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!!
I’m starting with BS too because of the possibility of correcting EPI distortions with T1-weighted images.
I used both the –dwi-mask and –t1-mask in order to improve the correction following your advice, but the outcome was pretty the same. In fact, the outcome was even worse when I used one (–dwi-mask) or both masks (dwi+t1) than when I did not use any of them.
Maybe without a fieldmap and only a T1 little correction could be made? Don’t get me wrong, I’m quite glad with correcting at least a little of such distortions than leave my DWI volumes with such disturbances.