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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