is it OK if I correct my dwi images for eddy currents in FSL, rotate my bvecs with fdt_rotate_bvecs.sh (FSL script) and then use that output (eddy corrected dwi volumes and rotated b-vecs) in BS-BDP for further processing?
I read a response in this same thread that says that bvecs are rotated (again) when registered to the T1-weighted image (.bfc.nii.gz).
Would my pipeline (FSL->BS) of preprocessing suppose any kind of problem? Thanks!!