Analysis, Tractography and Applications in Diffusion Imaging Flashcards
What can be exploited by diffusion MRI?
Entire white matter tracts which can be several millimetres across, often have a coherent orientation in any particular part of brain
What is magnetic resonance signal sensitive to?
Random thermal motion of water molecules within neural tissue
Since structures such as cell walls and myelin impede such motion, observing the characteristics of this self-diffusion in a particular part of brain provides insight into the underlying tissue microstructure
What confers a strong orientiental dependence of anisotropy on the mobility of free water ?
Very linear structure of white matter tracts
When are water molecules freer to move along cyclinders than across them?
Very loosely, a millimetre or so of tract may be thought of as resembling a bundle of cyclinders with a single orientation
What does MR brain diffusion utilise?
The principle of microscopic water movement in the brain tissue
Under normal conditions, water in the brain tissue moves rather freely. When a disruption to the blood supply of the brain occurs, the tissue will swell
The swelling will decrease the freedom with which the water can move about
The restriction in movement is visible on the MT diffusion scan images
What is diffusivity in the brain?
- Mean diffusivity which can be collected from ADC analysis
- Get bright area In the centre of the brain at the surface of cerebrospinal fluid where the diffusivity is high
- Dark areas in the remaining areas
What are we interested from tractography?
Anisotropy
What do we want to get the orientation of?
White matter structures
Why do we rely on the anisotropy of diffusion?
We can’t see the white matter structures directly
What is found in CSF?
Relatively equal freedom to move in all directions
What is fractional anisotropy?
A scalar value between zero and one that describes the degree of anisotropy of a diffusion process
A value of zero means that diffusion is isotropic I.e. it is unrestricted (or equally restricted) in all directions
A value of one means that diffusion occurs only along one axis and is fully restricted along all other directions
What is FA thought to measure in diffusion imaging?
- Fiber density
- Axonal diameter
- Myelination in white matter
What occurs in structured spaces?
The probability of water diffusion is constrained in some directions but unconstrained in others
What happens in brain tissue?
Water molecules diffuse more freely along the axons but are relatively constrained from escaping it or moving across the walls of axons
How can the diffusion tensor be calculated?
By calculating the diffusivity along multiple directions and it becomes possible to estimate the orientation of axon bundles
What does white matter have?
Relatively high FA
What do CSF and grey matter have?
Low FA
What are the basis of anisotropy in tissue?
- Neural white matter, arranged in bundles of fibres, is particularly linear
- Diffusion perpendicular to bundles is more impeded
- Myelin and neural filaments contribute
What does anisotropy reflect?
Microstructure
What is diffusion MRI in the clinic?
- Effective diffusivity is affected by oedema or the presence of tumours
- Diffusion MRI widely used in acute ischaemic stroke
- Effects visible earlier in diffusivity map than in T2-weighted images
- Also used to monitor tumour progression and response to treatment
What is voxel-based analysis?
- Whole-brain group contrast analysis can be used to find differences between patients and control, or correlations
What are two features used in voxel-based analysis?
- SPM - applicable with care, but may not be ideal for FA maps
- TBSS - designed for use with DTI data: uses an FA “skeleton”
What is the FA colour map?
- Red for left-right
- Green for anterior-posterior
- Blue for superior-inferior
- Orientation only, no information about direction
What is not obvious on structural image?
What is the effect on the white matter
Has the white matter taken over destroyed by the tumour or has the tumour moved things out of the way
What is vector FA map?
Superimpose principal direction vector
What can anisotropic be described by?
Mathematical tensor
What can diffusion be summarised as?
- MD
2. FA maps
What is tractography?
A technique that allows to identify fibre bundle tracts by connecting voxels based on the similarities in maximal diffusion direction
What is principal directions?
The direction in which there is greater diffusivity in each voxel
There is flow across the corpus callosum and follow other tracts similarly
Use this information and follow to reconstruct white matter tracts
What are streamlines?
To track through diffusion data, the track command requires seed points from which to initiate streamlined
These seed points are defined in an image that is in the same physical space as the diffusion data, but not always in the same voxel space
For example, your seed image could be of 1mm resolution, while your diffusion data is of 2mm resolution. But the physical space of both images should be aligned, even though the voxel indices are not.
What is the process of streamline?
- Begin at seed point
- Find the principal direction.
- Step a short distance
- Repeat until termination (leaving white matter or brain, excessive curvature, length limit, too little anisotropy
What is tractography?
- Follow principal directions in contiguous voxels to reconstruct fibre tracts
- Anatomically coherent bundles of fibres can be grouped together
- Allows visualisation, segmentation and analysis of brain connectivity
- Group analysis of FA/MD within specific tracts a common alternative to VBA
What are the two types of tractography ?
- Deterministic
2. Probabilistic
What is deterministic tractography?
A point estimate of the principal diffusion direction at each voxel is used to draw a single line
What is probabilistic tractography?
Provide a probability distribution on the diffusion direction at each voxel ( the higher the distribution, the higher the uncertainty of connections in that area) which is then used to draw thousands of streamlines to build up a connectivity distribution
What are the advantages of probabilistic tractography?
- Allows to continue tracking in area of high uncertainty (with very curvy tracts)
- Provide a quantitative measure of the probability of a pathway being traced between two points
What is noise and uncertainty?
Tracking process accumulates local errors
Trajectory can jump from one fasciculus to another
Probabilistic; gives a sense of these effects
What are the problems with probabilistic tractography?
- Various sources of uncertainty mix together
- Streamlines fall away with distance from the seed point
- Not reliable as a measure of connectivity
- Spurious branches may occur
What are used of ROIs?
- Typically, handawn
- Used to constrain the tracking to say we are only interested in a subset of streamline
- Can have false positives or under estimation of the tracts
What are more complex ROI constraints?
- Several ROI types may be needed for consistent results
- Waypoint, termination and exclusion masks are common
- ROIs not easily transferred between subjects and/or populations
- But “recipes” can be transferred
What are applications of tractography?
- White matter mapping and tract segmentation
- Studying effects of lesions, rumours etc
- Planning surgery and assessing recovery
- Feeds into neuronavigation along with structural and functional imaging
What are development and aging?
- Brain continues to develop after birth and throughout childhood
- Developmental processes in white matter include: myelination, synaptogenesis, and synaptic pruning
- FA generally increases and MD decreases with age; tracts vary together
- Some small gender differences in certain age ranges
- Opposite effect during aging
What are limitations of diffusion MRI and tractography ?
- Relatively low image resolution (2-3mm voxels)
- Complex relationship to tissue microstructure
- Sensitive to damage, but not very specific (degeneration, inflammation, oedema)
- Cannot tell direction of communication
- Tractography works best in major tracts
- False positive/negative connections
What are limitations of DTI?
- DTI is diffusion MRI + tensor model
- Extremely useful method, providing information about white matter orientation and “integrity”
- But if two fibres cross within a voxel then lamda1 ~ lamda 2 > lamda 3 and there is no true principal directions (oblate ellipsoid)
- More recent approaches can model the signal in the presence of 2+ fibre populations
What are improved models and HARDI?
- Greater angular resolution (I.e. more directions) and less restrictive assumptions than in DTI produce more convincing results
- Subject to diminishing returns
- Greater b-value also often used when fitting these models
- Multiple fibre directions observable
- Can result in more true positives, but also more false positives
What is the crossing-fibre problem?
- The diffusion tensor cannot represent multiple fibre orientations within a single image voxel
- But in real data these are very common
- People try to overcome the problem using more sophisticated models (e.g. multiple tensors) or taking up a model-free approach (q-space imaging)
What is structural connectivity graphs?
- Weight of a connection between cortical region (e.g.) the number of streamlines connecting the two
- Can also be derived from correlations in cortical thickness or grey matter volume
