Dear Colm,
what does the very last line of the “topup guidance” say?
Jesper
> On 11 Dec 2019, at 12:26, Colm McGinnity <[log in to unmask]> wrote:
>
> Dear FSL Experts,
>
> I would like to ask for help with the following problem, apologies if already answered or due to a silly mistake. I am trying to run topup on some fMRI data; I have data that was acquired AP and PA. I try to run topup using the following command:
>
> topup --imain=fMRI_memory_long_PA_short_rvols_merged.nii.gz --datain=datain.txt --config=b02b0.cnf --iout=fMRI_memory_long_PA_short_rvols_merged_unwarped --out=fMRI_topup_output
>
> However, on clicking enter the topup guidance is displayed, as if I had entered "topup --help" only, but without any error message. Nothing seems to have run.
> Has anyone else encountered and solved this issue?
>
> Many thanks in advance,
> Colm McGinnity
> King's College London
>
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