Hi,
I'm not sure exactly how you are trying to pass the variables, but they are typically expanded on the command line before being passed to any program. Hence it shouldn't be anything specific to eddy_openmp. Are you trying to run it via fsl_sub or some other way?
All the best,
Mark
> On 18 Feb 2017, at 18:22, gj <[log in to unmask]> wrote:
>
> Hi,
>
> I am having problems passing shell variables as values for the options to eddy (eddy_openmp to be exact), so that it fails complaining that the input files do not exist (but they do and when I don't pass variables but hardcode the paths and files, it works fine). What is the trick?
>
> Thanks!
> g
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