Add FastSurfer-CC to the FastSurfer repository #727
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
m-reuter
reviewed
Sep 18, 2025
m-reuter
reviewed
Sep 18, 2025
m-reuter
reviewed
Sep 19, 2025
m-reuter
reviewed
Sep 19, 2025
m-reuter
reviewed
Sep 20, 2025
m-reuter
reviewed
Sep 20, 2025
m-reuter
reviewed
Sep 20, 2025
m-reuter
reviewed
Sep 26, 2025
m-reuter
reviewed
Sep 26, 2025
m-reuter
reviewed
Sep 26, 2025
Member
Author
|
All required features should be present at right now. I'm still running tests - in the meanwhile we can move forward with the --seg_only integration. |
Contributor
There was a problem hiding this comment.
Pull Request Overview
This PR adds FastSurfer-CC, a comprehensive corpus callosum segmentation, head pose normalization, and analysis module to the FastSurfer repository. The implementation includes deep learning models for AC/PC localization and CC segmentation, along with detailed morphometric analysis capabilities.
- Deep learning-based AC/PC localization and corpus callosum segmentation pipeline
- Comprehensive morphometric analysis with thickness measurements and shape metrics
- Interactive 3D visualization and surface mesh generation capabilities
Reviewed Changes
Copilot reviewed 40 out of 49 changed files in this pull request and generated 5 comments.
Show a summary per file
| File | Description |
|---|---|
| requirements.mac.txt | Adds new dependencies for mesh processing and visualization |
| recon_surf/recon-surf.sh | Updates CC processing path and comments out old commands |
| recon_surf/align_points.py | Adds verbose parameter and debugging output to rigid alignment function |
| pyproject.toml | Adds corpus callosum dependencies to project configuration |
| env/fastsurfer.yml | Adds conda environment dependencies for mesh processing |
| doc/conf.py | Updates documentation to include corpuscallosum module |
| doc/api/*.rst | Adds API documentation for new CorpusCallosum modules |
| FastSurferCNN/download_checkpoints.py | Integrates CC model checkpoint downloading |
| Docker/build.py | Adds logging improvements for docker build process |
| CorpusCallosum/* | Complete corpus callosum analysis implementation with segmentation, localization, and shape analysis |
Tip: Customize your code reviews with copilot-instructions.md. Create the file or learn how to get started.
dkuegler
reviewed
Nov 11, 2025
Member
dkuegler
left a comment
dkuegler
left a comment
There was a problem hiding this comment.
This is an incomplete review :( it is currently 250 comments long, but a lot are minor changes that are just having to be applied ... I will do that myself.
This comment was marked as duplicate.
This comment was marked as duplicate.
Sorry, something went wrong.
dkuegler
reviewed
Nov 12, 2025
dkuegler
reviewed
Nov 12, 2025
dkuegler
force-pushed
the
dev
branch
3 times, most recently
from
92f81b1 to
8ee1f0b
Compare
m-reuter
reviewed
Nov 12, 2025
m-reuter
reviewed
Nov 12, 2025
m-reuter
reviewed
Nov 12, 2025
dkuegler
force-pushed
the
dev
branch
4 times, most recently
from
9232375 to
fc81092
Compare
… during review + merge
resolving several issues from the review, like using concurrent.futures.* Cleanup, optimizations and formatting (e.g. variable names)
change the default settings of various output files to lighter default settings while keeping the ability to have those outputs, e.g. for qc output. rename, standardize and improve "meaningfulness" of variable names Update typing and docstrings Remove unwanted extra empty lines and debugging plots (comments) Use suppress_stdout from FastSurfer (which uses redirect_stdout) instead of the new implementation HidePrints add and optimize parallelization across multiple files (halfs processing time of fastsurfer-cc.py) move some constant values from various files into constants or just use the constants that were already available fix several functions broken by myself in review or other commits make plotly html plots use cdn-delivered javascript to significantly reduce he size of files Remove redundant function parts in recon_cc_surf_measures_multi Reorder arguments in recon_cc_surf_measure Integrate FastSurferCC into run_fastsurfer, create stats files of updated aseg and asegdkt Update on-demand execution of FastSurferCC in recon-surf Add additional option to also reduce asegdkt to aseg in paint_cc_into_pred
Fix typos in typing and docstrings
improve type annotations of brainvolstats. Fix CC measure computation Fix conform check in paint_cc_in_pred
…surfer_cc.py CLI interface and internal code complexity.
update plotting in localization of ac pc
other fixes?!
…ur, fsaverage. Fixed multithreading bug. Documentation
…, multiple bugfixes
- Add types with documentation - Move contour documentation into contour module
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
3 participants
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.
This PR contains corpus callosum segmentation, head pose normalization and corpus callosum analysis modules.
This is work in progress. Integration in the run_fastsurfer.sh script is pending, and weights are not online yet.