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Hi, I guess it will depend on what you wanna do with the data. It won't be easy to combine the two runs - because of voxel intensity AND diffusion gradient issues. So I would probably analyze the two runs separately and combine them (e.g. by using the FA image or whatever) later on. Having said this, you may wanna try the CATNAP toolbox from the BIRN (which uses flirt, of course;). Cheers- Andreas ________________________________ Von: FSL - FMRIB's Software Library [mailto:[log in to unmask]] Im Auftrag von Paul Geha Gesendet: Donnerstag, 31. Mai 2007 02:06 An: [log in to unmask] Betreff: [FSL] Motion correction for DTI Hello, I have DTI data collected with 68 ( 8 no diffusion scans) different directions, with two consecutive scans, that are interleaved to cover the whole brain. In some of them the subject moved from one scan to the other so that when I reconstruct the image there is an obvious shifts between the 2. How can I correct for that. Can I use Flirt with 6 DOF only to register one to the other and then scramble them into one image? Is this transformation going to change the voxel values due to interpolation? thanks for the help Paul Paul Geha M.D. Northwestern University The Feinberg School of Medicine Department of Physiology M211 303 E. Chicago Ave. Chicago, IL 60611 Tel:312-503 2886 Fax: 312-503-5101