It isn't clear to me exactly what you want, but if you want a fixed rotation of a general ROI (or image of any form) then using makerot is the best option. You just need to specify your angle and axis of rotation and then save the matrix output. Then
you use this matrix with flirt via the -applyxfm and -init options (or you can use applywarp). See the FSL wiki and course docs for more info on how to use flirt and applywarp.
HI all could anyone help me to find a method to rotate a ROI with fsl command? Or could anyone help me to find a method to make a fine transformation matrix? I found a makerot function in a forum but I don't understand how to use it. Thank.