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| == Windows Subsystem for Linux (WSL) Install & Setup == | == Windows Subsystem for Linux Install & Setup == |
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| The Windows Subsystem for Linux (WSL) enables a Unix distribution to run in a "virtualized" environment under Windows OS. Some common linux distributions, e.g., CentOS and Ubuntu, are currently available from the Windows App store for download and use in WSL. The WSL terminal window looks much like what you would see in a virtual machine running on Windows, but includes access to your home directory on the Windows side via NTFS. So if your Windows username was "bill" then from the WSL terminal window you can see bill's download folder as /mnt/c/Users/bill/Downloads. The username you pick to run in the WSL linux environment has sudo/admin privileges and need not be the same as your username, e.g., "bill" on the Windows side. | The Windows Subsystem for Linux (WSL) enables a Linux distribution to run in a "virtualized" environment under Windows OS without utilizing a VM host application such as VirtualBox. Common Linux distributions such as Ubuntu, CentOS and Fedora are available from the Windows App store for download and use in WSL; some like Ubuntu Linux are free. |
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| To setup WSL, the PowerShell must first be used to enable WSL. Then a linux distribution needs to be installed in the WSL environment. Subsequently additional software may need to be installed to run on the Windows side and/or in the Linux distribution running under WSL depending upon what you want to run under Linux. | WSL is primarily intended to give Windows developers a way to test their applications with Linux based services but not reproduce a complete X-Windows based Linux GUI/desktop environment such as Gnome or KDE (which you see on your linux workstation). For Linux running inside WSL on windows, the desktop and terminal window will look like what you see for the default desktop and terminal settings for that particular linux distribution. |
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| In order to run X-windows based graphics programs in WSL, an X server needs to be installed on the Windows side (since the Windows OS is driving the graphics hardware and there is no native X server in Windows). Accordingly, the WSL linux environment needs to be set/tested to run X based graphics in WSL with the X server running under Windows (instead of under Linux). | WSL includes access to your home directory on the Windows side via NTFS. So if your Windows username was "bill" then from the WSL linux terminal window you can see bill's download folder as the linux path /mnt/c/Users/bill/Downloads in your default shell, e.g., bash, tcsh. This mount point is a convenient way to share files between your Windows home directory and Linux running in WSL. The username you pick when you setup the WSL environment has sudo/admin privileges in the linux environment and need not be the same as your username on the Windows side. |
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| The instructions below will show how to setup the WSL environment (under Windows 10) with a linux distribution in order to run Freeview (using a 3rd party X server running under Windows 10). | Steps for Setting Up WSL to run freesurfer: i. Enable WSL on the windows machine + i. Install WSL on the windows machine + i. Download/install a linux distribution into WSL ++ i. Download/install an X-server on the windows machine +++ i. From a terminal window running inside the linux distribution, download and install freesurfer ++++ |
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| WSL is still under development and changing with each release. WSL was not (at least initially) intended to reproduce a fully functional X based Linux GUI/desktop environment such as Gnome or KDE; it was primarily intended to give Windows developers a way to test their applications with Linux based services. That being said, WSL can be setup to display graphics with varying degrees of success for different Linux distirbutions. | ''+ These steps may be combined into a single command for WSL version 2; see the link to the MS documentation. Your windows machine will be updated and re-booted.'' |
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| === Enable WSL from PowerShell === | ''++ For a linux distribution we recommend Ubuntu 22.'' |
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| Bring up a PowerShell window, | ''+++ An example of installing the Xming X-server is listed below. These steps may vary depending upon the network settings on the Windows machine. Please check that you have given Xming permission to connect through the Firewall using Windows Defender.'' |
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| {{attachment:WSL_setup_2.png}} | ''++++ We recommend using the freesurfer installer packages, i.e., the *.deb file for Ubuntu linux.'' |
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| Run the "enable optional feature" command. You should be able to cut and paste the command from the MS documentation, [[https://docs.microsoft.com/en-us/windows/wsl/install-on-server|WSL_install]] |
=== Setup and Install WSL version 2 === |
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| {{attachment:WSL_setup_3.png}} | As of this writing, WSL version 2 is available. If no version of WSL is currently installed on your Windows machine, then follow the MS documentation to install WSL version 2, |
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| [[https://surfer.nmr.mgh.harvard.edu/fswiki/FS7_wsl_ubuntu|Freesurfer WSL2]] | |
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| === Install a Windows X Server and Fonts === | Previous instructions for the manual setup and install of WSL version 1 (skip if using WSL version 2), [[https://surfer.nmr.mgh.harvard.edu/fswiki/FSL_wsl_version_1|Enable WSL version 1 from PowerShell]] |
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| Use of the Xming X server will be shown in the examples below. Please note there are other X-servers available for Windows. | === Install and Run an X-Server in Windows === |
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| Download a copy of the X-server and the corresponding X-fonts from the (Xming) web site, [[http://www.straightrunning.com/XmingNotes|Xming]]. The paid 7.x version is preferable to the free 6.X version, however the 7.x version is not free. The examples below will show using the 6.x version, i.e., the 6.x version of the X-server and the 7.x version of the fonts have been downloaded into the Downloads folder in the screen shot below. | [[https://surfer.nmr.mgh.harvard.edu/fswiki/FSL_wsl_xming|Install X-server (Xming)]] |
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| {{attachment:xming_and_fonts.png}} | === Install and Run a Linux OS in WSL - Install and Run Freesurfer in Linux === |
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| Example OS's running under WSL and installing freesurfer on them: | |
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| First install the Xming server. You can accept the defaults presented by the installer menus including allowing it to install "Xming" and 'Xlaunch" shortcuts on the desktop. | [[https://surfer.nmr.mgh.harvard.edu/fswiki/FS7_wsl_ubuntu|WSL_Ubuntu_freesurfer]] |
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| [[https://surfer.nmr.mgh.harvard.edu/fswiki/FS7_wsl_centos|WSL_CentOS_freesurfer]] | |
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| {{attachment:xming_install_1.png}} | You can choose a freesurfer distribution to install from the following links: |
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| {{attachment:xming_install_2.png}} | Freesurfer releases have gone through testing for recon-all and freeview. We recommend installing the latest release unless you have some work in progress that requires installing an older release. [[https://surfer.nmr.mgh.harvard.edu/fswiki/rel7downloads|Freesurfer 7.X.X current release installers]] |
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| {{attachment:xming_install_3.png}} {{attachment:xming_install_4.png}} {{attachment:xming_install_5.png}} {{attachment:xming_install_6.png}} You should have both an '''Xming''' and an '''Xlaunch''' icon on your desktop after the successful install of Xming. {{attachment:X_desk_icons.png}} Next install the corresponding X-fonts, {{attachment:install_xfont_1.png}} {{attachment:install_xfont_2.png}} {{attachment:install_xfont_3.png}} {{attachment:install_xfont_4.png}} {{attachment:install_xfont_5.png}} Now double click the '''Xlaunch''' icon and go through the steps below to create and save an X configuration file in the same folder where Xming is installed. {{attachment:xlaunch_2.png}} {{attachment:xlaunch_3.png}} {{attachment:xlaunch_4.png}} {{attachment:xlaunch_6.png}} === Test Launching Xming === Test to see if the Xming server will run by double clicking on its desktop launch icon. You will probably get a message from Windows Defender reporting it has been blocked from running by default. Give Xming permission to run on both local and public networks. {{attachment:xming_run_test_1.png}} Once Xming is running, it should be visible by clicking on the small up arrow like symbol in the lower left hand corner of the Windows 10 desktop. This will reveal "hidden" items that are running and Xming (with the X icon) should be one of them. You can right click on it to exit Xming. {{attachment:xming_run_test_2.png}} === Install and Run a Linux OS in WSL === With both WSL enabled and an X server setup under Windows, you are now ready to install and run a Linux distribution in WSL. [[https://https://surfer.nmr.mgh.harvard.edu/fswiki/FS7_wsl_centos|WSL_CentOS_intsall]] [[https://https://surfer.nmr.mgh.harvard.edu/fswiki/FS7_wsl_ubuntu|WSL_Ubuntu_intsall_TBD]] |
Development stream builds contain ongoing development work and code changes that are the basis for future freesurfer releases. The development stream packages have not gone through the same testing and Q/A for stability as an actual freesurfer release. [[https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/|Freesurfer 7.X.X development stream nightly build installers]] |
Windows Subsystem for Linux Install & Setup
The Windows Subsystem for Linux (WSL) enables a Linux distribution to run in a "virtualized" environment under Windows OS without utilizing a VM host application such as VirtualBox. Common Linux distributions such as Ubuntu, CentOS and Fedora are available from the Windows App store for download and use in WSL; some like Ubuntu Linux are free.
WSL is primarily intended to give Windows developers a way to test their applications with Linux based services but not reproduce a complete X-Windows based Linux GUI/desktop environment such as Gnome or KDE (which you see on your linux workstation). For Linux running inside WSL on windows, the desktop and terminal window will look like what you see for the default desktop and terminal settings for that particular linux distribution.
WSL includes access to your home directory on the Windows side via NTFS. So if your Windows username was "bill" then from the WSL linux terminal window you can see bill's download folder as the linux path /mnt/c/Users/bill/Downloads in your default shell, e.g., bash, tcsh. This mount point is a convenient way to share files between your Windows home directory and Linux running in WSL. The username you pick when you setup the WSL environment has sudo/admin privileges in the linux environment and need not be the same as your username on the Windows side.
Steps for Setting Up WSL to run freesurfer:
- Enable WSL on the windows machine +
- Install WSL on the windows machine +
- Download/install a linux distribution into WSL ++
- Download/install an X-server on the windows machine +++
- From a terminal window running inside the linux distribution, download and install freesurfer ++++
+ These steps may be combined into a single command for WSL version 2; see the link to the MS documentation. Your windows machine will be updated and re-booted.
++ For a linux distribution we recommend Ubuntu 22.
+++ An example of installing the Xming X-server is listed below. These steps may vary depending upon the network settings on the Windows machine. Please check that you have given Xming permission to connect through the Firewall using Windows Defender.
++++ We recommend using the freesurfer installer packages, i.e., the *.deb file for Ubuntu linux.
Setup and Install WSL version 2
As of this writing, WSL version 2 is available. If no version of WSL is currently installed on your Windows machine, then follow the MS documentation to install WSL version 2,
Previous instructions for the manual setup and install of WSL version 1 (skip if using WSL version 2), Enable WSL version 1 from PowerShell
Install and Run an X-Server in Windows
Install and Run a Linux OS in WSL - Install and Run Freesurfer in Linux
Example OS's running under WSL and installing freesurfer on them:
You can choose a freesurfer distribution to install from the following links:
Freesurfer releases have gone through testing for recon-all and freeview. We recommend installing the latest release unless you have some work in progress that requires installing an older release.
Development stream builds contain ongoing development work and code changes that are the basis for future freesurfer releases. The development stream packages have not gone through the same testing and Q/A for stability as an actual freesurfer release.