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Contrast Mechanisms in MRI. Introduction to Cardiovascular Engineering Michael Jay Schillaci, PhD Managing Director, Physicist Tuesday, September 16 th , 2008. Overview. Image Acquisition Basic Pulse Sequences Unwrapping K-Space Image Optimization Contrast Mechanisms

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Contrast mechanisms in mri

Contrast Mechanisms in MRI

Introduction to Cardiovascular Engineering

Michael Jay Schillaci, PhD

Managing Director, Physicist

Tuesday, September 16th, 2008


Overview
Overview

  • Image Acquisition

    • Basic Pulse Sequences

    • Unwrapping K-Space

    • Image Optimization

  • Contrast Mechanisms

    • Static and Motion Contrasts

      • T1 & T2 Weighting, Field Strength, T2*, Dephasing

    • Endogenous Contrasts

      • BOLD Imaging

    • Motion Contrasts

      • Time of Flight, Diffusion, Perfusion



Image formation
Image Formation

  • Integrate magnetization to get MRI signal

    • Select a z “slice” and form image of XY plane variations

    • Contrast from difference in magnetization in different tissues

      • Image at several times to get average

Horizontal density

Vertical density


Basic mri scan terminology
Basic MRI Scan Terminology

  • Orientation:

    • Coronal

    • Sagittal

    • Axial

  • Matrix Size:

    • # of Voxels in dimension

  • Field of view (FOV):

    • Spatial extent of dimension

  • Resolution:

    • FOV/Matrix size.

Coronal

Sagittal

Axial

Axial Orientation

64x64 Matrix

192x192mm

FOV

3x3mm Resolution

Sagittal Orientation

256x256 Matrix

256x256mm

FOV

1x1mm Resolution


Image creation
Image Creation

  • The scanning process

    • Protocol sets Gradients and Encodes K-Space Weights

    • Signal is Determined with Fourier Transform

    • Image Created with Inverse Transform

Step 2

Step 1

Step 3


Image acquisition
Image Acquisition

Gy varies in each cycle

Data Acquisition (DAQ)


Slice selection gradient g sl
Slice Selection Gradient: Gsl

  • Gradient Field

    • Ensures Field Greater on “Top”

  • Larmor Frequency

    • Depends on z Position

  • RF pulse

    • Energizes “Matched” Slice

Field Strength

Z Position


Frequency encoding gradient g ro
Frequency Encoding Gradient: Gro

  • Apply transverse gradient when we wish to acquire image.

  • Slice emits signal at Larmor frequency, e.g. lines at higher fields will have higher frequency signals.

X Position

Field Strength


Phase encoding gradient g pe
Phase Encoding Gradient: Gpe

  • Apply Orthogonal RF pulse

    • Apply before readout

    • Adjusts the phase along the dimension (usually Y)

Y Position

Field Strength


Unwrapping k space

Choose phase encoding time so that

Unwrapping K-Space

Field of View:

Pixel Size:

Image Adapted from Prof. Yao Wang’s Medical Imaging course notes at: http://eeweb.poly.edu/~yao/EL5823


Maximizing the signal

gives the: Ernst Angle:

Image Optimization

  • Adjustment of Flip Angle Parameter

    • Maximum SNR typically between 30 and 60 degrees

    • Long TR sequences (2D)

      • Increase SNR by increasing flip angle

    • Short TR sequences (TOF & 3D)

      • Decrease SNR by increasing flip angle


Gradient echo imaging
Gradient Echo Imaging

  • Assume perfect “spoiling” -transverse magnetization is zero before each excitation:

  • Spin-Lattice (T1) Relaxation occurs between excitations:

  • Assume steady state is reached during repeat time (TR):

  • Spoiled gradient rephases the FID signal at echo time (TE):


Spin echo imaging
Spin Echo Imaging

  • Spin echo sequence applies a 180º “refocusing pulse”

    • Half way between 90º pulse and DAQ

    • Allows measurement of true T2 time

T2

T2*


The refocusing pulse

Actual Signal

1

T2

Signal

T2*

0

0.5 TE

0.5 TE

The “Refocusing Pulse”

Spins Rotate at Different Rates

Refocusing Pulse Re-Aligns Spins


Volume reconstruction
Volume Reconstruction

  • 3D volumes

    • composed of 2D slices

  • Slice thickness.

    • Thicker slices have more hydrogen so more signal (shorter scan time)

    • Thinner slices provide higher resolution (longer scan time)

  • Optional: gap between slices.

    • Reduces RF interference (SNR)

    • Fewer slices cover brain

1mm Gap

2mm Thick

3mm



T1 and t2 weighting
T1 and T2 Weighting

  • T1 Contrast

    • Echo at T2 min

    • Repeat at T1 max

  • T2 Contrast

    • Echo at T2 max

    • Repeat at T1 min

  • Net Magnetization is

T1 Contrast Weighting

TR

TE

Max T1 Contrast

Min T2 Contrast

T2 Contrast Weighting

TR

TE

Min T1 Contrast

Max T2 Contrast


Static contrast images
Static Contrast Images

  • Examples from the Siemens 3T

T1 Weighted Image (T1WI)

(Gray Matter – White Matter)

T2 Weighted Image (T2WI)

(Gray Matter – CSF Contrast)

“Diagnostic Image”

“Anatomical Image”


Flip angle variation

+z

M

B0

q

MZ

+y

MXY

BC

+x

Flip Angle Variation

  • RF Pulse Magnitude Determines Flip Angle

    • Duration and magnitude are important

q

Adapted from: http://www.mri.tju.edu/phys-web/1-T1_05_files/frame.htm


Field strength effects
Field Strength Effects

  • Increased field strength

    • Net magnetization in material is greater

    • Increased contrast means signal is increased

    • Image1 resolution is better

Muscle

Tissue

1MRI adapted from: http://www.mri.tju.edu/phys-web/1-T1_05_files/frame.htm


Tissue contrast and dephasing
Tissue Contrast and Dephasing

  • Dephasing of H2O and Fat

    • MRI signal is a composite of Fat and H2O signals

    • H2O and Fat resonate at different frequencies

      • T1F = 210 ms, T1W = 2000 ms ( T1F > T1W→ fat is brighter)

    • Relative phase gives TE dependence

MF

ΦFW

MW

Parallel ( ΦFW = 0o )

@ TE = 13.42 ms

Anti-Parallel (ΦFW = 180o )

@ TE = 15.66 ms



Bold imaging
BOLD Imaging

  • Blood Oxyenation Level Dependent Contrast

    • dHb is paramagnetic, Hb is less

    • Susceptibility of blood increases linearly with oxygenation

    • BOLD subject to T2* criteria

  • Oxygen is extracted from capillaries

    • Arteries are fully oxygenated

    • Venous blood has increased proportion of dHb

    • Difference between Hb and dHb is greater for veins

    • Therefore BOLD is result of venous blood changes


Blood flow

Metabolism

Neuronal

activity

BOLD

signal

[dHb]

Blood volume

Sources of the BOLD Signal

BOLD is a very indirect measure of activity…


Neuronal Origins of BOLD

BOLD response predicted by

dendritic activity (LFPs)

Increased neuronal activity results in increased MR (T2*) signal

LFP=Local Field Potential; MUA=Multi-Unit Activity;SDF=Spike-Density Function

Adapted from Logothetis et al. (2002)


The bold signal
The BOLD Signal

ACTIVE

BASELINE


BOLD Imaging

  • Blood Oxyenation Level Dependent Contrast

    • Susceptibility of blood changes with oxygenation

    • Blood flow correlated with task performance

    • Differential activations can be mapped

BASELINE

ACTIVE


Static contrast t2 relaxation
Static Contrast - T2* Relaxation

  • T2* accounts for magnetic defects and effects

    • T2 is relaxation due to spin-spin interaction of nuclei

    • T2M is relaxation induced by inhomogeneities of main magnet

    • T2MS is relaxation induced by magnetic susceptibility of material


Bold artifacts
BOLD artifacts

  • fMRI is a T2* image – we will have all the artifacts that a spin-echo sequence attempts to remove.

  • Dephasing near air-tissue boundaries (e.g., sinuses) results in signal dropout.

BOLD

Non-BOLD



Flow weighting
Flow Weighting

  • Time-of-Flight Contrast

Acquisition

Excitation

Saturation

No Flow

Medium Flow

High Flow

No

Signal

Medium Signal

High

Signal

Vessel

Vessel

Vessel


Diffusion Tensor Imaging

ADC

Anisotropy

  • Diffusion Coefficients

    • Magnitude (ADC) Maps “Proton pools”

    • Direction (Anisotropy) Maps “Velocity”

    • Reconstruct Fiber Tracks with “Clustering”


Indices of diffusion anisotropy
Indices of Diffusion Anisotropy

Relative anisotropy:

Fractional anisotropy:

Vector

MD

FA


Dti in stroke research

Examine integrity of fiber tracts

Tractography - trace white matter paths in gray matter

Assess neglect as a disconnection syndrome

Healthy

DTI in Stroke Research

Stroke


Arterial Spin Labeling

  • Perfusion

    • Flow of fluid into vessels to supply nutrients/oxygen

    • The amount and direction of flow matters


Pulsed Labeling

Imaging Plane

Alternating

Inversion

Alternating

Inversion

EPISTAR

EPI Signal Targeting with Alternating Radiofrequency

FAIR

Flow-sensitive Alternating IR


180o

180o

90o

RF

Gx

Image

Gy

Alternating

Proximal Inversion

Odd Scan

Even Scan

Gz

90o

180o

180o

RF

Gx

Image

Gy

Odd

Scan

Alternating opposite

Distal Inversion

Gz

Even

Scan

ASL Pulse Sequences

EPI Signal Targeting with Alternating Radiofrequency

EPISTAR

Flow-sensitive Alternating IR

FAIR


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