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Dear Kim, I've had a look at your data and there are a couple of things that puzzle me there, and which I think are the explanation for your results. When I look at your two SE-EPI images (b0 images) in slices ~7-11 there seems to be substantial signal loss in the odd images compared to the even images. In an SE-EPI image I expect to see little/negligible signal loss, and that is what topup expects too. topup attempts to "solve" this by stretching signal outside the FOV, thereby getting rid of it, but that is clearly wrong so your BOLD images end up being "corrected" wrongly. If I set the fslview windowing quite low (max of 100) I can also see streaks/lines of intensity in the left-right direction extending outside the brain. These streaks/lines move up-down in a consistent manner between the PE+ and PE- images, which explains the strange "stripes" in the estimated field. I think the first thing you need to do is to find out why you have that signal loss. I know you have some excellent physicists at MGH so I suggest talking to one of them. Jesper