In this two-days workshop, you will learn how to use different diffusion MRI (dMRI) techniques in an open-source environment. During the workshop, I will explain the theory behind different diffusion MRI techniques. This will be followed by practical tutorials based on the Diffusion in Python (Dipy) package (dipy.org).
To participate in the workshop, you will need to install Dipy and Fury. To install the dependencies of these two packages, I suggested that you install anaconda (in the anaconda website you will find the installers for different operative systems).
After installing anaconda, open an anaconda prompt terminal and type:
conda install -c conda-forge dipy
For some Dipy visualization tools you also need to have Fury installed. For this, in the anaconda prompt terminal, type:
conda install -c conda-forge fury
If this does not work try
pip install fury
More information on Dipy and Fury installation can be found in the following page).
The workshop will start with a 30 min warm-up at 9:00 am UTC on both days. During this warm-up, we can resolve technical difficulties you might be experiencing. The actual workshop will start at 9:30. Lunch break is from 12 to 1, and we will continue until 3:30.
Below you can find the topics discussed on the two days:
- Workshop introduction
- Diffusion MRI data as 4D images and simple Apparent Diffusion Coefficient calculation
- Diffusion Tensor Imaging (DTI)
- Introduction to DTI tractography
(Lunch)
- Exploration of different reconstruction techniques for tractography
- Probabilistic vs Deterministic Tractography
- High angular resolution diffusion imaging (DSI, Q-ball, CSA)
- Open questions and discussion
- Diffusion MRI pre-processing
- Diffusion MRI signal representation techniques (DTI, DKI, MAP-MRI)
- Diffusion MRI microstructural models (WMTI, SMT, fw-DTI)
(Lunch)
- Combining advanced dMRI metrics and tractography
- Overview of other tools available in Dipy
- Discussion of the future directions on Dipy development
- Open questions and discussion