fmri acquisition
DESCRIPTION
FMRI acquisition. Richard Wise FMRI Director [email protected] +44(0)20 2087 0358. Why do we need the magnet?. d. Inside an MRI Scanner. z gradient coil. r.f. transmit/receive. x gradient coil. super conducting magnet. subject. gradient coils. Common NMR Active Nuclei. - PowerPoint PPT PresentationTRANSCRIPT
FMRI acquisitionFMRI acquisition
Richard WiseFMRI Director
+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