Comments for Imaging and a little bit of OSS

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

slash_boot — Wed, 09 May 2012 12:39:28 +0000

If you have freesurfer installed I would run the following script in terminal in the directory where you have your .nii files:
#!/bin/bash
for infiles in `ls *.nii`
do
fname=`echo $infiles | cut -d ‘.’ -f1`;
mri_convert $infiles -ot nifti1 $fname;
done

Now if you have a 4D image, and have FSL installed, things are even easier. Suppose your 4D file is named series.nii, run the following script at the terminal:

#!/bin/bash
export FSLOUTPUTTYPE=ANALYZE
fslsplit series.nii output_basename -t

Hope this helps!

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

Lena — Thu, 26 Apr 2012 11:03:50 +0000

Hi there,

I was wondering how do I convert nii files into their respective hdr and img files?

many thanks

Comment on Normalization in FSL by Gustava

Gustava — Wed, 04 Apr 2012 23:56:48 +0000

Hi,

Thanks for this

Where you register the T1 to MNI, and are running fnirt, should that be run on my_betted_structural, instead of my_structural (I would think so).

Cheers!

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

Jon Duke — Wed, 21 Mar 2012 15:33:44 +0000

After many days of looking for a “RDP” like solution for the 11.X builds of ubuntu I finally found a very elegant solution on another site. I wanted to share it in hopes of saving others like myself a little time.

Source
http://mlepicki.com/2011/10/remote-vnc-login-to-ubuntu-11-10/

“Today I’ve installed Ubuntu 11.10 Oneiric Ocelot on my ASrock 100HT nettop. I’ve wanted to remotely control this box via VNC protocol.
My solution was x11vnc server, so I could share one one session between remote and physical access. I’ve found useful thread about x11vnc on Ubuntu 11.10 – I’ve just added some upstart magic to start x11vnc after lightdm.
First of all, I’ve installed x11vnc:
apt-get install x11vnc
Then, I’ve created /etc/init/x11vnc.conf file:
start on login-session-start
script
x11vnc -xkb -noxrecord -noxfixes -noxdamage -display :0 -auth /var/run/lightdm/root/:0 -forever -bg -o /var/log/x11vnc.log
end script
After restart, x11vnc shoud listen on vnc startard port – 5900.
This script is of course based on upstart event mechanism. Lightdm emits login-session-start event (you can find it in lightdm.conf), and we start x11vnc when this event is emited – that’s first line of x11vnc.conf file.”

Comment on When gvfsd-metadata starts using 100% processor by Peter

Peter — Sat, 03 Mar 2012 19:55:45 +0000

Thanks. This fixed an issue I had with gvfs-metadata hogging 100% CPU usage when working with files.

The partition in question was indeed almost 97% full.

Comment on Change “Linux Mint flavoured” Google search to original Google search by Adrian

Adrian — Fri, 24 Feb 2012 15:17:23 +0000

Thanks, that was very helpful.

Comment on Bounding box for wfu-pickatlas masks by Valerie

Valerie — Thu, 23 Feb 2012 01:16:04 +0000

Hi Rishi,

I was wondering, could you also make a mask of the anterior hippocampus this way? How would you go about determining those dimensions? Thank you very much for any advice,

Valerie

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