Dear Scott,
I am afraid there is no ready made solution for this situation. What you can try is to resample the reversed PE data to have the same resolution as the dti data and then run topup on that. Resampling can be done either with flirt or applywarp supplying it with a unity transformation matrix and using for example one of your DTI data volumes as -ref.
I _think_ that would work, but I haven’t tested using it like that so I can’t say for certain.
Jesper
On 20 Apr 2015, at 00:13, Scott Quadrelli <[log in to unmask]> wrote:
> Hi,
>
> I am still hoping to find and answer to this questions, if anyone has any idea.
>
> Cheers,
>
> Scott
>
>
>
> Dear Experts,
>
> I’m new to DTI processing, apologies for the basic question.
>
> I am trying to preprocess using TOPUP/EDDY. I have run into an issue where the DTI data has different dimensions (possibly changed during acquisition to decrease SAR, but I am not entirely sure why, the dimensions should have been the same) from the reverse phase encoded B0 acquisition.
>
> Dimensions reverse phase encode acquisition:
> <Screen Shot 2015-04-03 at 7.50.19 am.png>
>
> Dimensions: DTI acquisition
> <Screen Shot 2015-04-03 at 7.49.45 am.png>
>
> Is there a way around this so I can still pre-process using TOPUP and EDDY?
>
> Cheers,
>
> Scott
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