analysis methods in functional magnetic resonance imaging...

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Sprint 2007 fMRI Analysis Course Sprint 2007 fMRI Analysis Course 1 Sprint 2007 fMRI Analysis Course Sprint 2007 fMRI Analysis Course 2

Analysis Methods in Functional Magnetic Resonance ImagingAnalysis Methods in Functional Magnetic Resonance ImagingECE595/CS591/PSYCH650ECE595/CS591/PSYCH650

Sprint 2007 fMRI Analysis Course Sprint 2007 fMRI Analysis Course 3








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OutlineOutline•• MR Basic PrinciplesMR Basic Principles

•• HardwareHardware•• SpinSpin•• SequencesSequences


Puzzle PiecesPuzzle Pieces

Helmholtz

Golay


The MagnetThe Magnet

•• Goal: align the protonsGoal: align the protons•• Coils Coils

•• Super conductance: Super conductance: HeliumHelium

•• 1.5T, 1.5T, 3T3T, 7T , 7T (Earth magnetic field = (Earth magnetic field = 0.0005T) 0.0005T)

•• Side Effects (FDA : <8T, Side Effects (FDA : <8T, neonates <4T )neonates <4T )•• NauseaNausea•• VertigoVertigo•• TinglingTingling•• HeadacheHeadache•• Pain in tooth fillingsPain in tooth fillings


Not harmful?Not harmful?


The Gradient CoilsThe Gradient Coils•• Goal: Goal:

•• Slice selectionSlice selection•• Frequency encodingFrequency encoding•• Phase encodingPhase encoding

Side EffectsSide Effects•• Induced currents (dynamo; small) Induced currents (dynamo; small) •• Nerve stimulation Nerve stimulation •• PhosphenesPhosphenes•• Acoustic NoiseAcoustic Noise


The RF CoilThe RF Coil•• Goal: Goal:

•• Turn longitudinal Turn longitudinal magnetization into magnetization into transverse magnetizationtransverse magnetization

•• Measure the signal Measure the signal generated by the generated by the precessingprecessingspins. spins.

•• Side Effects Side Effects •• Induced currents: Specific Induced currents: Specific

Absorption Rate (SAR) Absorption Rate (SAR) limits limits

•• Heating: avoid loops.Heating: avoid loops.

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CoilsCoils

Head coil•homogenous signal•moderate SNR

Surface coil•highest signal at hotspot•high SNR at hotspot


Basic TheoryBasic Theory

•• Protons have a property called spinProtons have a property called spin•• LarmorLarmor Equation: Equation:

ωω = = γγBB00•• ωω = = LarmorLarmor frequencyfrequency•• γγ = = gyromagneticgyromagnetic ratioratio

•• 42MHz/T for protons (42MHz/T for protons (11H) H) •• 11MHz/T for 11MHz/T for 1313CC•• 176GHz/T for electrons (e176GHz/T for electrons (e--))









180°90°

z

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MoMz

t

63%

T1

Longitudinal Relaxation Time T1

Longitudinal Relaxation = Energy transfer between excited spins andTissue (Spin-Lattice-Relaxation)

Reestablishing of longitudinal magnetization with time constant T1

1-e-t/T1


Mxy

37%

T2t

Transverse Relaxation Time T2

Transverse Relaxation = Decay of magnetization by interaction between nuclei (Spin-Spin-Relaxation)


Mz S

Tissue 1

Tissue 2

TR Short TE Medium TE Long TE

Longitudinal Relaxation Transverse Relaxation

Tissue 2

Tissue 1

Relaxation Times are Tissue Specific


30002000100000.0

0.2

0.4

0.6

0.8

1.0

TR (msec)

Sign

al

gray matterT1 = 1000

CSFT1 = 3000

white matterT1 = 600

T1T1--relaxation timerelaxation time

•• Depends on tissue typeDepends on tissue type•• White matter: 70 msWhite matter: 70 ms•• Gray matter: Gray matter: 90 ms90 ms•• CSF: CSF: 400 ms400 ms

•• T2 << T1T2 << T1

•• Measure the signal Measure the signal 200 ms after the RF pulse. 200 ms after the RF pulse.

•• White matter: eWhite matter: e--200/70 200/70 = 5% = 5% •• Gray matter: eGray matter: e--200/90 200/90 = 10%= 10%•• CSF:CSF: ee--200/400 200/400 = 60= 60 Sprint 2007 fMRI Analysis Course Sprint 2007 fMRI Analysis Course 24

TR

Long

Short

Short LongTE

ProtonDensity

T1 poor!

T2

Image contrastImage contrast

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NMR Signal

B0

z’ z’ z’

X’ X’ X’

y’ y’ y’

S(t) S(t) S(t)

M0

S(t)

t

S0≈M0 T2*

0

T0=1/f0

Spin refocusing

z’

X’

y’ y’

z’

X’

y’y’

B0z’

X’

z’

X’

12

3

45

123

45

z’

X’

y’1

23

45

90°x 180°y

Hahn echoCPMG (Carr-Purcell-Meiboom-Gill) modification : multiple π

t = TEt = TE/2t = 0

Spin echo

90° 180°

t = TE/2

t = TE

υ1

υ2 = υ1 / 2

Spin echo

FID Spin echo

readout

Signal

Gradient

TransversalMomentsPhase

+

-

0t

1

2

3

4

5

1

4

5

2

3

T2

T2*

90° 180°

Gradient echo

α readoutGradient

FID gradientecho

Signal

TransversalMomentsPhase t

T2*

Longitudinal Relaxation

B0

t=t0 t=t1Mz=0

t=t2Mz=a

t=t3Mz=b

t=∞Mz=1

….

t

Mz(t)

t0 t1 t2 t3

90°M0

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Making an image1. Slice selection with a gradient field

B0

0

a) Set a z-gradient b) Choose the frequency of the RF pulsec) Switch off the z-gradient

Resonance at ω = γ(B0+ 1)

B0+1

B0+2

z

Making an image2. Frequency encoding with a gradient field

0x

Faster precession: fast changing signal

Slower precession: slow changing signal

Bx

a) When measuring the signal, set a gradientb) Measure only fast signals -> back of headc) Measure only slow signals -> front of head

Making an image3. Phase encoding with a gradient field

0y

By

a) After the RF pulse, set a gradient for a brief timeb) Measure the signal

The phase of the signal depends on the y-position : sin(…+y)c) Repeat, with ever stronger gradient

The signal : sin(…+2y), sin(…+3y), sin(…+4y)d) Signals that change rapidly with the repeat number have large ye) Signals that change slowly with the repeat number have small y

Phase advance


1 2 N

ky

kx

Raw Data Matrix (k-Space)

Raw data matrix or k-space is filled line by line by variation of the Phase Encoding Gradient

Line Information =Frequencies of the Readout Gradient


Fourier Transformation

K_x

K_y

x

y


EPI imaging and kEPI imaging and k--spacespacex = frequency and y = phase or angle

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Frequency and phase encoding merely Frequency and phase encoding merely plots a trajectory across kplots a trajectory across k--space.space.

frequ. encode

phase encode


EPI


EPI and SpiralsEPI and Spirals

kx

ky

Gx

Gy

kx

ky

Gx

Gy


EPI SpiralsSusceptibility: distortion, blurring,

dephasing dephasing

Eddy currents: ghosts blurring

k = 0 is sampled: 1/2 through 1st

Corners of kspace: yes no

Gradient demands: very high pretty high


OutlineOutline•• MR Basic PrinciplesMR Basic Principles

•• HardwareHardware•• SpinSpin•• SequencesSequences

•• Basics of BOLD fMRIBasics of BOLD fMRI•• Signal mechanismSignal mechanism•• Sequences usedSequences used•• ArtifactsArtifacts

•• A few tradeA few trade--offsoffs

analysis methods in functional magnetic resonance imaging...

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