Hi,
We include a matlab function named call_fsl() which sets up the rest of the environment correctly for calling FSL commands, as it is actually very difficult to get it right. So I recommend that you use this instead of 'system' and you should be fine.
All the best,
Mark
> On 23 Jan 2017, at 05:49, Jason Stockmann <[log in to unmask]> wrote:
>
> Hello,
>
>
> I'm trying to execute system UNIX commands from within Matlab using the 'system' Matlab command. I set up the environment variables as prescribed on the FSL install page, and the FSL commands are being successfully called, but unfortunately they crash with the following error:
>
>
> 'ERROR:: Environment variable FSLOUTPUTTYPE is not set!
> Please make sure that the appropriate configuration file is sourced by
> your shell (e.g. by putting it in .profile).
> e.g. bash or sh users add the line ". ${FSLDIR}/etc/fslconf/fsl.sh"
> e.g. tcsh or csh users add the line "source
> ${FSLDIR}/etc/fslconf/fsl.csh"'
>
>
> I tried running both the bash and tcsh commands, but it doesn't seem to help. For starters, I don't know whether calling Unix within Matlab uses bash or tcsh shells. Has anyone experienced this problem before?
>
> -- Jason Stockmann
|