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Hi, you can apply these transforms to images using the -applyxfm option in FLIRT. There is a detailed explanation of how to do that on the FSL course practical http://www.fmrib.ox.ac.uk/fslcourse/lectures/practicals/reg/index.html#applying Cheers, Stam On 28 Mar 2011, at 20:24, R. Duke wrote: > Hello FSL Experts, > > I am currently running ProbtrackX and was wondering about checking the registration from seed space (standard space) to diffusion space (native space). I am also using ROI's from the HarvardOxford Template that I would also like to check. After following the steps outlined on the FMRIB web page I only have transformation matrix files (*.mat) in my xfms folders. Is there a way that I can check to see if these standard space ROI's are covering the appropriate anatomical regions in diffusion space? > > Cheers! >