Add FastSurfer-CC to the FastSurfer repository #727
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m-reuter
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Sep 18, 2025
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m-reuter
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m-reuter
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m-reuter
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Sep 26, 2025
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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. |
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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 |
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dkuegler
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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.
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dkuegler
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m-reuter
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update plotting in localization of ac pc
…nified and clearer also fixing broken transformation matrices Renaming of functions and variables for better description of function prepare processing of non-isotropic images Use lapy 1.4 function to save surface in vox2ras_tkr coordinates Rename centroid_registration to register_centroids_to_fsavg Fix vox_size arguments in multiple places Use FastSurfer's thread_executor to perform parallelization Fix generation of aseg_auto_statsfile in run_fastsurfer Add a commented solution to vectorize subsegment_contour.subsegment_midline_orthogonal Improve Error messages Update/fix docstrings improve type annotations, including additional overload signatures Add a CCMeasurementsDict TypedDict for CC Measures Reformatting Various fixes to CC generation (messages to be edited)
other fixes?!
…ur, fsaverage. Fixed multithreading bug. Documentation
…, multiple bugfixes
Cleanup of - typing - docstrings - function names - variable names
- Add types with documentation - Move contour documentation into contour module
…it a class method Remove vox2ras_tkr from fsaverage information Fix surface saving Fix --slice_selection type function Fix mapping from upright to orig space Change types of ndarrays from python to numpy Scalar types
- change instatiation of CCContour to from_* syntax - update io functions for CCContour - Optimize CCContour - Fix vox2ras_tkr application for surface to save - Add and use alternative implementation for CC endpoint finding (requires no image rotation) - Remove resolution, where it is not needed and build all vox2vox and vox2ras operations on transformation matrices (including surfaces and image to midslab/midslice)
- Resolved outstanding issues where vox_size was used, but correct application of vox2ras should have been used (subdivision mask, cc_image) - Fix cc_image - Fix subdivision mask - vectorize get_unique_contour_points - Remove resolved FIXME comments - Remove unused variables
Update CorpusCallosum to use the new lapy.Polygon interface
m-reuter
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Dec 23, 2025
FastSurfer is not compatible with numpy 2 right now, because numpy 2 has changed some of the names of datatypes.
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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.