Hi Emily,
You seem to have come across an inconsistency in how eddy and eddy_quad handle it when extensions are included in the basename. In the future I would not include the '.nii.gz' extension in the basename when running eddy.
For now, if you want to run eddy_quad on this eddy output directory, you would first have to rename "Eddycorrect.nii.gz" to "Eddycorrect.nii.gz.nii.gz". You should then be able to run eddy_quad with "${dir}/Eddycorrect.nii.gz" as basename.
Best wishes,
Michiel
> On 2 Jun 2022, at 21:55, Emily Dennis <[log in to unmask]> wrote:
>
> Yes I did try that too, and oddly get this error
>
> ValueError: ${dir}/Eddycorrect.nii.gz does not appear to be a valid EDDY output basename
>
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