Dear Erik,
>
> We’re looking to use spin-echo HCP style fieldmaps, and are comparing the application of a fieldmap calculated with topup in two methods:
>
> 1. `applytopup` - Using the fieldmap and the single phase correction as shown in the help text
> 2. FEAT - Using FEAT’s stream and inputting the fieldmap directly.
>
> When comparing the outputs, it seems that FEAT produces a “gentler” correction than applytopup, including taking signal out of OFC less aggressively. Can you tell us the exact steps FEAT is performing in its correction (or give suggestions on how to dig into it), and if there are any adjustments that can be made to applytopup to make it resemble FEAT more closely?
>
> For example, we’ve seen in various documents that FEAT expects a fieldmap in radians / second, but applytopup doesn’t specify. Is there some extra unit checking that adjusts the fieldmap to within sane / expected values that might explain this?
there are a couple of reasons why the outputs might be different.
1. Applytopup will do both a “relocation” of the intensity (i.e. moving it to the right place) and a “Jacobian modulation” (i.e. a compensation for stretching/compression of the signal). FEAT will only do the former.
2. When using a " spin-echo HCP style fieldmap” in FEAT it is crucial that you get both the fourth column in the --acqp file (the total readout time) and the “effective EPI echo spacing” in FEAT right. Also, FEAT expects the field in radians/s whereas the field generated by topup (provided the readout time is correct) is in Hz. So you would need to multiply it by 2pi.
Jesper
>
> Thanks in advance for any detail you could give us on how to unify these and apply correction accurately. Happy to share snapshot examples of it would help,
>
> Erik
>
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