Hello,
Have you setup up your .tcsh to source the fsl environment? The commands needed to make can be found at:
https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FslInstallation/ShellSetup#csh.2Ftcsh
Hope this helps,
Kind Regards
Matthew
--------------------------------
Dr Matthew Webster
FMRIB Centre
John Radcliffe Hospital
University of Oxford
> On 5 May 2017, at 12:48, Amber B <[log in to unmask]> wrote:
>
> Dear all,
>
> I am trying to run a script in terminal to get a list of p-values from my ICA dual regression results.
>
> I want to run the following script:
> foreach subj (dr_stage3_ic00??_tfce_corrp_tstat?.nii.gz)
> foreach? echo $subj `fslstats $subj -R`
> foreach? end
>
> (terminal produces the ‘foreach? ‘ after submitting each line)
>
> However, this script is for a t-shell terminal, and my terminal is in bash. The bash terminal doesn’t recognize the ‘foreach’ command.
> (It produces the error: -bash: foreach: command not found)
>
> When I change my terminal to t-shell, I get the following error:
> fslstats: Command not found.
> Thus, FSL won’t run in my t-shell terminal. I have tried reinstalling FSL in the t-shell terminal, but that didn’t help.
>
> Does anyone know either how to change the script so it will run in a bash terminal, or how to make FSL run in my t-shell terminal?
>
> Any help would be greatly appreciated!
>
> Best,
> Amber
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