ENH: integrate left-right flip detection #3313
Draft
Conversation
This file contains 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
enh: rerun registration using this flipped functional image
…on with original and flipped functional image to detect left-right flip enh: propagate the flip_info through the workflow so it can be integrated into the visual report
…ithin visual report enh: report costs in registration with original and flipped functional image
Codecov ReportAttention: Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## master #3313 +/- ##
===========================================
- Coverage 73.79% 56.86% -16.94%
===========================================
Files 56 56
Lines 4263 4284 +21
===========================================
- Hits 3146 2436 -710
- Misses 1117 1848 +731 ☔ View full report in Codecov by Sentry. |
…of the workflow initialisation fails complaining this connection does not exist. The output is the dictionary with the same keys as the flip_info for the bbr_wf except the value associated with the keys are empty.
celprov
force-pushed
the
enh/left-right-flip-detection
branch
from
94ac539 to
4232b3a
Compare
…to avoid duplicating this part of the code when additionally outputting the transform betweeen the flipped bold and the t1w.
…T1w image when I was actually flipping the BOLD, any previous commit that states the T1w was flipped is a mistake. enh: plot the alignment between the flipped BOLD and T1w as a complement to left-right flip check through cost comparison. The plot is hidden in a drop down section.
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Outdated suggestions cannot be applied.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.
The left-right flip detection runs the alignment algorithm after flipping the BOLD image and compares the costs of aligning the T1w with the flipped BOLD and with the original BOLD. In the summary of the visual report, we emit a warning if the cost related to the flipped image is lower than the cost related to the original image. We also report the two costs and provide the visualization of the flipped alignment.
Strongly inspired by the AFNI implementation of the left-right detection tool (Glen et al. 2020)