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.
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
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
Review Day 2
Introducing Testkraken: Test your Workflow
Using Nipype on HPC and Cloud with public data
Blitz Intros: Neuroscout, OpenNeuro
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.
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.
Introduction to neuroimaging meta-analysis
FIU’s BBC is located 17 miles from the Miami International Airport (MIA) or 19 miles from the Fort Lauderdale-Hollywood International Airport (FLL).
The events will be held in the Wolfe University Center, WUC 155.
January weather in Miami is simply spectacular and an excellent choice for a winter getaway. This is our coolest and driest time of the year, with lots of sunshine and clear skies. Average highs are 76 degrees F (25 degrees C) and average lows are 60 degrees F (16 degrees C). UV levels will be high so bring plenty of sunscreen.
FIU’s BBC is located right on Biscayne Bay, and offers many outdoor recreational opportunities, an Aquatic Center, and a Fitness Center. The BBC is adjacent to the Oleta River State Park, a gorgeous natural oasis of hardwood hammocks and mangroves. Visitors can enjoy hiking, off-road bicycling trails, or paddling along lush mangrove forests on the Oleta River. Kayak and SUP (paddleboard) rentals are available through the Blue Moon Outdoor Center.
Attendees interested in staying on the beach may want to consider hotels just south of the BBC, in Bal Harbour and Surfside, or just north in Sunny Isles.
Transportation between the FIU BBC and the recommended hotels will not be provided. Attendees are encouraged to factor these additional costs into their travel budget. Both Lyft and Uber are available in the greater Miami metropolitan area.
Registration: $125 for one event, $200 for both events
Fees cover breakfast, lunch, snacks, and plenty of coffee
Questions? Contact us!