Update Win10 WSL installation information (Move from Wiki to RTD, update recommendations for FSLEyes/WSL1) #2952
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joshuacwnewton
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| #. Install FSL | ||
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| FSL contains fsleyes which is the default viewer for NIfTI image in SCT. |
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is FSLeyes still part of the whole FSL package? and by the way: now that FSLeyes is a standalone package, shouldn't we recommend instead of install FSLeyes (much lighter)?
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Ah, good observation! From the FslWiki:
FSLeyes can either be installed as part of FSL, installed into a conda environment, or installed into a Python environment (for advanced users).
Since we already use a conda environment for the SCT install, this does indeed seem like a much simpler way of going about it.
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@lrouhier @gaspardcereza can you confirm installation of FSLeyes with conda within WSL is seamless?
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I didn't try to run FSLeyes yet (WSL2 is not really mean to run GUIs...). I think there's a way to do so but the few tutorials I saw were very advanced stuff (at least to me). I can only say that installing FSL following their instructions went well (even if it required ~1h on my end) and that prelude is working. Maybe @lrouhier managed to launch FSL eyes on his end (if so that would be of interest to me because I don't really have a good nifti viewer).
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Last time installing with conda wasn't working really well because I had some dependency issues.. I can try again if need be.
Fsleyes works really well once you installed (At least it is still working on my end). I am still using WSL 1 however (an old discussion about the why: #2747)
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Thank you for your feedback @mariehbourget! If you found an easy solution to install FSLeyes within WSL, then we should definitely replace the current approach with your suggestion. Do you mind modifying the current SOP with your approach? here. Thank you so much!
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That is interesting as the newest conda version might work great (I tested it back in March). It might have been a wxpython install as mentionned in your link. That's why I went with the fsl install.
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I don't have permissions to modify directly in this PR, should I use a fork?
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@alexfoias or @joshuacwnewton can you add Marie Helene please? thanks
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@jcohenadad I added @mariehbourget on the repo with WR.
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@mariehbourget thank you so much! 🎉 @gaspardcereza I don't see any of your investigations on this thread, so I'm copy/pasting what you wrote in your our internal meeting:
Could you please try installing FSLeyes based on @mariehbourget instructions. If you experience any issue, please report it immediately (don,t try to fix it on your end, because if you're having the issue, it means that anyone on the planet could have the same issue-- the goal here is to reproduce and document-- then we can fix if necessary). @lrouhier could you please also try on your end thanks! |
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Sorry @jcohenadad I was still trying to make it work. Note that it will require to deactivate you're firewalls under Public network settings (might be risky...). |
so i gather WSL2 is more complicated than WSL1? Can anyone confirm? if this is confirmed, then we'll support WSL1 (not 2) |
Not necessarily more complicated once you know what you're dealing with (but I admit that the risk related to turning off the firewall might be a big drawback...). |
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OK, we need to put ourselves in the shoes of our user base: most of those using Windows are not computer savvy. So, more than "what we want to do", the question is: "what is less complicated for our users".
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In that case I would definitely go with |
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(My apologies for being absent in the discussion. I have not used WSL personally and so I don't have much to add, but I really appreciate everyone's contributions to this PR!) |
joshuacwnewton
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@gaspardcereza @lrouhier can you please try to install FSLeyes according to @mariehbourget instructions? |
I followed the conda installation instructions and it worked. Contrary to @mariehbourget I did it on |
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thank you for the feedback @gaspardcereza ! |
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Not yet I am trying it now. I have but one concern: will it work in another conda-env (e.g., if I have an ivadomed-env and a "side-project" env will it work in both ? or do I need it to install it twice? (I will check that as well but as anyone tried ?) |
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The conda install works fine ! (apologies for the delay I needed to figure out how to avoid using the already installed version). It does not seem to work in multiple env however, which means that you need to have to reinstall it every time you change env (if you need it or change env every time you want to use it) |
jcohenadad
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@joshuacwnewton I think this PR is good to go. Can you please update with master branch, and I'll review. Thanks! |
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Sure thing, @jcohenadad. Thank you again for your additions (ditto for other team members). |
Related Issues/PRs
Fixes #2950.
Fixes #2747.
Description
Currently, we link to the developer Wiki from RTD for WSL installation steps. But, if information is meant for our users, then we should be putting it directly on RTD instead. (The developer Wiki updates frequently, so broken links are an inevitable issue.)
This PR moves the page from the Wiki to RTD as a long-term fix. (The information is a verbatim copy of https://github.com/neuropoly/spinalcordtoolbox/wiki/Misc:-SCT-on-Windows-10:-Installation-instruction-for-SCT-on-Windows-subsytem-for-linux with some formatting tweaks.)
At the same time, this is a good opportunity to address our recommendations regarding:
➤ Rendered doc: https://spinalcordtoolbox.com/en/jn-2950-move-win10-installation-info/