How to run FreeSurfer on Windows with WSL2 | GB Negrini

[utterances-bot]

How to run FreeSurfer on Windows with WSL2 | GB Negrini

Freesurfer is available only for the Linux and Mac OS X operating systems. You can run FreeSurfer in Windows using a virtual machine, but that can slow down the processing a little. One alternative is to use Windows Subsystem for Linux. Here, I'll show you how to do it!

https://gbnegrini.com/post/how-to-run-freesurfer-windows-wsl/

[CS-Rorita]

Thank you for this content provided

I followed the installation steps in the link however in the last step to view freeview I get this error. Can you direct me to a solution to this problem?
"Segmentation fault (core dumped)"
Thank you very much

[gbnegrini]

Hi @CS-Rorita!
Could you please try running the commands below just so we can check if FS was completely installed? It should print the help text for freeview and freesurfer.

freeview -h
freesurfer -h

"Segmentation fault (core dumped)" usually hints at a memory access error. I have found some people experiencing this issue with freeview (in Mac, though). I hope this discussion topic can help you!

[ghost]

Hello

I have two issues :

1. I get this message error and I do not understand what is wrong ?

This application failed to start because no Qt platform plugin could be initialized. Reinstalling the application may fix this problem.

Available platform plugins are: eglfs, linuxfb, minimal, minimalegl, offscreen, vnc, wayland-egl, wayland, webgl, xcb.
Aborted

2. I do not know how to access the installed data on my computer. Where does ubuntu WSL install everything ?

Thank you

[CS-Rorita]

Hi Not a definitive judgment, but an advice On windows 10 system, I tried a lot to install freesurfer with WSL, but it didn't work. The solution was much easier and smoother using the virtual machine https://surfer.nmr.mgh.harvard.edu/fswiki/VM_67 Good luck

…

On Sat, Feb 5, 2022, 4:44 AM libetue ***@***.***> wrote: Hello I have two issues : 1. I get this message error and I do not understand what is wrong ? This application failed to start because no Qt platform plugin could be initialized. Reinstalling the application may fix this problem. Available platform plugins are: eglfs, linuxfb, minimal, minimalegl, offscreen, vnc, wayland-egl, wayland, webgl, xcb. Aborted 1. I do not know how to access the installed data on my computer. Where does ubuntu WSL install everything ? Thank you — Reply to this email directly, view it on GitHub <#1 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AQBU5B5K65F5IDQLHVZLAVLUZR6GNANCNFSM5MI4L3XA> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>. You are receiving this because you were mentioned.Message ID: ***@***.***>

[ghost]

Hi Not a definitive judgment, but an advice On windows 10 system, I tried a lot to install freesurfer with WSL, but it didn't work. The solution was much easier and smoother using the virtual machine https://surfer.nmr.mgh.harvard.edu/fswiki/VM_67 Good luck
…
On Sat, Feb 5, 2022, 4:44 AM libetue @.> wrote: Hello I have two issues : 1. I get this message error and I do not understand what is wrong ? This application failed to start because no Qt platform plugin could be initialized. Reinstalling the application may fix this problem. Available platform plugins are: eglfs, linuxfb, minimal, minimalegl, offscreen, vnc, wayland-egl, wayland, webgl, xcb. Aborted 1. I do not know how to access the installed data on my computer. Where does ubuntu WSL install everything ? Thank you — Reply to this email directly, view it on GitHub <#1 (comment)>, or unsubscribe https://github.com/notifications/unsubscribe-auth/AQBU5B5K65F5IDQLHVZLAVLUZR6GNANCNFSM5MI4L3XA . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub. You are receiving this because you were mentioned.Message ID: @.>

Thank for your advise. I wait a bit if anyone could help with WSL and windows 10, so frustrating to do 3 hours of installation and be blocked at the end !

[gbnegrini]

Hi @libetue!
Could you provide more details? This error occurred while installing WSL, Xserver, or FreeSurfer? If you are already inside Ubuntu WSL, try running sudo apt-get install qt5-default and then repeat the step that caused this error.
To access your computer data, you have to navigate from within Ubuntu WSL using bash. Your drives should be available in the /mnt/ folder.

As @CS-Rorita mentioned, using a VM can be more straightforward for some people. However, when using a full VM you can end up wasting precious resources, especially considering FreeSurfer's intensive use of memory and CPU.

[andyhagen11]

Hi gbnegrini,

I get al the way through the installation and everything seems to work excpet when I try the command freeview I get this error:

QXcbConnection: Could not connect to display :0
Could not connect to any X display.

I have tried the solution of adding my IP to DISPLAY as outlined in the wiki instructions but I continue to get the same error. Any suggestions?

Thanks so much!

Andy

[gbnegrini]

Hi @andyhagen11!
Sorry, I can't reproduce this issue in my machine. Adding the IP usually worked for me.
Maybe the solutions in these two threads (unrelated to FreeSurfer, but issue seems the same) can help you:

• WSL mrview, could not connect to any X display
• WSL 2 Error: Can't open display: localhost:0.0

[andyhagen11]

The first link worked! I used Nicks solution and restarted my WSL and freeview finally pulled up!

[marmara228]

Thank you for this great article. I managed to load a few subjects properly into freeview. However, for most it says

QXcbConnection: XCB error: 170 (Unknown), sequence: 174, resource id: 90, major code: 146 (Unknown), minor code: 20
QXcbConnection: XCB error: 170 (Unknown), sequence: 174, resource id: 90, major code: 146 (Unknown), minor code: 20

And then there is an endless number of

error: freadFloat: fread failed

Ultimately, freeview freezes and gets shut down.

Is this an Xming problem? What puzzles me the most, is that it seems to work for some subjects, but it doesn't for others.

Thank you!

[SimonaNedelcheva]

Hi gbnegrini,

I have installed FreeSurfer on Ubuntu22 in wsl in Windows 11, but after it starts and I load the files, nothing shows up. Do you have any advice how to troubleshoot the issue?

Thank you!

https://ibb.co/nRT8QzD - here is a link with the issue