Comments for Imaging and a little bit of OSS

Comment on VNC server setup for Ubuntu 10.04 (Lucid Lynx) by slash_boot

slash_boot — Wed, 25 Jan 2012 23:51:07 +0000

Hi Anand:

I have encountered similar problems when the network speeds have been painfully slow. If your server or client are using upload speeds less than 512 kbps, you can get the unresponsive gray screen.

Comment on VNC server setup for Ubuntu 11.04 (Natty Narwhal) by slash_boot

slash_boot — Wed, 25 Jan 2012 23:47:12 +0000

Yes. One important step would be to make sure you always shutdown with a restart option if you want to have the servers running again. Always use:

shutdown -r 0

Comment on VNC server setup for Ubuntu 11.04 (Natty Narwhal) by Buddy

Buddy — Sun, 22 Jan 2012 13:33:06 +0000

Will this allow me to run a headless server?

Comment on VNC server setup for Ubuntu 10.04 (Lucid Lynx) by Anand

Anand — Tue, 10 Jan 2012 00:21:10 +0000

Thanks for the tips. I started a VNC server with you xstartup and I can connect to it with the gnome session. Although the desktop background is all grey without any icons. It doesn’t respond to right-button click either. I have unset “SESSION_MANAGER” and “DBUS_SESSION_BUS_ADDRESS” to no avail. Note that the default gnome terminals which were started via xstartup work fine (even with multiple tabs).

Comment on VNC server setup for Ubuntu 11.04 (Natty Narwhal) by slash_boot

slash_boot — Thu, 05 Jan 2012 19:43:31 +0000

Jagan: If you want to connect to the Ubuntu machine using a macbook, you need to launch the vnc session on your macbook. The VNC client for OSX is Chicken of the VNC.

Fire up the terminal and connect to your Ubuntu machine using ssh like you did.
You then need to start a vnc session. You’ll do that by typing:

vncserver :3 -geometry 1200×800

I am assuming that you have already made changes to the xstartup file in .vnc folder.

Once vncserver session has been started on Ubuntu side, you need to launch Chicken of the VNC on your mac.

In there, you connect to localhost :3, give your password, and you should be in.

Hope this helps.

Comment on VNC server setup for Ubuntu 11.04 (Natty Narwhal) by Jagan Reddy

Jagan Reddy — Thu, 05 Jan 2012 12:18:22 +0000

Hi,
My goal is to allow some authorized people to connect to home PC for training purposes. I need a VNC environment so that they can use when required X-windows for practice lessons.

As for my testing: Via my own local network I am able to do desktop sharing and controlling from my macbook. Here again, it requires the user already connected to remote desktop. But I need the person to connect afresh. I have already setup secure shell and I can do ssh via port 22.

I want to follow your approach, that I should initiate a ssh and then start vncviewer on the remote machine to get the desktop. This way the user is in control to start X display only when required and it iss secure as well. But I am not able to achieve this. Please see my attempts from my macbook pro.

Any help is highly appreciated.

OS-X-Leopard:~ admin$ ssh -L 5903:192.168.2.6:5903 bab4l8m@192.168.2.6
bab4l8m@192.168.2.6′s password:
Welcome to Ubuntu 11.04 (GNU/Linux 2.6.38-13-generic x86_64)

* Documentation: https://help.ubuntu.com/

19 packages can be updated.
14 updates are security updates.

New release ‘oneiric’ available.
Run ‘do-release-upgrade’ to upgrade to it.

Last login: Thu Jan 5 07:09:34 2012 from os-x-leopard.local
bab4l8m@ubuntu:~$ export DISPLAY=os-x-leopard.local
bab4l8m@ubuntu:~$ vncviewer localhost:3
Error: Can’t open display: os-x-leopard.local
bab4l8m@ubuntu:~$ export DISPLAY=localhost:3
bab4l8m@ubuntu:~$ vncviewer localhost:3
No protocol specified
No protocol specified
No protocol specified
No protocol specified
Error: Can’t open display: localhost:3
bab4l8m@ubuntu:~$ export DISPLAY=0:3
bab4l8m@ubuntu:~$ vncviewer localhost:3
No protocol specified
No protocol specified
No protocol specified
No protocol specified
Error: Can’t open display: 0:3
bab4l8m@ubuntu:~$

Comment on VNC server setup for Ubuntu 10.04 (Lucid Lynx) by slash_boot

slash_boot — Thu, 29 Dec 2011 15:18:34 +0000

I used to get a grey screen on rare occasions, but in most circumstances it worked fine.

The small hack with “unset DBUS_SESSION_BUS_ADDRESS” is quite useful in cases when you can’t make the grey screen go away.

Thanks for the helpful suggestion.

Comment on VNC server setup for Ubuntu 10.04 (Lucid Lynx) by Krishnamohan Bandi

Krishnamohan Bandi — Thu, 29 Dec 2011 10:57:06 +0000

The above xstartup configuration did not work for me and I was seeing a grey screen with the following error “could not acquire name on session bus”.

To fix this, I have added the following line just after the # exec /etc/X11/xinit/xinitrc

unset DBUS_SESSION_BUS_ADDRESS

and I could get a full blown desktop now without any issues

Hope this helps

Comment on Converting .hdr/.img files to .nii by slash_boot

slash_boot — Thu, 15 Sep 2011 13:27:00 +0000

You can use the .img file as the freesurfer input. Infact you can even get away without specifying the extensions.

Comment on VNC server setup for Ubuntu 11.04 (Natty Narwhal) by joe

joe — Sun, 04 Sep 2011 19:58:49 +0000

if I change “gnome-session &” to “xfce-session &” it’ll still work, right? The computer I’m running as a server is a salvaged Pentium 3 with only 384MB of RAM running Xubuntu with XFCE sessions to save RAM, so it’s important that I at least try to use XFCE instead of the heavier Gnome, so I don’t unnecessarily bog down my machine

Comment on Converting .hdr/.img files to .nii by tony

tony — Thu, 01 Sep 2011 00:58:53 +0000

If I want to use nifti hdr/img files as input, could you please tell me which of the following is right?

recon-all –i $FREESURFER_HOME/subjects/subj1/file.hdr –subject subj1 –all

recon-all –i $FREESURFER_HOME/subjects/subj1/file.img –subject subj1 –all

Comment on Bounding box for wfu-pickatlas masks by slash_boot

slash_boot — Wed, 31 Aug 2011 17:17:22 +0000

@joyce
Hi Joyce,

What I did was I created a binary mask of the template brain, and then overlaid the binary mask obtained by applying my transformation. Then I overlaid them with some transparency to see if they were matching up or not. I kept playing with the numbers until they had a match. I tried it the empirical way rather than develop a sequencial logic for it

Comment on VNC server setup for Ubuntu 11.04 (Natty Narwhal) by Sz

Sz — Fri, 26 Aug 2011 07:10:04 +0000

@הורדות Start Applications/Accessories/Terminal from the "start menu".

Comment on VNC server setup for Ubuntu 11.04 (Natty Narwhal) by dave

dave — Sun, 21 Aug 2011 21:52:42 +0000

why is it so hard? On windows you download tightvnc .. install.. boom it works.

I don’t understand all this

Comment on Moebius (Möbius) strip in art and culture by Julie

Julie — Sun, 07 Aug 2011 18:27:29 +0000

Thank you so much for this very cool post! I’m researching Jose de Rivera’s “Infinity” sculpture for my blog. Very cool to see the various representations of the mobius strip in art, playgrounds and most importantly, CAKE!!