class 1: introduction of fmri 2012 spring, fmri: theory & practice
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Class 1: Introduction of fMRI
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
MRI studies brain anatomy.Functional MRI (fMRI) studies brain function.
MRI vs. fMRI
2012 spring, fMRI: theory & practice
Brain Imaging: Anatomy
Photography
CAT
PET
MRI
Source: modified from Posner & Raichle, Images of Mind2012 spring, fMRI: theory & practice
MRI vs. fMRI
neural activity blood oxygen fMRI signal
MRI fMRI
one image
many images (e.g., every 2 sec for 5 mins)
high resolution(1 mm)
low resolution(~3 mm but can be better)
fMRI Blood Oxygenation Level Dependent (BOLD) signal
indirect measure of neural activity
…
2012 spring, fMRI: theory & practice
E = mc2
???
The First “Brain Imaging Experiment”
“[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)
Angelo MossoItalian physiologist
(1846-1910)
… and probably the cheapest one too!
2012 spring, fMRI: theory & practice
History of NMR
NMR = nuclear magnetic resonanceFelix Block and Edward Purcell
1946: atomic nuclei absorb and re-emit radio frequency energy1952: Nobel prize in physics
nuclear: properties of nuclei of atomsmagnetic: magnetic field requiredresonance: interaction between magnetic field and radio frequency
Bloch PurcellNMR MRI: Why the name change?
most likely explanation: nuclear has bad connotations
less likely but more amusing explanation: subjects got nervous when fast-talking doctors suggested an NMR
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
Ogawa2012 spring, fMRI: theory & practice
First fMRI paper
Time
BrainActivity
Source: Kwong et al., 1992
Flickering CheckerboardOFF (60 s) - ON (60 s) -OFF (60 s) - ON (60 s) - OFF (60 s)
2012 spring, fMRI: theory & practice
Year of Publication Done on Jan 13, 2012
The Continuing Rise of fMRI
2012 spring, fMRI: theory & practice
# of
Pub
licat
ions
fMRI Setup
2012 spring, fMRI: theory & practice
fMRI intro movie
2012 spring, fMRI: theory & practice
Necessary Equipment
Magnet Gradient Coil RF Coil
Source for Photos: Joe Gati
RF Coil
4T magnet
gradient coil(inside)
2012 spring, fMRI: theory & practice
x 80,000 =
Robarts Research Institute 4T
The Big Magnet
Source: www.spacedaily.com
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
2012 spring, fMRI: theory & practice
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
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
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
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
CSF has low signal dark
T1-WEIGHTED ANATOMICAL IMAGE T2-WEIGHTED ANATOMICAL IMAGE
fat has low signal dark
CSF has high signal bright
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
Step 4: Use Gradients to Encode Space
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.
lower magnetic field;
lower frequencies
higher magnetic field;
higher frequencies
space
field strength
2012 spring, fMRI: theory & practice
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
K-Space
Source: Traveler’s Guide to K-space (C.A. Mistretta)2012 spring, fMRI: theory & practice
Review
Tissue protons align with magnetic field(equilibrium state)
RF pulses
Protons absorbRF energy
(excited state)
Relaxation processes
Protons emit RF energy(return to equilibrium state)
Spatial encodingusing magneticfield gradients
Relaxation processes
NMR signaldetection
Repeat
RAW DATA MATRIX
Fourier transform
IMAGE
Magnetic field
Source: Jorge Jovicich2012 spring, fMRI: theory & practice
Susceptibility Artifacts
-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…
sinuses
earcanals
T1-weighted imageT2*-weighted image
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
BOLD signal
Source: fMRIB Brief Introduction to fMRI
neural activity blood flow oxyhemoglobin T2* MR signal
Blood Oxygen Level Dependent signal
2012 spring, fMRI: theory & practice
Hemodynamic Response Function
% signal change = (point – baseline)/baselineusually 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 peaksignal peaks 4-6 sec after stimulus begins
post stimulus undershootsignal suppressed after stimulation ends
2012 spring, fMRI: theory & practice
BOLD signal
Source: Doug Noll’s primer2012 spring, fMRI: theory & practice
The Concise SummaryWe sort of understand this
(e.g., psychophysics, neurophysiology)
We sort of understand this (MR Physics)We’re *&^%$#@ clueless here!
2012 spring, fMRI: theory & practice
Gazzaniga, Ivry & Mangun, Cognitive Neuroscience
Spatial and Temporal Resolution
2012 spring, fMRI: theory & practice
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