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Functional MRI: Image

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Functional MRI: Image Contrast and Acquisition Karla L. Miller FMRIB Centre, Oxford University Other Nuclei of interest for Spectroscopy 23Na in Rat Brain (low ... – PowerPoint PPT presentation

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Title: Functional MRI: Image


1
Functional MRI Image Contrast and Acquisition
Karla L. Miller FMRIB Centre, Oxford University
2
Functional MRI Acquisition
  • Basics of FMRI
  • FMRI Contrast The BOLD Effect
  • Standard FMRI Acquisition
  • Confounds and Limitations
  • Beyond the Basics
  • New Frontiers in FMRI
  • What Else Can We Measure?

Basics of FMRI FMRI Contrast The BOLD
Effect Standard FMRI Acqusition Confounds and
Limitations Beyond the Basics New Frontiers in
FMRI What Else Can We Measure?
3
The BOLD Effect
BOLD Blood Oxygenation Level Dependent Deoxyhemog
lobin (dHb) has different resonance frequency
than water dHb acts as endogenous contrast
agent dHb in blood vessel creates frequency
offset in surrounding tissue (approx as dipole
pattern)
4
The BOLD Effect
Frequency spread causes signal loss over
time BOLD contrast Amount of signal loss
reflects dHb Contrast increases with delay (TE
echo time)
5
Vascular Response to Activation
capillary
6
Sources of BOLD Signal
Very indirect measure of activity (via
hemodynamic response to neural activity)! Complica
ted dynamics lead to reduction in dHb during
activation (active research area)
7
BOLD Contrast vs. TE
15 change
  • BOLD effect is approximately an exponential
    decay
  • S(TE) S0 eTE R2 ?S(TE) ? TE R2
  • R2 encapsulates all sources of signal dephasing,
    including sources of artifact (also increase with
    TE)
  • Gradient echo (GEGREFE) with moderate TE

8
Functional MRI Acquisition
Basics of FMRI FMRI Contrast The BOLD
Effect Standard FMRI Acquisition Confounds and
Limitations Beyond the Basics New Frontiers in
FMRI What Else Can We Measure?
9
The Canonical FMRI Experiment
  • Subject is given sensory stimulation or task,
    interleaved with control or rest condition
  • Acquire timeseries of BOLD-sensitive images
    during stimulation
  • Analyse image timeseries to determine where
    signal changed in response to stimulation

10
What is required of the scanner?
1
2
3
image
  • Must resolve temporal dynamics of stimulus
    (typically, stimulus lasts 1-30 s)
  • Requires rapid imaging one image every few
    seconds (typically, 24 s)
  • Anatomical images take minutes to acquire!
  • Acquire images in single shot (or a small number
    of shots)

11
Review Image Formation
Fourier transform
k-space
image space
  • Data gathered in k-space (Fourier domain of
    image)
  • Gradients change position in k-space during data
    acquisition (location in k-space is integral of
    gradients)
  • Image is Fourier transform of acquired data

12
BOLD Signal Dropout
Dephasing near air-tissue boundaries (e.g.,
sinuses) BOLD contrast coupled to signal loss
(black holes)
13
DTI Basics Water Diffusion(DTI Diffusion
Tensor Imaging)
Einstein on Brownian Motion
1905 five important papers
14
Why USE DTI MRI Detection of Acute Stroke
Diffusion Weighted Imaging (DWI) has proven to
be the most effective means of detecting early
strokes Lehigh Magnetic Imaging Center
Conventional T2 WI
DW-EPI
Sodium ion pumps fail - water goes in cells and
can not diffuse DW image gets bright (note
much later cells burst and stroke area gets very
dark)
15
Why USE DTI MRI Tumor
T2 (bright water)
T2 (bright water)
DWI (x direction) (T2 (bright water)(diffusion))
Contrast (T1 Gadolinium)
16
Why DTI MRI (more recently) Fiber
Tracking
17
1st level of complexity
Diffusion Weighted Image X direction
  • Higher diffusion in X direction ? lower signal

Artifact or Abnormality
David Porter - November 2000
18
T2
T2 diffusion
Sequence
T2 Image
Measure diffusion
Regular T2 image
Excite
(gradient strength)
19
2nd Level of complexity DWI 3 Direction
Measuring Diffusion in other directions (examples)
  • single-shot EPI diffusion-weighted (DW) images
    with b 1000s/mm2 and diffusion gradients
    applied along three orthogonal directions
  • Higher diffusion ? lower signal

Dxx
Dyy
Dzz
?
courtesy of Dr Sorensen, MGH, Boston
David Porter - November 2000
20
3rd level of complexityDiffusion Tensor Imaging
Basics
How can we track white matter fibers using DTI
  • Measures water diffusion in at least 6 directions
  • Echo-planar imaging (fast acquisition)
  • Collecting small voxels (1.8 x 1.8 x 3mm),
    scanning takes about 10 minutes

21
  • Higher diffusion ? lower signal

water
Diffusion ellipsoid
Diffusion ellipsoid
White matter fibers
  • Useful for following white matter tracts in
    healthy brain

22
  • Higher diffusion ? lower signal

White matter fibers
Isotropic
Anisotropic
Adapted from Beaulieu (2002). NMR in Biomed
15435-455
23
DTI ellipsoidmeasure 6 directions to describe
z
no diffusion
y
x
Ellipsoid represents magnitude of diffusion in
all directions by distance from center of
ellipsoid to its surface.
24
Ellipsoid Image
Information available through DTI
Tract
Pierpaoli and Basser, Toward a Quantitative
Assessment of Diffusion Anisotropy, Magn. Reson.
Med, 36, 893-906 (1996)
25
Tractography
Superior view color fiber maps
Lateral view color fiber maps
Zhang Laidlaw http//csdl.computer.org/comp/pro
ceedings/vis/2004/8788/00/87880028p.pdf.
26
axial
cor
sag
Diffusion Tensor Imaging data for cortical spinal
tract on right side blue superior inferior
fibers green anterior posterior fibers red
right left fibers Note tumor is darker mass on
left side of axial slice
MRISC
27
FA color (largest diffusion direction)
red right left green anterior
posterior blue superior - inferior
28
MRS Magnetic Resonance Spectroscopy
  • Proton spectroscopy (also can do C, O, Ph,..
    Nuclei)
  • Looking at protons in other molecules ( not
    water)
  • (ie NAA, Choline, Creatine, .)
  • Need
  • gt mmol/l of substances
  • high gyromagnetic ratio ( )
  • Just like spectroscopy used by chemist but
    includes
  • spatial localization

29
Just looking at Proton Spectroscopy
  • Just excite small volume
  • Do water suppression so giant peak disappears
  • Compare remaining peaks

precession
Frequency
Frequency
30
MRS Magnetic Resonance Spectroscopy
NAA N-acetyl aspartate, Cr Creatine, Cho
Choline
amplitude
NAA
Cr
Cho
Frequency of precession
31
Multi Voxel Spectroscopy (aka Chemical Shift
Imaging CSI)
  • Do many voxels at once
  • Can be some disadvantages with signal to noise
    (S/N) and voxel bleeding

32
Evaluate Health of Neurons (NAA level) Normalize
with Creatine (fairly constant in brain)
Red means High NAA/CR levels
33
  • Epilepsy Seizures (effects metabolite levels)
  • find location
  • determine onset time

34
Other Nuclei of interest for Spectroscopy
35
23Na in Rat Brain (low resolution images are
sodium 23 images) (high resolution images are
hydrogen images)
36
Common Metabolites used in Proton Spectroscopy
37
Important Concepts
  • What energies are used in each modality?
  • How does the energy interact with the tissue?
  • How is the image produced?
  • What is represented in the image?
  • What are important advantages and disadvantages
    of the major imaging modalities?
  • What are the fundamental differences between the
    Xray technologies (2D vs 3D, Radiography vs CT vs
    Fluoroscopy)?
  • What are the two major types of MRI images (T1,
    T2), and how are they different?
  • How are Angiograms produced (both Xray and MRI)?
  • Why are the advantages of combining imaging
    modalities?

38
Important Concepts
  • What does DTI, diffusion tensor imaging,
    measure?
  • What structures that we are interested in effect
    DTI images?
  • What does the DTI ellipsoid represent?
  • How might DTI be useful for clinical application
    or research?
  • What are we looking at with proton spectroscopy?
  • What are the three major metabolites we
    typically measure?
  • What do we need to be able to do proton
    spectroscopy?
  • What might proton spectroscopy be used for?
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