Tools for reproducible research

• From interactive exploration to reproducible data science: Jupyter, Binder, Travis and friends. by Fernando Perez within Neurohackademy 2018

  • duration: 1 hr 25 min
  • type: {video}

• Jupyter tutorial by Eshin Jolly within MIND 2018

  • duration: 31 min
  • type: {video}

Containers

• Docker for scientists 1 by Chris Gorgolewski within Neurohackweek 2016

  • duration: 1 hr 13 min
  • type: {video}

• Docker for scientists 2 by Chris Gorgolewski within Neurohackweek

• Docker tutorial by Lucy Owen within MIND 2018

  • duration: 20 min
  • type: {video}

• Neurodocker allows you to easily create containers suited to your neuroimaging needs. Here is a tutorial on how to use it.

Tools for reproducible neuroimaging

• ReproNim - A Center for Reproducible Neuroimaging Computation (a good site to get up to date on doing reproducible neuroimaging research)

• Code-ocean - A research collaboration platform that uses docker containers to let you run your analysis online

• NeuroLinks - Resources for computational neuroscience

Presentations

• Improving the Reproducibility of Neuroimaging Research by Russ Poldrack within Neurohackweek 2016

  • duration: 1 hr 23 min
  • type: {video}

• GNU Make for Neuroimaging Workflows by Tara Madhyastha within Neurohackweek 2016

  • duration: 48 min
  • type: {video}

• Introduction to web technologies by Anisha Keshavan within Neurohackademy 2018

  • duration: 56 min
  • type: {video}

• Neuroimaging pipelines by Satra Ghosh within Neurohackweek 2017

  • duration: 1 hr 33 min
  • type: {video}

• Reproducibility in fMRI: What is the problem? 1 by Russ Poldrack within Neurohackweek 2017

  • duration: 1 hr 40 min
  • type: {video}

• Same Data - Different Software - Different Results? Analytic Variability of Group fMRI Results by Alexander Bowring

  • duration: 12 min
  • type: {video}

• Software pipelines for reproducible neuroimaging by Satra Ghosh and Chris Gorgolewski within Neurohackademy 2016

  • duration: 1 hr 14 min
  • type: {video}

• Neuroimaging Workflows & Statistics for reproducibility by Dorota Jarecka, Satrajit Ghosh, Celia Greenwood and Jean-Baptiste Poline at OHBM

  • duration: 3 hr 45 min
  • type: {video}

• Tools from the Center for Open Neuroscience by Yaroslav Halchenko within MIND 2018

  • duration: 59 min
  • type: {video}

• Allen Institute Data and Software by Nicolas Cain within Neurohackweek 2017

  • duration: 53 min
  • type: {video}

• Allen Institute Datasets by Terri Gilbert within Neurohackweek 2016

  • duration: 1 hr 8 min
  • type: {video}

• Allen Institute RNAseq data by Jeremy Miller within Neurohackweek 2016

  • duration: 52 min
  • type: {video}

• AllenSDK and the Allen Brain Observatory by Nicolas Cain and Justin Kiggins within Neurohackademy 2018

  • duration: 1 hr 42 min
  • type: {video}

• Integrating Allen Institute Datasets with MRI data by Kirstie Whitaker within Neurohackweek 2016

  • duration: 28 min
  • type: {video}

Tutorials/instructions/slides

• Advance Unix and Make by Valentina Staneva and Tara Madhyastha within Neurohackweek 2016

• CRN resources by Chris Gorgolewski within Neurohackweek

• Reproducibility in fMRI: What is the problem? 2 by Russ Poldrack within Neurohackweek 2017

• Reproducible research pipelines by Chris Gorgolewski and Satra Ghosh within Neurohackweek 2016

• Reproducible fMRI analysis with Code Ocean by Stephan Heunis describing how he did that with an SPM pipeline.

Other

• Challenges to open data and how to respond