fslswapdim should be the correct tool for this, although it can get complex. I'd suggest reading the help page http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Fslutils , and exploring the effects of different options.
What was the full command that you used? Were the brains in correct orientation beforehand (try fslreorient2std)?
Cheers
On 2 January 2015 at 07:17, SUBSCRIBE FSL Anonymous <[log in to unmask]> wrote:
