The Basics of MRIIves Levesque

BIC Seminar Series, October 5th, 2009

McConnell Brain Imaging CentreMontreal Neurological InstituteMcGill University

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Acknowledgments for material

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

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MRI: a simple overview

somethinghappens

put subjectin scanner

knock!buzz! knoc

k!

bang!

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MRI: behind the scenes

Fourier transform

B0

NMRGx

z

y

encoding

x

z

y

M

B1

excitation

detection

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Outline

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

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NMR Physics

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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

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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

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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

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• Superconducting solenoid magnet

• Liquid helium cooling

• Many km’s of wire• 1.0 – 9.4 tesla

The main magnet

B0NOT

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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

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Excitation (stationary frame of reference)

B1 field in yellow, magnetization vector in red

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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

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Excitation (rotating frame of reference)

B1 field in yellow, magnetization vector in red

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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!

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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)

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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)

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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*

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Relaxation in the lab frame

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

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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”

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T1 & T2 relaxation in CNS at 3 T

0 0.6 0.80

0.1

0.2

0.3

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0.5

0.6

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1

Time (s)

T2 relaxation

0 1 2 3 40

0.1

0.2

0.3

0.4

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0.7

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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

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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)

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• 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

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Spatial Encoding and Reconstruction

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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

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Gradients modify the amplitude of B0

B0

Gz= dB0/dz

B0 Gy= dB0/dy

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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

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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

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3D-FT imaging

3D FT

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3D-FT imaging

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Echo-planar imaging (EPI)

• Acquire entire 2D space in one shotky

kx

RF

Gy

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Example of alternate k-space trajectory

• interleaved spirals

kx

ky

RF

Gx

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Basic MRI sequences

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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

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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

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GE images depend on T1 and T2*

T1w FLASH

Localizer (“scout”) Post-gadolinium T1w

GE EPINO

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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 ′

+=

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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”

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Turbo spin echo

acq. acq. acq.

2D FT

N2 / 3 repetitions of TR N2 voxels

3 × N1 samples per TR N1 voxels

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Turbo spin echo images

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

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

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Diffusion contrast in MRI

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Gradients and phaseGy

timeB0 B0 + Gy

Gy

B0

Total:Total:

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Gradient dephasing and rephasingG

time

B0

Total:

B0 - G B0

Total:

B0 + G

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Gradients, phase, and motionG

time

B0B0 + G B0 B0 - G

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Diffusion MRI SE sequence

EPI

diffusion encoding gradients

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Diffusion indices

FA: anisotropy

index

RGB plot: principal direction,

scaled by FA

trace of diffusion tensor ~ Dav

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BOLD MRI

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O2

at rest

O2

ACTIVATED

BOLD contrast

∆T2*

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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

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fMRI acquisition

• series of stimulus conditions–activation and baseline

off

on

stimulus

rapid image acquisition NO

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fMRI example: finger tapping task

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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

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Choices, trade-offs and limitations

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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

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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!

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+ 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

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Artefacts:what’s wrong with my image?

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Subject motion affects images

phase encoding

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

imagingNO

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Flow artefacts

2D SETR 3s

TE 50ms

3D slab-selective FLASHNO

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Ghost sightings in EPI imagesphase encoding

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

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Magnetic susceptibility artefacts

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

• Solutions: parallel imaging, shorter TE, angulation

GR

EE

PI

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MRI Safety

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

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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

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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∝

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Summary

Fourier transform

B0

NMR Gy

z

x

encoding

y

z

x

M

B1

excitation

detection

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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/

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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