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Introduction
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README.md

README.md

READ THIS FIRST! NEWER VERSION IS AVAILABLE

This is a now archived version of the workshop materials as were used at OHBM 2018. No further changes would be done to it. For an updated version, please visit/follow e.g. a SfN 2018 version.

Instructions

Install VirtualBox

  • Go to the VirtualBox Download page: https://www.virtualbox.org/wiki/Downloads

  • Select the link from the "VirtualBox 5.2.12 platform packages" section that matches your system.

  • For Windows 10 users:

    1. Double-click the downloaded executable file (Windows Installer 1.1 or higher is required)
    2. Select default options in installation dialog.
    3. The installer will create a "VirtualBox" group in the Windows Start menu.
    4. For more detailed step-by-step instructions, look here
  • For Mac users:

    1. Double-click on the downloaded dmg file to have its contents mounted
    2. A window will open telling you to double click on the VirtualBox.pkg installer file displayed in that window.
    3. This will start the installer, which will allow you to select where to install VirtualBox to.
    4. After installation, you can find a VirtualBox icon in the "Applications" folder in the Finder.
  • For Ubuntu users:

    • Step-by-step instructions can be found here

Download and import the VM image file

  • Download from https://training.repronim.org/reprotraining.ova
  • To import the reprotraining.ova file:
    1. Open VirtualBox on your computer
    2. select "File" -> "Import Appliance" from the VirtualBox menu.
    3. Click through the import wizard dialog leaving the default settings (see here for example step-by-step instructions here).

Starting the VM

  • Open VirtualBox on your computer
  • Choose "reprotraining" from the menu on the left and press "start" (the green arrow) to start the Ubuntu virtual machine.

Issues:

  • if you have a windows 10 pro 64 bit (eg Lenovo X1C) machine and get an error like: vt-x/amd-v hardware acceleration is not available on your system, look here
  • if you are unable to install VirtualBox due to virtualization technology (VT-x) not being enabled on your system, look here

The Presentations

Introduction - David Kennedy (UMass Medical) and JB Poline (McGill)

Link

FAIR Data - BIDS datasets - Jeffrey Grethe, UCSD

Link.

Computational basis - Yaroslav Halchenko, Dartmouth College and Michael Hanke, Magdeburg

Neuroimaging Workflows - Dorota Jarecka and Satrajit Ghosh, MIT

Statistics for reproducibility - Celia Greenwood and Jean-Baptiste Poline, McGill

  • Basics Link
  • Positive Predictive Value (PPV) Link