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Dear Andreas, Thank you for replying. Yes, we use the BBR option in the registration step. Lucia ________________________________________ From: FSL - FMRIB's Software Library [[log in to unmask]] on behalf of Andreas Bartsch [[log in to unmask]] Sent: Monday, April 20, 2015 4:36 PM To: [log in to unmask] Subject: Re: [FSL] B0 unwarping misalignment Hi, this looks like bad z-shift. Do you use FSL's latest version, i.e. BBR? Cheers, Andreas Am 20.04.15 15:31 schrieb "Lucia M Li" unter <[log in to unmask]>: >Dear FSL users & experts, > >We were hoping to get some help on an issue we've had with our unwarping >step (run as part of running a single-session melodic). > >We noticed that for a couple of people in our study, the "fieldmap to >highres" registration looks seriously displaced - see link: >https://dl.dropboxusercontent.com/u/22466029/FieldmapAlignment/Missalignme >nt.jpg > >The majority of our scans have registered very well however - see link: >https://dl.dropboxusercontent.com/u/22466029/FieldmapAlignment/GoodAlignme >nt.png > >We were wondering if anyone could advise on what might have caused this >displacement in a few people only (scanned using the same scanner/ >parameters, fieldmaps prepared using the same parameters & unwarped with >the same parameters)? >We were also wondering what effect this has on the final data (the final >func to highres looks ok) and what we can do to correct it? > >Many thanks in advance for your help. > >Kind regards, >Lucia