nii-masker: A command-line wrapper for nilearn's Masker tools

[danjgale]

nii-masker

Project Description

niimasker is a command-line wrapper for nilearn's Masker objects, which let you easily extract out time series from your functional data (and gives you a number of options for post-processing during extraction). I'm in a lab with a number of non-Python users who would benefit greatly from this ability, and this project was a spur-of-the-moment project idea I had a couple of weeks ago when discussing my fMRI pipeline with my colleagues (we're trying to get a more standardized workflow going – fmriprep, etc). Because niimasker is run via the command-line, pretty much anyone with some bash knowledge can use it (or at least that's what I'm working towards).

I developed much of this last week in a "mini-sprint" (i.e. a colleague needed data "yesterday"). While its core functionality is working, there's lots to be done. I've included a number of issues in the repo already: https://github.com/danjgale/nii-masker/issues. So, there are some exciting features to add (e.g., a visual report à la fmriprep) as well as some testing/CI to set up. These outline some of the things I'd like to accomplish at the hackathon.

Skills required to participate

• Any experience with Python and nilearn
• Any HTML knowledge would be helpful for development of the visual report!

Integration

The goal is to create a totally intuitive tool for anyone, so all contributions from all backgrounds and perspectives are encouraged. Non-expert/technical users can contribute by providing feedback and design ideas to make niimasker more approachable and user-friendly.

Preparation material

• Nilearn’s user guide, in particular the masker guide
• argparse info
• The project's README

Link to your GitHub repo

https://github.com/danjgale/nii-masker/

Communication

I can set up a channel on the brainhack mattermost/slack if this gains interest. I would also like to keep a lot of conversation "in the open" directly in github issues as well.