class 1: introduction of fmri 2012 spring, fmri: theory & practice

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


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

MRI vs. fMRI


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

…


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!


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


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)


Year of Publication Done on Jan 13, 2012

The Continuing Rise of fMRI


# of

Pub

licat

ions

fMRI Setup


fMRI intro movie


Necessary Equipment

Magnet Gradient Coil RF Coil

Source for Photos: Joe Gati

RF Coil

4T magnet

gradient coil(inside)


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


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 “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.


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.


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


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

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


Step 5: Convert Frequencies to Brain Space

k-space contains information about

frequencies in image

We want to see brains, not frequencies


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


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

Source: fMRIB Brief Introduction to fMRI

neural activity blood flow oxyhemoglobin T2* MR signal

Blood Oxygen Level Dependent signal


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


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!


Gazzaniga, Ivry & Mangun, Cognitive Neuroscience

Spatial and Temporal Resolution


class 1: introduction of fmri 2012 spring, fmri: theory & practice

Documents

theory practice2012

theory practicethe

theory practiceoutlinepart

publications2012 spring

overviewqa2012 spring

images of mind2012 spring

bold signalogawa2012

theory practicebrain