Hi Torsten,

What problems would you foresee in using epiunwarp for fMRI? If I understand correctly, there is signal dropout in gradient echo images the way there isn't in spin echo -- I guess you're also saying that epiunwarp would not deal with these situations (but what does it do when it encounters them?)? We have quite a bit of distortion in our functional images (multiband factor 4).....

We do have images with opposing phase encoding directions (perhaps, though, the reverse phase encoding image got flipped during conversion). The --no-flip switch didn't help, but I ran convertx with --flip-y on the reverse phase-encoding image before running epiunwarp -- that helped with the mirror effect.

The correction with the additional gradient echo image in the reverse phase encoding direction as our functional scans, seems decent to my naive eye -- could I get your expert opinion (see attachment, p.1, left side)?

However, now I have a problem and a question.
When correcting the functional scans with the deformation matrix calculated from the pair of spin echo images (one A->P, other P->A), it seems like the correction is going in the wrong direction for the functional scans (though the correction on the SE images look pretty good -- see attachment, p.1, right side)

I also am wondering whether one should use reverse or forward Jacobian (attachment, p.2)?

I thought I'd continue this thread (as all related to SDC for BOLD images)....

Thanks a lot again!
Gina