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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.
http://www.fmrib.ox.ac.uk/fsl/flirt/examples.html
 
On Thu, Oct 7, 2010 at 3:56 PM, Mike Sugarman <[log in to unmask]> wrote:
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



--
Xiaowei.Zou

Department of Biomedical Engineering
Columbia University
New York, NY, 10027