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2 commits

Author SHA1 Message Date
695bbb6e11 refactor(nnu): transition to native volume processing for Pipeline B
Update the nnU-Net pipeline to operate on native (unprocessed) volumes
instead of preprocessed ones. This allows nnU-Net to utilize its own
`plan_and_preprocess` logic for resampling, cropping, and normalization,
ensuring Pipeline B remains distinct from Pipelines A and C.

- Update `scripts/05_build_splits.py` to include native `img` and `label`
  paths in the manifest rows.
- Modify `scripts_nnu/01_nnu_prepare_dataset.py` to symlink native
  volumes and implement a label fix-up mechanism for non-conforming grids.
- Update `scripts_nnu/04_nnu_pseudo_label.py` and `05_nnu_eval_test.py`
  to use native image paths and perform selection/evaluation in physical
  mm on the native grid.
- Refactor `scripts_nnu/nnu_common.py` to handle native-grid label
  alignment and volume-based selection gates.
- Update `README.md` to document the preprocessing differences between
  Pipelines A/C and Pipeline B.
2026-09-26 12:44:40 +08:00
b6fa62a763 feat: initial project structure
Add .gitignore, AGENTS.md, scripts directory, and src directory to initialize the repository.
2026-09-25 16:00:37 +08:00