Outline of the module
The diffusion weighted Magnetic Resonance Imaging (dwMRI) signal can be used to probe the microstructure of biological tissue. It is sensitive to tissue characteristics on the micrometre scale, such as intracellular and extracellular volume and the direction of oriented structures. As such it has potential applications in the human brain ranging from diagnosis of stroke, tumour and degenerative white matter diseases to delineating axonal fibre bundles that connect remote regions in the brain. These applications find interest in the fields of neuroradiology, neuroanatomy and cognitive neuroimaging. Some dwMRI techniques, such as mean diffusivity contrast maps, have already entered clinical practice. Other techniques, although promising, are debated for their practicality, interpretability or usefulness even within exploratory frontier research fields. This module provides in-depth treatment of the full range of modern-day diffusion MRI techniques, with a focus on human neuroimaging applications and attention to their acquisition requirements, post-processing and modelling, and biophysical interpretability.
The module covers the following topics:
• How to choose diffusion MRI sequences and set their parameters for various diffusion MRI data models?
• Recognising, preventing or correcting artefacts that occur in diffusion MRI data
• Deriving physiological microstructure characteristics from diffusion MRI data
• Interpreting various diffusion MRI data models in term of biological microstructure and its pathology or change
• Combining diffusion modelling results with other MRI modalities such as T1 contrast, SWI, fMRI, etc.
Learning objectives
At the end of this module, students will have knowledge of:
• The physics of hindered and restricted diffusion in biological tissue
• Diffusion MRI sequences and their practical usage
• Typical artefacts in diffusion MRI data and their correction
• The various contrasts calculated from diffusion MRI data
• Models that can be applied to diffusion MRI data and the interpretation of their parameters
• Fibre tractography, its potential and its pitfalls
Content
In diffusion weighted MRI, signal is sensitised to the microscopic thermal motion (or self-diffusion) of water. At diffusion times on the order of tens of milliseconds, this signal can be employed to measure the powder average - over millimetre-scale voxels - of micrometre-scale tissue properties. Diffusion MRI is often used to characterise the white matter in the human brain. Oedema, cell swelling or tissue deterioration can leave detectable traces in the dwMRI signal. In addition, water diffuses more easily parallel to the direction of surrounding axon bundles than perpendicularly. Thus, by measuring the directional anisotropy of the diffusion signal, inferences can be drawn about the local direction and even the complete trajectories of fibre-bundles through the brain. A typical imaging voxel in the human brain will often contain diffusion MRI signal contributions from multiple microstructural compartments. Different compartments can have free, hindered or restricted diffusion on several length-scales and different directional anisotropy. This makes the relation of the diffusion MRI signal to the underlying physiology complex and sometimes hard to interpret. Beyond the simplest contrasts calculated from diffusion-weighted images, signal models have to employed to extract interpretable parameters. These models vary in their complexity, basic assumptions and interpretability.
This module will treat a great majority of the models currently applied to voxel-wise diffusion MRI data, their acquisition requirements, and biophysical interpretation based on their modelling assumptions. Tractography, the delineation of fibre-bundle trajectories through the brain from local directional information, will also get extended treatment, with a focus on both its potential added benefit and its pitfalls.
Overview of tasks and lectures
There will be 10 lectures of 2 hours distributed over 5 days.
• Introduction to diffusion weighted MRI
• Diffusion weighted MRI sequences
• Diffusion tensor Imaging I: scalar diffusion indices
• Preprocessing and correction of diffusion weighted images
• Diffusion tensor Imaging II: directional information
• Beyond DTI: DSI, HARDI and tractography
• Connectomics and Tract Density Imaging
• Microstructural compartment models I
• Microstructural compartment models II
• Summary and introduction of post-module assignments
Position within the programme
This module deals with the physical processes and micro-anatomy underlying the diffusion MRI signals. Because of the variety of ways in which biological tissue can influence the signal, modelling and analysis is important in deriving interpretable biological microstructure parameters from acquired data. This module is complementary to general modules dealing with MRI physics and clinical applications, and focuses in-depth on the analysis and modelling aspects of diffusion MRI.
Teaching format
Structure
The module is a one week-long residential module consisting of 10 lectures of 2 hours. In addition, each day the students will perform hands-on exercises in data acquisition and analysis of dwMRI data and software simulations guided by tutors. The residential part is combined with a preparatory reading phase and post-module marked assignments.
Grading
Passing the module requires an 85% attendance to the lectures and practical sessions, and a satisfactory completion of the practical sessions and the module assignments. Students will report on the module assignments in written form which will be evaluated by the module coordinator(s).