Dear Lara,
> I'm emailing to ask for some advice about phase encoding in topup and creating the datain file.
>
> In the collection of DTI scans I'm working with, some of the scans I have were acquired with A-P and P-A phase encoding direction which seems straightforward and topup works fine, but some of the scans are 1 run of A-P and then 1 run of R-L phase encoding. I realise the latter of these is less ideal but wondering if I can use topup with these at all?
>
> In the Topup users guide, it states that you can use 1 scan acquired in AP and one scan acquired in LR. However when I have tried to use the latter of these with the parameter text file (datain file) as below, using your FAQ answer about making the datain file with an AP and RL phase encoding to help me:
>
> 0 -1 0 0.095
> 1 0 0 0.122
>
> I then get the following error message in apply topup:
> terminate called after throwing an instance of 'TOPUP::ApplyTopupException'
> what(): ApplyTopup:: msg=Invalid combination of phase-encode vectors for least-squares restoration.
I assume this is an error message from applytopup and not topup itself? If so, add --method=jac to your applytopup comman line and you'll be fine.
Jesper
>
> Can anyone help with this?
>
> Many thanks
>
> Lara
>
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