Dipy

Dipy is a diffusion MRI data analysis. It is similar to MRtrix. One of Dipy’s main authors and contributors, Eleftherios Garyfallidis, was a post-doc in our lab in 2014-2015. It offers many functions coded in python/cython that you can import as a library when analysing your data. It doesn’t offer complete end-to-end scripts, but you can check their official website’s tutorials for scripts examples. You can also check our videos tab in the Teams’ General channel for a tutorial.

Dipy will be installed automatically when installing Scilpy. However, you might have to modify Dipy at some point in your research. If so, you will need to fork the Dipy repository and clone it somewhere on your computer. If you want your modification to become a part of the official Dipy, you will have to set up your upstream remote (see Git) and do a pull request in Dipy.