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Functional MRI: Image Contrast and Acquisition. Karla L. Miller FMRIB Centre, Oxford University. Functional MRI Acquisition. Basics of FMRI FMRI Contrast: The BOLD Effect Standard FMRI Acquisition Confounds and Limitations Beyond the Basics New Frontiers in FMRI

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Functional MRI: Image

Contrast and Acquisition

Karla L. Miller

FMRIB Centre, Oxford University


Functional mri 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?

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?


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)


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)


Vascular response to activation

neuron

HbO2 = oxyhemoglobin

dHb = deoxyhemoglobin

HbO2

HbO2

HbO2

HbO2

HbO2

dHb

HbO2

HbO2

HbO2

dHb

dHb

dHb

dHb

HbO2

HbO2

HbO2

HbO2

HbO2

HbO2

HbO2

HbO2

dHb

HbO2

dHb

dHb

HbO2

HbO2

dHb

HbO2

HbO2

HbO2

HbO2

HbO2

HbO2

HbO2

O2 metabolism

blood volume

[dHb]

blood flow

Vascular Response to Activation

capillary


Blood flow

Metabolism

Neuronal

activity

BOLD

signal

[dHb]

Blood volume

Sources of BOLD Signal

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 t e
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


Functional mri acquisition1
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?


The canonical fmri experiment

on

on

on

on

Stimulus

pattern

off

off

off

off

off

Predicted

BOLD signal

time

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


What is required of the scanner
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)

image

1

2

3 …


Review image formation

ky

kx

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

Fourier

transform

imagespace

k-space


Raster scan 2dft k space acquisition

ky

kx

Raster-scan (2DFT) k-space 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


Echo planar imaging epi

ky

kx

Echo-planar imaging (EPI)

  • “Single-shot”: Collect entire image each TR

  • Increase in acquisition speed (good for FMRI)

  • Longer readout each TR (introduces image artifacts)


Partial k space

ky

kx

Partial k-space

c+id

a+ib

aib

cid

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


Partial k space epi

ky

kx

Partial k-space EPI

Reduces TE (sacrifices some functional contrast)

Must acquire slightly more than half (Hermetian symmetry is approximate)

Slight blurring added to image


Spiral fmri
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)



Trajectory considerations
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


Typical fmri parameters
Typical* FMRI Parameters

* These values are typical, not fixed!!


Functional mri acquisition2
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?


The BOLD Effect

BOLD contrast is based on signal dephasing

BOLD imaging requires long delay (TE) for contrast


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 air-tissue boundaries (e.g., sinuses)!


Bold signal dropout

Non-BOLD

BOLD

BOLD Signal Dropout

Dephasing near air-tissue boundaries (e.g., sinuses)

BOLD contrast coupled to signal loss (“black holes”)


EPI

Multi-shot

Image Warping

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


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)


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

[Jenkinson et al]


Timing errors

2DFT

EPI

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…

Spiral


Epi ghosting

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


Physiological noise

7T

7T

3T

1.5T

3T

1.5T

Physiological “Noise”

Thermal SNR

Timecourse SNR

  • Respiration, cardiac pulsation, neural networks

  • Thermal SNR linear in voxel volume, B0

  • Physiological noise tends to be “BOLD-like”: increases with TE and B0

voxel volume

voxel volume


Functional mri acquisition3
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?


Receive rf coils and snr

Volume coil

8-channel array

Receive RF coils and SNR

SNR  receive volume

Volume coils

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

Surface coil


Parallel imaging sense smash etc

Surface coils

Single coil

8-channel array

Parallel imaging (SENSE, SMASH, etc)

  • 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 at high field 3t
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…


High resolution fmri at 7t
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


Functional mri acquisition4
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?


Blood flow

Metabolism

Neuronal

activity

BOLD

signal

[dHb]

Blood volume

Sources of BOLD Signal

Yes! (ASL)

Maybe…

No…?

Probably (VASO)

BOLD ([dHb]) is a very indirect measure of activity

Can MRI get closer to the action?


Fmri of blood flow asl

z (=B0)

inversion

slab

excitation

y

x

inversion

imaging

plane

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

blood


Fmri of blood flow asl1

white matter

(low perfusion)

grey matter

(high perfusion)

Perfusion

image

FMRI of Blood Flow: ASL

ASL “kinetic curve”

  • Represents an interesting physiological parameter

  • Quantitative: fit kinetic curve for perfusion in ml/100g/min

  • Lower SNR than BOLD

  • Limited coverage (~5 slices)

0.8

0.6

Signal change (%)

0.4

0.2

0.0

0

1

2

3

4

Time (s)


Fmri of blood volume vaso
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]


Diffusion tensor imaging dti
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


Diffusion tensor imaging dti1

z

y

x

Color-coded directions

Tract-based connectivity

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


Recommended reading
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/


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