Functional Magnetic Resonance Imaging
Albert Parker
February 26, 2002
Sources
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Functional Magnetic Resonance Imaging
Mark S. Cohen, Ph.D
Susan Y. Bookheimer, Ph.D.
UCLA Brain Mapping Division
Trends in Neurooscience
http://spinwarp.ucsd.edu/fmri/FMRI-TINS.html)
•
Journey to the Center of My Mind
Stephen S. Hall
The New York Times, 6/1999
http://www.fmri.org/jounrey.html
•
Basics of NMR
Joseph P. Hornak
Department of Chemistry and Imaging Science
Rochester Institute of Technology
http://www.cis.rit.edu/htbooks/nmr/bnmr.htm
•
A Primer on MRI and fMRI
Douglas C. Noll, Ph.D.
Departments of Biomedical Engineering and Radiology
University of Michigan, Ann Arbor, MI
6/2001
http://www.bme.umich.edu/~dnoll/primer2.pdf
How does fMRI form an image of Neural
Activity in the brain??
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Overview of the Physics
Encoding of spatial location
Encoding of neural activity
Experimental procedure
fMRI technology is based on …
• Nuclear Magnetic Resonance (NMR) phenomenon (1946, 1950)
• high concentration of hydrogen nuclei in biological systems and its high
sensitivity to NMR signals.
• magnetic susceptibility of oxyhemoglobin and deoxyhemoglobin (1936)
The Physics of NMR
Bloch (1946) and Hahn (1950)
1. Atomic nuclei with an odd number of neurons and/or protons have:
•
a small magnetic moment.
• an angular momentum called nuclear spin
= electron
= neutron
= proton
The Physics of NMR
Bloch (1946) and Hahn (1950)
2. Magnetic moments will align (anti) parallel to an applied static
magnetic fields.
3. Random atomic collisions and other perturbations allow the system to
reach an equilibrium with an excess of protons aligned with the static
magnetic field.
The Physics of NMR
Bloch (1946) and Hahn (1950)
4. If one applies a static magnetic field to nuclei with spin, the
magnetization of each nucleus has a resonance (or Larmor) frequency
f defined by
f =  B0
proportionality constant for
specific nuclear species (MHz/Tesla)
strength of static magnetic field
(typically about 1.5 Tesla)
Nuclei
Unpaired Protons
Unpaired Neutrons
Net Spin
1H
1
1
0
2
1
0
0
0
1
1
1
1
1
1
1/2
1
1/2
3/2
1
1/2
1/2
2H
31P
23Na
14N
13C
19F
 MHz/T
42.58
6.54
17.25
11.27
3.08
10.71
40.08
The Physics of NMR
Bloch (1946) and Hahn (1950)
5. Excitation: If an oscillating magnetic field (called a radio frequency
pulse) is applied to nuclei at their resonance frequency, their spins
absorb energy, causing the magnetization of the nuclei to precess in
phase about the static magnetic field.
The precessing magnetization can be measured by a nearby coil.
The Physics of NMR
Bloch (1946) and Hahn (1950)
6. Decay: Following excitation, the precessing magnetization returns to
equilibrium according to exponential decay.
– s(t) be an magnetic resonance (MR) signal
– T2 is the MR signal decay rate (from a few to tens of ms)
The T2 rates are different for different biological tissues!
(in particular, for oxyhemoglobin and deoxyhemoglobin!!)
How does fMRI form an image
of neural activity?
How to form an image of neural
activity using NMR?
Need to measure:
1. Spatial Location
2. Neural Activity Magnitude
Spatial Location in 1-D
• Frequency Encoding (Lauterbur 1973)
– relate frequency linearly to spatial location by
B(x) = B0 + Gx· x
“base” strength
of the static
magnetic field
gradient strength
of the static magnetic
static field strength
location
in 1-D
– So the resonance frequency of the nuclei at location x is given by:
f(x) =  B(x) = (B0 + Gx· x)
Spatial Location in 1-D
measure s(t)
F [s(t)]
amplitude
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Take the Fourier transform of the MR signal s(t), F[s(t)], to decompose s(t)
into its power spectrum (a signal’s frequencies and associated amplitudes).
In the case of an object composed of a particular medium, we get an image of
that object at a particular instant in time: a 1-D distribution of the
magnetization intensity at location x:
frequency
intensity
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Spatial Location in 1-D
Frequency Encoding in practice
Phase Encoding
Spatial Location in 2-D
Echo Planar Imaging (Mansfield 1977): use frequency encoding to
determine the “x” direction and echo encoding to determine the “y”
direction.
sampling windows
Spatial Location in 3-D
• Since most humans are 3-D, the third dimension is incorporated into
the procedure by performing slice-selective excitation: apply the RF
pulse as a function of position in the 3rd dimension (or by moving the
static magnetic field along the 3rd dimension).
How to measure neural activity?
• The physiology of neural activity involves many complex processes.
• MR has the capability to measure parameters related to several neural
physiological functions, including:
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changes in phosphorus metabolism and metabolic byproducts
blood flow
blood volume
blood oxygenation
Blood oxygen level dependent contrast
(BOLD)(Ogawa et al. 1990)
• The most common technique used in fMRI.
• Takes advantage of the magnetic susceptibility of oxyhemoglobin and
deoxyhemoglobin (Pauling 1936). Deoxy Hb has a higher precess
magnitization decay rate than does oxy Hb. (They have different T2
rates!)
During periods of neuronal activity, local blood flow and volume increase with little or no
change in oxygen consumption. As a consequence, the oxygen content of the venous blood
is elevated, resulting in an increase in the MR signal.
Experimental Procedure …
so fMRI works like this …
1.
Use EPI and slice selective excitation
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2.
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4.
5.
Apply a static magnetic field with intensity B0.
Use an RF pulse with frequency matching resonance frequency of the
desired medium (e.g. hydrogen nuclei) for the given static magnetic
field intensity B0.
Apply magnetic field gradients in x and y directions.
Use coils to measure the MR signal s(t).
Calculate F[s(t)] over each sampling window to determine MR
signal location in the 2-D slice we have selected.
Take into account how fast the signal has decayed since the RF
pulse (T2 decay) when interpreting MR signal “strength” at each
location.
Give image intensity
Issues!
There is not a one-to-one
correspondence between T2 and
the neural activity that we are
trying to measure. There are
pathways that might decrease
the decay rate and hence results
in a decreased MR signal!
Issues!
• Small size in of activation related response leaves it susceptible to
noise (low SNR) from:
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thermal and electromagnetic noise from the subject
reception coil, preamps and other electronics
quantization noise from analog to digital conversion
cardiac and respiratory cycles
head movement (problem especially for speech tasks)
• uncontrolled neuronal events
– differences in the manner in which a task is performed
– neuronal events associated with behavior unrelated to the task
– spontaneous firing of networks
• MRI response is delayed and relatively slow compared to brain activity
Dealing with the issues!
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rapid data acquisition techniques
special reception coils
increasing static magnetic field intensity
SNR depends on temporal resolution - lower temporal resolution
post-processing techniques, movement correction algorithms,
different gradient systems
multi-shot techniques
head restraints and bite bars
use cortical landmarks
Comparison: temporal and spatial resolution; and invasiveness
This figure relates the temporal and spatial resolution of methods for the study of brain function to the
size scale of neuronal features and to the “invasiveness” of the methods.
How fMRI stacks up:
• temporal resolution: seconds
• spatial resolution: cortical columns
• invasiveness: apparently completely safe, barring pacemakers
“Though few Neuroscientists will be able to afford MR devices of their
own … with fMRI it will be possible to perform longitudinal studies
on individual subjects advancing the practical spatial resolution of
functional imaging and enabling vastly more complex experimental
designs …” - Mark Cohen
fMRI will not map the cortical and subcortical functions of the human
brain, but it has moved us closer to the ideal.