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