fmri acquisition functional mri: image contrast and acquisition functional mri: image contrast and...
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FMRI Acquisition
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
FMRI 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?
Functional MRI Acquisition
FMRI 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)
FMRI Acquisition
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
FMRI Acquisition
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
FMRI Acquisition
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)
FMRI Acquisition
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
FMRI 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?
Functional MRI Acquisition
FMRI 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
FMRI Acquisition
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
FMRI Acquisition
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
FMRI Acquisition
• Collect separate line each repetition period (TR)
• “Multi-shot”: image pieced together over multiple TR
• Images have few artifats, but take minutes to acquire
Raster-scan (2DFT) k-space acquisition
ky
kx
FMRI Acquisition
ky
kx
• “Single-shot”: Collect entire image each TR
• Increase in acquisition speed (good for FMRI)
• Longer readout each TR (introduces image artifacts)
Echo-planar imaging (EPI)
FMRI Acquisition
Partial k-space
If data doesn’t have phase errors, quadrants of k-space contain redundant information (Hermetian symmetry)
Partial k-space: acquire half of k-space and “fill in” missing data based on symmetry
a+ib
aib
c+id
cidky
kx
FMRI Acquisition
ky
kx
Reduces TE (sacrifices some functional contrast)
Must acquire slightly more than half (Hermetian symmetry is approximate)
Slight blurring added to image
Partial k-space EPI
FMRI Acquisition
Spiral FMRI
• Currently, only serious alternative to EPI
• Short apparent TE (center of k-space acquired early)
• Fast and efficient use of gradient hardware
• Reconstruction must resample onto grid before FFT
• Different artifacts than EPI (not necessarily better)
FMRI Acquisition
Multi-shot trajectories
FMRI Acquisition
Trajectory considerations
• Longer readout = more image artifacts– Single-shot (EPI & spiral) warping or blurring – PR & 2DFT have very short readouts and few artifacts
• Cartesian (2DFT, EPI) vs radial (PR, spiral)– 2DFT & EPI = ghosting & warping artifacts– PR & spiral = blurring artifacts
• SNR for N shots with time per shot Tread :
SNR Ttotal = N x Tread
FMRI Acquisition
Typical* FMRI Parameters
Parameter Value Notes
TE(echo time)
1.5T: 60 ms3.0T: 30 ms
Determines functional contrast, set ≈T2*
TR(repeat time)
1–4 s No extra info < 1s; Poor resolution > 6s
Matrix size 64x64 Limited by incurred warping/blurring
Resolution 3x3x4 mm Limited by SNR, FOV and matrix size
Flip angle 60-90º Set to Ernst angle (max tissue signal)
* These values are typical, not fixed!!
FMRI 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?
Functional MRI Acquisition
FMRI Acquisition
The BOLD Effect
BOLD contrast is based on signal dephasing
BOLD imaging requires long delay (TE) for contrast
FMRI Acquisition
Dephasing also occurs near air-tissue boundaries due to abrupt shift in magnetic susceptibility
Sensitivity to BOLD effect implies problems near air-tissue boundaries (e.g., sinuses)!
Signal Dropout in BOLD
FMRI Acquisition
BOLD Signal Dropout
BOLDNon-BOLD
Dephasing near air-tissue boundaries (e.g., sinuses)
BOLD contrast coupled to signal loss (“black holes”)
FMRI Acquisition
Image Warping
Multi-shotEPI
Position information is encoded in local frequency
Imperfections in magnetic field (frequency offsets) masquerade as information about position
Signal from regions with offset gets misplaced
Longer readouts leads to greater displacement
FMRI Acquisition
Field Offset
Field map
field offset local warping
EPI Spiral
localblur
• Object interacts with magnetic field, introduces local imperfections (first-order correction with “shim” fields)
• Field offset introduces phase accrual during readout
• EPI: field offsets warp image (PSF linear phase along y)
• Spiral: field offsets blur image (PSF has conical phase)
FMRI Acquisition
EPI Unwarping
field map uncorrected
Can measure local frequency (“field map”)Estimate distortion from field map and remove itField map correction introduces blurring
corrected
[Jenkinson et al]
FMRI Acquisition
Timing Errors
• Timing errors delay readout along kx and/or ky
• Analyze via k-space point-spread function (PSF)
• Shift in k-space PSF modulates image phase
• Phase cancellation patterns in image (can be complicated)
• Many causes: hardware delays, eddy currents…
2DFT Spiral EPI
FMRI Acquisition
EPI
EPI Ghosting
Odd and even lines mismatch (e.g., due to timing errors, eddy currents)
Causes aliasing (“ghosting”)
To fix: measure shifts with reference scan, shift back in reconstruction
“ghost”
= +
undersampled
FMRI Acquisition
Physiological “Noise”
• Respiration, cardiac pulsation, neural networks
• Thermal SNR linear in voxel volume, B0
• Physiological noise tends to be “BOLD-like”: increases with TE and B0
7T
3T
1.5T
7T
3T1.5T
Thermal SNR
voxel volume voxel volume
Timecourse SNR
FMRI 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?
Functional MRI Acquisition
FMRI Acquisition
Receive RF coils and SNR
Surface coil
8-channel array
SNR receive volume
Volume coilssignal and noise from entire volumegood coverage, moderate SNR
Surface coilslocalize signal and noisereduced coverage, good SNR
Multi-channel coilsarray of “independent” surface coilsgood coverage
Volume coil
FMRI Acquisition
• Coil sensitivity encodes spatial information
• Can “leave out” large parts of k-space– Theory: For n coils, only need 1/n of k-space– Practice: Need at least ~1/3 of k-space– In general, incurs loss of SNR
• More coverage, higher resolution, faster imaging, etc.
Parallel imaging (SENSE, SMASH, etc)
Single coil 8-channel array
Surface coils
FMRI Acquisition
FMRI at High Field (>3T)
• SNR and BOLD increase with field strength
• Physiological noise means practical gain is less
• Benefits: Resolution
• Problems: Artifacts, RF heating, wavelength effects…
FMRI Acquisition
High-resolution FMRI at 7T
High-res 7T: 0.58 x 0.58 x 0.58 mm3 = 0.2 mm3
High-res 3T: 1 x 1 x 1 mm3 = 1 mm3
Conventional 3T: 3 x 3 x 3 mm3 = 27 mm3
FMRI 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?
Functional MRI Acquisition
FMRI Acquisition
Sources of BOLD Signal
Neuronal activity Metabolism
Blood flow
Blood volume
[dHb]BOLDsignal
BOLD ([dHb]) is a very indirect measure of activity
Can MRI get closer to the action?
Yes! (ASL)
Probably (VASO)
Maybe…
No…?
FMRI Acquisition
FMRI of Blood Flow: ASL
• Perfusion: delivery of metabolites (via local blood flow)
• Arterial Spin Labeling (ASL): invert of in-flowing blood
• IMAGEperfusion = IMAGEuninverted - IMAGEinverted
inversionslab
imagingplane
excitation
inversion
xy
z (=B0)
bloodblood
FMRI Acquisition
FMRI of Blood Flow: ASL
• Represents an interesting physiological parameter
• Quantitative: fit kinetic curve for perfusion in ml/100g/min
• Lower SNR than BOLD
• Limited coverage (~5 slices)
grey matter(high perfusion)
white matter(low perfusion)
Perfusionimage Time (s)
0.0
0.2
0.4
0.6
0.8
0 1 2 3 4
Sig
na
l cha
nge
(%
) ASL “kinetic curve”
FMRI Acquisition
FMRI of Blood Volume: VASO
• Vascular Space Occupancy (VASO): null blood volume
• Invert everything (blood + tissue)
• Image when blood is at null point (no blood signal)
• Change in blood volume causes signal change
[Lu et al, MRM 2003]
FMRI Acquisition
Diffusion Tensor Imaging (DTI)
• Water diffusion restricted along white matter
• Sensitize signal to diffusion in different directions
• Measure along all directions, infer tracts
Diffusion direction
FMRI Acquisition
Diffusion Tensor Imaging (DTI)
• Complementary information to FMRI
– FMRI: gray matter, information processing
– DTI: white matter, information pathways
• Tractography: tracing white matter pathways between gray matter regions
Tract-based connectivity
Color-coded directionsx
y
z
FMRI Acquisition
Recommended Reading
Introduction to Functional Magnetic Resonance Imaging, by Buxton
Handbook of MRI Pulse Sequences, by Bernstein, King & Zhou
These slides:
http://www.fmrib.ox.ac.uk/~karla/