Hi,
This is definitely a bug and you've identified the correct solution to it.
We'll make sure this also gets fixed in our next release.
All the best,
Mark
> On 4 Jan 2018, at 17:45, Allison Jack <[log in to unmask]> wrote:
>
> Hi FSL experts,
>
> FIRST is working fine for me on my local machine. However, I've been having trouble with it on the server I've been using, and I think it's because of a sourcing issue. I have contacted the HPC team about it, but I thought I'd get your sense of things as well. Basically, I'm getting an error when I try to run either run_first_all or first_boundary_corr that it can't find fslstats, and it points to line 105 of first_boundary corr. I noticed that unlike all other parts of the script, which include $FSLDIR in paths to tools it calls, in this line it just calls fslstats "naked" so to speak:
>
> lb=`fslstats ${imout}_grot -R | awk '{ print $2 }'`
>
> Am I right that things would work if I get the HPC team to edit this line of the script to say
>
> lb=`${FSLDIR}/bin/fslstats ${imout}_grot -R | awk '{ print $2 }'
>
> ?
>
> Thanks!
> A
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