CC documentation & final testing #763
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…r consistency (identical results) Add --conformed_name with orig image to fastsurfer_cc.py call in run_fastsurfer.sh
Fix output files formatting
Fix more formatting of Markdown files
m-reuter
previously requested changes
Jan 14, 2026
m-reuter
approved these changes
Jan 14, 2026
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Pull request overview
This PR cleans up the Corpus Callosum (CC) module documentation and fixes a coordinate transformation bug in preparation for release. The changes reorganize documentation across multiple files, fix a critical bug in AC/PC coordinate calculation, and improve code consistency in the subdivision logic.
Changes:
- Fixed coordinate transformation bug where AC/PC coordinates were incorrectly calculated by mixing RAS and voxel coordinates
- Reorganized CC documentation into three focused sections: module overview, advanced options, and output files
- Improved subdivision code consistency by always transforming midline to ACPC space before subdivision
Reviewed changes
Copilot reviewed 7 out of 7 changed files in this pull request and generated 3 comments.
Show a summary per file
| File | Description |
|---|---|
| run_fastsurfer.sh | Added --conformed_name parameter to fastsurfer_cc.py call |
| doc/scripts/fastsurfer_cc.rst | Cleaned up and expanded documentation with quality control and analysis mode sections |
| doc/overview/modules/CC.md | Restructured to focus on JSON output structure, removed duplicate content |
| doc/overview/OUTPUT_FILES.md | Updated file naming conventions and descriptions for CC module outputs |
| CorpusCallosum/shape/postprocessing.py | Fixed subdivision to consistently use ACPC space for all subdivision methods |
| CorpusCallosum/fastsurfer_cc.py | Fixed AC/PC coordinate transformation bug, removed unused TypeVar import |
| CorpusCallosum/README.md | Updated documentation structure with clearer organization |
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Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
Member
|
@m-reuter all items from co-pilot are resolved/fixed. |
Remove dev flag from run_fastsurfer.sh
Member
|
I found another issue in CC, halting merge for now. |
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I updated the CC documentation to clean it up and match the status for the release.
This PR also serves as point to commit last changes before I run final tests, therefore I'm putting it into draft mode. I will remove the draft label when all tests ran successfully.