College 1: Technical background of fMRI
MRI = Magnetic Resonance Imaging
The human body is mostly water. Water molecules (H2O) contain hydrogen nuclei (protons),
which become aligned in a magnetic field. An MRI scanner applies a very strong magnetic
field which aligns the proton "spins."
The scanner also produces a radio frequency current that creates a varying magnetic field. The
protons absorb the energy from the magnetic field and flip their spins. When the field is
turned off, the protons gradually return to their normal spin, a process called precession. The
return process produces a radio signal that can be measured by receivers in the scanner and
made into an image.
Protons in different body tissues return to their normal spins at different rates, so the scanner
can distinguish among various types of tissue (e.g. fat or water). The scanner settings can be
adjusted to produce contrasts between different body tissues. Additional magnetic fields are
used to produce 3-dimensional images that may be viewed from different angles.
MRI for the neuroscience?
1. Understanding anatomy
2. Depiction of pathology/neurodiseases
3. Localizing brain activity
4. White matter fibers = structural connectivity
5. Neuronal networks = functional connectivity
6. Measuring cerebral blood flow
7. Microstructure (axonal diameter etc.)
Four MRI rules
1. Rotation frequency scales are linearly with local magnetic field strength
- 3 Tesla = 128 Mhz
- 7 Tesla = 300 Mhz
- Susceptibility differences lead to large magnetic field variations
- Body in magnet will make spinning slightly faster
2. Only magnetization in the transverse plane is measured
3. Relaxation processes determine contrast
- Different tissue will respond different to this rule (quantitative)
- Basic MRI parameters of tissue are determined by 3 parameters:
1) Proton Density (PD) = percentage of protons to detect
PD (%)
White matter 70 - Number of protons present
in a voxel
Gray matter 85
- Frequently expressed
CSF 100 relative to pure water
Skeletal muscle 70
Bone narrow 40
, 2) T1 = how fast does the magnetization regrow in the direction of the main
magnetic field (anatomical)
> 1 images can be thought of as a map of proton energy within fatty tissues of
the body
> 1 tissue is bright = fat
> T1 recovery: tissue contrast controlled by sequence timing (longitudinal)
- T1 short = fast relaxation
- T1 long = slow relaxation
3) T2 = how fast do we lose our transversal magnetization
> Fatty tissue is distinguished from water-based tissue by comparing with the
T1 images – anything that is bright on the T2 images but dark on the T1 images
is fluid-based tissue (e.g. CSF)
> 2 tissues are bright = fat AND water
> Transversal relaxation: tissue contrast by echo time
- T2 short = fast relaxation
- T2 long = short relaxation (lot of dephasing after only short time,
blocking each other signals)
4. Spatial localization is based on spatial variation of the magnetic field strength
- Spatially varying the magnetic field in all directions
- Local precession frequency will depend on location in space
- Careful analysis of the signal (Fourier transform) or by the interplay with the
frequency of the RF (rotation frequency), the spatial distribution of the MR-
signal can be deduced ( = MR images)
Typical fMRI acquisition
- 20 – 35 slices
- In plane resolution of 3 x 3 mm
- Slice thickness 3-5 mm
- Dynamic scan time was: 2-3 sec, more recent approximately 1 sec
, - Gradient echo imaging
- Use of single shot EPI (echo planar imaging)
- Slice by slice
- Fast switching gradients
- Loud
- Distortions
- However, the sequence is frequently tuned to specific applications
BOLD contrast related to both blood oxygenation, blood flow
Blood and blood volume
Oxygenation - difficult relation with neuronal activity
Level
Dependent
- Blood flow increase larger than increase in oxygen consumption
- Deoxy-hemoglobin has slightly different magnetic properties than oxy-hemoglobin
(= better MRI signal)
- Presence of deoxy-hemoglobin can be detected as MRI signal, decreases due to
magnetic field inhomogeneities (-> dephasing)
- Shape of BOLD response: - Chain
of fMRI effects:
- BOLD contrast correlates (primarily)
with the input of neurons
MRI = Magnetic Resonance Imaging
The human body is mostly water. Water molecules (H2O) contain hydrogen nuclei (protons),
which become aligned in a magnetic field. An MRI scanner applies a very strong magnetic
field which aligns the proton "spins."
The scanner also produces a radio frequency current that creates a varying magnetic field. The
protons absorb the energy from the magnetic field and flip their spins. When the field is
turned off, the protons gradually return to their normal spin, a process called precession. The
return process produces a radio signal that can be measured by receivers in the scanner and
made into an image.
Protons in different body tissues return to their normal spins at different rates, so the scanner
can distinguish among various types of tissue (e.g. fat or water). The scanner settings can be
adjusted to produce contrasts between different body tissues. Additional magnetic fields are
used to produce 3-dimensional images that may be viewed from different angles.
MRI for the neuroscience?
1. Understanding anatomy
2. Depiction of pathology/neurodiseases
3. Localizing brain activity
4. White matter fibers = structural connectivity
5. Neuronal networks = functional connectivity
6. Measuring cerebral blood flow
7. Microstructure (axonal diameter etc.)
Four MRI rules
1. Rotation frequency scales are linearly with local magnetic field strength
- 3 Tesla = 128 Mhz
- 7 Tesla = 300 Mhz
- Susceptibility differences lead to large magnetic field variations
- Body in magnet will make spinning slightly faster
2. Only magnetization in the transverse plane is measured
3. Relaxation processes determine contrast
- Different tissue will respond different to this rule (quantitative)
- Basic MRI parameters of tissue are determined by 3 parameters:
1) Proton Density (PD) = percentage of protons to detect
PD (%)
White matter 70 - Number of protons present
in a voxel
Gray matter 85
- Frequently expressed
CSF 100 relative to pure water
Skeletal muscle 70
Bone narrow 40
, 2) T1 = how fast does the magnetization regrow in the direction of the main
magnetic field (anatomical)
> 1 images can be thought of as a map of proton energy within fatty tissues of
the body
> 1 tissue is bright = fat
> T1 recovery: tissue contrast controlled by sequence timing (longitudinal)
- T1 short = fast relaxation
- T1 long = slow relaxation
3) T2 = how fast do we lose our transversal magnetization
> Fatty tissue is distinguished from water-based tissue by comparing with the
T1 images – anything that is bright on the T2 images but dark on the T1 images
is fluid-based tissue (e.g. CSF)
> 2 tissues are bright = fat AND water
> Transversal relaxation: tissue contrast by echo time
- T2 short = fast relaxation
- T2 long = short relaxation (lot of dephasing after only short time,
blocking each other signals)
4. Spatial localization is based on spatial variation of the magnetic field strength
- Spatially varying the magnetic field in all directions
- Local precession frequency will depend on location in space
- Careful analysis of the signal (Fourier transform) or by the interplay with the
frequency of the RF (rotation frequency), the spatial distribution of the MR-
signal can be deduced ( = MR images)
Typical fMRI acquisition
- 20 – 35 slices
- In plane resolution of 3 x 3 mm
- Slice thickness 3-5 mm
- Dynamic scan time was: 2-3 sec, more recent approximately 1 sec
, - Gradient echo imaging
- Use of single shot EPI (echo planar imaging)
- Slice by slice
- Fast switching gradients
- Loud
- Distortions
- However, the sequence is frequently tuned to specific applications
BOLD contrast related to both blood oxygenation, blood flow
Blood and blood volume
Oxygenation - difficult relation with neuronal activity
Level
Dependent
- Blood flow increase larger than increase in oxygen consumption
- Deoxy-hemoglobin has slightly different magnetic properties than oxy-hemoglobin
(= better MRI signal)
- Presence of deoxy-hemoglobin can be detected as MRI signal, decreases due to
magnetic field inhomogeneities (-> dephasing)
- Shape of BOLD response: - Chain
of fMRI effects:
- BOLD contrast correlates (primarily)
with the input of neurons
