Physiopy/phys2denoise: Automated pipeline to create BIDS-formatted physiological regressors for neuroimaging denoising

Project info

Title:

Physiopy/phys2denoise: Automated pipeline to create BIDS-formatted physiological regressors for neuroimaging denoising

Project lead:

Stefano Moia @smoia (@SteMoia on twitter)

Project collaborators:

Katie Bottenhorn @62442katieb François Lespinasse @sangfrois

Registered Brainhack Global 2020 Event:

Brainhack Donostia

Project Description: The aim of this project is to restart the development of physiopy/phys2denoise, an automated pipeline to create BIDS-formatted physiological regressors for neuroimaging denoising. In practice, some folks might like to collect physiological recordings (e.g. pulse, chest expansion, % of gasses breathed out, skin conductance, …) while performing fMRI (fun MRI) experiments (or any other technique for which it’s relevant to consider physiological data). Those same folks might want to use the data they collected to implement impressive preprocessing pipelines and clean MRI data from physiological artefacts. If the data get BIDSified, for instance using physiopy/phys2bids, we can set up a pipeline that read such data and prepares all of the regressors that might be used in that same preprocessing pipeline (e.g. RETROICOR, RVT, RV, CRF, …). During the BHD week, we’ll re-draft and code the skeleton of the pipeline, and merge the contributions that have been proposed during the OHBM Hackhathon. We’ll also start drafting the documentation of the repository (explaining all those funny acronyms reported above), and write a couple of tests. Later in the week we’ll do some user testing too, and if we’ll have time, start working on a proposal to make fMRIprep ready files - in order to work toward a possible integration. If there is an arts-and-crafts oriented person, we are in need of logo!

Moreover:

• no limits in the number of participants, although we’ll work in parallel in smaller teams should we become too many or the task requires it.
• we ac(q)knowledge (inside joke) all contributions using a Turing-way-inspired, all-contributors based system.
• we have a (quite extensive) documentation for contributors in physiopy/phys2bids, like:
  • Contributing to phys2bids
  • Developer installation
  • Contributor guide
  • Code of Conduct
  • Developer calls calendar

Data to use:

Later during the week, we might use some of the data we have in OSF. We’ll evaluate together which one to use.

Link to project repository/sources: https://github.com/physiopy/phys2denoise Also have a look at: https://github.com/physiopy/phys2bids https://github.com/physiopy/peakdet

Goals for Brainhack Global 2020:

We’ll have a milestone and a dedicated label to indicate those issues we can tackle during this BHG, but as a summary:

• Design the repo
• Code the skeleton of the pipeline
• Merge open PRs and complete the list of metrics that can be computed
• Write documentation about the pipeline, but also about physiological denoising and techniques (and whatnot)
• Extra: deisign the logo!

Good first issues:

No GFI for the moment, however if someone is interested in reading and writing documentation about denoising, it could be a great way to move their first steps in a Git(Hub) based development environment.

Skills:

Code contributions:

• python (mandatory)

Documentation:

• Reading papers
• Writing skills
• Becoming acquainted with ReStructured Text before starting could be helpful.

Logo design:

• Creativity
• Any software that handles images (also MS paint, although, I mean, MS paint?!?)
• Be familiar with the existing logos of physiopy.

Communication channels:

We’ll discuss over mattermost where to videochat.

Project labels

• I added all of the labels I want an associate to my project

Project Submission

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• Link to your project: could be a code repository, a shared document, etc.
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• Flesh out at least 2 “good first issues”: those are tasks that do not require any prior knowledge about your project, could be defined as issues in a GitHub repository, or in a shared document.
• Skills: list skills that would be particularly suitable for your project. We ask you to include at least one non-coding skill. Use the issue labels for this purpose.

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• Number of participants required.
• Twitter-size summary of your project pitch.
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• Specify how you will acknowledge contributions (e.g. listing members on a contributing page).

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