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ENH: Refactor workflow to adopt *SDCFlows*' new correction workflow #2547

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merged 6 commits into from
Sep 23, 2021

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@oesteban oesteban commented Sep 16, 2021

This PR addresses the problem reported in #2210.

Along with the specific changes in SDCFlows, this PR:

  • Resamples BOLD data in its native space using new SDCFlows' utilities.
  • Introduces a new IdentityInterface node called bold_final that acts as buffer to reduce LoC and branches when dealing with data with/without fieldmaps (and helpful too for ME-EPI, although this is not fully implemented).
  • ROIs plot now uses the output of unwarping through a RobustAverage node, therefore fixing one issue reported in Susceptibility distortion correction (SDC) using Spin Echo Fieldmaps  #2210.
  • preproc datasink of BOLD in native space now connected to the bold_final node, which contains HMC'ed + SDC'ed (if fieldmaps found) BOLD in native space. Now, it is matched with the ROIs plot, reducing a little the opportunities for divergence.

This PR DOES NOT solve (or even leaves without implementation):

@oesteban oesteban changed the title enh: update workflows to account for new resampling ENH: Refactor workflow to adopt *SDCFlows*' new correction workflow Sep 17, 2021
@oesteban oesteban marked this pull request as ready for review September 21, 2021 08:27
oesteban added a commit to oesteban/fmriprep that referenced this pull request Sep 22, 2021
oesteban added a commit that referenced this pull request Sep 22, 2021
STY: Run black on ``workflows.bold.base`` to clarify diff in #2547
@oesteban oesteban force-pushed the fix/sdc-resampling-2210 branch from 87addcf to a4526c9 Compare September 22, 2021 07:52
@oesteban oesteban requested a review from mgxd September 22, 2021 07:53
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@mgxd I've rebased on master after running black on workflows/bold/base.py, so the diff should be much cleaner now. Some little stylistic changes remained, but now they are just residual changes I don't think will disturb the review process.

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This is holding me up a little, so I'll merge.

@oesteban oesteban merged commit f12a042 into nipreps:master Sep 23, 2021
@oesteban oesteban deleted the fix/sdc-resampling-2210 branch September 23, 2021 07:37
oesteban added a commit that referenced this pull request Oct 7, 2021
This PR builds on top of #2547, unifying the final BOLDref computation.
oesteban added a commit to effigies/fmriprep that referenced this pull request Oct 18, 2021
This PR builds on top of nipreps#2547, unifying the final BOLDref computation.
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