fmri acquisition richard wise fmri director [email protected] +44(0)20 2087 0358

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FMRI acquisition FMRI acquisition Richard Wise FMRI Director [email protected] +44(0)20 2087 0358

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FMRI acquisitionFMRI acquisition

Richard WiseFMRI Director

[email protected]

+44(0)20 2087 0358

Why do we need the magnet?Why do we need the magnet?

d

Inside an MRI ScannerInside an MRI Scanner

subject

super conducting magnet

x gradient coil

z gradient coil

r.f. transmit/receive

gradient coils

Common NMR Active NucleiCommon NMR Active Nuclei

Isotope Spin % g I abundance MHz/T

1H 1/2 99.985 42.5752H 1 0.015 6.5313C 1/2 1.108 10.7114N 1 99.63 3.07815N 1/2 0.37 4.3217O 5/2 0.037 5.7719F 1/2 100 40.0823Na 3/2 100 11.2731P 1/2 100 17.25

Nuclear SpinNuclear Spin

spin

magnetic moment

M

M=0

If a nucleus has an unpaired proton it will have spinand it will have a net magnetic moment or field

ResonanceResonance

• If a system that has an intrinsic frequency (such as a bell or a swing) can draw energy from another system which is oscillating at the same frequency, the 2 systems are said to resonate

Spin TransitionsSpin Transitions

Low energy

High energy

The Larmor FrequencyThe Larmor Frequency

ω = γ B

Frequency Field strength

128 MHz at 3 Tesla

Tissue magnetizationTissue magnetizationB0 M

90º RF excitation pulse

Tissue magnetizationTissue magnetizationB0 M

90º RF excitation pulse

MR signal ω = γ B

Tissue magnetizationTissue magnetizationB0

90º RF excitation pulse

MR signal ω = γ B

M

.

Tissue magnetizationTissue magnetizationB0

90º RF excitation pulse

MR signal ω = γ B

Signal decay: time constant T2

signal

time

Tissue contrast: TE &TTissue contrast: TE &T22 decay decay

TE

EchoAmplitude

Long T2 (CSF)

Medium T2

(grey matter)

Short T2

(white matter)

Contrast

TT22 Weighted Image Weighted Image

TT22 Weighted Image Weighted Image

SE, TR=4000ms, TE=100ms

grey matter

CSF

T2/ms

500

8090

SE, TR=4000ms, TE=100ms

1.5T

white matter 7080

Tissue magnetizationTissue magnetizationB0 M

Magnetization recovery: time constant T1

M

time

Tissue magnetizationTissue magnetizationB0 M

Magnetization recovery: time constant T1

M

time

Tissue contrast: TR & TTissue contrast: TR & T11 recovery recovery

TR

Medium T1 (grey matter)

Long T1 (CSF)

Short T1 (white matter)

Mz

Contrast

TT11 Weighted Image Weighted Image

SPGR, TR=14ms, TE=5ms, flip=20º

TT11 Weighted Image Weighted Image

SPGR, TR=14ms, TE=5ms, flip=20ºSPGR, TR=14ms, TE=5ms, flip=20º

white matter

grey matter

CSF

T1/s R1/s-1

4

1

0.7

0.25

1

1.43

1.5T

Short TR

Short TE

Long TE

Long TR

T1

T2

PD

From Frequencies to ImagesFrom Frequencies to Images

• Vary the field by position

• Decode the frequencies to give spatial information

Gradient coilsGradient coils

subject

super conducting magnet

x gradient coil

z gradient coil

r.f. transmit/receive

gradient coils

Image formationImage formation

FourierTransform

frequency

time

Signal Spectrum

The Fourier TransformThe Fourier Transform

FFT

2 x 2nn

Slice selectionSlice selection

0time frequency

G

RF excitation

ω = γ B

(Gradient echo) Pulse sequence(Gradient echo) Pulse sequence

The Pulse Sequence ControlsThe Pulse Sequence Controls

• Slice location• Slice orientation• Slice thickness• Number of slices• Image resolution

– Field of view (FOV)– Image matrix

• Echo-planar imaging

• Image contrast– TE, TR, flip angle,

diffusion etc

• Image artifact correction– Saturation, flow

compensation, fat suppresion etc

TT22* : pleasure …..* : pleasure …..

TT22* : ….. and pain* : ….. and pain

T2* contrastT2* contrast

T2* contrastT2* contrast• Field variation across the sample• Decay of summed NMR signal

GE-EPI is T2* weightedGE-EPI is T2* weighted

Wilson et al Neuroimage 2003

Neural activity to FMRI signalNeural activity to FMRI signal

Neural activity Signalling Vascular response

Vascular tone (reactivity)Autoregulation

Metabolic signalling

BOLD signal

glia

arteriole

venule

B0 field

Synaptic signalling

Blood flow,oxygenationand volume

FMRI and electrophysiologyFMRI and electrophysiology

Logothetis et al, Nature 2001

Haemodynamic responseHaemodynamic response

Buxton R et al. Neuroimage 2004

balloon model

%

-1

initial dip undershoot

Blood oxygenationBlood oxygenation

Bandettini and Wong. Int. J. Imaging Systems and Technology. 6:133 (1995)Bandettini and Wong. Int. J. Imaging Systems and Technology. 6:133 (1995)

Rest

Active: 40% increase in CBF, 20% increase in CMRO2

O2 Sat 100% 80% 60%

O2 Sat 100% 86% 72%

CMRO2 = OEF CBF

O2 O2 O2

CMROCMRO22: : CBF ratioCBF ratio

Hoge R et al

Signal evolutionSignal evolution

• Gradient echo

S = Smax . e-TE/R2*

• Deoxy-Hb contribution to relaxation

R2* (1-Y) CBVY=O2 saturationb~1.5

• Longer TE, more BOLD contrast but less signal and more dropout/distortion. TE=T2*

Vessel densityVessel density

500 m

100 m Harrison RV et al. Cerebral cortex. 2002

Resolution IssuesResolution Issues

• Spatial Resolution– How close is the blood flow response to the

activation site (CBF better?)– Most BOLD signal is on the venous side– EPI is “low res”– Dropout and distortion

• Slice orientation• Slice thickness

• Temporal Resolution

Factors affecting BOLD signal?Factors affecting BOLD signal?

• Physiology– Cerebral blood flow (baseline and change)– Metabolic oxygen consumption– Cerebral blood volume

• Equipment– Static field strength– Field homogeneity (e.g. shim dependent T2*)

• Pulse sequence– Gradient vs spin echo– Echo time, repeat time– Resolution

Physiological baselinePhysiological baseline• Baseline CBF, • But CBF CMRO2 unchanged (Brown et al JCBFM 2003)

• BOLD response

Cohen et al JCBFM 2002

Noise sourcesNoise sources• What is noise in a BOLD experiment?

– Unmodelled variation in the time-series– Intrinsic MRI noise

• Independent of field strength, TE• Thermal noise from subject and RF coil

– Physiological noise• Increases with field strength, depends on

TE• At 3T physiological noise > intrinsic• Cardiac pulsations• Respiratory motion and B0 shift• Vasomotion, 0.1Hz• Blood gas fluctuations• “Resting state” networks

– Also• Scanner drift (heating up)

BOLD Noise structureBOLD Noise structure

• 1/f dependence– BOLD is bad for

detecting long time-scale activation

frequency

BOLD noise

Spatial distribution of noiseSpatial distribution of noise• Motion at intensity boundaries

– Head motion– Respiratory B0 shift

• Physiological noise in blood vessels and grey matter

Thanks to …

John Evans

Rami Niazy

Martin Stuart

Spiro Stathakis