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Furen Xiao e7721760f2 Enhance MONAI training scripts and models for Pipeline B and C 
- Updated `05_monai_run_iterative.py` to include legacy mode and improved configuration options for training.
- Introduced `UNetBAligned` class in `monai_common.py` for deep supervision and instance normalization.
- Modified `train_transform` and `make_dataloader` in `monai_common.py` to support B-aligned data protocol with Z-score normalization and augmentation.
- Added new loss functions `nn_dc_and_ce` and `b_dc_and_ce` in `losses.py` for improved training performance.
- Enhanced `Unet3D` architecture in `unet3d.py` to support leaky ReLU and deep supervision.
- Created new augmentation functions in `augment_b.py` for Pipeline B's training, including rotation, scaling, and noise.
- Implemented new training scripts `run_b_100ep_stages.sh` and `run_c_bloss_100ep_after_b.sh` for structured training and evaluation.
- Updated dataset handling in `dataset.py` to accommodate new augmentation and normalization strategies.
2026-10-08 05:28:15 +08:00
..
01_build_ntuh_manifest.py feat: refactor path handling and add configuration for external data directories 2026-09-27 10:17:33 +08:00
02_build_m6_dataset.py feat(registration): implement best-of-ANTs registration for CT to T1c alignment and enhance benchmarking scripts 2026-10-04 22:22:11 +08:00
03_scan_lee_t1c.py fix(t1c): exclude TOF MRA and subtraction series 2026-09-27 18:45:09 +08:00
04_reconstruct_lee.py fix(lee): exclude SSFP sequences and enhance T1c exclusion notes 2026-09-27 15:29:02 +08:00
05_build_splits.py feat(dataset): add row-level exclusion curation for labeled volumes 2026-10-05 16:53:56 +08:00
06_pseudo_label.py feat: refactor path handling and add configuration for external data directories 2026-09-27 10:17:33 +08:00
07_train.py feat: initial project structure 2026-09-25 16:00:37 +08:00
08_eval.py feat: initial project structure 2026-09-25 16:00:37 +08:00
09_run_iterative.py feat: refactor path handling and add configuration for external data directories 2026-09-27 10:17:33 +08:00
bench_registration.py Enhance MONAI training scripts and models for Pipeline B and C 2026-10-08 05:28:15 +08:00
benchmark_pipelines.py Enhance MONAI training scripts and models for Pipeline B and C 2026-10-08 05:28:15 +08:00
investigate_synthmorph.py Refactor code structure for improved readability and maintainability 2026-10-02 19:00:07 +08:00
investigate_synthmorph_mm.py Refactor code structure for improved readability and maintainability 2026-10-02 19:00:07 +08:00
make_screenshots.py feat: refactor path handling and add configuration for external data directories 2026-09-27 10:17:33 +08:00
make_tv_slices.py feat(dataset): add row-level exclusion curation for labeled volumes 2026-10-05 16:53:56 +08:00
preprocess.py feat(registration): align CT to T1c and add benchmarking 2026-09-28 16:20:30 +08:00
qa_label_interpolation.py fix(label_qa): resample TV warps to the 0.5 mm T1c grid 2026-10-04 14:59:39 +08:00
run_b_100ep_stages.sh Enhance MONAI training scripts and models for Pipeline B and C 2026-10-08 05:28:15 +08:00
run_c_bloss_100ep_after_b.sh Enhance MONAI training scripts and models for Pipeline B and C 2026-10-08 05:28:15 +08:00
scan_procs.py feat: refactor path handling and add configuration for external data directories 2026-09-27 10:17:33 +08:00
test_dataloader.py feat: refactor path handling and add configuration for external data directories 2026-09-27 10:17:33 +08:00