installation fails due to dependency issue in Precise

Installing through the NeuroDebian repository with synaptic works

Thanks for reporting this issue. I get the same error message when attempting to install fsl on Ubuntu 12.04. (Works fine on Ubuntu Quantal though):

The following packages have unmet dependencies:
 fsl : Depends: fsl-4.1 (>= 4.1.6-4~) but it is not going to be installed
E: Unable to correct problems, you have held broken packages.

I also got the error but I managed to fix it on my machines:

First I realised, that
"wget -O- http://neuro.debian.net/lists/precise.de-md | sudo tee /etc/apt/sources.list.d/neurodebian.sources.list
sudo apt-key adv --recv-keys --keyserver pgp.mit.edu 2649A5A9" (as recommended on http://neuro.debian.net/index.html)
left a blank neurodebian.sources.list. So I copied my working Lucid-entries and replaced "lucid" by "precise":
"deb http://apsy.gse.uni-magdeburg.de/debian data main contrib non-free
# deb-src http://apsy.gse.uni-magdeburg.de/debian data main contrib non-free
deb http://apsy.gse.uni-magdeburg.de/debian precise main contrib non-free
# deb-src http://apsy.gse.uni-magdeburg.de/debian precise main contrib non-free"
after that I did:
"sudo apt-get update"
"sudo apt-get install neurodebian-keyring"
"sudo apt-get update"
"sudo apt-get install fsl"

...worked for me, hope it helps.