ENH: Refactor the distortion estimation workflow #53
Conversation
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
oesteban
force-pushed
the
fix/sdc-wf
branch
2 times, most recently
from
c2f48fd to
c093c19
Compare
oesteban
added a commit
to oesteban/sdcflows
that referenced
this pull request
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).
5 tasks
oesteban
added a commit
to oesteban/sdcflows
that referenced
this pull request
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).
oesteban
added a commit
that referenced
this pull request
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).
oesteban
added a commit
to oesteban/sdcflows
that referenced
this pull request
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
added a commit
to oesteban/sdcflows
that referenced
this pull request
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.
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
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.