Dear Mohammad,
>
> In our DWI data acquisition, we forgot to acquire the b0 image with PA phase encoding for some subjects.
> Now we want to add the b0-PA data to our previously acquired data but we are afraid that due to the changes in the subject head position in the new acquisition, TOPUP fail to work properly. Since the miss position of the subjects head can be corrected with a rigid body registration, can we register the newly acquired b0-PA to our b0-AP with a rigid body transform and next merge b0-PA and b0-AP?
>
> My main question is:
> Which of this methods is the most optimized solution for our problem in order that the FSL's DWI data preprocessing pipeline work properly?
>
> 1) Only acquiring the b0-PA.
> 2) Acquiring b0-PA and a new b0-AP.
> 3) Acquiring the whole DWI dataset again. (requiring DWI, b0-AP, and b0-PA)
>
the truly stringent way of doing it would be 3, i.e. reacquire the whole DWI dataset. Though I can see that it might not be practical/possible.
The problem with bringing the subjects back to do only the b0-PA scan is not so much the rigid body registration between the two (topup has a built in rigid body registration), but rather that the exact susceptibility field will depend on the location of the subject (see for example https://www.ncbi.nlm.nih.gov/pubmed/29277648 for an explanation). That means that the assumption (that topup makes) that both images were acquired in the same field, but that it manifests itself differently because of different acquisition parameters is not true.
I suspect that in practice the effect (of a separate acquisition) is relatively small and that the results would still be much better than if not having the b0-PA scan at all. But this has not been tested so I don’t know for a fact how big a problem it is.
Jesper
> Thank you for considering my request!
>
> Best regards,
> Mohammad
>
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