Dear Matt,
I meant the second problem (the first is achieved inside topup), i.e. I meant registration between the spin-echo EPI field map and the EPI data I am correcting.
Could you please guide me how to achieve that?
As I looked to HCP pipeline script TopupPreprocessingAll.sh
https://github.com/Washington-University/Pipelines/blob/master/global/scripts/TopupPreprocessingAll.sh
and it seems (if I understand it correctly) that simple flirt 6 DOF registration between EPI data (named "scout" there) and one of the spin echo epi "fieldmap" datasets is done to correct for motion between "scout" and "fieldmap". So the effect of different distortion is neglected in current version of HCP pipeline scripts?
On the other hand, I suppose the effect is indeed small provided the datasets are acquired in the same session and there is not a gross subject movement (which would lead to exclude the dataset due to motion artifacts anyway). What do you think?
Antonin
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