Support for optional intensity modulation in B0FieldTransform.apply()
#238
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oesteban
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unwarping
impact: high
oesteban
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Oct 20, 2021
Although I brought up the issue within #2530 and got some mildly opposed initial opinion from @effigies (#2530 (comment)), I've come to think that we should provide the T2star workflow with HMC'ed and SDC'ed echos (confirmation awaiting: #2608 (review)). This comes as an issue related to #2606. This PR proposes that individual echoes are HMC'ed (and SDC'ed when fieldmaps are available) before calculating the optimal combination and the T2star map. I believe this may be beneficial when we combine SDC with modulation by the Jacobian of the distortion (nipreps/sdcflows#238) because that might help restore some (little, admittedly) of the dropout of the later echoes in distorted regions. I would expect more voxels will be deemed as acceptable for the exponential fitting for this reason. It also conceptually simplifies a little, as both SE and ME paths look more alike, and only the little hacks to generate ME iterables and the ``boldbuffer`` are now necessary. Otherwise, SDC would be inserted at a much later stage for ME only.
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