Lectures on MR > Courses 2018 > Diffusion: From acquisition to tissue microstructure
Diffusion: From acquisition to tissue microstructure

September 3-5, 2018

Course venue
Champalimaud Centre for the Unknown

Course organiser
Valerij G. Kiselev
University Medical Center

Local organiser

Noam Shemesh
Champalimaud Neuroscience Programme
Champalimaud Centre for the Unknown

Preliminary faculty
E. Fieremans, V.G. Kiselev, D.S. Novikov, R.G. Nunes, N. Shemesh, M.Weigel

Goals of the course

The course Diffusion: From acquisition to tissue microstructure is an in-depth overview of measuring and
interpreting molecular diffusion in tissues with MRI, providing a solid background in this rapidly expanding research field.
Fundamental physics of molecular diffusion serves as a basis for the presentation of acquisition and post processing
methods. This course focuses on how to use diffusion MRI for probing tissue microstructure that is much finer than the
imaging resolution. The course is designed for basic scientists who already have experience in MRI and wish to extend their
knowledge of the physics of tissue microstructure mapping with diffusion MRI.

Attendance of the course on Diffusion: From acquisition to tissue microstructure will provide you with background on:
• Relation between diffusion-weighted signal and diffusion propagator
• Diffusion pulse sequences and acquisition strategies
• Practical sequence design and parameter optimisation
• Artefacts: Symptoms, mechanisms and remediation
• Relation between diffusion propagator and structure of heterogeneous media
• Diffusion models versus signal representations
• Parameter estimation: strategies, pitfalls, “orthogonal” measurements
• Model validation in phantoms and in animals
• Clinical translation and applications

Educational levels
This course is intended for MR physicists, other scientists and PhD students who already have experience in basic MR methods and knowledge of MR excitation and acquisition principles, and who wish to extend their knowledge on diffusion weighted imaging. This advanced course provides a detailed introduction into the field of diffusion measurements, which covers the physical principles of diffusion in heterogeneous media, measurement techniques and applications to investigation of the cellular structure of living tissues.

Course description

The basic idea of MR diffusion measurements is easy to explain, but its practical implementations require real know-how. How to design experiments? How to extract diffusion properties from the measured signal? How do these properties reflect the cellular structure of biological tissues? What is a model and how to model? How to validate models? How to translate model-based approaches into the clinic?
The course will begin with an introduction to the basic concepts of the physics of diffusion. The fundamental quantity, the diffusion propagator, will be discussed in the context of its relation to a diffusion-weighted NMR measurement. The cumulant expansion will serve as a basis to understand the relation between the genuine diffusion measures, such as diffusion tensor and higher-order metrics, and their measurable “apparent” counterparts.
From this moment on, the course will develop two alternating tracks, devoted to modelling and to acquisition. During the modelling track, students will be exposed to the concept of coarse-graining over an increasing diffusion length, the associated time evolution of the diffusion metrics, and the effective medium way of thinking about the diffusion process. During the acquisition track, basic and advanced experimental techniques, their advantages and disadvantages, optimisation, imaging artefacts and their remediation, will be presented.
The two tracks will inform and complement each other, and will be accompanied by numerous exercises to be solved and further discussed in class. Parameter estimation for microstructural models will be discussed from the point of their pitfalls, degeneracies and “orthogonal” measurements to resolve such degeneracies.
The course will culminate with lectures on model validation using phantoms and animal experiments, as well as about the clinical translation of the discussed quantitative approaches.

Learning objectives
Diffusion basics
• Gaussian diffusion and the central limit theorem
• Non-Gaussian diffusion: origins and examples
• Diffusion propagator and the diffusion-weighted signal; q-space imaging
• Basic gradient waveforms (pulsed and oscillating gradients)

Biophysical modelling
• Models versus representations
• The cumulant expansion as a default representation
• Diffusion as coarse-graining. Origin of time dependence
• Effective medium theory
• Multiple Gaussian compartments and the Standard Model
• Multiple diffusion encodings: what kind of independent information can they provide?

Acquisition methods
• Diffusion-weighted imaging sequences
• Single shot and multi-shot sequences
• Single shot diffusion-weighted EPI sequence
• Practical sequence design and parameter optimisation
• Alternative diffusion-weighted imaging methods: Multi-band acquisitions, multi-shot EPI, TSE, PROPELLER, SSFP and others
• Challenges of diffusion measurements outside the brain

Post-processing, correction of artefacts, parameter estimation
• Correction of susceptibility related distortions of EPI images
• Correction of eddy currents distortions
• Artefacts of multi-shot/segmented DWI and possible methods of compensation
• Linear parameter estimation: DTI, DKI
• Non-linear parameter estimation: pitfalls and degeneracies
• “Orthogonal” measurements with generalised gradient wave forms

Validation and applications
• Monte Carlo simulations
• Validation in phantoms
• Validation in animals
• Pilot studies in humans and clinical translation
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