Dear Jose,
> I have computed the fieldmap coefficients from a set of b0 images with reversed phase polarity. I would like to use this to correct my fMRI dataset. I have to questions regarding that.
>
> 1. I have done this using fugue, and all seems ok. Would there be any difference between applying fugue or applytopup in this stage?
yes, a quite big difference is that applytopup will take “Jacobian modulation” into account, and fugue will not. Jacobian modulation refers to the effect of stretching/compression of signal as a consequence of the distortions. For fMRI data it is not clear if there is any advantage in taking this into account, so it is not that one is necessarily better. But it means that your corrected data would look quite different post correction depending on which way you chose.
> 2. In order to use applytopup I need to set as input the output from the topup run. But this run was computed for a set of 8 b0 images, and thus the movparam correspond to these images. Should I modify the movparam file to include the motion within the fMRI series, or in case it was already modified, should I set all to zeros?
I think the best would be to just be in the space of the first of your 8 b0 images. In order to do that your fMRI time series would need to be aligned to that b0 image. You then set --inindex=1 to indicate that all your images are in the space of that first b0.
Good luck
Jesper
>
> Many thanks!
>
> bw
>
> Jose
>
> --
> José Angel Pineda-Pardo
> Postdoctoral Researcher
> hmCINAC - HM Puerta del Sur
> Av Carlos V 70, Móstoles, Spain
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