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?
Many thanks in advance for all the help,
Ines
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