There is a simple way of manually determining and applying an affine registration to the currently viewed volume in FreeView. That feature is mostly used for reorienting infant and ex-vivo scans.
Highlight the volume that you want to work with, and then select on the top menu the Tools and Transform Volume options. This will provide you with a panel to specify rotation, displacement and scaling parameters. After specifying the required parameter values, hit Apply and then view the result in the visualization panel. You can undo the transformation by selecting Restore to Original. When you are satisfied with the transformation, you have to save the volume and/or the transformation that you have just created. Use the Save volume as... and/or Save Reg... buttons respectively.