> Dear David,
> > 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.
Thanks. Ok! Could you help me understand how can I write the command line for eddy without topup step? Eddy talking about compulsory arguments, but I don't know if I have all compulsory files to fill all blanks of eddy command line:
The following COMPULSORY options have not been set:
--imain (Ok! it's just uncorrected image)
--mask (Ok! brain mask obtained on bet step)
--index File containing indices for all volumes in --imain into --acqp and --topup (I don't know how to make this!)
--acqp File containing acquisition parameters (I don't know how obtain thin either!)
--bvecs File containing the b-vectors for all volumes in --imain (ok! I have this)
--bvals File containing the b-values for all volumes in --imain (ok! I have this)
--out Basename for output (ok! just a basename)
> 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.
I will love to make this but how? I will send a list of files extracted from DICOM file. Any of those files can do the job?
> > 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.
I attached a screenshot showing the part I talking about to your email (very large image to post here), but if you search for pipeline on the page you will probably find what I talking about
Thank you vey much
> > Thank you
> > Best Reagards
> > David