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Hi, 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. All the best, Mark From: FSL - FMRIB's Software Library <[log in to unmask]<mailto:[log in to unmask]>> on behalf of Carmine Pagliaro <[log in to unmask]<mailto:[log in to unmask]>> Reply-To: FSL - FMRIB's Software Library <[log in to unmask]<mailto:[log in to unmask]>> Date: Thursday, 3 September 2015 11:04 To: "[log in to unmask]<mailto:[log in to unmask]>" <[log in to unmask]<mailto:[log in to unmask]>> Subject: [FSL] Random rotation ROI 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.