 128 MHzX
Z Z
128 MHz
Y Y
X X
127.9999 MHz 128.0001 MHz
Z
Y
X
Explanation of T2* decay
3.000 T 3.000 T
After 3 ms 3.000 T 3.000 T
Vectorsum
3.000 T 3.000 T 3.000 T 3.000 T
Af3+10-6 T 3.000 T
After 3 ms
Vectorsum3+10-6 T 3.000 T
3+2×10-6 T 3-10-6 T 3+2×10-6 T 3-10-6 T
Spin Echo Techniques(Obtain the effect of T2 instead of T2* )
Spins fan out (dephasing) ZZ
M
Initial 90°
p ( p g)
T2* decay
Y
180° RF excitation
TE/2
M
Y
B0
Initial 90RF excitation
X
TE/2
X
ZZ
YY
TE/2XX
Spin Echo Technique
Courtesy of Brian Hargreaves. http://www-mrsrl.stanford.edu/~brian/mri-movies/
Spin Echo
TE 13 TE 90
Proton density weighted
T2 weighted T1 weightedTE = 13 msTR 900TE = 13 ms TE = 90 ms
TR = 3 s
TR = 900 ms
TR 3 s21 )1(0
TTE
TTR
eekMS −−−=
Laboratory Frame
Courtesy of Brian Hargreaves. http://www-mrsrl.stanford.edu/~brian/mri-movies/
Rotating Frame
Courtesy of Brian Hargreaves. http://www-mrsrl.stanford.edu/~brian/mri-movies/
Long
T1
Relaxationtime
1
T2
Short
Molecular motion: slow intermediate fastllMolecular size:
Molecular interactions:
large intermediateintermediate
small
bound free
JT Bushberg, JA Seibert, EW Leidholdt Jr., and JM Boone. The Essential Physics of Medical Imaging
B
B B G Zz= + ⋅0
Slice Selection
Z
- Z1
Z1B0
B G Zz0 1+ ⋅
2 1G Zz ⋅
ω
ω ω γ= + ⋅0 G Zz
B G Zz0 1− ⋅
Z
- Z1
Z1ω0
ω γ0 1+ ⋅G Zz
G Z
2 1γG Zz ⋅
(a)
ω γ0 1− ⋅G Zz
(b)
RF coil
M
Gradient coils
RF with a narrow bandwidth Slice-select gradient
Y Magnet
B0ZX
Y
Excite a slice of tissue
B0
X
ZSpatial encoding using a gradient pulse
G
ωxYrotγ ⋅ ⋅ ⋅G X tx 1
Gx
ω ω γ= + ⋅0 G Xx
ω γ0 1+ ⋅G Xx
Xrot
x 1
X
- X1
X1
ω0
ω γ− ⋅G X
(b) At X1
Zω γ0 1− ⋅G XxZ
G X t(a)
Yrot
γ ⋅ ⋅ ⋅G X tx 1
Phase offset relative to rotating frame at ω0Xrot
(c) At –X1
g 0
00 Bγω =
TR (time of repetition)
TE (time of echo)
Xgradient
( )
Gx
Gx tTx/2 Tx/2
Tx/2
Ygradient
t = 0
Gy Gradient Echo Sequence
Zgradient
Ty
TGz
Sequence
RF
g Tz
Tz/2
RF
DataAcquisitionAcquisition
Data acquisitionwindow
Acquire signal (Fourier Transform)
Frequency domain (k space)
Inverse Fourier Transform
Space domain
Dr. Seiji Ogawa
cycles/millimeter
millimeter
Transformation
Britney Spears on earth Britney Spears on Mars
ky (Δky = 1/yfov)
(yres-1)/2
K space (Spatial Frequency Domain)
1st ky line
2nd ky line
3rd ky line
Xgradient
Gx
Gx tTx/2 Tx/2
Tx/2
-(xres-1)/2 (xres-1)/2Y
gradient
t = 0
Gy
kx (Δkx = 1/xfov)
( )
Ty
(k -2)th k line ∫=t
xx dGk02
τγπ
ykixkixyxy
yxTt
eeeyxMtyxM ππ 222)0,,(),,( −−−=
(kymax)th ky line
(kymax -1)th ky line
(kymax 2)th ky line
(yres 1)/2
∫∫
∫
∫
=t
yy dGk0
0
2
2
τγπ
π
-(yres-1)/2
dxdyeeeyxMk
dxdytyxMktSykixki
xy
xy
yxTt ππ 22
0
0
])0,,([
),,()(
2 −−−
∫∫∫∫
=
=
EPI Pulse Sequence
X Grad
Y Grad
Z GradZ Grad
RF
Time
EPI Pulse SequenceK space
Typical 64 × 64
KyTE
X Grad
Y Grad
63rd Ky line
Z Grad33rd Ky line
Kx
RF
Kx
Time
1st Ky line2nd Ky line
30 slices
Slice #30Sli #2Slice #1 Slice #3Slice #2
Slice #29
2 sec = TR
2 sec
Repeat many titimes
2 sec
Bimanual finger tapping motor study (P ≤ 10-7)(12 s resting and then 24 s finger tapping at 1 Hz, TR = 2 s)
2 sec
Artifacts due to back-and-forth trajectory in k space
Susceptibility artifacts
Image artifacts due to field variation
NormalNormal
Variation along X
Variation along Y
Variation l Zalong Z
Another common technique for fMRI: spiral imaging
GoalsGoalsGoalsGoals
1. Basic concepts of MRI2. Basic meanings of TE, TR, T1, T2, T2*, k space, EPI
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