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Dear Greve,
Thank you very much for your reply, yes indeed i found the problem which was connected to the deletion of 1 slice of the functional data in order to run the FSL "topup" b02b0.cnf flag. I solved it by changing this step, using the b02b0_2.cnf for odd number of slices.
Many thanks again
Best Giorgio
freesurfer@nmr.mgh.harvard.edu