2. 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. MRI vs. fMRI
Functional MRI (fMRI)
MRI studies brain anatomy.
studies brain
function.
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
high resolution
MRI fMRI low resolution
(1 mm) (~3 mm but can be better)
one image
…
fMRI many images
(e.g., every 2 sec for 5 mins)
Blood Oxygenation Level Dependent (BOLD) signal
indirect measure of neural activity
↑ 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
(1846-1910)
“[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:
most likely explanation: subjects got nervous when fast-talking doctors suggested an NMR
nuclear has bad connotations 2012 spring, fMRI: theory & practice
8. 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
Ogawa
2012 spring, fMRI: theory & practice
9. First fMRI paper
Flickering Checkerboard
OFF (60 s) - ON (60 s) -OFF (60 s) - ON (60 s) - OFF (60 s)
Brain
Activity
2012 spring, fMRI: theory & practice
Source: Kwong et al., 1992 Time
10. # of Publications
The Continuing Rise of fMRI
Year of Publication Done on Jan 13, 2012
2012 spring, fMRI: theory & practice
13. 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. 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 Robarts Research Institute 4T
x 80,000 = B0
Source: www.spacedaily.com
2012 spring, fMRI: theory & practice
15. Metal is a Problem!
Source: www.howstuffworks.com
Source: http://www.simplyphysics.com/
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 When you put a material (like
“spins” (like tops). They have your subject) in an MRI
an orientation and a frequency. 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
After you turn off the radio waves, as the
change the orientation of the spins as the
protons return to their original
protons absorb energy.
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 T2 measures how quickly the
protons realign with the main protons give off energy as they
magnetic field recover to equilibrium
fat has high fat has low
signal bright signal dark
CSF has low CSF has high
signal dark signal bright
2012 spring, fMRI: theory & practice
T1-WEIGHTED ANATOMICAL IMAGE T2-WEIGHTED ANATOMICAL IMAGE
19. 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 higher
magnetic field; magnetic field;
lower higher
frequencies 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 We want to see brains,
information about not frequencies
frequencies in image
2012 spring, fMRI: theory & practice
22. 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
Relaxation Spatial encoding
RF energy
processes using magnetic
(excited state)
field gradients
Relaxation
processes
Protons emit RF energy
(return to equilibrium state)
NMR signal
detection
Repeat
RAW DATA MATRIX
Fourier transform
IMAGE
2012 spring, fMRI: theory & practice
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. 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. 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 time to rise
= (point – baseline)/baseline signal begins to rise soon after stimulus begins
usually 0.5-3%
time to peak
initial dip signal peaks 4-6 sec after stimulus begins
-more focal and potentially a better
measure
post stimulus undershoot
-somewhat elusive so far, not
signal suppressed after stimulation ends
everyone can find it 2012 spring, fMRI: theory & practice
28. BOLD signal
2012 spring, fMRI: theory & practice
Source: Doug Noll’s primer
29. The Concise Summary
We sort of understand this
(e.g., psychophysics, We sort of understand this
neurophysiology) We’re *&^%$#@ clueless here! (MR Physics)
2012 spring, fMRI: theory & practice
30. Spatial and Temporal Resolution
Gazzaniga, Ivry & Mangun, Cognitive Neuroscience
2012 spring, fMRI: theory & practice