Please enable JavaScript.
Coggle requires JavaScript to display documents.
Biophysics of Neuroimaging - Coggle Diagram
Biophysics of Neuroimaging
Neuroimaging
Neuroimaging
Measurements of neural structure/activity in form of images
Each pixel corresponds to quant measurement of structure/activity
Pixel = Picture/image element
Often used specifically to refer to non-invasive techniques
To image human brain structure & function
What Measures
Tissue composition
Tissue structure
Neural population activity
Metabolite concentration
Specific Techniques
MRI
PET
Neuroimaging Terminology
Image
Pixel
Voxel
Spatial resolution
Temporal resolution
Signal-to-noise ratio
Contrast-to-noise ratio
Image
Rectangular array of pixels
Can also be higher-dimensional/3-dimensional
Pixel
Picture/image element
Voxel
Volume element
Pixel from a 3D image
Spatial Resolution
Smallest distance that can be resolved
Temporal Resolution
Smallest time interval that can be resolved
Signal-to-Noise Ratio
Contrast-to-Noise Ratio
Measuring Neural Signal
Spikes the currency of neural communication
Neurones the units of neural computation
But can only measure correlates of neural signals
Fundamental limitation of all neuroimaging methods
What to Consider
Which level of spatial data necessary to understand brain function
Which level of temporal detail necessary
Measuring Correlates
All signals measure some correlate of average neuronal population activity
Not activity of single neurones
Example: Measuring Correlates
Pooled synaptic activity
Metabolic rate
Blood flow
Blood volume
Blood oxygenation level
Pooled Synaptic Activity
Optical imaging
MEG
EEG
Metabolic Rate
Autoradiography
SPECT
PET
Blood Volume
PET
Blood Oxygenation Level
fMRI
MRI
Limitation
Provide relative measurement of blood flow
Magnetic Field
Magnetic field strength measured in Tesla (T)/Gauss (G)
Magnetic flux density/magnetic field per unit time per unit area
Magnetic Field of MRI
Uses superconducting magnets
Creates strong magnetic fields
Orientation of magnets in longitudinal
MRI Scanner Constituents
Big magnet
Smaller magnets
Radio transmitter
Radio receiver
Shielded room
Fast computers
Tesla & Guass
1 T = 10,000 G
Example: Gauss of Objects
Earth magnetic field = 0.5 G
Refrigerator magnet = 200 G
MR magnet = 15,000 - 90,000 G
Magnetic Field in MRI Use
3 separate electromagnetic coils (magnets)
Allow applying much weaker magnetic field in any gradients
Gradients
Direction that vary over space
Have 2 uses
Uses of Gradient Magnetic Fields
Restrict measurement to specific spatial region
Encode spatial location to allow reconstructing image from measured, non-spatial radiofrequency signal
Risk of Strong Magnetic Field
Most common cause of MRI injury is metal object drawn into magnet at high speed
Stronger fields increase risk
Effects of strong fields include nausea & peripheral nerve stimulation
When Need Strong Magnetic Field
High SNR
Nuclear Magnetic Resonance
Nuclei of some atoms behave like little magnets
Line up w. external magnetic field B0
Flip direction when excited by radiofrequency pulse (radiowave) of right frequency
Over time relax & flip back which emits radio signal
Signal known as nuclear magnetic resonance
Echo of radio signal what scanner measures
Strength of signal depend in part on chemical composition of tissue
NMR Primer
Atomic nuclei spin around an axis
Spins are vectors (w. magnitude & direction)
For some nuclei the spin causes them to behave like magnets/dipoles
Polarisation
Aligns magnets
W/out. magnetic field spins orient randomly
External magnetic field lines up spins/nuclei
Slightly more align w. than against field
Spin & Spin Packet
Individual spins too weak to be detectable on own
Spin Packet
Group of spins experiencing same magnetic field strength
Net Magnetisation Vector
Vector sum of all spins in spin packet
Large if all spins aligned
Point in same direction
Zero if spins not aligned
Point in random direction
Precession
Source of MRI signal
Spins & spin packets precess about applied magnetic field along Z axis
Pecession causes magnetic field transverse to Z axis to change over time
Changing magnetic field the same as radio wave
Picked up my radio receiver in MRI scanner
Excitation
Radio transmitter in scanner sends out radiowave at specific freuqency that exactly matches precission frequency
Pulse causes spins to tilt in accordance w. XY plan
90 degree pulse = Into XY plane
180 degree pulse = Away from XY plane
By varying scanner magnetic field only spins in particular locations can be exited
Relaxation
After excitation spins slowly re-align w. magnetic field while emitting radio signal
Emitted signal strength increases w. magnetic field strength
Higher SNR at high field strength
Measuring Relaxation Speed
T1
T2
T2
Decay in XY
In MRI due to dephasing by 'spin-spin' interaction
In fMRI also due to dephasing due to blood oxygen levels
T1
Recover along Z
Due to spins returning to original direction
Tissue Contrast
Diff tissues have diff values
So relative strength of radio echo diff for diff tissues
Basis for making anatomical MR images w. diff contrasts
Contrast
Varied by modifying time between excitations (repetition time) & time between excitation & measurement (echo time)
Types of Contrast
T1
T2
T1 Contrast
White matter is bright
Strong signal
Gray matter is intermediate
Cerebrospinal fluid is dark
Weak signal
T2 Contrast
White matter is dark
Gray matter is intermediate
Cerebrospinal fluid is bright
Pulse Sequences
Particular sequence, strength, & duration of RF pulses & gradient application
Can vary image contrast & signal by changing parameters
By applying gradient fields at specific times can select specific regions of space to excite & measure from
Changing Parameters
TR (repetition time)
How often apply RF pulse
TE (echo time)
How long wait to measure echo
Flip angle
Strength of excitation pulse
Critical Evaluation
Limitations of Neuroimaging
Indirect measures
Population-based
Determine what can deduce
Indirect Measures
Reconstruct neural activity from blood flow depend on many assumptions
Population-Based
Can only measure correlates of neural activity averaged over many neurones & over time
But many single-unit measurements suggest activity of individual neurones is significant
Level of observational detail in orders of magnitude
Slower/coarser than that of neuronal processing
How Overcome
Make educated guess to interpret data
Brain Function
Historical Experiment (Field & Inman, )
A: Replication study of Mosso's experiement
R: Not replicate
Mosso Experiment
Tilt head back & cradle fall as blood flow increase
Explanation
Blood flow increase but brain doesn't expand
Doesn't get heavier when think
Cerebral Blood Flow
Basis of modern neuroimaging technique
Brain consumes about 20% of energy of body
Brain receives about 20% of blood flow
Neural Activity & Blood Flow
Neural activity result in pronounced increases in metabolism
Aerobic
Anaerobic
Neural activity increase global blood flow marginally but locally dramatically
Redistribute blood flow w/in. brain
Regulation of Cortical Blood Flow
Microvasculature
Cortex densely packed w. blood vessels
Distribution mirrors neuronal organisation
Evidence that blood flow highly locally regulated
Potentially at columnar level
Study: Brain Metabolism & Energy Consumption (Attwell & Laughlin, 2001)
R: Distribution of ATP consumption indicate brain energy consumption
Neuroimaging Methods
Types of Methods
Invasive
Sem-invasive
Non-invasive
Invasive
Use on animals only
Example: Invasive
Optical imaging
Calcium imaging
Autoradiography
Semi-Invasive
Can be used on humans
Example: Semi-Invasive
SPECT
PET
CT
Non-Invasive
Example: Non-Invasive
fMRI
NIRS
Tomographic Techniques
Tomography the reconstruction of shape of object from projection images
Based on Radon transform algorithm
Example: Tomographic Techniques
CT
SPECT
PET
Originally MRI
But diff method underlies modern MRI
Computerised Tomography (CT)
Beams of X-rays rotate around head
X-ray computed tomography
Image contrast depend on tissue density
Limitation
Only structural info
Uses harmful radiation
Single Photon Emission Computer Tomography (SPECT)
Use short-lived radioactive tracers that emit gamma rays
Detectors in ring around head measure intensity of gamma rays
Image of tracer concentration reconstructed w. tomographic techniques
First method that allowed measure related to function
Advantage
Many clin use
Limitation
Low resolution
~1cm
Require radioactive tracers
Positron Emission Tomography
Short-lived radioactive tracers that emit positrons (anti-electrons)
Positrons collide w. electrons emitting 2 gamma rays in opposite directions (annihilation)
Pairs of detectors identify coincident gamma rays allowing location of annihilation to be reconstructed
Intensity of radiation at each point reflect metabolic rate/blood flow
Depend on tracer used
Advantage
Provide absolute (true) measurement of blood flow & metabolism
Tracers can be bound to skin-specific metabolites
Allow measurement of uptake & kinetics
Better resolution than SPECT
Mainly clin use
Radiotracer short-lived so can detect in and decrease in response to things
Disadvantage
Require injecting radioactive tracer
Require cyclotron to make tracer
Expensive
Temporal resolution v. low
~1 min
Spatial resolution poor
~ 5mm
Low SNR
Poor image quality
Superseded by fMRI
Random Transform
How much light gets through tissue & take measurement from many diff angles
Plot profiles (images taken at diff angles)
Image is direct representation of object
Take profiles to make it in context of light absorption to form projection
Combine projections to form object
Imaging
Echoplanar Imaging
First problem how to take images
Use echoplanar imaging
V. quick
Build stack of images that cover entire brain in seconds
Limitation
Lower resolution & bigger voxels
Imaging
Measurement of neural structure/activity in form of images
Imaging Jargon
Biophysics of fMRI
fMRI
Generate images where local intensity affected/influenced by amount of O2 in tissue
Changes in local magnetic environment due to blood that change signal
BOLD Signal
SAME AS fMRI BOLD page
Deoxyhaemoglobin & BOLD Signal (Ogawa, 1992)
Deoxyhaemoglobin is paramagnetic
Acts like magnet to influence protons to move
More deoxyhaemoglobin means less disturbed signal
Less deoxyhaemoglobin means reduction in signal