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:
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:
What will participants learn:
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