Introduction to MRI

Purpose
overview MRI fundamentals and current research areas

Outline
NMR net magnetization (M) T1 and T2 relaxation (other than mechanisms) FID, SE, IR, GRE T1W, T2W, PDW image contrast image formation (excitation, k-space, phase-encode, etc.) 2D, multislice, 3D motion and flow (artifacts, angiography, quantitative flow) functional MRI other effects (magnetization transfer, chemical shift, etc.) discussion

Joseph Fourier, 1768-1830

Nuclear Magnetic Resonance (NMR)

nuclei with odd number of protons and/or neutrons nuclear spin angular momentum nuclear magnetic moment biological tissue
hydrogen (1H) phosphorus (31P) sodium (23Na)

NMR
N

NMR
when placed in a magnetic field, B0, a net magnetization vector M forms spins exhibit resonance (precess) at Larmor frequency = B
where = gyromagnetic ratio /2 = 42.58 MHz/T for hydrogen

NMR
B0
M

no external field

external field B 0

Net Magnetization (M)

static magnetic field B0 produces a net magnetization vector M (along z-axis)
z M B0

NMR
excitation
a rotating magnetic field (RF), perpendicular to B0 , with frequency 0 can rotate M into the x-y plane

evolution
M will then precess freely and decay back to its equilibrium position along the z-axis

Excitation
excitation z B0 M B0 T1 T2 x 0 y
stationary (lab) frame of reference

evolution z

x RF (B1) y
rotating frame of reference

T1 and T2
90o 90o

RF
TR Mz recovery: T1
1 1 0.8 0.8

...

Mxy decay: T2

0.6 Mz

Signal (Mxy )

0.6

0.4

0.4

e-t/T2

(1-e-t/T1)

0.2

0.2

0 0 1 2 TR (s) 3 4

0 0 0.1 0.2 0.3 0.4 Time (s)

Free Induction Decay s(t) = exp(-t/T2*)

1 0.8

(envelope) FID

z
Signal

0.6 0.4 0.2 0 -0.2 -0.4 -0.6 -0.8 -1 0 0.2 0.4 Time 0.6 0.8 1

x 0 y
Signal 60 50

FFT

40

spectrum

30

stationary (lab) frame of reference

20

10

0.2

0.4 Frequency

0.6

0.8

Notes
Larmor equation

T1 = spin-lattice relaxation time T2 = spin-spin relaxation time T2* = observed FID decay time constant T2 <= T1

T1 Contrast
1 GM 0.8 WM CSF

Mz

0.6 0.4 0.2 0 0 2

TR (s)

Signal (Mxy)

1 0.8 0.6 0.4 0.2 0 0 WM 0.1 0.2 0.3 0.4 GM CSF

SE: TR/TE = Short/Short

Time (s)

T2 Contrast
1 GM 0.8 WM CSF

Mz

0.6 0.4 0.2 0 0 2

TR (s)

Signal (Mxy)

1 0.8 0.6 0.4 0.2 0 0 WM 0.1 0.2 0.3 0.4 GM CSF

SE: TR/TE = Long/Long

Time (s)

PD Contrast
1 GM 0.8 WM CSF

Mz

0.6 0.4 0.2 0 0 2

TR (s)

Signal (Mxy)

1 0.8 0.6 0.4 0.2 0 0 WM 0.1 0.2 0.3 0.4 GM CSF

SE: TR/TE = Long/Short

Time (s)

Spin-Echo
TE/2 90x TE 180y

z B0 M

b
x RF (B1) 90 y y x RF (B1) 180

b
x

a
x x

FID T2* e -t/T2*

T2 e -t/T2

Spin-echo

Spin-Echo Contrast
converts Mz at time TR into Mxy and then measures it at a time TE later long TR, short TE -> PDW long TR, long TE -> T2W short TR, short TE -> T1W

Inversion Recovery (IR)

180 RF TI 90 180

z B0 M

RF (B1) 180 y y

SE

Mz

1-2e-t/T1

Inversion Recovery
can create good tissue contrast can null tissue of a selected T1 beware of real vs magnitude images and bounce artifact scan time can be rather long

Gradient Recalled Echo (GRE)

RF

z B0 M

TR

z M z

z M

x y

gradient FID signal GRE

Gradient Recalled Echo

faster imaging sequence (TRs as low as 1015ms) reduced flip angle shorter TR -> more T1W larger flip angle -> more T1W longer TE -> more T2*W

GRASS Images
T1W TR/TE/ = 300ms/13ms/60o

T2*W TR/TE/ = 30ms/13ms/60o

T2*W TR/TE/ = 300ms/35ms/15o

PDW TR/TE/ = 400ms/13ms/10o

MPGR Images
TR/TE=400/9ms

= 10

30

60

90

Scanner Hardware
main magnet (Tesla) gradient coils (mT/m) RF coils (T (Rx))

Gradient amps

RF amp

Receiver

Computer

Display

Typical MRI Scanner

Image Formation
gradients cause a position dependent frequency relationship via the Larmor equation

slice select gradient frequency encode (a.k.a. readout, measurement) phase encode

Selective Excitation
apply a gradient perpendicular to desired slice excite using an RF pulse containing a range of frequencies pulse bandwidth and gradient strength result in a slice thickness

Slice Selection
RF slice profile

time FFT frequency

distance

G-slice B0

MRI: 1D Localization
NMR
Real

B0 Gx Project

Imag

FFT time frequency

Frequency Encode Gradient

gradient on during data acquisition Larmor equation gives relationship between frequency and location in one direction

GRE Pulse Sequence

RF
slice selection

Gz Gy Gx S(t)
phase encode frequency encode signal

Phase Encode
for each sequence repetition apply a short gradient pulse orthogonal to the frequency encode gradient increment amplitude of this pulse for each TR collect N (typically 128-256) phase encode lines reconstruct image using Fourier Transform (FFT)

ky

2-D Imaging

FFT kx x

magnitude raw data

magnitude reconstructed image

K-space Interpretation
received time domain signal represents the spatial frequency domain Fourier data the position in n-D k-space is given by the time integral of the gradient waveforms

MRI
Signal equation (ignoring relaxation)

S (t ) =

vol

M ( r , t ) dr
jB0t j

S (t ) = M ( x , y , z , t ) e
x y z

G ( t ' )rdt '

dxdydz

MRI
Fourier interpretation of the signal equation (2D)
s(t ) = M ( x, y,)e
x y j 2 [ k x ( t ) x + k y (t ) y ]

dxdy

2D Fourier transform of M(x,y) is

M ( k x , k y ) = M ( x , y ,)e
x y

j 2 ( k x x + k y y )

dxdy

therefore

s(t ) = M ( k x (t ), k y ( t ))
where k (t ) =

Gx ( t ' )dt ' 2 0

t t

k y (t ) = Gy (t ' )dt ' 2 0

2-D Imaging Sequence: k-space Interpretation

ky RF Gy Gx S(t) A/D kx

Fourier Sampling: Resolution

256x256 128x128 64x64

FFT

FFT

FFT

Fourier Sampling: FOV & Aliasing

FFT

FFT

3D Imaging Sequence: k-space Interpretation

ky RF Gz Gy Gx S(t) A/D kz kx

3D Imaging

3D FFT

3D Imaging

3D Imaging

Alternate k-space Trajectories

echo planar imaging (EPI)
ky
RF Gy Gx

kx

Alternate k-space Trajectories

ky

interleaved spirals

RF Gx Gy

kx

Image Quality: SNR & CNR

SNR: Signal to Noise Ratio CNR: Contrast to Noise Ratio SNR = (signal mean) / (signal standard deviation)
Ideal: signal & no noise noise
1.5 1.5

actual: signal & noise

1.5

image intensity

noise intensity

image intensity

0.5

0.5

0.5

0 0

50
X

100

0 0

50 X

100

0 0

50 X

100

SNR
signal strength
tissue type sequence parameters coil etc

noise variance
thermal noise in patient and coil electronics total measurement time

SNR: Acquisition Parameters

signal
voxel (resolution element) volume coil sensitivity

signal averaging
e.g. add two noisy signals signal doubles noise variance doubles SNR increase by root 2 (~1.4)

SNR: Acquisition Parameters

FOV & matrix size slice thickness signal averages 2D vs 3D sequence type and timing excitation pulse angles

SNR: Example

1 signal average relative SNR = 1

4 signal averages relative SNR = 2

8 signal averages relative SNR = 2.8

16 signal averages relative SNR = 4

SNR: Example

Increasing resolution Decreasing SNR

SNR: Example
partial volume

256x256, 12cm FOV

256x256, 24cm FOV

SNR: Example

a: 512x512 b: 512x384 c: 512x256 d: 256x256 a b

Fast Spin Echo

multiple echo spin echo sequence apply a different phase encoding for each echo reduce total scan time by ETL (TF) good SNR more complex contrast effects

FSE
phased array spine coil 512x512 sat. bands ant. TR: 4s TEeff: 102ms ETL: 16 NEX: 2 Sl th: 3mm Scan time: 2:08

Chemical Shift
basis on NMR spectroscopy local chemical environment causes shifts in magnetic field and hence resonant frequency data acquired in absence of gradient e.g. in vivo proton spectroscopy
metabolites such as NAA, creatine, choline, lactate, etc.

In Vivo Proton Spectrum

Normal Control NAA Zellweger Disease NAA

Cho Cr

Cho

Cr

La La Lip

*Courtesy Nicola DeStefano, McGill

Chemical Shift Imaging (CSI)

2 spatial + 1 spectral ky

RF Gx Gy S(t)
kf kx

A/D

Spectroscopic Imaging (MRSI)

*Courtesy Nicola DeStefano, McGill