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SDC: Unify unwarping workflows #21

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oesteban opened this issue May 28, 2019 · 2 comments · Fixed by #115
Closed

SDC: Unify unwarping workflows #21

oesteban opened this issue May 28, 2019 · 2 comments · Fixed by #115
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effort: high Estimated high effort task impact: high Estimated high impact task unwarping
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2.0.0

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@oesteban
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oesteban commented May 28, 2019 •
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After estimation of the displacements field map (either via phase1/2, phasediff, PE-polar, or SyN), the unwarping should happen with a unique workflow.

This requires #19.
@oesteban oesteban transferred this issue from nipreps/fmriprep Jul 9, 2019
@oesteban oesteban added this to the 1.0.0 milestone Aug 7, 2019
oesteban added a commit to oesteban/sdcflows that referenced this issue Nov 20, 2019
@oesteban
ENH: Refactor the distortion estimation workflow
1bd8274 
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.
@oesteban oesteban mentioned this issue Nov 20, 2019
Merged
oesteban added a commit to oesteban/sdcflows that referenced this issue Nov 21, 2019
@oesteban
ENH: Refactor fieldmap-unwarping flows, more homogeneous interface
8e9a82e 
This PR closes nipreps#19, reorganizing the unwarping tools for fieldmap-based
solutions:

  - [x] Separate the displacements field generation from actual
        unwarping (i.e., applying the nonlinear transform).
        By doing this, we are not only addressing nipreps#19 directly, we are
        also readying the ground for tackling nipreps#21 since now all the
        unwarping paths (pepolar, fieldmaps/phases/phasediff, or syn)
        have more consistent interfaces.
  - [x] Update the root workflow to reflect these changes.
  - [x] Unloaded ``unwarp.py`` of the workflow to write reports, which
        has been moved to a new module called ``outputs.py`` following
        some of the latest *fMRIPrep* non-written standards.
  - [x] Polished some minor documentation and stylistic issues within
        the scope of the proposed changes.
@oesteban oesteban mentioned this issue Nov 21, 2019
Merged
5 tasks
oesteban added a commit to oesteban/sdcflows that referenced this issue Nov 22, 2019
@oesteban
ENH: Refactor fieldmap-unwarping flows, more homogeneous interface
4945039 
This PR closes nipreps#19, reorganizing the unwarping tools for fieldmap-based
solutions:

  - [x] Separate the displacements field generation from actual
        unwarping (i.e., applying the nonlinear transform).
        By doing this, we are not only addressing nipreps#19 directly, we are
        also readying the ground for tackling nipreps#21 since now all the
        unwarping paths (pepolar, fieldmaps/phases/phasediff, or syn)
        have more consistent interfaces.
  - [x] Update the root workflow to reflect these changes.
  - [x] Unloaded ``unwarp.py`` of the workflow to write reports, which
        has been moved to a new module called ``outputs.py`` following
        some of the latest *fMRIPrep* non-written standards.
  - [x] Polished some minor documentation and stylistic issues within
        the scope of the proposed changes.
oesteban added a commit to oesteban/sdcflows that referenced this issue Nov 23, 2019
@oesteban
ENH: Refactor fieldmap-unwarping flows, more homogeneous interface
29f2d0b 
This PR closes nipreps#19, reorganizing the unwarping tools for fieldmap-based
solutions:

  - [x] Separate the displacements field generation from actual
        unwarping (i.e., applying the nonlinear transform).
        By doing this, we are not only addressing nipreps#19 directly, we are
        also readying the ground for tackling nipreps#21 since now all the
        unwarping paths (pepolar, fieldmaps/phases/phasediff, or syn)
        have more consistent interfaces.
  - [x] Update the root workflow to reflect these changes.
  - [x] Unloaded ``unwarp.py`` of the workflow to write reports, which
        has been moved to a new module called ``outputs.py`` following
        some of the latest *fMRIPrep* non-written standards.
  - [x] Polished some minor documentation and stylistic issues within
        the scope of the proposed changes.
@oesteban oesteban modified the milestones: 1.0.0, 1.1.0 Nov 25, 2019
@oesteban oesteban added impact: high Estimated high impact task effort: high Estimated high effort task labels Apr 2, 2020
@oesteban
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oesteban commented Apr 2, 2020

Very related: #26

@oesteban oesteban mentioned this issue Oct 14, 2020
Closed
oesteban added a commit to oesteban/sdcflows that referenced this issue Oct 23, 2020
@oesteban
ENH: New objects for better representation of fieldmap estimation
e827bf7 
This PR attempts to provide a more reliable framework to build
fieldmap estimation workflows.
Implicitly, it will help addressing issues regarding data conformity
(e.g., nipreps#63, nipreps#64, nipreps#65) and also ease larger refactors such as #20, nipreps#21,
 nipreps#26, and nipreps#101.
@oesteban oesteban mentioned this issue Oct 23, 2020
Merged
oesteban added a commit to oesteban/sdcflows that referenced this issue Oct 23, 2020
@oesteban
ENH: New objects for better representation of fieldmap estimation
3c51023 
This PR attempts to provide a more reliable framework to build
fieldmap estimation workflows.
Implicitly, it will help addressing issues regarding data conformity
(e.g., nipreps#63, nipreps#64, nipreps#65) and also ease larger refactors such as #20, nipreps#21,
 nipreps#26, and nipreps#101.
oesteban added a commit to oesteban/sdcflows that referenced this issue Oct 26, 2020
@oesteban
ENH: New objects for better representation of fieldmap estimation
a52066c 
This PR attempts to provide a more reliable framework to build
fieldmap estimation workflows.
Implicitly, it will help addressing issues regarding data conformity
(e.g., nipreps#63, nipreps#64, nipreps#65) and also ease larger refactors such as #20, nipreps#21,
 nipreps#26, and nipreps#101.
@oesteban oesteban linked a pull request Nov 12, 2020 that will close this issue
ENH: New estimation API (featuring a TOPUP implementation!) #115
Merged
@oesteban
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Actually, this is essentially implementing #26. Closing in favor of that one.

oesteban added a commit to oesteban/sdcflows that referenced this issue Nov 14, 2020
@oesteban
ENH: New objects for better representation of fieldmap estimation
7091ed0 
This PR attempts to provide a more reliable framework to build
fieldmap estimation workflows.
Implicitly, it will help addressing issues regarding data conformity
(e.g., nipreps#63, nipreps#64, nipreps#65) and also ease larger refactors such as #20, nipreps#21,
 nipreps#26, and nipreps#101.
oesteban added a commit to oesteban/sdcflows that referenced this issue Nov 18, 2020
@oesteban
ENH: New objects for better representation of fieldmap estimation
f4c0ca6 
This PR attempts to provide a more reliable framework to build
fieldmap estimation workflows.
Implicitly, it will help addressing issues regarding data conformity
(e.g., nipreps#63, nipreps#64, nipreps#65) and also ease larger refactors such as #20, nipreps#21,
 nipreps#26, and nipreps#101.
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ENH: New estimation API (featuring a TOPUP implementation!) oesteban/sdcflows
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