ENH: Deduplicating magnitude handling and fieldmap postprocessing workflows #52
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…kflows This PR splits the magnitude processing and the fieldmap postprocessing that is shared between phasediff (and phase1/2) and direct B0 mapping approaches. It also addresses some issues on the direct B0 mapping approach, where the fieldmap was converted between units and subject to PRELUDE (which is not correct as these fieldmaps are not phase-wrapped). Adding a test case of SE fieldmaps would be great for a future PR. Close nipreps#17
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Following nipreps#40, rolls back the changes most involved with PyBIDS also making the API evolve less abruptly. The PR builds on top of nipreps#52, and closes nipreps#16. This PR does not address #20, nor nipreps#19 and nipreps#21 although it is setting the necessary stepping stones.
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Putting together the lessons learned in nipreps#30, leveraging nipreps#52 and nipreps#53 (unfolded from nipreps#30 too), and utilizing nipreps#50 and nipreps#51, this workflow adds the phase difference map calculation, considering it one use-case of the general phase-difference fieldmap workflow. On top of this PR, we can continue the discussions held in nipreps#30. Probably, we will want to address nipreps#23 the first - the magnitude segmentation is sometimes really bad (e.g. see the phase1/2 unit test). Another discussion arisen in nipreps#30 is the spatial smoothing of the fieldmap (nipreps#22). Finally, the plan is to revise this implementation and determine whether the subtraction should happen before or after PRELUDE, and whether the arctan2 route is more interesting.
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Putting together the lessons learned in nipreps#30, leveraging nipreps#52 and nipreps#53 (unfolded from nipreps#30 too), and utilizing nipreps#50 and nipreps#51, this workflow adds the phase difference map calculation, considering it one use-case of the general phase-difference fieldmap workflow. On top of this PR, we can continue the discussions held in nipreps#30. Probably, we will want to address nipreps#23 the first - the magnitude segmentation is sometimes really bad (e.g. see the phase1/2 unit test). Another discussion arisen in nipreps#30 is the spatial smoothing of the fieldmap (nipreps#22). Finally, the plan is to revise this implementation and determine whether the subtraction should happen before or after PRELUDE, and whether the arctan2 route is more interesting.
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This PR splits the magnitude processing and the fieldmap postprocessing
that is shared between phasediff (and phase1/2) and direct B0 mapping
approaches.
It also addresses some issues on the direct B0 mapping approach, where
the fieldmap was converted between units and subject to PRELUDE (which
is not correct as these fieldmaps are not phase-wrapped).
Adding a test case of SE fieldmaps would be great for a future PR.
With thanks to @mattcieslak for providing the basis for this in #30.