Hello Jesper,
Thank you for your reply.
In the user guide (http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/eddy/UsersGuide) it was mentioned that " eddy attempts to combine the correction for susceptibility and eddy currents/movements ..". So, i expected the output to be corrected for both 1. eddy currents, motion and also 2. susceptibility artifact at one go. EDDY was successful in correcting the first part (eddy currents, motion) but not the second (susceptibility artifact).
As you have mentioned, i will add --resamp=lsr and --fep and that should solve my problem by merging the two input DTI scans with something similar to apply_topup. In this case will the eddy_rotated_bvecs output file also have 31 corresponding vectors? if so, how are these combined rotation and movement_rms parameters calculated?
Best wishes
Jay
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