The TAPAS PhysIO Toolbox for Physiological Noise Modeling in fMRI

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:

  1. Finding the best physiological noise model for your data using MACS
  2. Creating an interactive tutorial of PhysIO in action using Matlab Online and open datasets, for example based on this prototype code

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.

Goals for Brainhack Global

All of the following goals are equally worthwhile. We will base our prioritization on user interest and expertise:

  1. Model Selection of the best Physiological noise model for your data (tracked in this issue )
  1. Interactive Online Tutorial of the PhysIO pipeline with openly available fMRI data (tracked in this issue )
  1. Fulfilling some PhysIO users’ long-standing small, but impactful feature requests from the wish list , such as
    • A consistent interface for multiband fMRI data (this issue )
    • A direct read-in of BIDS scan timing data from .json sidecar files, similar to the CBRAIN implementation
    • Exporting preprocessed physiological traces and derived measures (heart-rate variability, respiratory volume per time) at base resolution before physiological modeling (this issue )

Good 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

AvatarPhysIO

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.


Date
Jan 1, 0001 12:00 AM