Dear Ariadna,
>
> Dear FSL experts,
>
> I have a question regarding topup. I have two acquisitions: My main dti data acquired R->L with one b0 and 64 volumes and an additional acquisition with different encoding direction (L->R) and one b0 and 5 volumes.
> After running the following commands:
> fslroi dwidata.nii nodif_RL 0 1
> fslroi dwidata_phaseshift.nii nodif_LR 0 1
> I ran "fslmerge -t RL_LRb0 nodif_RL.nii nodif_LR.nii"
>
> QUESTION 1: I was wondering if the order in which these images are merged matters for subsequent steps.
> When I ran TOPUP my acqparams file looks like this:
> 1 0 0 0.035
> -1 0 0 0.035
> Is this correct?
that looks fine.
>
> QUESTION 2:
> Does the acqparams for EDDY would look like this?:
> 1 0 0 0.035?
>
> (only one line?)
That looks fine too. Though there is nothing to stop you from using the same acqparams as you did for topup (two lines). If your index.txt file only contains ones it will simply ignore the second line. That is what I typically do, just to be certain there are no mistakes that make the two acqparams end up being different.
Good luck.
Jesper
>
> Thank you in advance,
>
> Ariadna
>
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