EXCITE Afternoon Hands-On MRI Sessions : fMRI & DTI
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Transcript of EXCITE Afternoon Hands-On MRI Sessions : fMRI & DTI
Institute for Biomedical Engineering
EXCITE
Afternoon Hands-On MRI Sessions: fMRI & DTI
Institute for Biomedical Engineering
Contrast in MRI - Relevant Parameters
Relaxation times: T1 Spin-lattice relaxation time (longitudinal relaxation time)
Return of spin system to equilibrium state
T2 Spin-spin relaxation time (transverse relaxation time)
Loss of phase coherence due to fluctuations of interacting
spins (‘phase memory time’)
T2* Decay time of free induction decay
Signal loss due to magnetic field inhomogeneity (difference
in magnetic susceptibility)
ADC Apparent diffusion coefficient
Signal loss due to diffusion of water molecules in an
inhomogeneous magnetic field
k water exchange rate
Exchange of water between macromolecule bound fraction and
bulk (free) water
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Sensitivity: Signal-to-Noise Ratio (SNR)
Spatial resolution
Temporal resolution
Signal: magnetization (number of spins, magnetic field strength, …. )Noise: thermal noise of receiver system, physiological noise, …
Relations and Limitations
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MRI Contrast
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MRI delivers good soft tissue contrast Tissue specific magnetic parameters for contrast
generation T2 / T2*: how fast is signal lost after excitation T1: how fast is magnetization gained back after excitation for next
experiments
Sequence parameters and sequence type determine contrast
Relaxation times
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0 0.5 1.0 0 0.5 1.0 0 0.5 1.0
+1.0
-1.0
0.0
time (s) time (s) time (s)
Mi(t)/Meq
Mx My Mz
The NMR signal
Relaxation Relaxation
exp(-t/T2*)
1-exp(-t/T1)
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Relevant parameters: Repetition time (TR) = time between two excitations Flip angle -> how much magnetization is left for next excitation
Strong T1 weighting for large flip angle and short TR
T1 weighting
Mxy
Mz
MzA
MzBθ
T1 Relaxation during TR
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T1 weighting: Example
Two metabolites with T1=500ms (blue) and T1=250ms (red) Flip angle: 60° Signal proportional to DMz
TR=3000ms
01.04.2010
time
Mz
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T1 weighting: Example
Two metabolites with T1=500ms (blue) and T1=250ms (red) Flip angle: 60° Signal proportional to DMz
TR=300ms
01.04.2010
time
Mz
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T1 weighting: Example
Two metabolites with T1=500ms (blue) and T1=250ms (red) Flip angle: 60° Signal proportional to DMz
TR=100ms
01.04.2010
time
Mz
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Relevant parameter: Echo time (TE) = time between excitations and data acquisition Strong T2 weighting for long TE
T2 / T2* weighting
Mxy
t / ms
TEshort TEmedium TElong
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Intensity scales with number of signal generating nuclei per volume element
Keep influence of relaxation times small: Short TE -> small effect of T2 / T2* on signal Long TR -> small effect of T1
Proton density weighting
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Functional MRI (fMRI)
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Uses echo planar imaging (EPI) for fast acquisition of T2*-weighted images.
Spatial resolution: 3 mm (standard 1.5 T scanner) < 200 μm (high-field systems)
Sampling speed: 1 slice: 50-100 ms
Problems: distortion and signal dropouts in certain regions sensitive to head motion of subjects during scanning
Requires spatial pre-processing and statistical analysis.
EPI(T2*)
T1
dropout
But what is it that makes T2* weighted images “functional”?
Functional MRI (fMRI)
Institute for Biomedical Engineering The BOLD contrast
Source: Jorge Jovicich, fMRIB Brief Introduction to fMRI
neural activity blood flow oxyhemoglobin T2* MR signal
REST
ACTIVITY
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The temporal properties of the BOLD signal
sometimes shows initial undershoot
peaks after 4-6 secs
back to baseline after approx. 30 secs
can vary between regions and subjects
BriefStimulus
Undershoot
InitialUndershoot
Peak
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MRI and Diffusion
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Brownian motion
Molecules or atoms in fluids and gases move freely Collisions with other particles causes trembling movement Brownian motion: microscopic random walk of particles in
fluids of gases (R. Brown 1827) Brownian motion depends on thermal energy, particle
properties and fluid density
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Diffusion
Diffusion: irreversible automatic mixing of fluids (or gases) due to Brownian motion
Root mean square displacement depends on diffusion coefficient D and time :t (A. Einstein)
Diffusion coefficient D affected by cell membranes, organelles, macromolecules (Le Bihan 1995)
2r D
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Anisotropy
Restrictions on water diffusion usually without spherical symmetry anisotropic diffusion in biological tissue
Diffusion tensor (=3x3-matrix) instead of diffusion coefficient accounts for anisotropic diffusion in 3D
Principal diffusion direction: direction with largest diffusion coefficient
Free Diffusion Restricted Diffusion
r1
r2
r3
2 , 1,2,3i ir D i
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Example: nerve fibre Diffusion perpendicular to fibre restricted Water diffusion indicates white matter organization
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Diffusion and MRI
Diffusion leads to signal loss in MRI
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Diffusion gradients Signal attenuation depends on diffusion coefficient and
gradient waveforms GE: sum of diffusion weighting gradients zero SE: diffusion weighting gradients have equal area Single shot techniques freeze out physical motion
TE
90° 180°diffusiongradient
diffusiongradient
EPI readout
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Diffusion weighted imaging DWI b-value (=b-factor) describes diffusion weighting
analogous to TE in T2 weighted sequences b-value determined by diffusion weighting gradients (i.e.
gradient form, strength, distance)
signal
b-factor [s/mm2] 0 200 400 600 800 1000
0bDS S e
S0: signal without diffusion weighting; D: diffusion coefficient in direction of gradient
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DTI
Ellipsoid represents diffusion tensor Fibre structure via map of diffusion anisotropy: calculate
fractional anisotropy (or relative anisotropy or volume ratio)
PM
MPS
MSPS
DWIs + Reference
l1l2
l33D ellipsoid
ADC
FA
Color-coded FA
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Principal diffusion coefficient and vector: longest axis of diffusion tensor
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Brain structures via analysis of principle diffusion vectors
Optic radiation
Pons
Middle cerebellarpeduncle
Corticospinal tract
Corpus callosum
MedullaSuperior cerebellarpeduncle
Superior longitudinal fasciculus
MedullaTapetum
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MR Angiography
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Blood flow
Image Slice
Image Slice
Saturation: apply 90°slice-selective pulse
Gradient echo imaging: Don’t wait for gradient echo Bright signal from unsaturated spins in slice
time
MzStationary spins
Inflowing spins
satu
ratio
n
ima
gin
g
MR Angiography