Dear FSL experts,
I am analysing rs-fMRI data in a study which include DWI data (acquired with a set of reversed-PE b0:s for correction with topup+eddy).
I understand from reading previous posts that I can use the susceptility field estimations from topup as field maps in the rs-fMRI pre-processing, preferably with epi_reg.
However, I cannot get my head around what would be the magnitude image to use?
The available output images from topup are: the field map and the unwarped b0 images.
What should I use as a magnitude image for epi_reg? It cannot be an unwarped b0 image, can it? Or should I take the original (warped) b0/s? Then chose those with distortions corresponding to the used -pedir in the fMRI? Could/Should they be averaged (what about alignment?) or ok with a 4D volume of b0:s?
Also, epi_reg wants the field map in rad/s but the -fout from topup is in Hz. How do I convert in between?
Thanks in advance!
Kind regards
Marika
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