Re: [Freesurfer] Freeview does not display image

2022-10-04 Thread fsbuild 
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With regards to WSL, there is probably something preventing the X-server from 
correctly displaying graphics. Instead of running freeview you could try 
a simpler command to test X-window graphics. One command is “xeyes” which 
you can look for and try running in the Ubuntu terminal window by typing,
$ which xeyes/usr/bin/xeyes$ xeyes

If a window does not open displaying something like a pair of eyes then the 
X-windows server is not working correctly.
There are 2 different versions of WSL, i.e. version 1 and 2. The setup 
for the X-server can be different depending upon which version you are running. 
You can try to find the version by typing the following command at the 
Windows command prompt. The number under VERSION should be the version of 
WSL you are running.
C:\Users\sam wsl -l -v NAME   STATE  
 VERSION* Ubuntu  Running 2  — means you are 
running WSL version 2
Down the bottom of this page are some instructions for setting up the Ubuntu 
shell environment for 
WSL,https://secure-web.cisco.com/1iKRwZpgN3zDuJlFspVtdJXrVV6ghp3nndYFCB19UUv0S_ZDUd_LyQflWBXOV2Ec9k9oguJAS9Wfh1JxC7S9wxuFfXpCUILrH9-cexgQn92l463Ch5Gr2lQn-XHFXD9dE6p6QUlj5oaIRqS2lWhFg--xR_sftxNpLbn21muMopMfiIkPPlS4f0pw2UGvA7-UFydNYWfu1-QRwV7b39O4-J2Qw2bkZ61RTVmdM9kLDq72IwZhIGJ7lH-lBHNqLjTtqdSgXCAZ8aBjKzGRyvB5ZCivTW5z6NzirccbCJLj-IJDFJqQAQ5JbMxd6E9ts3Wwh/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFS7_wsl_ubuntu
If you have not already run these 2 commands, then I would do so,
$echo "export XDG_RUNTIME_DIR=$HOME/.xdg"  
$HOME/.bashrc$echo "export DISPLAY=:0"  $HOME/.bashrc
Then exit your Ubuntu terminal window and start a new one so those settings 
take effect. Then try running the “xeyes” command again to see if it 
works. If it does work, then try running freeview again.

With regards to trying to use the VM, if uncompressing the image is crashing 
then you may be running out of disk space. You should check there is at 
least 40 Gig of free disk space in the location where you are trying to open 
the zip file.
- R.

On Oct 4, 2022, at 03:11, Justina Lee justinale...@gmail.com 
wrote:External Email - Use 
CautionHello R,Sorry I wasn’t 
so clear on my part. I am using ubuntu linux on the windows subsystem linux 
(WSL). I followed these instructions atMailScanner has detected a possible 
fraud attempt from "secure-web.cisco.com" claiming to 
behttps://surfer.nmr.mgh.harvard.edu/fswiki/FS7_wslto download the WSL, 
X-server, and the freesurfer.Is it still possible to fix the problem here 
internally or should I follow the instructions sent from the link previously to 
download Virtual Box and run freesurfer in this way? I have been trying to open 
the zip file Ubuntu compressed image but it seems to keep crashing as I load 
it. I will keep trying if the first way aforementioned is not 
possible.Thank you and hope this has become alittle 
clearer.Sincerely,JustinaOn Mon, Oct 3, 2022 at 8:35 PM fsbuild 
fsbu...@contbay.com 
wrote:External Email - Use 
CautionHello Justina,We need to 
know what your setup is on Windows for running Linux in order to help with 
running freeview. It reads like you are not using VirtualBox to run the 
Linux Ubuntu OS,I do not have VirtualBox installed So it’s not clear 
to me how you are currently running Ubuntu Linux on your Windows machine in 
order to run freeview or other freesurfer commands. Are you running 
Ubuntu linux with the Windows Subsystem for Linux (WSL)? Maybe you are 
connecting remotely to a linux machine via VNC or the like from your Windows 
machine ?If you don’t mind running freesurfer 7..2.0 (instead of the 
newest 7.3.2 release), there is a smaller version of the VM to download 
fromMailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to 
behttps://secure-web.cisco.com/1pDNeyyXnoU0PIQ7-rMdLh5tom581Kv0B3Mn8Rs7MprnKn-uT1AsFMEXN1z6iQArgATy5KV7HFg2cGHq78q-g3VX9AinZ7V0Bxa4EIXQiO3UdAQDoa00Zs7HZRkZ9XkzwKxYLtNBM0S4mZV54KcjnKyyDKFDQgBLezEsQS2ZD50o1zs_hbB9fcTqsw3suSoDAwWsZ3fcar4GR8SUP9KKhs1Kqpmd0xOsvsFUxzls5Y-u3lryPzutEkuO0Vcz4-4FjqP-8u0Rzp5fygoIJ0Dmk-Wrk1VE-QvdMCIMM67fFazyTCcyyYB3iMB4zcygRcD8Y/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FVM_67%26nbsp;
 with setup instructions under that link. But you would still need 
to download and install VirtualBox on your Windows machine and then download 
and install the Freesurfer Software.- R.On Oct 3, 2022, at 09:35, Justina Lee 
justinale...@gmail.com 
wrote:External Email - Use 
CautionTo whom that can provide 
any insight,I am currently using Ubuntu on windows to open freeview to show 
some data. My issue at hand is that freeview does not show any images, despite 
changing the window levels (contrast and brightness). Using the command 
freeview -v works, and I am able to run it smoothly.. When I try to open an mgz 
file, it runs fine, but I am unable to see anything.I do not have 
VirtualBox installed and tried to take this advice from previous but I ran

Re: [Freesurfer] Freeview does not display image

2022-10-04 Thread Justina Lee 
External Email - Use Caution

Hello R,

Sorry I wasn’t so clear on my part. I am using ubuntu linux on the windows
subsystem linux (WSL). I followed these instructions at
https://secure-web.cisco.com/1p8Cin-EJEpeRx1cZi8s231xYYwEa73Ljn6cCDVMGOudNzx-clBR6sZUCDMeSmSC85H7RtRtyEHdxO6j7DqYMFXEEle0HWR03qo71o_mjxHnvDmseEhe6KVuhPF3a9EM59Nka9FTcsYt1gVTr_HvvTbhHKoEmZ7oV9i3KeY7rIQGCvfTf9bQme8kx7TWvoWnm5VKZSHSvq48kfOuo2C6lIY_MAf92M9I1KgyaWazv2MhWZWGikJgOV2nw4QC69vFLjpH3ctxn4UIMJLn7bY8klGzGH6U_lmVmi2m4Q1eV11REMBdDeMc-XzcjqJYUvXvg-Th-bs5WT8twMoaIT9Yw2A/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFS7_wsl
 to download the WSL,
X-server, and the freesurfer.

 Is it still possible to fix the problem here internally or should I follow
the instructions sent from the link previously to download Virtual Box and
run freesurfer in this way? I have been trying to open the zip file Ubuntu
compressed image but it seems to keep crashing as I load it. I will keep
trying if the first way aforementioned is not possible.

Thank you and hope this has become alittle clearer.

Sincerely,
Justina


On Mon, Oct 3, 2022 at 8:35 PM fsbuild  wrote:

> External Email - Use Caution
>
>
> Hello Justina,
>
> We need to know what your setup is on Windows for running Linux in order
> to help with running freeview.  It reads like you are not using VirtualBox
> to run the Linux Ubuntu OS,
>
>  I do not have VirtualBox installed 
>
>
> So it’s not clear to me how you are currently running Ubuntu Linux on your
> Windows machine in order to run freeview or other freesurfer commands.  Are
> you running Ubuntu linux with the Windows Subsystem for Linux (WSL)?  Maybe
> you are connecting remotely to a linux machine via VNC or the like from
> your Windows machine ?
>
> If you don’t mind running freesurfer 7..2.0 (instead of the newest 7.3.2
> release), there is a smaller version of the VM to download from *MailScanner
> has detected a possible fraud attempt from "secure-web.cisco.com" claiming
> to be* 
> https://secure-web.cisco.com/1paaB_cgPVQ7btidlPguZcJsmtliH8F8hjmenNiwMMKj6psPWB7PbCzz88mGy5PUxJ4_RYJHEnEgzOrASI38A31sVxjVmfxfUSo9L9FoxfPo2Av_MQ6ngrK-iKSLjkEbUggeuaoXemH1U78dhZuZM2A4CAL_oLkIUIFvyvWpHvLbzriR6DhJXh-EgzZuO82YSUqI3pVfRIQ1T5aFoSn8Y-hAXTf-f5_IS6TEMtEMFUpxxu98IMgpvc-KXmk-Wzm8NyBtiXkhuju9KJHm65VHaV7mHETaWMKcy3_JUxpNDLu3RFKJJlU9p2uLb6LOYUMWA_NvQjUVmIQKA27QoJS_YzA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FVM_67
> 
> with setup instructions under that link.   But you would still need to
> download and install VirtualBox on your Windows machine and then download
> and install the Freesurfer Software.
>
> - R.
>
> On Oct 3, 2022, at 09:35, Justina Lee  wrote:
>
> External Email - Use Caution
>
>
> To whom that can provide any insight,
>
> I am currently using Ubuntu on windows to open freeview to show some data.
> My issue at hand is that freeview does not show any images, despite
> changing the window levels (contrast and brightness). Using the command
> freeview -v works, and I am able to run it smoothly. When I try to open an
> mgz file, it runs fine, but I am unable to see anything.
>
>  I do not have VirtualBox installed and tried to take this advice from
> previous but I ran across the problem of downloading the course Virtual
> Machine. I do think that I do not need to download the VirtualBox and can
> continue using Ubuntu on Windows.
>
> What could be the issue with this? Should I be downloading the Virtual
> machine to run Freeview?
>
> Thank you so much for your time and I hope that my issue is not too big of
> a problem to solve.
>
> Sincerely,
> Justina
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://secure-web.cisco.com/1XBB9mVISZMBi-_VRhIEm62UucxuNsrx0F-92EzExHgsYK_1D4N3Dg9If49qUFuo11Cdn9sLRgmZ46jVvgxo6jP2o7lsQu7bhK6-Kmis1M884MqF9f3CYVJizJM92RHyc69rt33Kug3_Ex5lc4S1Lwy1cldPGDcO_12gxyVoS4xQ-hQmsLuMF7olr9OaTaR26WjwJWv4kYz5JakPSmgFQy7NhpuCBXaLebRmKHa1vfKdNlLrIUghVJSKuVtEfHAnLhlbZo47AY4-dhZ8SMj_Rj1aC0lyrwn1GLDDeTFoQpIZAmkO-44ho_t6mBBm3YoPQ8xfugoEGeHNuUuP6rwOAXw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
>

Re: [Freesurfer] Freeview does not display image

2022-10-03 Thread fsbuild 
External Email - Use Caution

Hello Justina,
We need to know what your setup is on Windows for running Linux in order to 
help with running freeview. It reads like you are not using VirtualBox to 
run the Linux Ubuntu OS,
I do not have VirtualBox installed ...
So it’s not clear to me how you are currently running Ubuntu Linux on your 
Windows machine in order to run freeview or other freesurfer commands. 
Are you running Ubuntu linux with the Windows Subsystem for Linux (WSL)? 
Maybe you are connecting remotely to a linux machine via VNC or the like 
from your Windows machine ? 

If you don’t mind running freesurfer 7.2.0 (instead of the newest 7.3.2 
release), there is a smaller version of the VM to download 
fromhttps://secure-web.cisco.com/1YWO9PWAWb2dUg45HhJ8-Uf5BVRKini-Plt5R0ZzrEI56U73eIIqsvtOabP978uAZGbMguO6zYQXj2qmsPJoTTh7XQB1Lfjd_GAeMNqapxT92fvVsg3gtB6o_K_TGqYKm52s7ec5nvDnfb305SkZY5SoJ35m3yTBjgDCFLbXXPxXkheXpgZ_WR53HyCMzoKJTA3AY00j28VO95fGeTZ7uWfvDvLe8v_Og6PX24DOCLRBZTaLzr9cWE2lBsMd6N0avVNQetV_emJ79GF0lrvGJSxK2kaC87ydb09ZWR2FVyUPprRlBNZm7zdFvyF1pcMsa/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FVM_67%26nbsp;
 with setup instructions under that link. But you would still need 
to download and install VirtualBox on your Windows machine and then download 
and install the Freesurfer Software.
- R.

On Oct 3, 2022, at 09:35, Justina Lee justinale...@gmail.com 
wrote:External Email - Use 
CautionTo whom that can provide 
any insight,I am currently using Ubuntu on windows to open freeview to show 
some data. My issue at hand is that freeview does not show any images, despite 
changing the window levels (contrast and brightness). Using the command 
freeview -v works, and I am able to run it smoothly. When I try to open an mgz 
file, it runs fine, but I am unable to see anything.I do not have 
VirtualBox installed and tried to take this advice from previous but I ran 
across the problem of downloading the course Virtual Machine. I do think that I 
do not need to download the VirtualBox and can continue using Ubuntu on 
Windows.What could be the issue with this? Should I be downloading the Virtual 
machine to run Freeview?Thank you so much for your time and I hope that my 
issue is not too big of a problem to 
solve.Sincerely,Justina___Freesurfer
 mailing 
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
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[Freesurfer] Freeview does not display image

2022-10-03 Thread Justina Lee 
External Email - Use Caution

To whom that can provide any insight,

I am currently using Ubuntu on windows to open freeview to show some data.
My issue at hand is that freeview does not show any images, despite
changing the window levels (contrast and brightness). Using the command
freeview -v works, and I am able to run it smoothly. When I try to open an
mgz file, it runs fine, but I am unable to see anything.

 I do not have VirtualBox installed and tried to take this advice from
previous but I ran across the problem of downloading the course Virtual
Machine. I do think that I do not need to download the VirtualBox and can
continue using Ubuntu on Windows.

What could be the issue with this? Should I be downloading the Virtual
machine to run Freeview?

Thank you so much for your time and I hope that my issue is not too big of
a problem to solve.

Sincerely,
Justina
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail.