1. Class 1: Introduction of fMRI
2012 spring, fMRI: theory & practice

2. 2012 spring, fMRI: theory & practice
Outline
part 1
Introduction of MRI and fMRI
Physics and BOLD
MRI safety, experimental design, etc
part 2
BVQX installation, sample dataset, GSG manual, and forum, etc overview
Q&A
2012 spring, fMRI: theory & practice

3. 2012 spring, fMRI: theory & practice
MRI vs. fMRI
Functional MRI (fMRI) studies brain function.
MRI studies brain anatomy.
2012 spring, fMRI: theory & practice

4. Brain Imaging: Anatomy
CAT
Photography
PET
MRI
2012 spring, fMRI: theory & practice
Source: modified from Posner & Raichle, Images of Mind

5. MRI vs. fMRI
MRI
fMRI
high resolution
(1 mm)
low resolution
(~3 mm but can be better)
one image …
fMRI
Blood Oxygenation Level Dependent (BOLD) signal
indirect measure of neural activity
many images
(e.g., every 2 sec for 5 mins)
 neural activity   blood oxygen   fMRI signal
2012 spring, fMRI: theory & practice

6. The First “Brain Imaging Experiment”
… and probably the cheapest one too!
E = mc2
???
Angelo Mosso
Italian physiologist
( )
“[In Mosso’s experiments] the subject to be observed lay on a delicately balanced table which could tip downward either at the head or at the foot if the weight of either end were increased. The moment emotional or intellectual activity began in the subject, down went the balance at the head-end, in consequence of the redistribution of blood in his system.”
-- William James, Principles of Psychology (1890)
2012 spring, fMRI: theory & practice

7. History of NMR NMR = nuclear magnetic resonance
Felix Block and Edward Purcell
1946: atomic nuclei absorb and re-emit radio frequency energy
1952: Nobel prize in physics
nuclear: properties of nuclei of atoms
magnetic: magnetic field required
resonance: interaction between magnetic field and radio frequency
Bloch
Purcell
NMR  MRI: Why the name change?
less likely but more amusing explanation:
subjects got nervous when fast-talking doctors suggested an NMR
most likely explanation:
nuclear has bad connotations
2012 spring, fMRI: theory & practice

8. 2012 spring, fMRI: theory & practice
History of fMRI
MRI
-1971: MRI Tumor detection (Damadian)
-1973: Lauterbur suggests NMR could be used to form images
-1977: clinical MRI scanner patented
-1977: Mansfield proposes echo-planar imaging (EPI) to acquire images faster
fMRI
-1990: Ogawa observes BOLD effect with T2*
blood vessels became more visible as blood oxygen decreased
-1991: Belliveau observes first functional images using a contrast agent
-1992: Ogawa et al. and Kwong et al. publish first functional images using BOLD signal
2012 spring, fMRI: theory & practice
Ogawa

9. First fMRI paper Flickering Checkerboard Brain Activity Time 
OFF (60 s) - ON (60 s) -OFF (60 s) - ON (60 s) - OFF (60 s)
Brain
Activity
2012 spring, fMRI: theory & practice
Time 
Source: Kwong et al., 1992

10. The Continuing Rise of fMRI
# of Publications
Year of Publication
Done on Jan 13, 2012
2012 spring, fMRI: theory & practice

11. 2012 spring, fMRI: theory & practice
fMRI Setup
2012 spring, fMRI: theory & practice

12. 2012 spring, fMRI: theory & practice
fMRI intro movie
2012 spring, fMRI: theory & practice

13. 2012 spring, fMRI: theory & practice
Necessary Equipment
4T magnet
RF Coil
gradient coil
(inside)
Magnet
Gradient Coil
RF Coil
Source for Photos: Joe Gati
2012 spring, fMRI: theory & practice

14. 2012 spring, fMRI: theory & practice
The Big Magnet
Very strong
1 Tesla (T) = 10,000 Gauss
Earth’s magnetic field = 0.5 Gauss
4 Tesla = 4 x 10,000  0.5 = 80,000X Earth’s magnetic field
Continuously on
Main field = B0 B0
Robarts Research Institute 4T
x 80,000 =
Source:
2012 spring, fMRI: theory & practice

15. Metal is a Problem!
Source:
Source:
flying_objects.html
“Large ferromagnetic objects that were reported as having been drawn into the MR equipment include a defibrillator, a wheelchair, a respirator, ankle weights, an IV pole, a tool box, sand bags containing metal filings, a vacuum cleaner, and mop buckets.”
-Chaljub et al., (2001) AJR
2012 spring, fMRI: theory & practice

16. Step 1: Put Subject in Big Magnet
Protons (hydrogen atoms) have “spins” (like tops). They have an orientation and a frequency.
When you put a material (like your subject) in an MRI scanner, some of the protons become oriented with the magnetic field.
2012 spring, fMRI: theory & practice

17. Step 2: Apply Radio Waves
When you apply radio waves (RF pulse) at the appropriate frequency, you can change the orientation of the spins as the protons absorb energy.
After you turn off the radio waves, as the protons return to their original orientations, they emit energy in the form of radio waves.
2012 spring, fMRI: theory & practice

18. Step 3: Measure Radio Waves
T1 measures how quickly the protons realign with the main magnetic field
T2 measures how quickly the protons give off energy as they recover to equilibrium
fat has high signal  bright
fat has low signal  dark
CSF has high signal  bright
CSF has low signal  dark
2012 spring, fMRI: theory & practice
T1-WEIGHTED ANATOMICAL IMAGE
T2-WEIGHTED ANATOMICAL IMAGE

19. 2012 spring, fMRI: theory & practice
Jargon Watch
T1 = the most common type of anatomical image
T2 = another type of anatomical image
TR = repetition time = one timing parameter
TE = time to echo = another timing parameter
flip angle = how much you tilt the protons (90 degrees in example above)
2012 spring, fMRI: theory & practice

20. Step 4: Use Gradients to Encode Space
field strength
space
lower magnetic field;
lower frequencies
higher magnetic field;
higher frequencies
Remember that radio waves have to be the right frequency to excite protons.
The frequency is proportional to the strength of the magnetic field.
If we create gradients of magnetic fields, different frequencies will affect protons in different parts of space.
2012 spring, fMRI: theory & practice

21. Step 5: Convert Frequencies to Brain Space
k-space contains information about frequencies in image
We want to see brains, not frequencies
2012 spring, fMRI: theory & practice

22. 2012 spring, fMRI: theory & practice
K-Space
2012 spring, fMRI: theory & practice
Source: Traveler’s Guide to K-space (C.A. Mistretta)

23. Review Magnetic field Tissue protons align with magnetic field
(equilibrium state)
RF pulses
Protons absorb
RF energy
(excited state)
Relaxation
processes
Spatial encoding
using magnetic
field gradients
Relaxation
processes
Protons emit RF energy
(return to equilibrium state)
NMR signal
detection
Repeat
RAW DATA MATRIX
Fourier transform
2012 spring, fMRI: theory & practice
IMAGE
Source: Jorge Jovicich

24. Susceptibility Artifacts
T2*-weighted image
T1-weighted image
sinuses
ear
canals
-In addition to T1 and T2 images, there is a third kind, called T2* = “tee-two-star”
-In T2* images, artifacts occur near junctions between air and tissue
sinuses, ear canals
In some ways this sucks, but in one way, it’s fabulous…
2012 spring, fMRI: theory & practice

25. 2012 spring, fMRI: theory & practice
What Does fMRI Measure?
Big magnetic field
protons (hydrogen molecules) in body become aligned to field
RF (radio frequency) coil
radio frequency pulse
knocks protons over
as protons realign with field, they emit energy that coil receives (like an antenna)
Gradient coils
make it possible to encode spatial information
MR signal differs depending on
concentration of hydrogen in an area (anatomical MRI)
amount of oxy- vs. deoxyhemoglobin in an area (functional MRI)
2012 spring, fMRI: theory & practice

26. 2012 spring, fMRI: theory & practice
BOLD signal
Blood Oxygen Level Dependent signal
neural activity   blood flow   oxyhemoglobin   T2*   MR signal
Source: fMRIB Brief Introduction to fMRI
2012 spring, fMRI: theory & practice

27. Hemodynamic Response Function
% signal change
= (point – baseline)/baseline
usually 0.5-3%
initial dip
-more focal and potentially a better measure
-somewhat elusive so far, not everyone can find it
time to rise
signal begins to rise soon after stimulus begins
time to peak
signal peaks 4-6 sec after stimulus begins
post stimulus undershoot
signal suppressed after stimulation ends
2012 spring, fMRI: theory & practice

28. 2012 spring, fMRI: theory & practice
BOLD signal
2012 spring, fMRI: theory & practice
Source: Doug Noll’s primer

29. The Concise Summary
We sort of understand this (e.g., psychophysics, neurophysiology)
We sort of understand this (MR Physics)
We’re clueless here!
2012 spring, fMRI: theory & practice

30. Spatial and Temporal Resolution
Gazzaniga, Ivry & Mangun, Cognitive Neuroscience
2012 spring, fMRI: theory & practice