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Hi, You should verify that the diffusion orientations are correct by running FDT in one of the scans and looking to see that the diffusion directions (line vectors, not just colors) make anatomical sense in all three planes of section. Peace, Matt. _____ From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of Suzanna Laycock Sent: Wednesday, July 11, 2007 12:44 PM To: [log in to unmask] Subject: [FSL] Orientation question Hi, I've just re-read the orienation advice / info on the FSL FAQ sections, and I was wondering if I could double check with someone if the following is correct. My data is saved in analyze format, and previously (probably when I was using FSL 3.2), I was only running the following to reorientate the data: Avwswapdim.exe filename -x -y z data Can I just confirm that avworient is not relevant for analyze-formatted files? Also, having done this, I need to change the sign of the x and y colums of my bvecs. Having done this, everything should be in the correct orientation to proceed with TBSS. Is there any other things I need to change before I proceed? Thanks for any help Suzanna