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
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