containerize bidspm

Project title:

containerize bidspm

Project leader:

Remi Gau

Email:

remi.gau@gmail.com

Collaborators:

Brainhack Global 2022 Event:

BrainHack Donostia

Topic:

Statistical modelling

What is the purpose of the project:

bidspm is an SPM centric automated pipeline to preprocess BIDS datasets and to run fmri statistical on them by relying on the BIDS stats model for model and contrast specification.Currently the pipeline can run on Matlab and Octave.The pupose of this project is to create containerized versions (Docker, Singularity) of the pipeline to help reusability and reproducibility.

Where can participants find key resources to work on this project:

https://bidspm.readthedocs.io/en/latest/

What stage is the project on:

4

Required programming skills for the project:

Advanced programming level

Background knowledge needed on the topic:

Advanced

Data to use:

The demos of the pipeline should automatically download and bidsify example data from either OSF or from the SPM website.

Link to project repository:

https://github.com/cpp-lln-lab/bidspm

Goals for Brainhack Donostia 2022:

• improve the octave based docker container to make it run like a bids app
• compile the pipeline matlab code to make it run without requiring a license

What will participants learn:

• learn how to use matlab without having to pay for it- learn to use neurodocker to more easily build a docker / singularity recipe for your project

Number of collaborators:

2

Credit to collaborators:

We use all contributors to keep track of people’s contribution. Contributing: https://github.com/cpp-lln-lab/.github/blob/main/CONTRIBUTING.md

Type of project:

Coding methods, Data management, Pipeline development

Programming languages:

Necessary git skills level for the project:

Advanced (continuous integration)

Modality:

fMRI

Software suites:

BIDS, fMRIPrep, SPM

Type

coding_methods

Development status

2_releases_existing

Topic

reproducible_scientific_methods

Tools

BIDS

Programming language

containerization, documentation, matlab, octave, docker

Git skills

1_commit_push, 2_branches_PRs, 3_continuous_integration