ENH: Refactor the distortion estimation workflow #53
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Nov 20, 2019
This PR: - [x] Refines the work in nipreps#53 addressing nipreps#40. - [x] Adds tests to cover the orchestration workflow. - [x] Fixes nipreps#7 (added regression tests for this bug). - [x] Updates the interface of phdiff workflows: removes the metadata input, which was defined for this workflow solely. - [x] Makes it trivial to extend the phdiff workflow to phase1/phase2 workflows (nipreps#15).
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oesteban
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Nov 20, 2019
This PR: - [x] Refines the work in nipreps#53 addressing nipreps#40. - [x] Adds tests to cover the orchestration workflow. - [x] Fixes nipreps#7 (added regression tests for this bug). - [x] Updates the interface of phdiff workflows: removes the metadata input, which was defined for this workflow solely. - [x] Makes it trivial to extend the phdiff workflow to phase1/phase2 workflows (nipreps#15).
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Nov 23, 2019
This PR: - [x] Refines the work in #53 addressing #40. - [x] Adds tests to cover the orchestration workflow. - [x] Fixes #7 (added regression tests for this bug). - [x] Updates the interface of phdiff workflows: removes the metadata input, which was defined for this workflow solely. - [x] Makes it trivial to extend the phdiff workflow to phase1/phase2 workflows (#15).
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Nov 25, 2019
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.
oesteban
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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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Following #40, rolls back the changes most involved with PyBIDS also making the API evolve less abruptly.
PR builds on top of #52, and closes #16.
This PR does not address #20, nor #19 and #21 although it is setting the necessary stepping stones.