basic fmri physics in bold fmri, we are measuring: the inhomogeneities introduced into the magnetic...
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Basic fMRI Physics
In BOLD fMRI, we are measuring: the inhomogeneities introduced into the magnetic field of the scanner… as a result of the changing ratio of oxygenated:deoxygenated blood… via their effect on the rates of dephasing of hydrogen nuclei.
Ehhh???
History of MRI
NMR = nuclear magnetic resonancenuclear: properties of nuclei of atomsmagnetic: magnetic field requiredresonance: magnetic field x radio frequency
1946: Block and Purcellatomic nuclei absorb and re-emit radio frequency energy
1992: Ogawa and colleaguesfirst functional images using BOLD signal
Bloch Purcell
NMR MRI: Why the name change?
most likely explanation: nuclear has bad connotations
Ogawa less likely explanation: NMR means Nouveau Mouvement Religieux
Necessary Equipment
Magnet Gradient Coil RF Coil
Source: Joe Gati, photos
RF Coil
3T magnet
gradient coil(inside)
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]
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 Cox’s web slides
x 60,000 =
The Big Magnet
Source: www.spacedaily.com
Main field = B0
• Continuously on
• Very strong : Earth’s magnetic field = 0.5 Gauss / 1 Tesla (T) = 10,000 Gauss
3 Tesla = 3 x 10,000 0.5 = 60,000 x Earth’s magnetic field
B0
Robarts Research Institute 3T
SafetyThe strength of the magnet makes safety essential : things fly – even big things!
Source: www.howstuffworks.com Source: http://www.simplyphysics.com/flying_objects.html
Anyone entering the magnet must be metal free
This subject was wearing a hair band with a ~2 mm copper clamp. Left: with hair band. Right: without.
Source: Jorge Jovicich
Develop screening strategies :do the metal macarena!
1H aligns with B0
longitudinalaxis
Outside magnetic field • randomly oriented
M = 0
transverseplane
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
Source: Mark Cohen’s web slidesMSource: Robert Cox’s web slides
Longitudinalmagnetization
Protons are abundant: high concentration in human body have high sensitivity: yields large signals
Larmor Frequency
Larmor equation : resonance frequency f = B0/2π for 1H = 42.58 MHz/T
Field Strength (Tesla)
127.7
63.8
1.5 3.0
Fre
quen
cy (
MH
z)
Turn your dial to 3T fMRI …… broadcasting at a frequency of 127.7 Mhz
Radio-Frequency Excitation
• 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
Transversemagnetization
longitudinalaxis
Source: Robert Cox’s 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 (realignment)transverse magnetization T2 signal decays (dephasing)
Source: Robert Cox’s web slides
Why the dephasing ?
Source: Mark Cohen’s web slides
• 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 that affect T2* only.
• over time, the frequency differences lead to different phases between the molecules (clock analogy)
• as the protons get out of phase, the transverse magnetization decays
• this decay occurs at different rates in different tissues
T1 and TR
Source: Mark Cohen’s web slides
T1 = recovery of longitudinal magnetization (B0)
due to realignment of spinsTR (time to repetition) = time to wait after excitation before sampling T1
= time before next RF excitation
≈ M0(1-exp(-t/T1))
T2 and TE
Source: Mark Cohen’s web slides
T2 = decay of transverse (B1) magnetization
due to dephasing of spinsTE (time to echo) = time to wait before sampling T2
(after refocusing of signal)
≈ exp(-t/T2))
Source: Mark Cohen’s web slides
TISSUE T1(s) T2(s)
grey matter 1.0 0.10
white matter 0.7 0.08
CSF 2.0 0.25
blood 1.2 0.25
water 4.7 3.50
T1 and T2 contrasts
T2* relaxation
Source: Jorge Jovicich
time
Mxy
Mo sinT2
T2*
• dephasing of transverse magnetization due to both:
- microscopic molecular interactions (as for T2)
- spatial variations of the external main field B (tissue/air, tissue/bone interfaces)
• exponential decay (T2* 30 - 100 ms, shorter for higher Bo)
Spatial Coding: Gradients
How can we encode spatial position?• Add a gradient to the main magnetic field• Excite only frequencies corresponding to slice plane• Use other tricks to get other two dimensions
left-right: frequency encode top-bottom: phase encode
Field Strength ~ z position
Fre
qu
en
cy
Gradient switching – that’s what makes all the beeping & buzzing noises during imaging => EAR PLUGS !
Echos
Source: Mark Cohen’s web slides
Echos = refocusing of signal
Spin echo (not shown) – measure T2
Gradient echo (shown) - measure T2*flip the gradient at t=TE/2measure after refocusing at t=TE
pulse sequence: series of excitations, gradient triggers and readouts
t = TE/2
A gradient reversal at this point will lead to a recovery of transverse magnetization
TE = time to wait to measure refocused spins
(left-right)
(top-bottom)
A walk through the K-space
(inverse Fourier transform)
Source: Traveler’s Guide to K-space (C.A. Mistretta)
Susceptibility
Source: Robert Cox’s web slides
Adding a nonuniform object (like a person) to B0 will make the total magnetic field nonuniformThis is due to susceptibility: generation of extra magnetic fields in materials that are immersed in an
external field
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
earcanals
Susceptibility variations can also be seen around blood vessels where deoxyhemoglobin affects T2* in nearby tissue
Hemoglobin
Source: http://wsrv.clas.virginia.edu/~rjh9u/hemoglob.html, Jorge Jovicich
A molecule to breathe with:
- four globin chains - each globin chain contains a heme group - at center of each heme group is an iron atom (Fe)
- each iron ion Fe2+ can attach an oxygen molecule (O2)
- oxy-Hemoglobin (four O2) is diamagnetic no B effects
- deoxy-Hemoglobin is paramagnetic if [deoxy-Hgb] local B
BOLD signal
Source: Brief Introduction to fMRI by Irene Tracey
neural activity blood flow oxyhemoglobin T2* MR signal
Blood Oxygen Level Dependent signal
time
Mxy
SignalMo sin
T2* taskT2* control
TEoptimum
Stask
ScontrolS
Source: Jorge Jovicich
BOLD signal
Source: Doug Noll’s primer
To take away
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 Jovicich
Kwong et al., 1992
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