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.
Introduce the third segmentation pipeline using MONAI (1.6.x) to allow
direct comparison with Pipelines A and B. This includes the implementation
of the iterative pseudo-labeling workflow, training scripts, and
inference protocols.
- Add `scripts_monai/` directory containing the MONAI pipeline scripts.
- Update documentation in `README.md` and `AGENTS.md` to include MONAI
package requirements and pipeline details.
- Configure `.gitignore` to exclude MONAI-specific run directories.
- Update data directory descriptions to include MONAI pseudo-labels.
Update README.md to include detailed project overview, environment
requirements, data sources, and a comprehensive directory layout.
Add nnU-Net pipeline documentation and directory descriptions.
Update .gitignore to exclude nnU-Net specific directories and add
new scripts directory for nnU-Net pipeline.
Add initial nnU-Net pipeline scripts.
