Physiopy/phys2denoise: Automated pipeline to create BIDS-formatted physiological regressors for neuroimaging denoising
Stefano Moia @smoia (
@SteMoia on twitter)
Katie Bottenhorn @62442katieb François Lespinasse @sangfrois
Registered Brainhack Global 2020 Event:
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!
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.
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:
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.
We’ll discuss over mattermost where to videochat.
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