Improved CC & AC/PC editing

[ClePol]

Summary

• add a manual correction workflow for upright corpus callosum segmentations
• recompute CC morphometry, subdivisions, surfaces, QC outputs, and original-space outputs from corrected segmentations
• support manually supplied 3D AC/PC voxel coordinates
• align the midsagittal plane to supplied AC/PC landmarks
• document native, Docker, and Singularity/Apptainer expert workflows

Manual-edit behavior

Manual segmentations use label 192 for the corpus callosum and optionally label 250 for the fornix.
This can be done through run_fastsurfer.sh --edits, finding the cc.upright.manedit.mgz or through the fastsurfer_cc.py script.

Validation

• CC editing and landmark tests pass
• Ruff & doc builds
• Automatic and manually corrected Docker workflows tested on a real FastSurfer subject

[Copilot]

⚠️ Human review recommended

It changes core geometric alignment and segmentation mapping behavior (midplane transforms + edited-segmentation remapping), which warrants domain-specific validation beyond what can be safely inferred from diff review alone.

Pull request overview

This PR extends the FastSurfer Corpus Callosum (CC) module with an expert-facing workflow for (1) manual correction of upright CC segmentations and (2) optionally supplying AC/PC voxel landmarks to condition processing and refine midsagittal-plane alignment, along with documentation updates to describe the new workflows and outputs.

Changes:

• Add support for manual upright CC edits (*.upright.manedit.mgz) and recompute CC-derived outputs, including generating callosum.CC.orig.manedit.mgz for downstream inpainting.
• Add expert CLI support for manually supplied AC/PC voxel coordinates and adjust midplane alignment to contain those landmarks.
• Update CLI help and documentation for native/Docker/Singularity expert workflows and new/updated output files/metadata.

File summaries

File	Description
run_fastsurfer.sh	Wires --qc_snap to emit an upright reference volume, enforces upright CC edit usage, and forwards upright manedit segmentation into fastsurfer_cc.py.
doc/scripts/fastsurfer_cc.rst	Documents expert AC/PC landmark input and the upright CC manual-edit workflow (including container examples).
doc/overview/OUTPUT_FILES.md	Adds callosum.CC.orig.manedit.mgz and clarifies when upright_volume.mgz is produced.
doc/overview/modules/CC.md	Documents new JSON metadata fields describing landmark and segmentation sources.
doc/overview/EDITING.md	Adds end-to-end CC upright edit instructions for the top-level run_fastsurfer.sh --edits workflow.
CorpusCallosum/utils/mapping_helpers.py	Adds mapping of edited upright hard segmentations back to original space with regenerated subdivision labels and fornix handling.
CorpusCallosum/utils/editing.py	New utilities for path suffixing, AC/PC validation, and robust loading/validation of manual upright segmentations.
CorpusCallosum/registration/midsagittal_plane_alignment.py	Extends midplane transform resolution to optionally incorporate supplied AC/PC landmark constraints.
CorpusCallosum/registration/landmarks.py	New landmark-based midplane adjustment logic plus diagnostics emission.
CorpusCallosum/README.md	Expands expert quickstart with native/Docker/Singularity commands and mentions landmark/manual-edit support.
CorpusCallosum/fastsurfer_cc.py	Adds expert CLI args (--segmentation_manedit, --ac_coords, --pc_coords), conditional model loading, and manual-edit reprocessing/mapping behavior.

Review details

• Files reviewed: 11/11 changed files
• Comments generated: 0
• Review effort level: Low

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[ClePol]

For human reviewers:
The default path outside of --edits is unchanged. Only two minor changes:

• The statistics JSON gains landmark_source: "model" and segmentation_source: "model"
• --qc_snap now additionally creates mri/upright_volume.mgz