Transcript No Slide Title

Functional MRI: Image
Contrast and Acquisition
Karla L. Miller
FMRIB Centre, Oxford University
FMRI Acquisition
Functional MRI Acquisition
Basics of FMRI
FMRI Contrast: The BOLD Effect
Standard FMRI Acqusition
Acquisition
Confounds and Limitations
Beyond the Basics
New Frontiers in FMRI
What Else Can We Measure?
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
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)
FMRI Acquisition
Vascular Response to Activation
neuron
capillary
HbO2 dHb HbO2 HbO2 HbO2
HbO2
dHb 2
HbO
dHb 2HbO HbO
HbO
dHb
dHb
2
2 HbO2
HbO2 HbO2 HbO2
HbO2 dHb HbO
dHb2
HbO2
dHb
HbO2 HbO
HbO
dHb 2
2
HbO2 HbO2 HbO
HbO2
2
HbO
HbO2
2
HbO2
O2 metabolism
blood flow
blood volume
FMRI Acquisition
HbO2 = oxyhemoglobin
dHb = deoxyhemoglobin
[dHb]
Sources of BOLD Signal
Blood flow
Neuronal
activity
Metabolism
[dHb]
BOLD
signal
Blood volume
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
1–5%
change
• 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
FMRI Acquisition
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?
FMRI Acquisition
The Canonical FMRI Experiment
on
Stimulus
pattern
off
on
off
on
off
on
off
off
Predicted
BOLD signal
time
• 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
FMRI Acquisition
What is required of the scanner?
image 1 2 3 …
• 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)
FMRI Acquisition
Review: Image Formation
Fourier
transform
ky
kx
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
FMRI Acquisition
Raster-scan (2DFT) k-space acquisition
ky
kx
• Collect separate line each repetition period (TR)
• “Multi-shot”: image pieced together over multiple TR
• Images have few artifats, but take minutes to acquire
FMRI Acquisition
Echo-planar imaging (EPI)
ky
kx
• “Single-shot”: Collect entire image each TR
• Increase in acquisition speed (good for FMRI)
• Longer readout each TR (introduces image artifacts)
FMRI Acquisition
Partial k-space
ky
c+id
a+ib
a ib
c id
kx
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
FMRI Acquisition
Partial k-space EPI
ky
kx
Reduces TE (sacrifices some functional contrast)
Must acquire slightly more than half (Hermetian
symmetry is approximate)
Slight blurring added to image
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 ms
3.0T: 30 ms
Determines functional
contrast, set ≈T2*
TR
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)
(repeat time)
FMRI Acquisition
* These values are typical, not fixed!!
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?
FMRI Acquisition
The BOLD Effect
BOLD contrast is based on signal dephasing
BOLD imaging requires long delay (TE) for contrast
FMRI Acquisition
Signal Dropout in BOLD
Dephasing also occurs near air-tissue boundaries
due to abrupt shift in magnetic susceptibility
Sensitivity to BOLD effect implies problems near airtissue boundaries (e.g., sinuses)!
FMRI Acquisition
BOLD Signal Dropout
Non-BOLD
BOLD
Dephasing near air-tissue boundaries (e.g., sinuses)
BOLD contrast coupled to signal loss (“black holes”)
FMRI Acquisition
Image Warping
EPI
Multi-shot
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 offset
local warping
local
blur
Field map
EPI
Spiral
• 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
corrected
Can measure local frequency (“field map”)
Estimate distortion from field map and remove it
Field map correction introduces blurring
FMRI Acquisition
[Jenkinson et al]
Timing Errors
2DFT
Spiral
EPI
• 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…
FMRI Acquisition
EPI Ghosting
Odd and even lines mismatch (e.g.,
due to timing errors, eddy currents)
“ghost”
Causes aliasing (“ghosting”)
To fix: measure shifts with reference
scan, shift back in reconstruction
EPI
=
+
FMRI Acquisition
undersampled
Physiological “Noise”
Thermal SNR
Timecourse SNR
7T
7T
3T
1.5T
3T
1.5T
voxel volume
voxel volume
• Respiration, cardiac pulsation, neural networks
• Thermal SNR linear in voxel volume, B0
• Physiological noise tends to be “BOLD-like”: increases
with TE and B0
FMRI Acquisition
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?
FMRI Acquisition
Receive RF coils and SNR
SNR  receive volume
Surface coil
Volume coils
Volume coil
signal and noise from entire volume
good coverage, moderate SNR
Surface coils
localize signal and noise
reduced coverage, good SNR
Multi-channel coils
array of “independent” surface coils
good coverage
FMRI Acquisition
8-channel array
Parallel imaging (SENSE, SMASH, etc)
Surface
coils
Single coil
8-channel array
• 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.
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
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?
FMRI Acquisition
Sources of BOLD Signal
Yes! (ASL)
Blood flow
Maybe…
Neuronal
activity
Metabolism
[dHb]
BOLD
signal
No…?
Blood volume
Probably (VASO)
BOLD ([dHb]) is a very indirect measure of activity
Can MRI get closer to the action?
FMRI Acquisition
FMRI of Blood Flow: ASL
inversion
slab
z (=B0)
excitation
y
blood
x
inversion
imaging
plane
• Perfusion: delivery of metabolites (via local blood flow)
• Arterial Spin Labeling (ASL): invert of in-flowing blood
• IMAGEperfusion = IMAGEuninverted - IMAGEinverted
FMRI Acquisition
white matter
(low perfusion)
grey matter
(high perfusion)
Perfusion
image
Signal change (%)
FMRI of Blood Flow: ASL
ASL “kinetic curve”
0.8
0.6
0.4
0.2
0.0
0
1
2
3
Time (s)
• Represents an interesting physiological parameter
• Quantitative: fit kinetic curve for perfusion in ml/100g/min
• Lower SNR than BOLD
• Limited coverage (~5 slices)
FMRI Acquisition
4
FMRI of Blood Volume: VASO
[Lu et al, MRM 2003]
• 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
FMRI Acquisition
Diffusion Tensor Imaging (DTI)
Diffusion direction
• Water diffusion restricted along white matter
• Sensitize signal to diffusion in different
directions
• Measure along all directions, infer tracts
FMRI Acquisition
Diffusion Tensor Imaging (DTI)
z
y Color-coded directions
x
Tract-based
connectivity
• Complementary information to FMRI
– FMRI: gray matter, information processing
– DTI: white matter, information pathways
• Tractography: tracing white matter pathways between gray
matter regions
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/
FMRI Acquisition