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Hi, Most of the message that Clark referred to was about the case where the labelling is wrong, but normally it is fine, so check that first. If the labels that you see in FSLView (L, R, A, P, S, I) are in the correct places in the image then all you need to do in order to reorient your images to axial is: fslswapdim invol RL PA IS outvol (as it says in the help for fslswapdim). If the labels are wrong then follow the instructions in the email that Clark pointed to. Also, note that BET does not care whether images are sagittal or axial, if it fails in one orientation it is almost certain to fail in the other. Cropping out the neck from images where there is a lot of neck can help BET to work a lot better. If you still cannot get BET to work (and try some of the other BET options first) then let us know. All the best, Mark On 12 Mar 2010, at 23:40, Clark Johnson wrote: > 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. >