You may use flirt in FSL. you can specificy the transformation matrix and apply it to your data.
here is the link of examples given in website.
On Thu, Oct 7, 2010 at 3:56 PM, Mike Sugarman
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Hello,
I have a library of structural scans and am trying to conduct some analyses. However, when I view my scans, in every image viewer I use, whenever I use Orthoview, my sagittal and coronal slices are improperly oriented; they are either rotated 90 or 180 degrees. I am also having problems getting clean skull strips from BET, and I suspect these two issues might be related. Does anybody know of a way to rotate my images so that they are the proper orientation?
Thanks,
-Mike Sugarman
Department of Psychology
Wayne State University