All code for this document is located here.

Here we will discuss how to get FSL (and other Linux only applications) onto a Windows machine using the Windows Subsystem for Linux (WSL). All of these instructions require Windows 10 or higher. Some of this content was adapted from http://www.nemotos.net/?p=1481.

1 Install Linux Subsystem

Information below can be found here (https://docs.microsoft.com/en-us/windows/wsl/install-win10)

  1. Enable “Windows Subsystem for Linux” feature using one of the options here
  • Option 1 (easy): Check the appropriate box within “Turn Windows features on or off” dialog box. (Open Settings -> Search “programs” -> Select “Turn Windows features on or off”) Step 1b: You will need to restart your computer, as prompted, after this feature is enabled.
  • Option 1 (faster but harder): Use Command-Line/PowerShell by pasting in the code below
Enable-WindowsOptionalFeature -Online -FeatureName Microsoft-Windows-Subsystem-Linux

  1. Download and install your preferred Linux distribution from the Windows Store – Ubuntu is the recommended distribution. There are other options to download from Command-Line/Script or download and manually Unpack/Install.

  2. Open Ubuntu. Here we will set up NeuroDebian using bash, which houses a ton of neuroimaging software:

sudo apt-get update -qq -y
sudo apt-get install -y wget git
OS_DISTRIBUTION=$(lsb_release -cs)
wget -O- http://neuro.debian.net/lists/${OS_DISTRIBUTION}.us-nh.full | sudo tee /etc/apt/sources.list.d/neurodebian.sources.list
sudo apt-key adv --recv-keys --keyserver hkp://pool.sks-keyservers.net:80 0xA5D32F012649A5A9
sudo apt-get update
  1. Install FSL:
sudo apt-get install fsl
  1. Run these following commands:
echo ". /etc/fsl/fsl.sh" >> ~/.bashrc
echo "export DISPLAY=localhost:0.0" >> ~/.bashrc

This will set up the FSL environment whenever you have bash opened up in a new window. Also, this will allow FSL to open displays on the machine.

2 Getting Windows to Pop up

  1. In Linux, Install x11 apps (https://virtualizationreview.com/articles/2017/02/08/graphical-programs-on-windows-subsystem-on-linux.aspx):
sudo apt-get install x11-apps
  1. Start Xming (or other x11 app) on the Windows side.

3 Setting up R

  1. Install R with OpenBLAS capabilities:
sudo apt-get install libopenblas-base r-base
  1. Install RStudio Server. Check https://www.rstudio.com/products/rstudio/download-server/ to make sure this is the most up-to-date version:
export RSTUDIO_VERSION=$(wget --no-check-certificate -qO- https://s3.amazonaws.com/rstudio-server/current.ver)
echo "VERSION ${RSTUDIO_VERSION}"
sudo wget -q http://download2.rstudio.org/rstudio-server-${RSTUDIO_VERSION}-amd64.deb
sudo gdebi --non-interactive rstudio-server-${RSTUDIO_VERSION}-amd64.deb
sudo rm rstudio-server-*-amd64.deb
  1. On the Windows side, navigate on a browser (e.g. Chrome) to https://localhost:8787, which should give you a login screen. Use the login information for the Ubuntu machine to use RStudio (with the Linux backend) on the Windows machine!

4 Installing Packages in R

  1. Install the requirements for the dependencies for devtools:
sudo apt-get update -qq -y
sudo apt-get install -y libgit2-dev 
sudo apt-get install -y libcurl4-openssl-dev libssl-dev
sudo apt-get install -y zlib1g-dev libssh2-1-dev libpq-dev libxml2-dev 
sudo apt-get install -y libhdf5
  1. In the RStudio server or R. Install devtools and fslr:
install.packages("devtools", repos = "https://cran.rstudio.com/")
source("https://neuroconductor.org/neurocLite.R") 
neuro_install("fslr")

Check this installation by trying to run some help file, such as:

fslr::fast.help()
  1. In the RStudio server or R. Install devtools and fslr:
neuro_install("extrantsr")

5 Session Info

devtools::session_info()