Setting up your .bashrc for Mturk on cercimage

Add these two lines on the end:

export PATH=/home/rcusack/software/aws-mturk-clt-1.3.0/bin:$PATH
export MTURK_CMD_HOME=/home/rcusack/software/aws-mturk-clt-1.3.0

Demystifying SPM variable names

A very useful post for SPM users... thanks Nikki!

Poisson disc in Matlab

Poisson disc sampling is a nice way of getting random yet even coverage.

Following the helpful page from devmag here are 2d and 3d implementations of Poisson disc (sphere?) sampling in Matlab. Also an implementation using SPM's grey mask to parcellate grey matter to an arbitrary degree.

Get rid of Unity under RealVNC

Go to the directory .vnc in your home directory.
Backup the file xstartup, make a new file, and replace it with:


#!/bin/sh

# Uncomment the following two lines for normal desktop:
# unset SESSION_MANAGER
# exec /etc/X11/xinit/xinitrc

#[ -x /etc/vnc/xstartup ] && exec /etc/vnc/xstartup
[ -r $HOME/.Xresources ] && xrdb $HOME/.Xresources
xsetroot -solid grey
vncconfig -iconic &
#xterm -geometry 80x24+10+10 -ls -title "$VNCDESKTOP Desktop" &
touch /home/rhodri/.vnc/haverunxstarup

gnome-session --session=gnome-classic &

On restarting your vncserver, you should get an old style desktop.

Ubuntu reanimates netbook

I had an essentially dead Acer Aspire One D257 netbook. With Windows 7 Starter, which it arrived with out of the box (along with lots of bloatware) it had become unbearably slow. There were two options: dustbin, or reanimation with Linux. After a failed diversion with Joli OS (which is very pretty but the Wifi resolutely refused to work), I installed Ubuntu 12.10. This works very immediately, and has made the machine a pleasure to use. I also found the preview version of Spotify for Linux, which seems to work well too.

Matlab/FSL + Ubuntu 12.04 library problem

Since upgrading to Ubuntu Precise 12.04, we've been getting an error on starting matlab of 

/usr/local/MATLAB/R2011b/bin/util/oscheck.sh: /lib64/libc.so.6: not found

This same problem also seemed to break bet from FSL.

Now in your matlab path, for us

/usr/local/MATLAB/R2011b/sys/os/glnxa64

you'll find

libstdc++.so.6

symbolically linked to

libstdc++.so.6.0.1.13

Ubuntu ships with a newer version of this library in

/usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.16

So, I symbolically linked the Matlab version through to the one shipped with Ubuntu

$ cd /usr/local/MATLAB/R2011b/sys/os/glnxa64

$ mv libstdc++.so.6.0.1.13 libstdc++.so.6.0.1.13.old

$ ln -s /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.16 libstdc++.so.6.0.1.13

This seems to fix it.

Ubuntu Precise 12.04 & VNC

When we upgraded to 12.04, the RealVNC desktop would come up blank. I found the solution here.