Warning

All of the shell scripts take a long time to complete. I suggest not making any attempt to run them if you need to restart your computer any time soon.
I don't recommend using any version of Windows 10 prior to release 1709 (also known as the Fall Creators Update) for this. These scripts and instructions were developed using that release. Even though earlier releases included a version of the subsystem for Linux, it was not very well polished and would not be a good overall experience.

A word of thanks

The AFNI developers were very kind, and provided a complete set of instructions for Windows 10. These scripts and instructions are derived from there. You will want to look their documentation over and have a close look at the sections labeled as "optional" because those changes are generally not included in these scripts, though some are included in the instructions below. I especially want to thank the AFNI developers for doing the hard work required to make this work on Windows 10.

AFNI Windows 10 instructions

Why not just use the instructions?

You're certainly welcome to. There's no question that the instructions provided are both detailed and complete. They can also be hard to follow, as the windows 10 instructions reference the Ubuntu 16 instructions - but only sections of them. My goal was to simplify the process for the end-user, who may not be a Windows or Linux expert, or may just be an IT person who knows nothing about AFNI. I happen to be the IT guy who needed to install AFNI for a user but didn't want to read and parse 2 sets of instructions every time this was required for a new computer. Everything up to the actual afni install shell scripts can be performed by an IT technician, but since the Ubuntu install is unique to each user profile in Windows, afni is installed per-user and cannot be done ahead of time for the user without having the user's credentials, which is generally recognized as a bad idea and bad policy.

Starting from the "Install AFNI environment" header, all actions can be performed by an end-user, without Windows administrative credentials. All instructions from the AFNI documentation are reproduced as faithfully as I can, and adapted where I couldn't (or an additional package install was needed for R packages to compile properly). The instructions should be easy enough for an end-user to follow without additional guidance from IT. Also, since they are scripts and not copy-paste code blocks, more actions can be placed into one step. Trying to copy and paste all code steps at once from the documentation page would result in errors, especially when any step involves using sudo. In script form, the full set of commands work as expected without breaking.

Pre-requisites

Linux Subsystem (tested in Windows 10, 1709)

Run the following command as an administrator in powershell (or run Install-WSLFeature.ps1 with powershell) :

Enable-WindowsOptionalFeature -FeatureName Microsoft-Windows-Subsystem-Linux -Online -All -LimitAccess -NoRestart -ErrorAction Stop

Ubuntu on Windows

Install Ubuntu on Windows (Store link) : https://www.microsoft.com/store/p/ubuntu/9nblggh4msv6
Install Ubuntu on Windows (AppX Download) : https://aka.ms/wsl-ubuntu-1604

X server for Windows

VcXsrv : https://sourceforge.net/projects/vcxsrv/files/latest/download
XMing (free or paid) is not recommended, because some of the afni windows will crash on launch, this includes the 'AFNI Tips' sheet.

Install AFNI environment

Set up the Environment

Clone this repo into your home folder of your Ubuntu user
cd into the new folder
Run sh ./initializeEnvironment.sh
Close your Ubuntu window and re-open
cd into the repo

Install R

Run sh ./installR.sh

Make AFNI profiles, prepare for bootcamp and evaluate system:

Run sh ./createAfniProfiles.sh

Run AFNI

Every time you run afni you need to be running your X server first.
Launch Ubuntu
run afni

Mounting network shares automatically

sudo mkdir /mnt/share
echo "\\server\share /mnt/share     drvfs   defaults        0 0" | sudo tee --append /etc/fstab
# Not a requirement starting in Windows 10 release 1809, if you place the following lines in /etc/wsl.com
# echo "sudo mount -a" >> ~/.profile

/etc/wsl.conf:

[automount]
enabled = true
mountFsTab = true

Notes

The AFNI developers really want you to use tcsh. If you want to do this, you'll need to run this at minimum (untested)

chsh -s /usr/bin/tcsh
echo 'setenv R_LIBS ~/R' >> ~/.cshrc

I've had some feedback from Paul Taylor on the AFNI forums, who tells me the following:

Re. the choice of shell and our frequent use of tcsh-- we do have some scripts in bash and some in tcsh, and the latter is more popular locally mainly because of its relative readability. In general, we recommend setting up both bash and tcsh environments for AFNIing, and that is what our main instructions do. That way, whichever shell a user is using, they should be good to go.

https://afni.nimh.nih.gov/afni/community/board/read.php?1,157848,157853#msg-157853

As these source instructions include steps that set up both bash and tcsh, these scripts should also be sufficient since they were built using those same instructions, aside from the steps included above.

Repairing R Packages (using bash)

export R_LIBS=$HOME/R
rPkgsInstall -pkgs ALL

Enabling Quick-Edit mode to make copying and pasting easier

This is on by default in release 1709, but if you need to enable it run the following command in powershell (or run Enable-QuickEdit.ps1 in powershell) :

Set-ItemProperty -path HKCU:\Console -Name QuickEdit -Value 1

This enables sane copying and pasting inside any Windows command shell (Ubuntu, CMD, Powershell)

Microsoft Documentation for QuickEdit mode

(Optional) "Niceify" the terminal

See AFNI developers explanation for this here: AFNI Documentation

sh ./niceifyTerminal.sh

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