phys2CVR: a BIDS-compliant python toolbox to compute cerebrovascular reacitvity mapping

Title

phys2CVR: a BIDS-compliant python toolbox to compute cerebrovascular reacitvity mapping

Leaders

Stefano Moia

Email: s.moia.research@gmail.com Twitter: @SteMoia Mattermost: @smoia

Collaborators

No response

Brainhack Global 2023 Event

Brainhack Donostia

Project Description

phys2cvr is a python toolbox that aims at offering various approaches to compute cerebrovascular mapping, starting from at least a functional MRI hypervolume.

While not the first toolbox to compute CVR out there, I’m aiming at making something easy to adopt, a swiss knife to compute all sorts of maps to image cerebral physiology (not to denoise fMRI timeseries, for that you can check phys2denoise ). phys2cvr should become one of the most complete tools for CVR mapping available, easy to adopt through a CLI (and, if possible, a GUI), with nice reports and plots, and allowing the highest automation through BIDS compliance. No repetition allowed thoough: for all python-based approaches out there, phys2cvr should only act as wrap around. All contributions are welcome - and all contributions are recognised via all-contributors guidelines (and authorship on publications).

The project is already in advanced beta stage - in fact, I’m aiming at writing and publishing a paper about it. There is a list of to-dos left, that I collected here , before submitting a manuscript.

If you want to collaborate, yaih! Feel free to reach out to me, and if you are attending Brainhack Donostia, we can get the party started!

Link to project repository/sources

https://github.com/smoia/phys2cvr

Goals for Brainhack Global

Go through this list as much as possible:

https://docs.google.com/document/d/1MFgwIjM5IaT7RlHtc5vzplPXZi8xaW76Fa-dLzknckA/edit?usp=sharing

Good first issues

1. issue one: add a code of conduct and a contribution guideline
2. issue two: check that licence is valid in all files
3. issue three: spellcheck CLI help and docstrings

Communication channels

https://mattermost.brainhack.org/brainhack/channels/bhg-phys2cvr

Skills

The list of todos is long, and each part requires different skills. In general, no skill is required, beside good will and interest in CVR mapping.

In practice, generally speaking git knowledge is welcome. To touch the code, python knowledge is fairly mandatory. For documentation and other parts, knowing markdown or restructured test would be nice, but not mandatory.

Onboarding documentation

No response

What will participants learn?

git, python, CVR mapping, pre-commit, sphinx based documentation writing, datalad, …

Data to use

No response

Number of collaborators

more

Credit to collaborators

I follow physiopy’s CoC, guidelines, and contribution recognition.

All contributions are recognised through all-contributors, all contributors are invited to be authors in outreach activities.

Image

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Type

pipeline_development

Development status

2_releases_existing

Topic

physiology

Tools

BIDS

Programming language

Python

Modalities

fMRI

Git skills

2_branches_PRs

Anything else?

No response

Things to do after the project is submitted and ready to review.

• Add a comment below the main post of your issue saying: Hi @brainhackorg/project-monitors my project is ready!
• Twitter-sized summary of your project pitch.