ENH: Do not use legacy demean function from old nipype workflows #51
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The new demean function works with the median or the mode (default) for a more robust result.
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mattcieslak
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If I'm not wrong, the demeaning comes from the historic Finally, I believe Jenkinson's 2003 paper would cover this. |
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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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The new demean function works with the median or the mode (default) for a more robust result (to revise after #50 is merged)