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Mark nailed the reorientation question a while back -- look at this message https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0912&L=FSL&D=0&P=29740 for some very useful specifics Clark -----Original Message----- From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of Jeff Eriksen Sent: Friday, March 12, 2010 3:06 PM To: [log in to unmask] Subject: [FSL] how reorient volume for input to BET? I have some questions regarding image orientation in fslview and BET. I have been processing 3T and 7T DTI scans successfully, but the BET does not work on the 7T ones very well since they are low contrast and not whole brain. So I thought I would try to register the 7T DTI images to some T1 or T2 images, do the BET on the T1/T2, then use that mask for the DTI. Trouble is, when I went to run BET on the T1/T2 it failed, most likely because (as I subsequently discovered) the DTI are acquired axially while the T1/T2 are saggital. I then viewed the T1/T2 in fslview 3.1.5 and noticed that they display differently than the DTI images. For DTI the upperleft is coronal, upper right is saggital (both with top of head up), and lowerleft is axial with front of head up. For T1/T2 (acquired saggitally) the upper left shows the axial with nose left, upper right show coronal with top of head right, and lower left shows saggital with nose left. It seems that the axial display is the most useful and intuitive, so how should I go about reorienting the T1/T2 so that 1) it displays in the axial mode like the DTI and 2) permits continued processing with BET and registration in the same space as the DTI axial images? I have searched the forum and found some items on using fslswapdim and fslorient, and read through the FAQ on left-right swapping, but I still do not have enough documentation and examples to help me come up with the exact transformation I think I need. Thanks for any tips, pointers to other documentation or examples, etc.