Installing ANTsR in Windows 10: A few minor bugs

[j-hegde]

I recently successfully installed ANTsR on my Windows 10 (Professional; 64-bit; Dell XPS15) laptop. The relevant installation instructions on this site (https://github.com/ANTsX/ANTsR/wiki/Installing-ANTsR-in-Windows-10-(along-with-FSL,-Rstudio,-Freesurfer,-etc).#here-are-the-instructions-to-get-antsr-running-on-windows-10) were very clear-cut and helpful. Having taken ANTsR for a spin, I like it so much that I consider myself an ANTsR groupie!

Here, I log a few minor problems I encountered during the installation process, so as to help other Windows users seeking to install ANTsR get past them more quickly than I did.

(1) The following sentence at the top of the instructions “This will work only if your Windows 10 is updated with the anniversary update (Aug 2016).” should perhaps read something like: “This will work only if your Windows 10 is updated with the anniversary update (Aug 2016 or later).”

This is because I had trouble with Ubuntu install until I updated my Windows to the latest available version, i.e., Microsoft Windows OS Version: 10.0.18363 ; Build 18363.

(2) Further down, the following sentence “You may need to disable antivirus software (Kaspersky, Avast, etc) to perform the next steps.” should perhaps add something like this: “You may also need to disable AcronisImage or similar software that create whole-disk backups.”

My AcronisImage turned out to be the final obstacle that was preventing me from a successful install of WSL (Ubuntu). I kept getting the error msg “Error installing WSL: Package is corrupted". (Occasionally I'd see variations of this message depending on the fix I was trying. But then I came across this page that said disabling Acronis Image might help: https://superuser.com/questions/1211201/wsl-bash-on-windows-10-creating-unix-user-failed-returned-error-code-10 So I disabled AcronisImage, rebooted my machine, and voila! The exact same Ubuntu install worked without a hitch.

(3) At the very bottom of the instructions, in the section “Add ANTs to the path:” (3a) cp -R ${PWD}/../ANTs/Scripts/ $PWD/bin should be changed to cp -R ${PWD}/../ANTs/Scripts/ $PWD #Both because the ‘bin’ in question is really #named ‘antsbin’, and because you cd’ed to this dir using the cd command above.

(3b) Also, echo "export ANTSPATH=$PWD/bin/" >> ~/.bashrc should be changed to echo "export ANTSPATH=$PWD" >> ~/.bashrc #Same reason as #3a above

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[dorianps]

Thanks for reporting this @j-hegde .

I think that page will need a major update soon. WSL has been outdated for a while with very slow performance. Microsoft is getting ready to roll out WSL2, which is very fast and comparable to docker. WSL2 should come out in April/May but you can get it now if you upgrade Windows to a pre-release version (see Windows Insiders).

As for ANTs, it is also much changed since 2016. The best would be to follow the instructions on the main ANTs page. I think currently the scripts are automatically installed in the bin folder, so no need to copy them anymore.

[ntustison]

Thanks @dorianps . So would you recommend we eliminate that page describing the Windows-specific install?

[dorianps]

I would not delete that Wiki yet. We can already address point 1 raised above, but I don't seem to have edit access for some reason. Yet, it is understood that Windows should be updated at any point in time.

Point 2 is a very specific scenario, Acronis is not installed on many computers. There can be other specific scenarios as well, which we can't address (I literally had an issue with WSL2 an hour ago not being able to access internet, and it was due to the VPN on Windows).

Point 3 is a matter of crossing away all the instructions and pointing people to the ANTs official installation instructions.

What we can do in a couple of months, though, is add another page with instructions for WSL2, and a big header on the existing page to point to the new, better, solution.

[dorianps]

Btw, even Rstudio is now at a newer version, which does not work at all in WSL. It works on WSL2 though.

[ntustison]

Sounds good. Thanks @dorianps

[s-j-choi]

I wonder if ANTsRNet works also. If so, it would be fantastic.