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

Institute for Biomedical Engineering

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

Institute for Biomedical Engineering

IBT

MRI Contrast

Institute for Biomedical Engineering

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

Institute for Biomedical Engineering

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)

Institute for Biomedical Engineering

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

Institute for Biomedical Engineering

8IBT

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

Institute for Biomedical Engineering

9IBT

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

Institute for Biomedical Engineering

10IBT

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

Institute for Biomedical Engineering

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

Institute for Biomedical Engineering

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

Institute for Biomedical Engineering

IBT

Functional MRI (fMRI)

Institute for Biomedical Engineering

14IBT

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

Institute for Biomedical Engineering

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

Institute for Biomedical Engineering

IBT

MRI and Diffusion

Institute for Biomedical Engineering

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

Institute for Biomedical Engineering

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

Institute for Biomedical Engineering

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

Institute for Biomedical Engineering

Example: nerve fibre Diffusion perpendicular to fibre restricted Water diffusion indicates white matter organization

Institute for Biomedical Engineering

Diffusion and MRI

Diffusion leads to signal loss in MRI

Institute for Biomedical Engineering

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

Institute for Biomedical Engineering

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

Institute for Biomedical Engineering

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

Institute for Biomedical Engineering

Principal diffusion coefficient and vector: longest axis of diffusion tensor

Institute for Biomedical Engineering

Brain structures via analysis of principle diffusion vectors

Optic radiation

Pons

Middle cerebellarpeduncle

Corticospinal tract

Corpus callosum

MedullaSuperior cerebellarpeduncle

Superior longitudinal fasciculus

MedullaTapetum

Institute for Biomedical Engineering

IBT

MR Angiography

Institute for Biomedical Engineering

29IBT01.04.2010

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