jsheunis commented 3 years ago

`fMRwhy`: BIDS-compatible multi-echo fMRI analysis and quality control with SPM12/MATLAB/Octave

fmrwhy

Project Description

With this hackathon I would like to onboard anyone who wants to join, contribute to, or learn more about the fMRwhy project: a toolbox for BIDS-compatible multi-echo fMRI analysis and data quality control with SPM12/MATLAB/Octave.

You can access more information about the toolbox here:

If you go through the documentation and code base you will notice that many aspects are lacking, poorly implemented, undocumented, and more. That's why the project is at a great stage to receive contributions, from updates to the documentation to setting up a testing framework.

Specific goal

During the weeks before the hackathon, I will create specific issues on the fMRwhy GitHub repo that will guide new contributors. These issues will likely relate to the following aspects that require improvement:

Creating a more user-friendly README
Testing the toolbox using your own or publicly available data
Writing unit tests (currently, there are none 😬)
Setting up a unit/integration testing framework
Contributing to the documentation, including:
- populating the section on multi-echo fMRI
- populating the section on real-time fMRI
- populating the API
Adding docstrings to most functions
Adding visualisation features to the fMRI QC report
Creating tutorials for using toolbox features

Skills required to participate

Anyone who wants to contribute should be able to contribute. There are, however, some required skills depending on the features that you'd like to contribute to:

For logging issues or feature requests: a keen interest and familiarity with describing issues via GitHub
For testing the toolbox: a basic understanding of fMRI analysis with SPM12/MATLAB and BIDS data
For contributing to the documentation: git/github, sphinx, sphinx-contrib/matlabdomain, reStructuredText
For contributing to the code: git/github, MATLAB, javascript, html, css
For creating tutorials: git/github, using MATLAB/Octave with Jupyter Notebooks

Specific levels of requirement for if you want to contribute to specific software features include:

language	level of expertise required
MATLAB	beginner / confirmed / expert
javascript	confirmed / expert
html	confirmed / expert
css	confirmed / expert
SPM	beginner / confirmed / expert
GIT - 2	comfortable working with branches and can do a pull request on another repository

If you don't have the required skills but are keen to acquire them while contributing, please feel free to reach out!

Integration

How would your project integrate a physicist/imager/clinician/psychologist/computational scientist/maker/artist/lawyer as collaborator?

...to be determined...

Preparation material

Link to your GitHub repo

fMRwhy on GitHub

Communication

Remi-Gau commented 3 years ago

@jsheunis

I might drop by to help you get started to set up unit tests, code coverage and CI for those if you want? :-)

jsheunis commented 3 years ago

That would be awesome!

Remi-Gau commented 3 years ago

A channel for this project was added in the openMR 2021 discord server

OpenMRBenelux / openmrb2021-hackathon