Coastal Coding for Reproducible Neuroimaging Posted By: David Kennedy - Dec 6, 2018Tool/Resource: ReproNim: A Center for Reproducible Neuroimaging Computation COASTAL CODING FOR REPRODUCIBLE NEUROIMAGING ReproNim+Nipype 2.0 / NiMARE @FIU in Miami 10-12 JANUARY 2019 - REPRONIM/NIPYPE WORKSHOP 14-16 JANUARY 2019 - NIMARE CODE SPRINT See https://coastal-coding.github.io/ for complete details 10-12 JANUARY 2019 REPRONIM/NIPYPE WORKSHOP The goals of this workshop are two-fold. First, to enable attendees to become familiar with best practices for reproducible analysis from ReproNim. Second, to learn how to create scalable and re-executable neuroimaging workflows with the upcoming Nipype 2.0 platform. This event is targeted towards novice neuroimaging users who meet the following requirements: 1. Working knowledge of Python 3 2. Familiarity with scripting in at least 1 neuroimaging package (e.g., AFNI, ANTS, FSL, FreeSurfer, SPM) Advanced users are welcome to learn about the changes and hack with Nipype developers. NIPYPE WORKSHOP AGENDA JAN 10TH - REPRONIM: TOOLS FOR REPRODUCIBLE PRACTICES BOOTCAMP - Introduction to the workshop - Reproducibility Basics 1: The UNIX Shell, Neurodocker containers (Docker, Singularity) - Reproducibility Basics 2: Datalad, Git/Git-Annex/GitHub - Introduction to FAIR data and BIDS JAN 11TH - NIPYPE 2.0 PART I - Review Day 1 - Introduction to Nipype 2.0 dataflow framework - Blitz Intros: fMRIPrep, CPAC - Graphical Nipype with Giraffe.tools - Using Interfaces and Workflows in a script - Introducing Pydra: Create your own Workflow - Introducing Niflows: Reuse, Create, and Package your own Workflow JAN 12TH - NIPYPE 2.0 PART II - Review Day 2 - Introducing Testkraken: Test your Workflow - Using Nipype on HPC and Cloud with public data - Blitz Intros: Neuroscout, OpenNeuro - Feedback session 14-16 JANUARY 2019 NIMARE CODE SPRINT ABOUT NIMARE - NiMARE (Neuroimaging Meta-Analysis Research Environment) is a new Python package for performing analyses using neuroimaging meta-analytic data. Current tools for neuroimaging meta-analyses are spread out across several packages and languages. NiMARE aims to provide a standardized interface for a broad range of algorithms, along with interfaces to open meta-analytic resources like Neurosynth, NeuroVault, and brainspell. ABOUT THE SPRINT - The three-day NiMARE coding sprint will occur after the Nipype workshop, with a one-day rest period between, in which participants can enjoy Miami. At the sprint, we’ll be working to design a standard for representing meta-analytic data, to add implementations for new tools, and to improve the documentation and test coverage of the existing codebase. Anyone interested in contributing to this new package is welcome to join. Experience with Python or neuroimaging meta-analysis recommended, but not necessary. NIMARE SPRINT AGENDA JAN 14TH - META-ANALYSIS BOOTCAMP AND HACKING - Introduction to neuroimaging meta-analysis - Hacking - Progress reports JAN 15TH - HACKING AND PROGRESS REPORTS - Hacking - Progress reports JAN 16TH - HACKING AND PRESENTATIONS - Hacking - Project presentations |
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