README.md

coco2019-training

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

Links to the presentations:

• Introduction to Reproducible Neuroimaging: Motivations
  • presentation
• The UNIX Shell:
  • presentation / hands-on exercises
• Containers (Docker, Neurodocker, Singularity):
  • presentation
  • hands-on exercises
  • Neurodocker on github
• Datalad/Git/Git-Annex/GitHub:
  • presentation / hands-on exercises
  • notes / commands
• BIDS:
  • presentation
  • BIDS website
  • notes / commands
• 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:
  • ipython notebook tutorial: interfaces
  • ipython notebook tutorial: workflows
  • entire Nipype tutorial
• Introducing TestKraken: Test your Workflow:
  • presentation
  • notes / useful commands
  • TestKraken on github
• Introducing Niflows: Reuse, Create, and Package your own Workflow:
  • presentation
• Neuroscout:
  • presentation
  • Neuroscout website
  • FitLins repo
• 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

Additional links:

• review qstions
• neurostars.org

Docker containers used during the workshop:

• kaczmarj/coco2019:day1
• kaczmarj/coco2019:day2
• kaczmarj/coco2019:day3
• kaczmarj/testkraken