The Basics of MRI - McConnell Brain Imaging Centre › ...10-05_-_The_Basics_of_MRI_-_Ives_Levesq… · The Basics of MRI Ives Levesque BIC Seminar Series, October 5th, 2009 McConnell

The Basics of MRIIves Levesque

BIC Seminar Series, October 5th, 2009

McConnell Brain Imaging CentreMontreal Neurological InstituteMcGill University

NOT F

ORRE

-USE

Acknowledgments for material

Prof. Bruce PikeIlana LeppertDr. Jennifer CampbellMichael FerreiraChristine TardifDr. Luis Concha

NOT F

ORRE

-USE

MRI: a simple overview

somethinghappens

put subjectin scanner

knock!buzz! knoc

k!

bang!

NOT F

ORRE

-USE

MRI: behind the scenes

Fourier transform

B0

NMRGx

z

y

encoding

x

z

y

M

B1

excitation

detection

NOT F

ORRE

-USE

Outline

• NMR physics• Spatial encoding and reconstruction• Basic MRI sequences: GE, SE• Special contrast: DWI, BOLD• Trade-offs and limitations• Image artefacts• SafetyN

OT FO

RRE

-USE

NMR Physics

NOT F

ORRE

-USE

NMR: Nuclear spin• “odd-numbered” nuclei have net angular

momentum• magnetic moment, or spin, designated by

vector µ

• In biological tissue: 1H, 23Na, and 31P

N

SNOT F

ORRE

-USE

NMR: spins in magnetic field• magnetic moments (spins) align to external magnetic• net excess of spins in parallel state (lower energy)

state of net magnetization, vector M

B0

external field B0

M

∑=i

inet µMNO

T FOR

RE-U

SE

Spins in a magnetic field experience a torque:

Static field produces precession about at Larmor frequency

γ/2π = 42.58 MHz/T for 1H, f ~ 64 MHz at 1.5 T

This is the resonance frequency

NMR - Free precession & resonance

0Bf γ=

BMM γ×=dt

dB0

NOT F

ORRE

-USE

• Superconducting solenoid magnet

• Liquid helium cooling

• Many km’s of wire• 1.0 – 9.4 tesla

The main magnet

B0NOT

FOR

RE-U

SE

Manipulating magnetization

• Apply magnetic field B1– Perpendicular to B0– Amplitude ~ 20µT– Alternating with frequency f1

• Rotate M from z-axis to transverse (xy) plane

– Most efficient on resonance (f1 = f0)

y

xz

NOT F

ORRE

-USE

Excitation (stationary frame of reference)

B1 field in yellow, magnetization vector in red

NOT F

ORRE

-USE

The rotating frame of reference

f0 = γ B0

y

x

z

B0y’

x’

z

M M

Mxy

Mz

• “laboratory” frame of reference

• vector M precesses at resonant frequency

• rotating frame of reference (at f0)

• “ignore” precession of M

NOT F

ORRE

-USE

Excitation (rotating frame of reference)

B1 field in yellow, magnetization vector in red

NOT F

ORRE

-USE

Relaxation

• M returns to equilibrium

• Recovery of Mz• Decay of Mxy• Each appens at

a different rate

y’

x’

z

B0 Recovery of Mz

Decay of Mxy

*rotating frame of reference!

NOT F

ORRE

-USE

T1 Relaxation: Recovery of Mz

• Energy exchange with surrounding medium

0 1 2 3 40

0.2

0.4

0.6

0.8

1Mz recovery: T1

ρ(1- e-t/T1)

Mz

y’

x’

z

B0 T1 relaxation

Time (s)

NOT F

ORRE

-USE

T2 Relaxation: Decay of Mxy

• Effect of spin-spin interaction

0 0.1 0.2 0.3 0.40

0.2

0.4

0.6

0.8

1Mxy decay: T2

ρe-t/T2

Mxy

y’

x’

z

B0

T2 relaxationTime (s)

NOT F

ORRE

-USE

T2* Relaxation: Faster decay of Mxy

• Additional effect of B0 inhomogeneity

• Reversible

y’

x’

z

B0

T2* relaxation > T2 relaxation

0 0.1 0.2 0.3 0.40

0.2

0.4

0.6

0.8

1

Time (s)

Mxy decay: T2, T2*

Mxy

ρe-t/T2*

NOT F

ORRE

-USE

Relaxation in the lab frame

Individual spins in blue, Mxy in yellow, Mz in red

NOT F

ORRE

-USE

Image contrast• Signal depends on:

– sequence parameters (TR, TE, α)– NMR parameters in tissue: PD, T1, T2, T2*– diffusion, MT, iron, contrast agents, etc.

• Each pulse sequence has its own behavior

T1W T2W PD or “Intermediate”

NOT F

ORRE

-USE

T1 & T2 relaxation in CNS at 3 T

0 0.6 0.80

0.1

0.2

0.3

0.4

0.5

0.6

0.7

0.8

0.9

1

Time (s)

T2 relaxation

0 1 2 3 40

0.1

0.2

0.3

0.4

0.5

0.6

0.7

0.8

0.9

1

Time (s)

T1 relaxation

WM

GM

GM

WM

CSF

CSF

0.2 0.4

Mz Mxy

GM: T1 = 1300 ms T2 = 100 ms ρ = 0.8WM: T1 = 800 ms T2 = 80 ms ρ = 0.7

CSF: T1 = 5500 ms T2 = 2200 ms ρ = 1.0NO

T FOR

RE-U

SE

NMR signal detection

f0x

y

z

B0

stationary (lab) frame of reference0 0.2 0.4 0.6 0.8 1

-1

0

1

Time (ms)

Sig

nal

“FID”

f0

T2* decay

NMR signal received in RF coil (Faraday’s Law)

NOT F

ORRE

-USE

• excitation– apply magnetic field B1, perpendicular to B0 , at

resonant frequency f0, to rotate M0 into x-y plane• evolution

– M0 precesses freely, relaxing to equilibrium on z-axis– energy released in relaxation process at frequency f0

• detection– detect signal: changing magnetic flux in x-y plane

produces a voltage in receive coil

• waiting (for TE) and spatial encoding

• repetition (after TR)

Beyond exploiting the resonance

NOT F

ORRE

-USE

Spatial Encoding and Reconstruction

NOT F

ORRE

-USE

Magnetic field gradients

• Linear variations in magnetic field (millitesla / meter)

• Manipulate frequency of precession• Encode spatial information in signal

– frequency (readout)– phase (prior to readout)NO

T FOR

RE-U

SE

Gradients modify the amplitude of B0

B0

Gz= dB0/dz

B0 Gy= dB0/dy

NOT F

ORRE

-USE

B0

frequency (Hz)

MRI: localization in 1-D

Paul Lauterbur

FT

f0time (ms)

sign

al

f0 = γ B0Gx f > f0f < f0

N samples N points

NOT F

ORRE

-USE

kx

ky

x

y

2D FT

magnitude k-space data magnitude reconstructed image

2D-FT imaging

N1 samples per TR

N2 repetitions of TR N2 voxels

N1 voxels

NOT F

ORRE

-USE

3D-FT imaging

3D FT

NOT F

ORRE

-USE

3D-FT imaging

NOT F

ORRE

-USE

Echo-planar imaging (EPI)

• Acquire entire 2D space in one shotky

kx

RF

Gy

Gx NOT F

ORRE

-USE

Example of alternate k-space trajectory

• interleaved spirals

kx

ky

RF

Gx

Gy NOT F

ORRE

-USE

Basic MRI sequences

NOT F

ORRE

-USE

Breakdown of MRI experiment: the “sequence”

acquisition

TETR

preparation

- inversion preparation- MT saturation

relaxation

- acquire other slices- spoil or rewind

excitation

- RF pulses

- refocusing pulses - selective or non-selective

encoding

- gradients

- diffusion encoding

acquisition

- gradients- signal detectionNO

T FOR

RE-U

SE

The gradient echo sequence

acquisition

TETR

preparation

- inversion preparation (MP-RAGE)

- MT saturation

relaxation

2D: acquire other slices

3D: spoil or rewind

excitation

- excitation pulse

2D: slice-selective3D: non- or slab-selective

encoding

- phase encoding gradients

acquisition

- read-out gradients- data acquisition

- single-line or EPI

NOT F

ORRE

-USE

GE images depend on T1 and T2*

T1w FLASH

Localizer (“scout”) Post-gadolinium T1w

GE EPINO

T FOR

RE-U

SE

Spin echo

• T2* decay caused by spin dephasing

• Any pair of RF pulses can reverse (or refocus) T2’ to some extent

• 90°-180° combination is most effective• SE signal decays with time T2

22*

2

111TTT ′

+=

NOT F

ORRE

-USE

The spin echo sequence

acquisition

TRTE/2TE/2

relaxation

2D: acquire other slices

excitation

- excitation pulse- refocusing pulse

2D: slice-selective

encoding

- phase encoding gradients

read-out

- read-out gradients- data acquisition

- single-line or “turbo”

NOT F

ORRE

-USE

NOT F

ORRE

-USE

Turbo spin echo

acq. acq. acq.

2D FT

N2 / 3 repetitions of TR N2 voxels

3 × N1 samples per TR N1 voxels

NOT F

ORRE

-USE

Turbo spin echo images

TR/TE = 2.7s/12ms, ETL 3, 256x256, 60 slices

TR/TE = 5.4s/83ms, ETL 7, 256x256, 60 slicesNO

T FOR

RE-U

SE

Diffusion contrast in MRI

NOT F

ORRE

-USE

Gradients and phaseGy

timeB0 B0 + Gy

Gy

B0

Total:Total:

NOT F

ORRE

-USE

Gradient dephasing and rephasingG

time

B0

Total:

B0 - G B0

Total:

B0 + G

NOT F

ORRE

-USE

Gradients, phase, and motionG

time

B0B0 + G B0 B0 - G

NOT F

ORRE

-USE

Diffusion MRI SE sequence

EPI

diffusion encoding gradients

×NO

T FOR

RE-U

SE

Diffusion indices

FA: anisotropy

index

RGB plot: principal direction,

scaled by FA

trace of diffusion tensor ~ Dav

NOT F

ORRE

-USE

BOLD MRI

NOT F

ORRE

-USE

O2

at rest

O2

ACTIVATED

BOLD contrast

∆T2*

NOT F

ORRE

-USE

Hemoglobin and T2*

deoxy-Hbχ ~ 1.6

oxy-Hbχ ~ -0.3

longer T2, T2*

↑ BOLD upon↑ activation

shorter T2,T2*

baseline BOLD

oxy-RBCdeoxy-RBC

B0

NOT F

ORRE

-USE

fMRI acquisition

• series of stimulus conditions–activation and baseline

off

on

stimulus

rapid image acquisition NO

T FOR

RE-U

SE

fMRI example: finger tapping task

NOT F

ORRE

-USE

GE-BOLD vs SE-BOLD

Vessel Radius [µm]

∆R2*

[s-1

]

GE BOLD (TE = 40ms)

Vessel Radius [µm]

∆R2

[s-1

]

SE BOLD (TE = 100ms)

• GE-BOLD offers greater sensitivity• SE-BOLD more specific to small vessels

Buxton, 2002NO

T FOR

RE-U

SE

Choices, trade-offs and limitations

NOT F

ORRE

-USE

Voxel-size, FoV, and scan time are linked

N2 voxelsN2 repetitions of TR

2D FT

N1 samples per TR N1 voxels

scan duration = TR × N2 × NslicesNO

T FOR

RE-U

SE

Voxel size & scan time: link to SNR

( )21,, TTfTVSSNR readvoxel

S

ρσ

∝≡

Basic T1w

1×1×1 mm3

256×256×160

1

1

15.7 minutes

Voxel size

Matrix size

# averages

rel. SNR

Acq. time

High-res

0.5×0.5×1 mm3

512×512×160

1

0.25

31.4 minutes

Thick slice

1×1×2 mm3

256×256×80

1

2

7.9 minutes

High-res + SNR

0.5×0.5×1 mm3

512×512×160

16

1

8.4 hours!

NOT F

ORRE

-USE

+ Better SNR (up to 2×)+ Higher BOLD sensitivity

• Longer T1

- Higher energy deposition- B1 less homogeneous- More B0 artefacts

Impact of field strength

MP-RAGE, C. Tardif

1.5 T 3 T

NOT F

ORRE

-USE

Artefacts:what’s wrong with my image?

NOT F

ORRE

-USE

Subject motion affects images

phase encoding

• Motion during scan corrupts phase encoding• Solutions: subject co-operation, immobilization, fast

imagingNO

T FOR

RE-U

SE

Flow artefacts

2D SETR 3s

TE 50ms

3D slab-selective FLASHNO

T FOR

RE-U

SE

Ghost sightings in EPI imagesphase encoding

signal × 10• Imperfect gradient behaviour results in ghosting• Solutions: select phase encode direction to avoid

NOT F

ORRE

-USE

Magnetic susceptibility artefacts

• Changes in susceptibility affect B0 homogeneity– Image distortion and signal pile-up

• Solutions: parallel imaging, shorter TE, angulation

GR

EE

PI

NOT F

ORRE

-USE

MRI Safety

NOT F

ORRE

-USE

MRI safety: the main magnetic fieldThe magnet is always on, and will “perturb” instruments

NOT F

ORRE

-USE

MRI safety: Peripheral nerve stimulation• Magnetic field variations in time (dB/dt) induce

currents– Gradient coils switch on/off in less than 1 millisecond

• Currents induced in the subject can produce nerve stimulus

• Effect is greatest at the ends of the coils, because gradient amplitude is greater there

B0

Gz=dB0/dz

NOT F

ORRE

-USE

MRI safety: Energy deposition

• B1 field deposits energy into the body, results in heating

• SAR = specific absorption rate– power per unit (subject) mass, W/kg

• Heat is dissipated by the body’s own cooling, with the help of ventilation

• Monitored by the scanner

TRPSAR RFRFτ∝

NOT F

ORRE

-USE

Summary

Fourier transform

B0

NMR Gy

z

x

encoding

y

z

x

M

B1

excitation

detection

NOT F

ORRE

-USE

Useful referencesMRI From Proton to Picture

DW McRobbie, EA Moore, MJ Graves, Cambridge Press, 2002 (preview on Googlebooks)

Introduction to Functional Magnetic Resonance Imaging: Principles and TechniquesRB Buxton, Cambridge Press, 2002 (preview on Googlebooks)

Principles of magnetic resonance imagingDwight Nishimura, 1996 (out-of-print )

Magnetic Resonance Imaging: Physical Principles and Sequence DesignEM Haacke, Wiley, 1999

FMRIB MRI physics lectureshttp://www.fmrib.ox.ac.uk/education/graduate-training-course/program/lectures/mri-physics/mri-physics-course

The Basics of MRI (Joseph Hornak)http://www.cis.rit.edu/htbooks/mri/

NOT F

ORRE

-USE

The Basics of MRIAcknowledgments for materialMRI: a simple overviewMRI: behind the scenesOutlineNMR PhysicsNMR: Nuclear spinNMR: spins in magnetic fieldNMR - Free precession & resonanceThe main magnetManipulating magnetizationExcitation (stationary frame of reference)The rotating frame of referenceExcitation (rotating frame of reference)RelaxationT1 Relaxation: Recovery of MzT2 Relaxation: Decay of MxyT2* Relaxation: Faster decay of MxyRelaxation in the lab frameImage contrastT1 & T2 relaxation in CNS at 3 TNMR signal detectionSpatial Encoding and ReconstructionMagnetic field gradientsGradients modify the amplitude of B0Basic MRI sequencesBreakdown of MRI experiment: the “sequence”The gradient echo sequenceGE images depend on T1 and T2*Spin echoThe spin echo sequenceTurbo spin echoTurbo spin echo imagesDiffusion contrast in MRIDiffusion MRI SE sequenceDiffusion indicesBOLD MRIBOLD contrastHemoglobin and T2*Choices, trade-offs and limitationsVoxel-size, FoV, and scan time are linkedVoxel size & scan time: link to SNRArtefacts:what’s wrong with my image?Subject motion affects imagesFlow artefactsGhost sightings in EPI imagesMagnetic susceptibility artefactsMRI SafetyMRI safety: the main magnetic fieldMRI safety: Peripheral nerve stimulationMRI safety: Energy depositionSummaryUseful references