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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 > > ######################################################################## > > To unsubscribe from the FSL list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1 ######################################################################## To unsubscribe from the FSL list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1