Section 2 Basic fMRI Physics

Other Resources
These slides were condensed from several excellent online sources. I have tried to give credit where appropriate. If you would like a more thorough introductory review of MR physics, I suggest the following:
Robert Coxs slideshow, (f)MRI Physics with Hardly Any Math, and his book chapters online. http://afni.nimh.nih.gov/afni/edu/ See Background Information on MRI section Mark Cohens intro Basic MR Physics slides http://porkpie.loni.ucla.edu/BMD_HTML/SharedCode/MiscShared.html Douglas Nolls Primer on MRI and Functional MRI http://www.bme.umich.edu/~dnoll/primer2.pdf

For a more advanced tutorial, see:

Joseph Hornaks Web Tutorial, The Basics of MRI http://www.cis.rit.edu/htbooks/mri/mri-main.htm

Recipe for MRI

1) Put subject in big magnetic field (leave him there) 2) Transmit radio waves into subject [about 3 ms] 3) Turn off radio wave transmitter 4) Receive radio waves re-transmitted by subject
Manipulate re-transmission with magnetic fields during this readout interval [10-100 ms: MRI is not a snapshot]

5) Store measured radio wave data vs. time

Now go back to 2) to get some more data

6) Process raw data to reconstruct images 7) Allow subject to leave scanner (this is optional)

Source: Robert Coxs web slides

History of NMR
NMR = nuclear magnetic resonance Felix Block and Edward Purcell 1946: atomic nuclei absorb and reemit 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 NMR MRI: Why the name change? Purcell

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

Ogawa

Necessary Equipment
4T magnet

RF Coil gradient coil (inside)

Magnet

Gradient Coil

RF Coil

Source: Joe Gati, photos

The Big Magnet

Very strong 1 Tesla (T) = 10,000 Gauss Earths magnetic field = 0.5 Gauss 4 Tesla = 4 x 10,000 0.5 = 80,000X Earths magnetic field Continuously on Main field = B0
Robarts Research Institute 4T

x 80,000 =

B0

Source: www.spacedaily.com

The whopping strength of the magnet makes safety essential. Things fly Even big things!

Magnet Safety

Source: www.howstuffworks.com

Source: http://www.simplyphysics.com/ flying_objects.html

Screen subjects carefully Make sure you and all your students & staff are aware of hazzards Develop stratetgies for screening yourself every time you enter the magnet

Do the metal macarena!

Subject Safety
Anyone going near the magnet subjects, staff and visitors must be thoroughly screened: Subjects must have no metal in their bodies: pacemaker aneurysm clips metal implants (e.g., cochlear implants) interuterine devices (IUDs) some dental work (fillings okay)
This subject was wearing a hair band with a ~2 mm Subjects must remove metal from their bodies copper clamp. Left: with hair band. Right: without. jewellery, watch, piercings Source: Jorge Jovicich coins, etc. wallet any metal that may distort the field (e.g., underwire bra)

Subjects must be given ear plugs (acoustic noise can reach 120 dB)

Protons
Can measure nuclei with odd number of neutrons 1H, 13C, 19F, 23Na, 31P
1H

(proton) abundant: high concentration in human body high sensitivity: yields large signals

Outside magnetic field

Protons align with field

randomly oriented

Inside magnetic field

spins tend to align parallel or anti-parallel to B0 net magnetization (M) along B0 spins precess with random phase no net magnetization in transverse plane only 0.0003% of protons/T align with field
longitudinal axis

Longitudinal magnetization

M=0

Source: Mark Cohens web slides Source: Robert Coxs web slides

transverse plane

Larmor Frequency
Larmor equation
f = B0 = 42.58 MHz/T At 1.5T, f = 63.76 MHz At 4T, f = 170.3 MHz

170.3

Resonance Frequency for 1H

63.8

1.5

4.0

Field Strength (Tesla)

RF Excitation
Excite Radio Frequency (RF) field
transmission coil: apply magnetic field along B1 (perpendicular to B0) for ~3 ms oscillating field at Larmor frequency frequencies in range of radio transmissions B1 is small: ~1/10,000 T tips M to transverse plane spirals down analogies: guitar string (Noll), swing (Cox) final angle between B0 and B1 is the flip angle

Transverse magnetization

B0

B1

Source: Robert Coxs web slides

Coxs Swing Analogy

Source: Robert Coxs web slides

Relaxation and Receiving

Receive Radio Frequency Field
receiving coil: measure net magnetization (M) readout interval (~10-100 ms) relaxation: after RF field turned on and off, magnetization returns to normal
longitudinal magnetization T1 signal recovers transverse magnetization T2 signal decays

Source: Robert Coxs web slides

T1 and TR
T1 = recovery of longitudinal (B0) magnetization used in anatomical images ~500-1000 msec (longer with bigger B0) TR (repetition time) = time to wait after excitation before sampling T1

Source: Mark Cohens web slides

add a gradient to the main magnetic field excite only frequencies corresponding to slice plane
Freq

Spatial Coding:Gradients
How can we encode spatial position?
Example: axial slice

Use other tricks to get other two dimensions

left-right: frequency encode top-bottom: phase encode Gradient switching thats what makes all the beeping & buzzing noises during imaging!

Field Strength (T) ~ z position

Gradient coil

Precession In and Out of Phase

protons precess at slightly different frequencies because of (1) random fluctuations in the local field at the molecular level that affect both T2 and T2*; (2) larger scale variations in the magnetic field (such as the presence of deoxyhemoglobin!) that affect T2* only. over time, the frequency differences lead to different phases between the molecules (think of a bunch of clocks running at different rates at first they are synchronized, but over time, they get more and more out of sync until they are random) as the protons get out of phase, the transverse magnetization decays this decay occurs at different rates in different tissues
Source: Mark Cohens web slides

T2 and TE
T2 = decay of transverse magnetization TE (time to echo) = time to wait to measure T2 or T2* (after refocussing with spin echo or gradient echo)

Source: Mark Cohens web slides

Echos
pulse sequence: series of excitations, gradient triggers and readouts
Gradient echo Echos refocussing of signal pulse sequence Spin echo: use a 180 degree pulse to mirror image the spins in the transverse plane when fast regions get ahead in phase, make them go to the back and catch up

-measure T2 -ideally TE = average T2

Gradient echo: flip the gradient from negative to positive
t = TE/2

make fast regions become slow and vice-versa

A gradient reversal (shown) or 180 pulse (not shown) at this point will lead to a recovery of transverse magnetization

-measure T2* -ideally TE ~ average T2*

TE = time to wait to measure refocussed spins
Source: Mark Cohens web slides

T1 vs. T2

Source: Mark Cohens web slides

K-Space

Source: Travelers Guide to K-space (C.A. Mistretta)

A Walk Through K-space

single shot two shot
K-space can be sampled in many shots (or even in a spiral) 2 shot or 4 shot less time between samples of slices allows temporal interpolation

Note: The above is k-space, not slices

vs.

both halves of k-space in 1 sec

1st half of k-space in 0.5 sec

2nd half of k-space 1st half of k-space in 0.5 sec in 0.5 sec

2nd half of k-space in 0.5 sec

1st volume in 1 sec

interpolated image

2nd volume in 1 sec

T2*
T2* relaxation dephasing of transverse magnetization due to both: - microscopic molecular interactions (T2) - spatial variations of the external main field B (tissue/air, tissue/bone interfaces) exponential decay (T2* 30 - 100 ms, shorter for higher Bo)
Mxy Mo sin T2 T2*

time
Source: Jorge Jovicich

Susceptibility
Adding a nonuniform object (like a person) to B0 will make the total magnetic field nonuniform This is due to susceptibility: generation of extra magnetic fields in materials that are immersed in an external field For large scale (10+ cm) inhomogeneities, scanner-supplied nonuniform magnetic fields can be adjusted to even out the ripples in B this is called shimming
Susceptibility Artifact -occurs near junctions between air and tissue sinuses, ear canals -spins become dephased so quickly (quick T2*), no signal can be measured

sinuses ear canals

Susceptibility variations can also be seen around blood vessels where deoxyhemoglobin affects T2* in nearby tissue
Source: Robert Coxs web slides

Hemoglobin

Hemoglogin (Hgb):
- four globin chains - each globin chain contains a heme group - at center of each heme group is an iron atom (Fe) - each heme group can attach an oxygen atom (O2) - oxy-Hgb (four O2) is diamagnetic no B effects - deoxy-Hgb is paramagnetic if [deoxy-Hgb] local B

Source: http://wsrv.clas.virginia.edu/~rjh9u/hemoglob.html, Jorge Jovicich

BOLD signal
Blood Oxygen Level Dependent signal neural activity blood flow oxyhemoglobin T2*
Mxy Signal

MR signal

Mo sin

T2* task T2* control

S time

Stask Scontrol
TEoptimum

Source: fMRIB Brief Introduction to fMRI

Source: Jorge Jovicich

BOLD signal

Source: Doug Nolls primer

First Functional Images

Source: Kwong et al., 1992

Hemodynamic Response Function

% signal change
= (point baseline)/baseline usually 0.5-3%

time to rise
signal begins to rise soon after stimulus begins

initial dip

time to peak

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

Review
Magnetic field Tissue protons align with magnetic field (equilibrium state) RF pulses Relaxation processes Protons absorb Spatial encoding RF energy 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