Dear Ines,
> I have multi shelled acquisition collected with AP-PA with 5 b0 in the PA direction. I have ran topup and after that created an average file and the mask based on that. Afterwards, I noticed 2 potential issues:
> eddy results (eddy_corrected_data.nii.gz) appear to have distortions.
> eddy_corrected_data.nii.gz is misaligned with the mask from topup.
>
> Is this expected? Do you have any advice to remove distortions?
you will need to supply much more information than this. I suggest you specify all the FSL commands that you have run in order to generate your eddy_corrected_data.nii.gz.
Jesper
>
> Many thanks in advance for all the help,
> Ines
>
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