Open mrikasper opened 9 months ago
Hi @brainhackorg/project-monitors my project is ready!
Twitter-sized summary of our project pitch:
Reduce noise to the MACS with PhysIO for fMRI: Ever overwhelmed by the vast selection of noise models in PhysIO for your fMRI data? Find the best model for your data in this project by integrating Bayesian model selection via the MACS toolbox into your PhysIO workflow.
Possible dataset to work on (see also this issue):
TODO:
sub-46
) and test whether it works with PhysIO, then basic SPM preprocessing (similar to this CUBRIC Demo), then MACS GLMUpdate: In the BrainHack23 Toronto, @likeajumprope and me managed to achieve the following:
👍
Title
The TAPAS PhysIO Toolbox for Physiological Noise Modeling in fMRI
Leaders
Collaborators
Brainhack Global 2023 Event
BrainHack Toronto
Project Description
TL;DR: Watch the videos on PhysIO and MACS to learn about these 2 toolboxes that we are trying to integrate and make more accessible in this Hackathon.
The PhysIO Toolbox offers model-based physiological noise correction for functional MRI (fMRI) data, based on peripheral physiological recordings, such as cardiac and respiratory traces (ECG, pulse oximeter, breathing belt). Major noise models, such as RETROICOR, respiratory volume per time (RVT) or heart-rate variability (HRV) modulations of BOLD are supported.
PhysIO is written in Matlab, but also offered as standalone version via a containerized solution (Neurodesk) or web-based processing interface (CBRAIN). Through its integration as a toolbox in SPM, it both offers interactive operation via the Batch Editor GUI, as well as batch execution within fMRI preprocessing pipelines.
Through its more than 10 years of development as part of the Translational Algorithms for Psychiatry-Advancing Science (TAPAS) Software Package, PhysIO has seen many improvements and new releases, but user requests for new features always outnumber our core developer capacity.
In this Brainhack, we would like to add two of the most highly-desired features to PhysIO:
If you want to start small, there is also a user wish list of changes to the interface and documentation that we would be happy to see implemented.
Link to project repository/sources
Goals for Brainhack Global
All of the following goals are equally worthwhile. We will base our prioritization on user interest and expertise:
.json
sidecar files, similar to the CBRAIN implementationGood first issues
Communication channels
https://mattermost.brainhack.org/brainhack/channels/physio
Skills
Onboarding documentation
What will participants learn?
Data to use
TBD (it's one of the tasks)
Number of collaborators
4
Credit to collaborators
As outlined in our TAPAS CONTRIBUTING document, new members shall add themselves to the Contributor License Agreement alongside their first pull request contribution to the TAPAS PhysIO Code. This document is also referenced in the PhysIO README.
Image
Type
documentation, method_development, pipeline_development, visualization
Development status
1_basic structure
Topic
bayesian_approaches, data_visualisation, MR_methodologies, physiology, statistical_modelling
Tools
BIDS, SPM
Programming language
documentation, Matlab
Modalities
fMRI
Git skills
1_commit_push
Anything else?
We aim at making the project development environment available via Matlab Online or standalone (browser- or container-based, no license required), but if there is specific expertise, we could also aim at full Octave-compatibility of the toolbox.
Things to do after the project is submitted and ready to review.
Hi @brainhackorg/project-monitors my project is ready!