Dear Jean,
>
> I am trying to do the topup, so I looked up the user guide, and it says topup is appropriate for the data having two b0 images with different directions.
> But, all of my data is showing one b0 at volume #0, from anterior to posterior.
>
> Question.
>
> 1) In this case, can I perform TOPUP ? or can I just simply move on to eddy_correct?
No, in this case you typically cannot run topup. However, if you have a T2 scan for the subjects there is a possibility that you can use that for topup.
You can go straight to eddy, but it will mean that one of the sources of distortion will not have been corrected.
>
> 2) According to the eddy user guide, I believe I need acqparams.txt, and topup result files. How can I use eddy without topup results?
> ""
> eddy --imain=data --mask=my_hifi_b0_brain_mask --acqp=acqparams.txt --index=index.txt --bvecs=bvecs --bvals=bvals --topup=my_topup_results --niter=8 --fwhm=10,8,4,2,0,0,0,0 --repol --out=eddy_corrected_data --mporder=6 --slspec=my_slspec.txt --s2v_niter=5 --s2v_lambda=1 --s2v_interp=trilinear
> ""
You can still create an acqparams.txt file. It will then only have a single line. The only thing you need to make sure is that you put the non-zero entry in the right column (the first or the second) and I would suggest to put 0.05 in the fourth column. Then you call eddy in the same way as above, but leave out the --topup parameter.
Jesper
>
> Thanks in advance!
>
> Sincerely,
> Jean
>
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