[Neurodebian-users] FSL and neurodebian

[Jonathan Brooks]

Dear neurodebian maintainers,

I wonder if I could make a plea to have 2 separate packages for fsl-core. One which still plays nice with SGE, and leaves the queue configuration in fsl_sub untouched, and the other which has the changes necessary for Condor (currently the default)? I think it is down to the user to make this choice, and not to have it forced on them.

As it stands there are plenty of people who still use SGE and would prefer to have the “vanilla” FSL.

Whilst we’re at it - there is one particularly annoying “feature” when attempting to run a lot of FSL scripts under Ubuntu…. the default shell is DASH, which doesn’t like the BASH-isms contained in a lot of the FSL scripts (e.g. randomise_parallel). Basically whenever you have #!/bin/sh this is running under DASH.

In the past I have explicitly edited the failing scripts to call #!/bin/bash, but more recently I have taken to reconfiguring system wide with:

$ sudo dpkg-reconfigure dash

selecting BASH as the default shell.

Could this either be fixed in the original shell scripts or guidance provided on how to change the default shell….?

Thanks for all your hard work - it’s much appreciated!

Best wishes,

Jon



--
Jonathan Brooks (PhD) - Senior Research Fellow
CRiCBristol, University of Bristol, St Michael's Hill, Bristol, UK
T: +44(0)117-342-1512 W: http://www.cricbristol.ac.uk