Coastal Coding for Reproducible Neuroimaging

ReproNim+Nipype 2.0 / NiMARE @FIU in Miami

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

Location

Coastal Coding 2019 will be hosted at the scenic Biscayne Bay Campus (BBC) of Florida International University (FIU), located at 3000 NE 151 st in Miami, FL.

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.

Accommodations

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.

Hotel Recommendations

Hotel Option #1: Grand Beach Hotel

(from $281/night Oceanfront, from $207/night West)
5.7 miles from workshop site

Hotel Option #2: Best Western Plus Windsor Inn

(from $166/night)
3.4 miles from workshop site

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.

Sign Up

Registration: $125 for one event, $200 for both events
Fees cover breakfast, lunch, snacks, and plenty of coffee

Register here.

Contact

Questions? Contact us!

alaird@fiu.edu