How to run FSL on Windows 10 using Bash on Ubuntu on Windows

Since Aug 2016, Bash is available inside Windows.
That means, several neuroimaging software such as FSL or AFNI can be run from Windows.

I gave a try and confirmed FSL can run on Windows 10.

Below is what I did.

1. Install Bash on Ubuntu on Windows

First of all, we need to install bash on Windows.

There is a good tutorial on this topic, so please follow the link below.

How to Install and Use the Linux Bash Shell on Windows 10

2. Install Xming

Next, we neet to get Xming and install it. It seems the latest version is not free, but FSL can run with free version.

You can get free version of Xming from here.

Installation is simple. Default setting should work.

After reboot, run xming. Though nothing seems to happen, please check the task bar of Windows on the right bottom corner.



If you move cursor on the icon of Xming, it shows something like “Xming Server:0.0”. We use the information “0.0” later.

3. Install FSL

Next we run bash. type

bash

in the command prompt. (You already did this when you install bash on the first step)

Ubuntu on Windows is based on Ubuntu 14.04 LTS, so we utilize Neurodebian repository for installation.

Type the following in the command prompt.

sudo apt-get update
sudo apt-get dist-upgrade
wget -O- http://neuro.debian.net/lists/trusty.us-nh.full | sudo tee /etc/apt/sources.list.d/neurodebian.sources.list
sudo apt-key adv --recv-keys --keyserver hkp://pgp.mit.edu:80 0xA5D32F012649A5A9
sudo apt-get update
sudo apt-get install fsl

(There are some mirrors of Neurodebian, so please check http://neuro.debian.net/ to find the closest mirror for you.)

Here we do

• Update repository
• Update the system to the latest
• Setup neurodebian repository
• Get key for neurodebian repository
• update repository again to enable neurodebian
• Install FSL
4. Add some lines to .bashrc

Finally, type the following.

echo ". /etc/fsl/fsl.sh" >> ~/.bashrc
echo "export DISPLAY=localhost:0.0" >> ~/.bashrc

This operation writes the following lines to .bashrc

. /etc/fsl/fsl.sh
export DISPLAY=localhost:0.0

First line is necessary to run FSL, and the second line is to show the system where display is for GUI.

5. Check the installation

To enable change on .bashrc you need to exit bash once.

exit

Then type “bash” again.

bash

Then type

fsl

will bring up FSL menu.

fslview

will bring up FSLView.