Dear Joel,
> I have DWI data collected but only one b0 image, with the same phase encoding direction. It's my understanding that I need two b0's with opposite phase encoding in order to use and apply topup. I do have a phase and magnitude fieldmap collected with the same orientation, direction and dimensions. Is there a way to apply this fieldmap to correct for distortion to the b0 and DWI data?
yes, but then you need to use different tools than applytopup. You can for example use fugue, or you can feed a 1D displacement field (shiftmap) into convertwarp if you want to combine it with registration into standard space.
> Along these lines, could I use this fieldmap with BBR to help in alignment to a 3D T2 that was also collected?
I don’t think there should be any problems to use BBR with a T2 image. As long as your segmentation (of the T2) works well you should be fine.
Jesper
> I can create the prepped fieldmap with fsl_prepare_fieldmap but I don't know what to use to apply this to the b0. epi_reg and the tools in that script look to be optimized for epi to T1 registration only. Is there a way to insert a prepped fieldmap into apply topup or use the current scans that I have to correct for distortion? Thanks for any and all responses.
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