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/