Magnetic Resonance Imagining (MRI)
Magnetic Fields
• Protons in atomic nuclei spin on axes
– Axes point in random directions
across atoms
• In externally applied magnetic field
– Spin axes tend to align to magnetic
field direction
– Most “pointing” in same direction, but
some “pointing” in opposite direction
– How many align depends in part on
strength of magnetic field
MRI Magnetic Fields Cont’d
• In an externally applied magnetic field, atomic nuclei
with an odd number of nucleons (protons + neutrons)
precess
– = Spin axis wobbles
– Rate determined both by properties of the atom
– And by the strength & homogeneity of the magnetic field
– Hydrogen atoms in a 1.5 Tesla field precess at ~64 MHz
= Radio frequency [rf]
– Timing (phase) of wobble still random across atoms
Resonance
• A radio frequency pulse (rf pulse) of a particular frequency is
applied to the aligned protons in the magnetic field
– When rf pulse frequency
= precession frequency
= Larmor frequency,
nuclei resonate to it
– Pushes spinning protons into phase with one another
– Amplitude of wobble of the whole magnetic field generated by the
spinning protons increases (= spin axis is pushed farther out)
• Increases “transverse component” of magnetic field
• Which is what’s measured
– How far spin axis moves (= flip angle) depends on rf pulse intensity
and duration
Why is this useful?
• Takes characteristic amount of time after rf pulse for protons:
– To get back out of phase (= de-phase)
– And to settle back to original
wobble amplitude in fixed field
– Depending on what other kinds of
atoms are nearby
• i.e, the kinds of molecules
the atoms are in, in part
• As protons settle back into alignment with fixed field, the
strength of the magnetic field they generated decreases
– Variations in how long it takes the protons to de-phase & to settle
back to original wobble amplitude in fixed field
– Can be used to distinguish among different substances
How does this make IMAGING possible?
• How know where magnetic field being measured comes from?)
• Use gradient magnetic fields (Lauterbur Nobel Prize)
– Generate field with gradation in
field strength with only a small
region at 1.5 Tesla
– Only hydrogen atoms within that
region respond to 64 MHz pulse
– So, response must come from protons
within 1.5 T region
– Keep moving position of 1.5 T area to localize source of responses to
repeated rf pulses
– Size of 1.5 T region determines granularity of localization of response
Siemens Allegra 3T
Biomedical Imaging Center (BIC)
Fixed field magnet is (almost) always on!
- Child killed in 2001 at Westchester
Medical Center when an oxygen tank
brought into magnet room was pulled
into center of magnetic field
- In 2000, police officer’s gun pulled
from his hand into magnet & discharged
a bullet into the wall on the way in
Structural MRI
• Anatomical scans generally measure hydrogen atoms in water
– Since different kinds of tissue have different proportions of water
• Typical anatomical scan voxel granularity = 1 x 1 x 3-5 mm
Functional MRI (fMRI)
• Substance measured is hemoglobin (iron) in blood
– Blood flow increases to active brain regions
– Increases more than is usually needed
– So ratio of de-oxygenated to oxygenated blood decreases
• Oxygenated & de-oxygenated hemoglobin respond
differently to magnetic field and rf pulses
– Use this to detect where more oxygenated blood goes after
some event
– Takes several seconds for the response to peak
• Timing seems to vary some across different brain regions
– Fastest reliably detectable pre-peak response so far = 2 - 4 sec
– Signal strength change very small – generally less than 1% change
• If signal strength large, probably due to draining vein
Important to avoid measuring
this instead of this
fMRI Cont’d
• Spatial resolution:
– Ultimate limit probably spatial specificity of the circulatory system
– Worse than structural MRI
– Typical functional scan voxels = 3 x 3 x 5 mm
• Temporal resolution:
– IF blood flow is what’s measured, never going to be faster than seconds
– Working on detecting the brief initial decrease in oxygenated blood
preceding increased blood flow
– Working on imaging other substances
fMRI Data Analysis
• Much of the brain is active much of the time
– (e.g., “default network”)
• Try to isolate regions that are specific to some aspect
of the event of interest
– One widely used approach is to look for voxels whose
time course of signal strength change after stimulus is
correlated with an idealized hemodynamic response
function
– Decide on a threshold
for correlation strength
and only further analyze
voxels exceeding that
threshold
Subractive Logic
- Construct 2 conditions that you believe differ in just 1 important way
- Treat one as baseline & subtract it from the other to get rid of all the
activity the 2 have in common
- And then analyze what’s left
- May only analyze part of what’s left because may threshold (again),
and/or may only analyze Regions of Interest (ROI)
- These are all ways to cut down the number of statistical comparisons done
Subtractive Logic, Cont’d
• Similar logic used in comparing conditions in most other kinds
of experiments, too
• But there’s been a very unfortunate tendency in much of the
imaging literature so far,
• For researchers who don’t have a good understanding of the
many ways that different kinds of stimuli and/or tasks and/or
situations can differ,
• To claim that they’ve located “phonological word processing”, or
“irregular morphological inflection processing”, or some such
aspect of language processing
• When other confounded differences between conditions are
equally good candidates (such as plain old difficulty) for
explaining the effects