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.
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.
nii-masker
Project Description
niimaskeris 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). Becauseniimaskeris 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
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
niimaskermore approachable and user-friendly.Preparation material
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.