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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