Thanks Mark for your quick reply.
So, correct me if I am wrong, the fieldmap is applied at each step of the optimisation to undistort the epi image regarding it's new tentative alignment taking into account the epi slicing direction.
I noticed the _warp file output in epi_reg which is the fieldmap flirted into the epi image space through the T1 image as reference.
Having also observed some inconsistent behavior using weighting, I will consider that it is partially taken into account by the signal loss causing low gradient values accounting less into the cost function.
Bests.
basile
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