3.1 t 127 mhz 3.0 t 123 mhz 2.9 t 119 mhz excite like a swing. got one of the 3 orthogonal spatial...
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3.1 T127 MHz
3.0 T123 MHz
2.9 T119 MHz
excite
Like a swing. Got one of the 3 orthogonal spatial dimensions whenwe excite. z
3.1 T127 MHz
3.0 T123 MHz
2.9 T119 MHz
phase encode(after we excitebefore we listen)
Got second of the 3 orthogonal spatial dimensions whenwe listen.
fast
slow
regular
y
3.1 T127 MHz
3.0 T123 MHz
2.9 T119 MHz
LISTEN
Got second of the 3 orthogonal spatial dimensions whenwe listen.
fast
slow
regular
ModelofHeadCoil
x
signalwe “hear”
Repeat 256 times for a 256x256pixel image
Different phase each time
scan = 4 minutes
180 Degree RF Pulse
correcting gradients
Excite
Z
Y
X
Listen
SPIN ECHO SEQUENCE
TE – echo time
TR – repeat time
Contrast
T1 weighted – (MPRAGE-anatomical)T2 weighted – (fmri)
Spin Relaxation• Spins do not continue to precess forever
• Longitudinal magnetization returns to equilibrium due to spin-lattice interactions – T1 decay
• Transverse magnetization is reduced due to both spin-lattice energy loss and local, random, spin dephasing – T2 decay
• Additional dephasing is introduced by magnetic field inhomogeneities within a voxel – T2' decay. This can be reversible, unlike T2 decay
T1 decay – “spins back down”
Collective MagneticMoment of Protons
end
start
B0
signalwe “hear”
V
Time
T1 Recovery
Longitudinal Magnetization
Time2.0s
T2 decay – separation (dephasing) of “collective magnetic moment”
sometime after RF excitationImmediately after RF excitation
=
collective magnecticmoment
individual spins
separation (dephasing)
a little time later
T2 Decay
Transverse Magnetization
Time0.2s
T2 Decay
Trans. Mag.
T1 Recovery
Long. Mag.
50 ms50 ms 1 s1 s
Image type: Proton Density Contrast
TE – echo time TR – repeat time
Proton Density Weighted ImageProton Density Weighted Image
T2 Decay
Trans.Mag.
T1 Recovery
Long.Mag.
50 ms50 ms 1 s1 s
T1 Contrast
time time
TE – echo time TR – repeat time
T1 Weighted ImageT1 Weighted Image
T2 Decay
Trans. Mag.
T1 Recovery
Long.Mag.
50 ms50 ms 1 s1 s
T2* and T2 Contrast
TE – echo time TR – repeat time
T2 Weighted IMageT2 Weighted IMage
ProtonProtonDensityDensityWeightedWeightedImageImage
T1 T1 Weighted Weighted ImageImage
T2 T2 Weighted Weighted ImageImage
Properties of Body TissuesTissue T1 (ms) T2 (ms)
Grey Matter (GM) 950 100
White Matter (WM) 600 80
Muscle 900 50
Cerebrospinal Fluid (CSF) 4500 2200
Fat 250 60
Blood 1200 100-200
MRI has high contrast for different tissue types!
Functional MRI: Image Contrast and AcquisitionFunctional MRI: Image Contrast and Acquisition
Karla L. Miller FMRIB Centre, Oxford University
Karla L. Miller FMRIB Centre, Oxford University
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?
Functional MRI Acquisition
The BOLD Effect
BOLD: Blood Oxygenation Level Dependent
Deoxyhemoglobin (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)
Frequency spread causes signal loss over time
BOLD contrast: Amount of signal loss reflects [dHb]
Contrast increases with delay (TE = echo time)
The BOLD Effect
HbO2
HbO2
HbO2
HbO2
Vascular Response to Activation
dHb
dHb
dHb
dHb
O2 metabolism
dHb
dHb
HbO2
HbO2
dHbHbO2
HbO2
dHbdHb
HbO2
blood flow
HbO2
HbO2
HbO2
HbO2
HbO2HbO2
HbO2 HbO2
HbO2
HbO2HbO2
HbO2
HbO2
HbO2
[dHb]
dHb = deoxyhemoglobinHbO2 = oxyhemoglobin
capillary
blood volume
HbO2
HbO2HbO2
neuron
Sources of BOLD Signal
Neuronal activity Metabolism
Blood flow
Blood volume
[dHb]BOLDsignal
Very indirect measure of activity (via hemodynamic response to neural activity)!
Complicated dynamics lead to reduction in [dHb] during activation (active research area)
BOLD Contrast vs. TE
• BOLD effect is approximately an exponential decay:
S(TE) = S0 e–TE R2* S(TE) TE R2*
• R2* encapsulates all sources of signal dephasing, including sources of artifact (also increase with TE)
• Gradient echo (GE=GRE=FE) with moderate TE
1–5% change
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?
Functional MRI Acquisition
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
PredictedBOLD signal
time
Stimuluspattern
on
off
on
off
on
off
on
offoff
What is required of the scanner?
• Must resolve temporal dynamics of stimulus (typically, stimulus lasts 1-30 s)
• Requires rapid imaging: one image every few seconds (typically, 2–4 s)
• Anatomical images take minutes to acquire!
• Acquire images in single shot (or a small number of shots)
1 2 3 …image
Review: Image Formation
• 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
k-space image space
Fouriertransform
ky
kx
BOLD Signal Dropout
BOLDNon-BOLD
Dephasing near air-tissue boundaries (e.g., sinuses)
BOLD contrast coupled to signal loss (“black holes”)
Einstein on Brownian Motion
1905 five important papers
DTI Basics – Water Diffusion(DTI – Diffusion Tensor Imaging)
Conventional TConventional T22 WI WI DW-EPIDW-EPI
Why USE DTI MRI : Detection of Acute StrokeWhy 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
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)
Why USE DTI MRIWhy USE DTI MRI Tumor
T2 (bright water)
DWI (x direction)(T2 (bright water)+(diffusion))
Contrast (T1 + Gadolinium)
T2 (bright water)
Why DTI MRI (more recently): Fiber Tracking
Diffusion Weighted Image X directionDiffusion Weighted Image X direction
David Porter - November 2000
Artifact or Abnormality
Higher diffusion in X direction lower signal
RF
Gx
Gy
Gz
-
Time
(gradient strength)
T2T2 + diffusion
T2Image
Sequence
Excite Measurediffusion
RegularT2 image
courtesy of Dr Sorensen, MGH, Boston
David Porter - November 2000
single-shot EPI diffusion-weighted (DW) images with b = 1000s/mm2 and diffusion gradients applied along three orthogonal directions Higher diffusion lower signal
Dzz Dxx Dyy
Measuring Diffusion in other directions(examples)
• 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
How can we track white matter fibers using DTI
• Useful for following white matter tracts in healthy brain
Higher diffusion lower signal
water
Diffusion ellipsoid Diffusion ellipsoid
White matter fibers
Isotropic Anisotropic
Adapted from: Beaulieu (2002). NMR in Biomed; 15:435-455
Higher diffusion lower signal
White matter fibers
x
yz
DTI ellipsoidmeasure 6 directions to describe
no diffusion
Ellipsoid represents magnitude of diffusion in all directionsby distance from center of ellipsoid to its surface.
Pierpaoli and Basser, Toward a Quantitative Assessment of Diffusion Anisotropy, Magn. Reson. Med, 36, 893-906 (1996)
Ellipsoid Image
Tract
Information available through DTI
Tractography
Zhang & Laidlaw: http://csdl.computer.org/comp/proceedings/vis/2004/8788/00/87880028p.pdf.
Superior view color fiber maps Lateral view color fiber maps
Diffusion Tensor Imaging data forcortical spinal tract on right side
blue = superior – inferior fibersgreen = anterior – posterior fibersred = right – left fibers
Note tumor is darker mass on leftside of axial slice
axial
sag
cor
MRISC
FA + color (largest diffusion direction)
red = right – leftgreen = anterior – posteriorblue = superior - inferior
• Proton spectroscopy (also can do C, O, Ph,.. Nuclei)• Looking at protons in other molecules ( not water)
(ie NAA, Choline, Creatine, …….)• Need
> mmol/l of substances
high gyromagnetic ratio ( )• Just like spectroscopy used by chemist but includes
spatial localization
MRS – Magnetic Resonance Spectroscopy
Just looking at Proton Spectroscopy
• Just excite small volume• Do water suppression so giant peak disappears• Compare remaining peaks
Frequency
Frequency
precession
MRS – Magnetic Resonance Spectroscopy
Frequency of precession
amplitude
NAA
CrCho
NAA = N-acetyl aspartate, Cr = Creatine, Cho = Choline
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”
Evaluate Health of Neurons (NAA level) Normalize with Creatine (fairly constant in brain)
Red meansHigh NAA/CRlevels
Epilepsy Seizures (effects metabolite levels)• find location• determine onset time
Other Nuclei of interest for Spectroscopy
23Na in Rat Brain(low resolution images are sodium 23 images)(high resolution images are hydrogen images)
Common Metabolites used in Proton Spectroscopy
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?
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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