Class 1 f_mri_intro

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 vs. fMRI

Functional MRI (fMRI)
MRI studies brain anatomy.
studies brain
function.


Brain Imaging: Anatomy

CAT

Photography PET

MRI

Source: modified from Posner & Raichle, Images of Mind

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

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)

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

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

First fMRI paper

Flickering Checkerboard
OFF (60 s) - ON (60 s) -OFF (60 s) - ON (60 s) - OFF (60 s)

Brain
Activity

Source: Kwong et al., 1992 Time 

# of Publications
The Continuing Rise of fMRI

Year of Publication Done on Jan 13, 2012

fMRI Setup


fMRI intro movie


Necessary Equipment
4T magnet

RF Coil

gradient coil
(inside)

Magnet Gradient Coil RF Coil

Source for Photos: Joe Gati


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


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

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.

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.


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

T1-WEIGHTED ANATOMICAL IMAGE T2-WEIGHTED ANATOMICAL IMAGE

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)


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.

Step 5: Convert Frequencies to Brain
Space

k-space contains We want to see brains,
information about not frequencies
frequencies in image


K-Space

Source: Traveler’s Guide to K-space (C.A. Mistretta)

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
Source: Jorge Jovicich

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…


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)


BOLD signal
Blood Oxygen Level Dependent signal

↑neural activity  ↑ blood flow  ↑ oxyhemoglobin  ↑ T2*  ↑ MR signal

Source: fMRIB Brief Introduction to fMRI

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

BOLD signal

Source: Doug Noll’s primer

The Concise Summary
We sort of understand this
(e.g., psychophysics, We sort of understand this
neurophysiology) We’re *&^%$#@ clueless here! (MR Physics)


Spatial and Temporal Resolution

Gazzaniga, Ivry & Mangun, Cognitive Neuroscience

Class 1 f_mri_intro

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