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Dear David, Let me post a follow up: The eddy on one PE direction in the DWIs with opposite PEs in B0s work perfectly! If I would like to run eddy on only the PA encoded DWIs should I put the PA encoded B0 image first in the topup, followed by the AP encoded B0? Does it matter which B0 is the first image for topup? yes. The first b0 passed to topup defines the space for the susceptibility field and the first volume (typically a b0) passed to eddy defines the reference space for all your diffusion data. You want those two spaces to be the same, so you should strive to have the same b0 as the first volume for both topup and eddy. Jesper Regards, Szabolcs On Thu, Feb 25, 2016 at 5:03 PM, Jesper Andersson <[log in to unmask]<mailto:[log in to unmask]>> wrote: Dear David, Also as I see there is 1 processed/ corrected *.nii (..\ConnectomeData\ * \T1w\Diffusion\data.nii.gz) and bvec for a subject from the 'connectome in the box'. How can I achive that with my own data (with opposing PEs in B0 s and DWIs of course), should I use the --resamp lsr option? From a previous thread it looks like yes (https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=fsl;feea3a93.1510), but then how can I get one bvec file ? Or it will be provided via eddy because of the --resamp lsr flag? Since you only have one PE-direction for each dwi you cannot use --resamp=lsr. Just use the default. The bvec file is not produced by eddy. It is something you need to supply. If you are using 5.09 you will get a file with rotated bvecs as part of your output. Sure I have data with opposing PEs and the original bvecs. Could I get one corrected *.nii and one rotated bvec (rotated by eddy) with the l east squares reconstruction (like the preprocessed HCP data)? And if so how is that one rotated bvec is generated from the 2 original bvecs? I'm using 5.09 . The rotated bvecs is quite new in eddy, and we haven’t yet decided how best to combine LSR and rotated bvecs yet. If you use --resamp=jac you won’t have that problem, but it means loosing a little resolution in areas with large susceptibility distortions. On the other hand I find that the rotation of bvecs have a very small impact on most data from healthy adults. Jesper Cheers, Szabolcs I hope that answers your questions. Jesper Regards , Szabolcs David UMC Utrecht