coco2019-training

Training materials for the ReproNim day at https://coastal-coding.github.io

Introduction to Reproducible Neuroimaging: Motivations
- presentation
The UNIX Shell:
- presentation / hands-on exercises
Containers (Docker, Neurodocker, Singularity):
Datalad/Git/Git-Annex/GitHub:
- presentation / hands-on exercises
- notes / commands
BIDS:
Heudiconv/ReproIn:
- presentation
Pybids:
- ipython notebook tutorial
- pybids website
FAIR publishing:
- presentation
fMRIPrep:
- presentation
CPAC:
- CPAC website
- TODO link to the presentation
Graphical Nipype with Giraffe.tools:
- Gitaffe website
- presentation
Using Interfaces and Workflows in a script:
Introducing TestKraken: Test your Workflow:
Introducing Niflows: Reuse, Create, and Package your own Workflow:
- presentation
Neuroscout:
OpenNeuro:
- OpenNeuro website
- The Open Brain Consent project
Using the cloud (NITRC in the cloud):
- presentation
- commands from the demo
Nipype in the cloud (SLURM, AWS batch):
- presentation
CSV to NIDM/JSON:
- demo