Dear Mr. Jesper Andersson,
I want to use eddy current correction using eddy command of FSL 5.0.10.
But, reading documentation, seems that is needed to use topup first and dataset I actually working don't have different phase encodings for b0 (just one scan per subject). So I can't use topup, because topup need at least two phase encoding directions. So, how I can use eddy correction on this kind of dataset?
Another question is:
Looking on documentation at https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FDT/UserGuide there have the necessary steps to processing DTI data using FDT. Steps 1 and 2 are ok. But step 3 says that its needed to do a dtifit before topup (step 4) and eddy correction (step 5) and after that another dtifit (step 6). So the corrections on steps 4 and 5 are made on fitted data obtained on step 3 and not on original dwi data?