1. Contrast and Acquisition
Functional MRI: Image
Contrast and Acquisition
Karla L. Miller
FMRIB Centre, Oxford University

2. Functional MRI Acquisition
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?
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?

3. 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)

4. 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)

5. Vascular Response to Activation
neuron
capillary
HbO2
HbO2
dHb
HbO2
HbO2
dHb
dHb = deoxyhemoglobin
HbO2 = oxyhemoglobin
[dHb]
O2 metabolism
blood flow
blood volume

6. Sources of BOLD Signal
Neuronal
activity
Metabolism
Blood flow
Blood volume
[dHb]
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)

7. S(TE) = S0 e–TE R2* S(TE)  TE R2*
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

8. 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?

9. The Canonical FMRI Experiment
Stimulus
pattern on
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

10. 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)

11. 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

12. BOLD Signal Dropout BOLD Non-BOLD
Dephasing near air-tissue boundaries (e.g., sinuses)
BOLD contrast coupled to signal loss (“black holes”)

13. DTI Basics – Water Diffusion (DTI – Diffusion Tensor Imaging)
Einstein on
Brownian
Motion
1905 five
important papers

14. Why 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
Conventional T2 WI
DW-EPI
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)

15. Why USE DTI MRI Tumor T2 (bright water) T2 (bright water)
DWI (x direction)
(T2 (bright water)+(diffusion))
Contrast
(T1 + Gadolinium)

16. Why DTI MRI (more recently): Fiber Tracking

17. 1st level of complexity Diffusion Weighted Image X direction
Higher diffusion in X direction  lower signal
Artifact or Abnormality
David Porter - November 2000

18. T2 + diffusion T2 Sequence RF Gx Gy Gz Time T2 Image-
Time T2
Image
Measure
diffusion
Regular
T2 image
Excite
(gradient strength)

19. 2nd Level of complexity Measuring Diffusion in other directions
DWI : 3 Direction
Measuring Diffusion in other directions
(examples)
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 
courtesy of Dr Sorensen, MGH, Boston
David Porter - November 2000

20. 3rd level of complexity Diffusion Tensor Imaging Basics
How can we track white matter fibers using DTI
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

21. Higher diffusion  lower signal
water
Diffusion ellipsoid
Diffusion ellipsoid
White matter fibers
Useful for following white matter tracts in healthy brain

22. Higher diffusion  lower signal
White matter fibers
Displacement of 4 particles starting at same origin
Similar molecular displacements in all directions
Greater molecular displacement along cylinders than across
Isotropic
Anisotropic
Adapted from: Beaulieu (2002). NMR in Biomed; 15:

23. DTI ellipsoid measure 6 directions to describez
no diffusion y x
Ellipsoid represents magnitude of diffusion in all directions
by distance from center of ellipsoid to its surface.

24. Information available through DTI
Ellipsoid Image
Information available through DTI
Tract
Monkey brain, in-vivo
Pixel by pixel map of the diffusion ellipsoids in the ROI shown in the image.
The Diffusion ellipsoids summarize all the information that we can obtain with DTI.
This presentation is focused on the scalar ones, but we can clearly see the direction of the fibers in the corpus callosum.
Pierpaoli and Basser, Toward a Quantitative Assessment of Diffusion Anisotropy, Magn. Reson. Med, 36, (1996)

25. Tractography Superior view color fiber maps
Lateral view color fiber maps
Zhang & Laidlaw:

26. axial
cor
sag
Diffusion Tensor Imaging data for
cortical spinal tract on right side
blue = superior – inferior fibers
green = anterior – posterior fibers
red = right – left fibers
Note tumor is darker mass on left
side of axial slice
MRISC

27. FA + color (largest diffusion direction)
red = right – left
green = anterior – posterior
blue = superior - inferior

28. MRS – Magnetic Resonance Spectroscopy
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

29. Just looking at Proton Spectroscopy
Just excite small volume
Do water suppression so giant peak disappears
Compare remaining peaks
precession
Frequency
Frequency

30. MRS – Magnetic Resonance Spectroscopy
NAA = N-acetyl aspartate, Cr = Creatine, Cho = Choline
amplitude
NAA Cr
Cho
Frequency of precession

31. 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”

32. Evaluate Health of Neurons (NAA level)
Normalize with Creatine (fairly constant in brain)
Red means
High NAA/CR
levels

33. Epilepsy Seizures (effects metabolite levels)
find location
determine onset time

34. Other Nuclei of interest for Spectroscopy

35. 23Na in Rat Brain (low resolution images are sodium 23 images)
(high resolution images are hydrogen images)

36. Common Metabolites used in Proton Spectroscopy

37. 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?

38. 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?