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?