Structual Neuroimaging Flashcards
MRI vs fMRI
MRI looks at anatomy, while fMRI looks at the brain function
Magnetic fields
Magnets produce these magnetic fields
- attraction and repulsion of materials
- MRI machine can be dangerous if used incorrectly, due to the strong magnetic pull
- influence on nuclei -> nuclear magnetic resonance imaging
Nuclear magnetic resonance imaging NMR
Part of nuclei align with direction of the magnetic field
=/= radioactivity
- can cause nausea
- but no consequent short- or long-term illness
Hydrogen in fMRI
- human body is 55-78% water
- water molecules contain hydrogen atoms
- hydrogen atoms only contain one single proton
- atoms with uneven number of protons act as dipoles (even cancel eachother out and are not magentic)
Precess
Nuclei with odd number of protons/neutrons spin (precess)
- Larmor frequency
- depends upon magnetic field strength of the magnet
What causes Nuclear magnetic Resonance Imaging
If additional magnetic field oscillates with the Larmor frequency, nuclei absorb energy from the field
Static magnetic field
Atoms align with direction magnetic field
Oscillating magnetic field
If you add another magnetic field = radio frequency pulse (RF)
-> atoms spin/recess and get in phase (they will synchronise)
-> atoms flip and take direction of oscillating field
-> increase in energy state
When you remove RF pulse
- dephasing of atoms (spinning will be random
- realigning to static field (flip back) and this emits energy which you can see in the scan!
–> small signals over all the re-aligning nuclei integrate (stronger signal, when less dephasing)
Gradient of field strenght
- where does the signal come from?
Gradients are additional magnetic field over space: 3 different ones
–> they rely on the fact that the Larmor frequency depends on the field strenght
- if you add magnetic fields the Larmor will become larger
If magnetic field strength differs across space
- nuclei in different locations have a different Larmor frequency
- RP fulse only affets the nuclei with matching Larmor frequency
Three orthogonal gradients of field strength
- slice sletion gradient (at time of RF pulse Z)
- phase selection gradient (dephasing after RF pulse Y)
- frequency encoding gradient (at time of read out to signal X)
Slice selection gradient
- Applied during RF pulse
- RF pulse only affects nuclei that experience a total field strength with matching Larmor frequency
- Slice: volume of excited nuclei
- one slice per RF pulse for 2D, for full 3D there are as many RF pulses as there are slices
Interleaved slice acquisition
To minimize cumulative effects due to cross-slice excitation
- first all the odd slices, then the even slices for better results
Phase encoding gradient
- applied after RF pulse
- change spin resonance frequency of excited nuclei depending on their location in the gradient, causing dephasing
- when removed, resonance frequencies are the same again, but differenes in phase persist
- all nuclei at a certain position in the gradient have same phase, that phase is informative about position
Frequency encoding gradient
- applied during data acquisition
- = the read-out direction
- all nuclei at a certain position in gradient have same resonane frequency, thus frequency at read-out is informative about position
Summary of the gradients
- z-gradient (slice) cause slice selection
- y-gradient (phase) shows different phases
- x-gradient (frequency) shows the different frequencies
Pulse sequence
Succession of RF pulses and gradient changes
- pulse sequences differ in a number of ways
Pulse sequenes differ in a number of ways
- what happend prior to the RF pulse
- form and amplitude of the RF pulse
- direction and the amplitude of the gradients
- occurrence of one or multiple so-called gradient reversals
Voxels
Unit of space
- the shorter the time in which an image has to be taken, the lower the number of slices that can be imaged
–> the number of voxels per row/column in the slice relates back to number of steps of phase/frequency encoding gradient
How do these physical principles give rise to an image with anatomical structure?
Emitted signal decays over time and signal intensity depends upon sevel factors:
- density of H protons
- T1-recovery
- T2-decay
Factors are different in different tissues, resulting in signal contrast
Pulse sequence and parameter choice determine which factor has most weight
T1-recovery
Recovery of longitudinal orientation = spin-lattice relaxation
- realign with static magnetic field
T2-decay
Loss of transverse magnetization due to the loss in phase coherence = spon-spin interctions.
- Immediately after application of 90* RF pulse, transverse magnetization is maximized. It then begins to dephase due to natural interaction at anatomic or molecular levels. The signals from these dephasing protons begin to cancel out => MR signal decreases
T1-recovery time
= time it takes the longitudinal magnetization to grow back to 63% if its final value (all flipped back is 100%)
= spin-lattice relaxation time
T1-weighted image
Images only the T1 recovery time
- Faster T1-recovery means less dephasing and therefor it will show up brighter on the image
- because this differs for different tissues, you can clearly see the differences between different tissues and you get a nice image
T2-decay time
= time that it takes the transverse magnetization to decrease to 37% of its starting value
= spin-spin relaxtion time
–> basically the opposite of T1
T2-weighted image
It is basically the same at T1, but the opposite.
Recap T1 and T2 time
T1-time: time it takes to relax back in alignment with B0
T2-time: time it takes to dephase
-> two processes, which happen simultaneously and are both tissue-dependent
- using various pulse sequences that orchestrate the gradient coils, we can measure location specific activations
- YT video slide 25
3 components MRI scanner
Magnet (static field)
Gradient coild (varying magentic field)
Radio frequency coil (RF pulse)
–> magnet and gradient coils create varying magnetic fields. Radio frequency coils transmits and measures radio frequency waves
Magnet
Electrons flow along a wire
- Faraday’s principle
Faraday’s principle
Electric current in a loop of wire generates transient magnetic fied perpendicular to the loop of wire
- left hand principle
Magnetic field strength
Proportional to number of loops
- increase in current also increases field strength
Higher field strength:
- higher signal, higher resolution and more contrast
- more expensive and also more artefacts
CT scans vs. MRI
Shows a difference in contrast
- CT scan mainly in clincial context (inflammation, infection, TBI, stroke, tumor, …)
3 structural imaging methods
- structural T1-weighted MRI
- diffusion weighted imagin DWI
- magnetic resonance spectoscopy MRS
Image artefacts
Things that can disrupt the outcome of the image
- due to fixed materials, like braces
- due to removable items, like hair pins
- due to movement
Finding anatomical abnormalities
Goal of study (clinical diagnostics) or incidental
Routine pulse sequences
Robust to acquisition problems
- but e.g. high-field scanners
Voxel based morphometry VBM
Morphometry = quantity specific properties of brain anatomy
- compare regional volumes of tissue and produce map of statistially significant differences among populations of subjects
Problems: normalization problems and tot brain volume differences
Relevance of brain structure for behavior
- reveal neuroanatomical abnormalities with devestating effects upon behavior
- normal brain structure: relation to various behavioral variables
Connectivity
‘Nothing defines the function of a neuron better than its connections’
- neurons gets input and gives output to and from other neurons as well
Pattern of action potentials
From wehre and to where are the action potentials
- Paths = axons
- in humans use DWI (non-invasive connectivity imaging)
Diffusion weighted imaging
Image with large bunderls of 1000s of axons
- axons that start and end in each other’s vicinity,s tay together
–> white-matter pathways or tracts
How to DWI
Pulse seqeunce is adapted to be sensitive for diffusion of molecules => DWI
- molecules move from parts with higher to parts with lower concentration
- Cell walls and myelin impede such motion –> anisotropy in diffusion
Types of diffusion
Isotropic diffusion: can go whereever, equal in all directions (restrictend an unrestricted)
Anisotropic diffusion: restricted so can only go in certain directions
Diffusion tensor imaging DTI
Quantify amount of diffusion in each possible direction in 3D space
- diffusion described by tensor
DTI indices
- mean diffusion MD
- fractional anisotrpy FA
- axial and radial diffusivity AD and RD
–> differential sensitivity to diffusion-related phenomena
Mean diffusion
Overall amount of diffusion
Axial and radial diffusivity (AD and RD)
Amount of diffusion in certain direction: main axis or other directions
Fractional anisotrpy (FA)
From zero (isotropic diffusion) to 1 (only diffusion along main axis)
Tractography
Trace a line following main diffusion direction
- projection: connect cortical with subcortical
- commissural: connect hemispheres
- association: connect distal areas
Orientation map
Slide 44
DWI relevance for behavior
- can look for disconnections (influences behavior)
- FA affected in various mental disorders (schizophrenia, depression, autism etc.)
Magnetic Resonance Spectroscopy MRS
Quantify concetration and spatial distribution of specific molecules in brain
- spectroscopy
- spectrum
Spectroscopy
Method in which a signal is decomposed into its freqeuncy components
Spectrum
Shows strength/amplitude of each frequency component
- abnormal ratios between the peaks prove metabolic dysfunction
Underlying principle of MRS
Similar to MRI: radio-frequency waves affect spin of nuclei in magnetic field
MRI: spin of H in water molecules <-> MRS reflects resonance of other molecules
Intended vs unintended variations in frequency
Signal generated by atom is affected by its local chemical environment
=> each molecule has different resonant freqeuncy = chemical shift
- use variation in frequency to measure checmical composition of brain tissue
MR spectrum
Reflects particle resonance (ppm; parts per million) of metabolites that are associated with specific neurottransmitters or other substances in the brain tissue
- reference: Larmor frequency of tetramethylsilane
