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Hello Matthew, Thank you for your help. I was using FSL6.0.0. I updated to FSL6.0.1 and it helped: now, when I use fslswapdim my right hemisphere volumes are flipped. But they remain in the right hemisphere. So the issue of loosing alignment to the template space remains. How can I transform my nifti files in order to keep this information while using fslswapdim or fslmerge? Thanks, Garance ######################################################################## To unsubscribe from the FSL list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1