Can not run FSL after successful UBUNTU installation

Codrin Mironiuc

10/29/23, 7:48 PM

I have just installed FSL on Ubuntu 18.04.05 following all the steps from the FSL tutorial. I never used Ubuntu before, but everything seemed to go fine.

Just to check, even when I run the command python "/mnt/c/Users/<WindowsUserName>/Downloads/fslinstaller.py" with my username it mentions that fsl is already installed.

However, when I try to run fsl, by typing for example 'fsl' in the command line in Ubuntu, it says that the command was not found. Any idea why this may be?

EDIT: https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FslInstallation/Windows

This is the link of the tutorial. I basically did all the steps starting from: wsl --install -d Ubuntu-18.04 and everything worked.

When I got here: Try running the fslmaths, fsl, and fsleyes commands though, it tells me that it can not find the commands.

I have no idea how Ubuntu or Linux work, but I thought that maybe, as I did everything from the root@, and at the last step they say FSL must be installed into the WSL file system - do not try and install FSL into a location in your Windows file system. The safest option is to accept the default location, which is /usr/local/fsl/. , which is also what I did, it may mean that if I simply open Ubuntu and run fsl, it won't work? Maybe I need to get to the WSL file system, set the path there, and then run? I do not think that I understand this part and why it does not work.

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ChanganAuto

10/29/23, 7:50 PM

First question: Why 18.04? Support ends April 2023.

Codrin Mironiuc

10/29/23, 8:20 PM

thanks to both of you! @ChanganAuto I did this version of Ubuntu as this was mentioned in the tutorial. I have now added edits with explanations, also with the link. Thanks so much.

Nmath

10/29/23, 8:28 PM

I don't know much about this software but there are inconsistencies in your own details. For example, you've quoted: *"FSL must be installed into the WSL file system - do not try and install FSL into a location in your Windows file system"* -- but you also tell us *"when I run the command python "/mnt/c/Users/<WindowsUserName>/Downloads/fslinstaller.py" with my username it mentions that fsl is already installed"* -- Well that's exactly where you've just said that it's not supposed to be installed. Could this be your problem? I also fail to see why 18.04 is necessary. It's about to lose support

Codrin Mironiuc

10/29/23, 8:36 PM

Thanks a lot! I am also very confused of where the installation actually took place. As I mentioned, I follow all the steps from the link: first they say '6. Run the fslinstaller.py script in the Ubuntu shell with this command. Replace <WindowsUserName> with your Windows account username: " so I did this, and then they also say right below this: 'FSL must be installed into the WSL file system - do not try and install FSL into a location in your Windows file system. The safest option is to accept the default location, which is /usr/local/fsl/. ' So then, where exactly should I go to run this?

Nmath

10/29/23, 8:59 PM

I would guess that you can run it anywhere that isn't under `/mnt/x` where `x` is a Windows "drive"

Codrin Mironiuc

10/29/23, 9:12 PM

I ran it in normal @root path that is by default and it does not work, and I think this is not under a Windows drive. Thanks for the help!

Nmath

10/29/23, 9:24 PM

I don't know what you mean by @root path because that's not a path in Ubuntu or Windows

Codrin Mironiuc

10/30/23, 7:59 AM

Thanks! What I mean is the root user, so whatever I am doing in Ubuntu without being logged in to a user

Elon Musk

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EN: Can not run FSL after successful UBUNTU installation

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