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Add documentation for window subsystem for linux (WIP) #52

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.. -*- coding: utf-8; indent-tabs-mode:nil; -*-

############################################################
Spinal Cord Toolbox for Windows : Windows subsystem for linux
############################################################

This documentation shows how to install the latest version of SCT. If you want to install a different version of SCT please specify the version number.

.. contents::
..
1 Windows subsystem for linux
2 environment preparation
3 SCT installation
4 FSL installation
5 Usage

Installation
************


#. Install `Xming <https://sourceforge.net/projects/xming/>`_.

#. Install `Windows subsystem for linux and initialize it <https://docs.microsoft.com/en-us/windows/wsl/install-win10>`_.

- Please install the Ubuntu 18.04 LTS distro.

Environment preparation
***********************

Run the following command to install various packages that will be needed to install FSL and SCT. This will require your password

.. code-block:: sh

sudo apt-get -y update
sudo apt-get -y install gcc
sudo apt-get -y install unzip
sudo apt-get install -y python-pip python
sudo apt-get install -y psmisc net-tools
sudo apt-get install -y git
sudo apt-get install -y gfortran
sudo apt-get install -y libjpeg-dev
echo 'export DISPLAY=127.0.0.1:0.0' >> .profile


Install SCT
***********

Download SCT:

.. code-block:: sh

git clone https://github.com/neuropoly/spinalcordtoolbox.git sct
cd sct

To select a [specific release](https://github.com/neuropoly/spinalcordtoolbox/releases), replace X.Y.Z below with the proper release number. If you prefer to use the development version, you can skip this step.

.. code-block:: sh

git checkout X.Y.Z

Install SCT:

.. code:: sh

yes | ./install_sct



Install FSL
***********

FSL contains fsleyes which is the default viewer for NIfTI image in SCT.
Download and execute the installer:

.. code-block:: sh

wget https://fsl.fmrib.ox.ac.uk/fsldownloads/fslinstaller.py
python fslinstaller.py

to complete the installation of these software run:

.. code:: sh

cd ~
source .profile
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source .bashrc

You can now use SCT. To use FSLeyes, run Xming from your computer before entering the fsleyes command.

Your local C drive is located under '/mnt/c'. You can access it by running

.. code:: sh

cd /mnt/c