My method consists of 3 parts, which I abbreviate as pre-scanning, segmentation, and refocusing amplitude determination. Finally, I like to show some examples of recovering signal intensities in dropout regions.
University of Washington
Department of Statistics
Brief Introduction toBrief Introduction to
Functional MRI DataFunctional MRI Data
Red slides are due to Peter Jezzard, PhD
FMRIB Centre, Oxford University,
Hopefully, he does not mind
The 2003 Nobel Prize in Physiology or Medicine
6 October 2003
The Nobel Assembly at Karolinska Institutet has today
decided to award The Nobel Prize in Physiology or Medicine for
Paul C Lauterbur and Peter Mansfield
for their discoveries concerning
"magnetic resonance imaging“
For their discoveries that have led to the development of modern
MRI, which represents a breakthrough in medical diagnostics
Nuclei of hydrogen atoms I
• The human body weight has a high water
content (about 2/3rd)
• There are differences in water content among
tissues and organs.
• In many diseases the pathological process
results in changes of the water content, and
this is reflected in the MR image.
Nuclei of hydrogen atoms II
• H2O molecule composed of H and O2 atoms.
• The nuclei of the hydrogen atoms acts as
• When the body is exposed to a strong magnetic field,
the nuclei of the hydrogen atoms are directed
• When submitted to pulses of radio waves, the energy
content of the nuclei changes. After the pulse, a
resonance wave is emitted when the nuclei return to
their previous state.
• The small differences in the oscillations of the nuclei
Nuclei of hydrogen atoms II
• Using computer processing, it is possible to
build up a 3-dim image that reflects the
chemical structure of the tissue
– differences in the water content
– movements of the water molecules.
• This results in a very detailed image of
tissues and organs.
• Pathological changes can be documented.
“… A brain MRI is a claustrophobic procedure in
which you are passed through a tunnel so tight that
it practically touches your nose and forehead and
makes you feel that you might suffocate. I hated it..”
Lance Armstrong My jorney back to life
A bit of NMR Physics I
• Water is the most important site for MRI
– concentration of protons in water
– the dynamical properties of water.
• The proton is a fundamental nuclear particle with
charge, mass and spin
• Spin can be thought of as a rotation of the nucleus
about its axis
• But the nucleus has a charge
• Spinning charged object creates a magnetic field
A bit of NMR Physics II
• spin J + mass of the proton, gives it an angular
• Direction of µ is random due to thermal random motion
• When exposed to the strong magnetic field B0(1.5-3.0 T)
the spins are lined up
• The angle between the magnetic dipole moment µ and B0
for the hydrogen protons is +/-53o
44’’ (H atoms point up or
• Magnetic moments precess around the applied field with
µ xy(t)= µxy(0)e-iγBot
µ z(t)= µz(0)
A bit of NMR Physics III
• To detect magnetization, a coil of wire is connected to a
sensitive amplifier, which is in turn tuned to the Larmor
• The rotating magnetic field will induce a tiny NMR
signal in the coil, which oscillates at the Larmor
• Only the time varying part of the magnetization is
capable of inducing a signal in the coil
• Only the transverse component in is detectable
A bit of NMR Physics IV
• The transverse component of the magnetization is 0
• To generate an NMR signal, the magnetization must be
tipped away away from the equilibrium alignment
• To achieve this, the object is exposed to an alternating
magnetic field B1 magnetic field tuned to the Larmor
frequency. (a.k.a RF pulse , since the Larmor frequencies
are typically in the Mhz range)
• The flip angle ~ duration and strength of B1 field
• The magnetization can be tipped to any angle
A bit of NMR Physics V
• Each spin experiences a slightly different magnetic field
• Each spin will have a slightly different precession
• When B1
is removed, the system returns to its original
• M precess around B0:
• Longitudinal relaxation: the recovery of the longitudinal
component (the projection on B0
• The transverse component is destructed: transverse
A bit of NMR Physics VI
In rotating frame the transverse and longitudinal component from
the Bloch’s equation
x'y' x'y' +M (t) = M (0 ) e
1 1-t/T -t/T0
z' z z' +M (t) = M (1-e ) + M (0 ) e
is the longitudinal magnetization at thermal equilibrium.
•This holds for “slowly” relaxing spins (liquid state molecules)
are defined by the tissue, T1
•The length of the precession period depends on T2
•Enables the detection of MR signal.
•The magnitude of the signal depends on the # of spins, B0, T2
A bit of NMR Physics VII
• Multiple RF pulses generate echoes, two sided signals,
where one side is due to the refocusing of the transverse
magnetization and another side is due to the dephasing
• Gradient field is a special kind of the magnetic field
whose z-component varies linearly along a gradient
• The external magnetic field and RF pulse excite the spins
at different spatial locations in the same way.
BOLD Contrast Mechanism IBOLD Contrast Mechanism I
• Objects counteract in the presence of the external
• These counteractions distort the applied field.
• Diamagnetism a weak (less then ten parts per million)
repulsion in a magnetic field generated by the current of
the orbiting electron. All materials are naturally
• Paramagnetic materials have a dipole aligned with the
magnetic field producing an additive internal field. Present
in materials which have unpaired electrons.
• Most proteins and tissue water are diamagnetic.
BOLD Contrast Mechanism IIBOLD Contrast Mechanism II
• BOLD (blood-oxygen-level-dependent) is based on physiological responses
related to brain activation.
• Deoxygenated Hb used as the source for the contrast.
• HbO2 acts like a typical diamagnetic.
• But Hb is paramagnetic.
• Hb makes up nearly 15gm/100cm3
of the blood content
• Deoxygenated red cells and blood vessels become a little magnets distorting
the magnetic field around them.
Deoxygenated blood, because of its paramagnetic nature, leads to local
magnetic field distortions between vasculature and surrounding brain
parenchyma. This creates increased spin-spin dephasing of the MR signal in
those regions, and as a result, there is reduced signal in these areas as
compared to oxygenated hemoglobin.
BOLD Contrast MechanismBOLD Contrast Mechanism
Distribution of Spins
in a Voxel
BOLD Contrast Mechanism IIIBOLD Contrast Mechanism III
• Activation Rapid depletion of oxygen
• The fraction of the paramagnetic Hb increases
• Signal goes down below the baseline
• Initial dip (~0.5-1.0s) very subtle, observed at the field strength > 2T.
• The feeding arteriole dilates
• Blood flow increases (due to the flow velocity rather than the volume)
• Increase in O2 consumption < increase in CBF
• The fraction of HbO2 increases in the capillary and veins
• Since Hb decreases the MRI signal goes up
•The signal increase ~2-3% of the baseline at
•Overshoot phase, due to the slow adjustment
of the CBV to the changes in the stimulation
state. (The stimulus is over, but the elevated
blood volume persist even though the blood