SE FB registration#113
Merged
Merged
Conversation
…er handling for epicardium and endocardium, updating plotting functions, and refining denoising parameters.
…dium and endocardium, and update image registration with mask support in the registration loop.
…ecord_image_registration
Pedro Ferreira (Pedro-Filipe)
added
the
backend
Copilot started reviewing on behalf of
Pedro Ferreira (Pedro-Filipe)
June 8, 2026 15:53
View session
Contributor
There was a problem hiding this comment.
Pull request overview
This PR explores improved registration strategies for SE free-breathing acquisitions by adding an ANTsPy-based non-rigid option and introducing a new Elastix non-rigid “FB” recipe, alongside updates to use newly-derived “true border” contours across visualisation and QC tooling.
Changes:
- Added new registration options:
ants_non_rigid(ANTsPy) andelastix_non_rigid_fb(new Elastix B-spline recipe). - Updated multiple plotting/QC paths to use
epicardium_true_border/endocardium_true_borderinstead of the spline-interpolated contours. - Tuned denoising behaviour (reduced NLM strength; skip denoising for SE) and made minor UI/visualisation tweaks.
Reviewed changes
Copilot reviewed 12 out of 12 changed files in this pull request and generated 3 comments.
Show a summary per file
| File | Description |
|---|---|
| src/indi/scripts/main.py | Removes commented ITK threading code from the entrypoint. |
| src/indi/extensions/select_outliers.py | Plots segmentation overlays using “true border” contours in the manual outlier UI. |
| src/indi/extensions/read_data/read_and_pre_process_data.py | Uses “true border” contours for montage overlays; adjusts DICOM comment handling. |
| src/indi/extensions/manual_lv_segmentation.py | Adds “true border” overlay outputs and minor UI label tweaks for manual LV segmentation. |
| src/indi/extensions/image_registration.py | Adds ANTsPy registration option; adds new Elastix FB recipe; adjusts denoising strategy. |
| src/indi/extensions/image_registration_recipes/Elastix_bspline_fb.txt | Introduces a new Elastix B-spline parameter file for FB use. |
| src/indi/extensions/heart_segmentation.py | Ensures/derives “true border” contours when loading or generating segmentations. |
| src/indi/extensions/extensions.py | Updates results plotting to use “true border” contours and insertion points. |
| src/indi/extensions/crop_fov.py | Crops/updates “true border” contour coordinates; enhances registration debug visualisations. |
| settings_template.yaml | Documents new registration modes in the template settings. |
| pyproject.toml | Adds antspyx dependency for ANTsPy registration. |
| .pre-commit-config.yaml | Updates the pinned isort hook revision. |
💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.
Comment on lines
+686
to
687
| if "image_comments" in info.keys(): | ||
| logger.debug("Dicom header comment found: " + info["image_comments"]) |
Alberto Di Biase (tito21)
left a comment
Alberto Di Biase (tito21)
left a comment
Collaborator
There was a problem hiding this comment.
Some of the comments from copilot look a bit concerning.
ANTsPy seems slow to install, maybe we could move it as an optional dependency (it took ~12min to reinstall indi).
| return denoised_img | ||
|
|
||
|
|
||
| def registration_loop( |
Collaborator
There was a problem hiding this comment.
This can be refactored. I think it could be one general function for the elastix methods and a different function for each other methods
Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>
…geLondon/INDI into se_fb_registration
…es and alpha values, and adding a colorbar for better clarity
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
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.
Trying to improve the registration for SE free-breathing acquisitions...
Added a new method, based on ANTsPy:
https://github.com/ANTsX/ANTsPy
But not sure it is better. Seems to use more and unecessary non-rigid deformations.
Also added a new elastix recipe with more non-rigid deformations.