Add documentation for window subsystem for linux (WIP)

[lrouhier]

For windows 10 user , it might be better to use windows subsystem for Linux (WSL) instead of docker especially since Docker is dropping the support on Docker toolbox.
This PR add documentation for the installation of FSLeyes and SCT in this context in a separate .rst file. It contains the following instruction :

• Link for the installation of WSL
• for Xming installation (still needed for FSLeyes)
• Command to run to set up the environement to install FSL and SCT dependencies (e.g., gcc, gtk..)
• Command to install sct from 4.2.1 archive
• Command to install FSL which will install FSLeyes
• A useful note about the location of certain files.

TO DO :

• Description of windows subsystem
• Add link in the readme for Windows user to redirect them here

[jcohenadad]

why pointing to a specific Xming release? in 1 year from now, the release will likely have changed

[lrouhier]

I use the same link that we used in the README that's why I took this one. I will change that.

[jcohenadad]

we should make the documentation version-agnostic. I anticipate many users will install 4.2.1 instead of the latest. Moreover, why not using git instead of wget? I will suggest some changes

[jcohenadad]

i believe this folder /home/sct/sct_dev is not valid based on the code above (cd spinalcordtoolbox-4.2.1)

[jcohenadad]

ideally we should have SCT installation support .profile files. See spinalcordtoolbox/spinalcordtoolbox#2622.

[lrouhier]

i believe this folder /home/sct/sct_dev is not valid based on the code above (cd spinalcordtoolbox-4.2.1)

Actually when using ./install_sct it creates a new folder named 'sct' in the 'home' folder that's why I was using it. At least while using the wget version. This does not happen with the git version and the Path is then correct but you don't really need to add it as explained below.

ideally we should have SCT installation support .profile files. See spinalcordtoolbox/spinalcordtoolbox#2622.

there is a .bashrc actually but I need to add to source it.

[jcohenadad]

Actually when using ./install_sct it creates a new folder named 'sct' in the 'home' folder that's why I was using it. At least while using the wget version. This does not happen with the git version and the Path is then correct but you don't really need to add it as explained below.

Here is what i get when launching the default install from package (4.2.2): (notice the /Users/julien/sct_4.2.2 folder)

julien-macbook:~/Desktop/spinalcordtoolbox-4.2.2 $ ./install_sct 


*******************************
* Welcome to SCT installation *
*******************************



Checking OS type and version...

Darwin julien-macbook.local 18.7.0 Darwin Kernel Version 18.7.0: Tue Aug 20 16:57:14 PDT 2019; root:xnu-4903.271.2~2/RELEASE_X86_64 x86_64
ProductVersion:	10.14.6

Checking requirements...


OK!


SCT version ......... 4.2.2
Installation type ... package
Operating system .... osx (14)
Shell config ........ /Users/julien/.bashrc

To improve user experience and fix bugs, the SCT development team is using a
report system to automatically receive crash reports and errors from users.
These reports are anonymous.

Do you agree to help us improve SCT? [y]es/[n]o: y

--> Crash reports will be sent to the SCT development team. Thank you!


SCT will be installed here: [/Users/julien/sct_4.2.2]

Do you agree? [y]es/[n]o: 

[jcohenadad]

note: if we end up using the git clone option, the install will be done locally (no more copied to another folder), which facilitates our task

[lrouhier]

Yes right!
I think it is better to go with git.

[jcohenadad]

@lrouhier thanks a lot for this documentation! i think we should host this documentation inside the spinalcordtoolbox repos since this has nothing to do with sct-docker, right? if you agree, can you please open a PR on the SCT repos and propose these changes? thanks!

[lrouhier]

Yes it might be more fitting I Will open a PR there with the changes requested.