> 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?
topup is used to estimate the susceptibility-induced field, whereas eddy is used to estimate the eddy current-induced fields and subject movement. For running topup it is necessary to have data with different phase encodings. It is not necessary for running eddy. You can simply run eddy without supplying topup output. That means your data will be corrected for eddy currents and movement, but it will still have the susceptibility-induced distortions.
If you have some other way of estimating the susceptibility-induced field (e.g. a traditional fieldmap) you can pass that to eddy using the --field option.
> 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?
I don’t quite understand this. When I look at the page you have linked to I don’t recognise the numbering you describe nor the instructions.
> Thank you
> Best Reagards