The ecosystem of open and collaborative neuroinformatic tools gets richer every day. Slowly but steadily, we all incorporate many open-source libraries and software packages into our work pipelines. This is only possible thanks to the dedication of people like Taylor Salo, who put in the time to create these tools we use. He is invested in the development of open tools for cognitive neuroscience, reproducible neuroimaging research, and semi-advanced fMRI denoising, and is coming to Brainhack Donostia 2020 to tell us how to get started and collaborate on an open-source Python project using GitHub.
A bit about Taylor Salo
Taylor Salo is a sixth-year doctoral student in the Department of Psychology at Florida International University working with Dr Angela Laird. He maintains NiMARE, a Python package for neuroimaging meta-analyses, and contributes to many other open-source projects such as BIDS (a standard for organizing and describing outputs of neuroimaging experiments), tedana (a library for denoising multi-echo fMRI data), and the physiopy suite (a set of tools to operate physiological files in MRI setups), among others. If you’re interested in getting to know Taylor better, have a look at his GitHub README.
There’s a bit more about Taylor’s talk in Brainhack Donostia in his abstract below!
In this talk, I will show you how you can start and work on a collaborative Python project from scratch using GitHub. With a little help from some colleagues, we will take the ICA-AROMA package, that is used in functional MRI data analysis but is no longer maintained, and make a new version of it that relies 100% on Python. In the process, we will refactor the code from a script into a package, add automatic tests that ensure the correct functionality of the changes we add, drop the FSL dependency, make the algorithm work in the subject space, and probably face a setback or two. In essence, it will be a complete GitHub collaboration experience condensed into a 1h15 tutorial.