Dear Justin,
> My question arises because I recall reading a while ago that there was some assumption that the first b0 and first diffusion weighted volume should be collected close in time because of some assumption that there was no movement between these two volumes?
>
> First instance, if we have a long example card and we first collect a single "blip-up" b0. Then, at the end of the example card, we collect a "blip-down" diffusion scan (with another b0). Assuming there is a decent deal of time/movement between the two b0s. If we:
I am not sure what an “example card” is, but I am going to assume it is a scan. So, what you are saying is that you have something like
b0-↑ dwi-↑dwi-↑ dwi-↑ dwi-↑ dwi-↑ dwi-↑ dwi-↑ dwi-↑ dwi-↑ ...
b0-↓
which means that some time, and hence possibly movement, has passed between the two b0 scans. I assume you then create a file
b0-↑ b0-↓
for topup. Is that correct?
It would have been even better if the b0-↓ had been acquired shortly before the start of the long diffusion scan. But it is certainly no disaster. There is a rigid-body movement model inside topup so if there has been movement that will be detected and corrected.
What it _cannot_ correct is the slight difference in susceptibility-induced field you will have for the two different scans of the movement is large and involves lots of head rotation. That is very much a second order effect though, and for most cases too small to worry about.
Jesper
>
> 1) run topup with the "blip-up" b0 first, followed by the "blip-down" b0 which might have significant movement between the two
> 2) run eddy with the outputs from topup and the "blip-down" diffusion scan
>
> The outputs from topup/eddy will be aligned to the "blip-up" b0 scan, but susceptibility corrected. Is this correct? And is there any issue with there being a decent amount of rigid body motion between the "blip-up" and "blip-down" b0? Assume for now that we've already collected this data and can't change anything...
>
> Thanks,
>
> -Justin
>
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