[Neurodebian-devel] Problem with fsl_app_wrapper

[Brendan Moloney]

I was quite excited to see the new FSL 5.0 release and started to plan our migration. During the transition 
period I would like the default commands (e.g. 'flirt') to use 4.1 and allow users to explicitly request the 
updated versions (e.g. by running 'fsl5.0-flirt'). To achieve this I made '/etc/fsl/fsl.sh' point to 
'/etc/fsl/4.1/fsl.sh' (our default bash.bashrc then calls '/etc/fsl/fsl.sh' to set up the environment).

This does not work because fsl_app_wrapper only sets up the correct environment if FSLDIR is not 
already defined. So calling 'fsl5.0-flirt' still runs the flirt command from 4.1.

Thanks,
Brendan Moloney