seqseg 2.1.6__tar.gz → 2.1.8__tar.gz

seqseg-2.1.8/PKG-INFO

@@ -0,0 +1,146 @@
+Metadata-Version: 2.4
+Name: seqseg
+Version: 2.1.8
+Summary: A deep learning-based medical image blood vessel tracking and segmentation tool.
+Author-email: Numi Sveinsson Cepero <numi@berkeley.com>
+License: Apache-2.0
+Project-URL: homepage, https://github.com/numisveinsson/SeqSeg
+Project-URL: repository, https://github.com/numisveinsson/SeqSeg
+Keywords: segmentation,deep learning,medical imaging,nnunet,medical image analysis,medical image segmentation,nnU-Net,blood vessel segmentation,vascular segmentation,vascular tracking,seqseg
+Classifier: Programming Language :: Python :: 3
+Classifier: License :: OSI Approved :: Apache Software License
+Classifier: Operating System :: OS Independent
+Classifier: Intended Audience :: Science/Research
+Classifier: Intended Audience :: Healthcare Industry
+Classifier: Topic :: Scientific/Engineering :: Artificial Intelligence
+Classifier: Topic :: Scientific/Engineering :: Image Recognition
+Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: vtk>9
+Requires-Dist: SimpleITK>2
+Requires-Dist: PyYAML==6.0.3
+Requires-Dist: nnunetv2>=2.5.1
+Requires-Dist: scipy
+Requires-Dist: vascular-segment-sampler>=0.6.0
+Provides-Extra: dev
+Requires-Dist: pytest>=7; extra == "dev"
+Provides-Extra: viz
+Requires-Dist: matplotlib>=3.5; extra == "viz"
+Dynamic: license-file
+
+![test seqseg without torch build](https://github.com/numisveinsson/SeqSeg/actions/workflows/python-app.yml/badge.svg)
+![test seqseg build](https://github.com/numisveinsson/SeqSeg/actions/workflows/test.yml/badge.svg)
+
+<p align="center">
+  <img src="https://raw.githubusercontent.com/numisveinsson/SeqSeg/main/seqseg/assets/seqseg_logo.png" alt="SeqSeg — Sequential Vessel Segmentation" width="480"/><br/>
+  <img src="https://raw.githubusercontent.com/numisveinsson/SeqSeg/main/seqseg/assets/coronary.png" alt="Example coronary segmentation (SeqSeg)" width="260"/>
+</p>
+
+<h1 align="center">SeqSeg: Sequential Vessel Segmentation and Tracking</h1>
+
+<p align="center">
+  <b>Automatic tracking and segmentation of blood vessels in CT and MR images using deep learning and geometric tracking.</b>
+</p>
+
+<p align="center">
+  <a href="https://rdcu.be/dU0wy"><img src="https://img.shields.io/badge/Paper-Annals%20of%20BME-blue" alt="Paper"/></a>
+  <a href="https://github.com/numisveinsson/SeqSeg/blob/main/LICENSE"><img src="https://img.shields.io/badge/License-Apache%202.0-green.svg" alt="License"/></a>
+  <a href="https://www.python.org"><img src="https://img.shields.io/badge/Python-3.9%2B-blue.svg" alt="Python 3.9+"/></a>
+</p>
+
+## Why SeqSeg?
+
+SeqSeg segments vessels **sequentially**, taking steps along vessel centerlines and detecting bifurcations to grow complete vascular trees from just **1–2 seed points**. By combining local deep-learning predictions (nnU-Net) with geometric tracking, it stays robust across vessel scales — from small coronaries to large aortas.
+
+- 🌱 **Minimal supervision** — only 1–2 seed points to initialize
+- 🌿 **Robust bifurcation detection** — automatically follows every branch
+- 🩻 **Multi-modal** — works with CT and MR 3D medical images
+- 📏 **Scalable** — vessels from ~1mm coronaries to ~30mm aortas
+- ✅ **Clinically validated** — coronary, aortic, cerebral, and pulmonary anatomies (pre-trained weights for aorta CT/MR and coronary CT)
+- ⚡ **Fast** — on CPU, about 2–5 minutes for an aorta, 5–15 for a coronary tree, and 10–30 for a cerebral tree. GPU is faster. Details in [Benchmarks](docs/benchmarks.md).
+
+A finished case includes a `simvascular/` project you can open directly in SimVascular, with pathlines and contours for every segmented branch.
+
+<p align="center">
+  <img src="https://raw.githubusercontent.com/numisveinsson/SeqSeg/main/seqseg/assets/mr_model_tracing_fast_shorter.gif" alt="SeqSeg Demo"/><br/>
+  <i>Real-time demonstration: automatic segmentation of an abdominal aorta in a 3D MR scan.</i>
+</p>
+
+## Start here
+
+- **First segmentation** — the [tutorial](seqseg/tutorial/tutorial.md) runs a sample abdominal-aorta MR scan.
+- **Your own images** — [Usage](docs/usage.md) describes `images/` and `seeds.json`. The command is in [Quick Start](#quick-start).
+- **Train a model** — [Training](docs/training.md).
+
+## Quick Start
+
+Python 3.9 or newer. 3.11 is the version used in the tutorial and conda example.
+
+The [tutorial](seqseg/tutorial/tutorial.md) is the sample run (abdominal-aorta MR, seed points, and Windows notes). Plan on 15–20 minutes including setup. Tracing is capped, so that part finishes in a few minutes; a real case should use the defaults.
+
+Install SeqSeg and the aorta weights below, then run `seqseg run batch` on your own data. The folder needs `images/` and `seeds.json` ([Usage](docs/usage.md)). This example is an aorta MR case. Change `-train_dataset`, `-config_name`, and `-img_ext` to match your images and weights.
+
+```bash
+pip install seqseg
+
+# Aorta and femoral weights (MR and CT)
+curl -L -o nnUNet_results.zip https://zenodo.org/records/15020477/files/nnUNet_results.zip
+unzip nnUNet_results.zip
+```
+
+[Aorta and femoral weights](https://zenodo.org/records/15020477) (`nnUNet_results.zip`). [Coronary CT weights](https://zenodo.org/records/19547894) are a separate archive, `nnUNet_results_coronary.zip`.
+
+`-nnunet_results_path` is the folder that contains `Dataset005_SEQAORTANDFEMOMR` (and the other dataset folders in that zip).
+
+```bash
+seqseg run batch \
+    -data_dir your_data/ \
+    -nnunet_results_path nnUNet_results/ \
+    -train_dataset Dataset005_SEQAORTANDFEMOMR \
+    -config_name global_aorta \
+    -img_ext .mha \
+    -outdir results/
+```
+
+| Anatomy | `-train_dataset` | `-config_name` |
+|---------|------------------|----------------|
+| Aorta / femoral MR | `Dataset005_SEQAORTANDFEMOMR` | `global_aorta` |
+| Aorta / femoral CT | `Dataset006_SEQAORTANDFEMOCT` | `global_aorta` |
+| Coronary CT | `Dataset010_SEQCOROASOCACT` | `global_coro` |
+
+The tutorial uses `-config_name aorta_tutorial` for its sample scan. The trainer-folder layout is in [Installation](docs/installation.md). The full command list and flag spelling are in [Usage](docs/usage.md).
+
+## Documentation
+
+| Job | Guide | Description |
+|-----|-------|-------------|
+| Run | [Installation](docs/installation.md) | Setup, dependencies, and pre-trained model weights |
+| Run | [Tutorial](seqseg/tutorial/tutorial.md) | End-to-end aorta example with sample data |
+| Run | [Usage](docs/usage.md) | Data layout, seeds, CLI arguments, and output files |
+| Run | [Configuration](docs/configuration.md) | YAML configs and tracking parameters |
+| Train | [Training](docs/training.md) | Train nnU-Net models on a new dataset |
+| Understand | [Algorithm Overview](docs/algorithm.md) | Methodology, workflow, and training strategy |
+| Understand | [Performance & Benchmarks](docs/benchmarks.md) | Accuracy, timing, and qualitative comparisons |
+| Integrate | [API](docs/api.md) | Call tracing from Python |
+| Integrate | [Research & Development](docs/development.md) | SimVascular, 3D Slicer, and repository layout |
+
+## Citation
+
+When using SeqSeg, please cite the following [paper](https://rdcu.be/dU0wy):
+
+```
+@Article{SveinssonCepero2024,
+author={Sveinsson Cepero, Numi
+and Shadden, Shawn C.},
+title={SeqSeg: Learning Local Segments for Automatic Vascular Model Construction},
+journal={Annals of Biomedical Engineering},
+year={2024},
+month={Sep},
+day={18},
+issn={1573-9686},
+doi={10.1007/s10439-024-03611-z},
+url={https://doi.org/10.1007/s10439-024-03611-z},
+}
+```

seqseg-2.1.8/README.md

@@ -0,0 +1,114 @@
+![test seqseg without torch build](https://github.com/numisveinsson/SeqSeg/actions/workflows/python-app.yml/badge.svg)
+![test seqseg build](https://github.com/numisveinsson/SeqSeg/actions/workflows/test.yml/badge.svg)
+
+<p align="center">
+  <img src="https://raw.githubusercontent.com/numisveinsson/SeqSeg/main/seqseg/assets/seqseg_logo.png" alt="SeqSeg — Sequential Vessel Segmentation" width="480"/><br/>
+  <img src="https://raw.githubusercontent.com/numisveinsson/SeqSeg/main/seqseg/assets/coronary.png" alt="Example coronary segmentation (SeqSeg)" width="260"/>
+</p>
+
+<h1 align="center">SeqSeg: Sequential Vessel Segmentation and Tracking</h1>
+
+<p align="center">
+  <b>Automatic tracking and segmentation of blood vessels in CT and MR images using deep learning and geometric tracking.</b>
+</p>
+
+<p align="center">
+  <a href="https://rdcu.be/dU0wy"><img src="https://img.shields.io/badge/Paper-Annals%20of%20BME-blue" alt="Paper"/></a>
+  <a href="https://github.com/numisveinsson/SeqSeg/blob/main/LICENSE"><img src="https://img.shields.io/badge/License-Apache%202.0-green.svg" alt="License"/></a>
+  <a href="https://www.python.org"><img src="https://img.shields.io/badge/Python-3.9%2B-blue.svg" alt="Python 3.9+"/></a>
+</p>
+
+## Why SeqSeg?
+
+SeqSeg segments vessels **sequentially**, taking steps along vessel centerlines and detecting bifurcations to grow complete vascular trees from just **1–2 seed points**. By combining local deep-learning predictions (nnU-Net) with geometric tracking, it stays robust across vessel scales — from small coronaries to large aortas.
+
+- 🌱 **Minimal supervision** — only 1–2 seed points to initialize
+- 🌿 **Robust bifurcation detection** — automatically follows every branch
+- 🩻 **Multi-modal** — works with CT and MR 3D medical images
+- 📏 **Scalable** — vessels from ~1mm coronaries to ~30mm aortas
+- ✅ **Clinically validated** — coronary, aortic, cerebral, and pulmonary anatomies (pre-trained weights for aorta CT/MR and coronary CT)
+- ⚡ **Fast** — on CPU, about 2–5 minutes for an aorta, 5–15 for a coronary tree, and 10–30 for a cerebral tree. GPU is faster. Details in [Benchmarks](docs/benchmarks.md).
+
+A finished case includes a `simvascular/` project you can open directly in SimVascular, with pathlines and contours for every segmented branch.
+
+<p align="center">
+  <img src="https://raw.githubusercontent.com/numisveinsson/SeqSeg/main/seqseg/assets/mr_model_tracing_fast_shorter.gif" alt="SeqSeg Demo"/><br/>
+  <i>Real-time demonstration: automatic segmentation of an abdominal aorta in a 3D MR scan.</i>
+</p>
+
+## Start here
+
+- **First segmentation** — the [tutorial](seqseg/tutorial/tutorial.md) runs a sample abdominal-aorta MR scan.
+- **Your own images** — [Usage](docs/usage.md) describes `images/` and `seeds.json`. The command is in [Quick Start](#quick-start).
+- **Train a model** — [Training](docs/training.md).
+
+## Quick Start
+
+Python 3.9 or newer. 3.11 is the version used in the tutorial and conda example.
+
+The [tutorial](seqseg/tutorial/tutorial.md) is the sample run (abdominal-aorta MR, seed points, and Windows notes). Plan on 15–20 minutes including setup. Tracing is capped, so that part finishes in a few minutes; a real case should use the defaults.
+
+Install SeqSeg and the aorta weights below, then run `seqseg run batch` on your own data. The folder needs `images/` and `seeds.json` ([Usage](docs/usage.md)). This example is an aorta MR case. Change `-train_dataset`, `-config_name`, and `-img_ext` to match your images and weights.
+
+```bash
+pip install seqseg
+
+# Aorta and femoral weights (MR and CT)
+curl -L -o nnUNet_results.zip https://zenodo.org/records/15020477/files/nnUNet_results.zip
+unzip nnUNet_results.zip
+```
+
+[Aorta and femoral weights](https://zenodo.org/records/15020477) (`nnUNet_results.zip`). [Coronary CT weights](https://zenodo.org/records/19547894) are a separate archive, `nnUNet_results_coronary.zip`.
+
+`-nnunet_results_path` is the folder that contains `Dataset005_SEQAORTANDFEMOMR` (and the other dataset folders in that zip).
+
+```bash
+seqseg run batch \
+    -data_dir your_data/ \
+    -nnunet_results_path nnUNet_results/ \
+    -train_dataset Dataset005_SEQAORTANDFEMOMR \
+    -config_name global_aorta \
+    -img_ext .mha \
+    -outdir results/
+```
+
+| Anatomy | `-train_dataset` | `-config_name` |
+|---------|------------------|----------------|
+| Aorta / femoral MR | `Dataset005_SEQAORTANDFEMOMR` | `global_aorta` |
+| Aorta / femoral CT | `Dataset006_SEQAORTANDFEMOCT` | `global_aorta` |
+| Coronary CT | `Dataset010_SEQCOROASOCACT` | `global_coro` |
+
+The tutorial uses `-config_name aorta_tutorial` for its sample scan. The trainer-folder layout is in [Installation](docs/installation.md). The full command list and flag spelling are in [Usage](docs/usage.md).
+
+## Documentation
+
+| Job | Guide | Description |
+|-----|-------|-------------|
+| Run | [Installation](docs/installation.md) | Setup, dependencies, and pre-trained model weights |
+| Run | [Tutorial](seqseg/tutorial/tutorial.md) | End-to-end aorta example with sample data |
+| Run | [Usage](docs/usage.md) | Data layout, seeds, CLI arguments, and output files |
+| Run | [Configuration](docs/configuration.md) | YAML configs and tracking parameters |
+| Train | [Training](docs/training.md) | Train nnU-Net models on a new dataset |
+| Understand | [Algorithm Overview](docs/algorithm.md) | Methodology, workflow, and training strategy |
+| Understand | [Performance & Benchmarks](docs/benchmarks.md) | Accuracy, timing, and qualitative comparisons |
+| Integrate | [API](docs/api.md) | Call tracing from Python |
+| Integrate | [Research & Development](docs/development.md) | SimVascular, 3D Slicer, and repository layout |
+
+## Citation
+
+When using SeqSeg, please cite the following [paper](https://rdcu.be/dU0wy):
+
+```
+@Article{SveinssonCepero2024,
+author={Sveinsson Cepero, Numi
+and Shadden, Shawn C.},
+title={SeqSeg: Learning Local Segments for Automatic Vascular Model Construction},
+journal={Annals of Biomedical Engineering},
+year={2024},
+month={Sep},
+day={18},
+issn={1573-9686},
+doi={10.1007/s10439-024-03611-z},
+url={https://doi.org/10.1007/s10439-024-03611-z},
+}
+```

{seqseg-2.1.6 → seqseg-2.1.8}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "seqseg"
-version = "2.1.6"
+version = "2.1.8"
 description = "A deep learning-based medical image blood vessel tracking and segmentation tool."
 readme = "README.md"
 requires-python = ">=3.9"
@@ -42,6 +42,7 @@ dependencies = [
     "PyYAML==6.0.3",
     "nnunetv2>=2.5.1",
     "scipy",
+    "vascular-segment-sampler>=0.6.0",
 ]
 
 [project.scripts]
@@ -62,9 +63,6 @@ dev = [
 viz = [
   "matplotlib>=3.5",
 ]
-train = [
-  "vascular-segment-sampler>=0.1.0",
-]
 
 [tool.pytest.ini_options]
 testpaths = ["seqseg/tests"]

{seqseg-2.1.6 → seqseg-2.1.8}/seqseg/cli.py

@@ -225,7 +225,8 @@ def _validate_trace_batch(ns: argparse.Namespace) -> None:
             + "\n  ".join(missing)
             + "\n\nMinimal example:\n"
             "  seqseg paths init\n"
-            "  seqseg paths set --data-dir /path/to/dataset --outdir /path/to/out\n"
+            "  seqseg paths set --nnunet-root ~/nnunet_data "
+            "--data-dir /path/to/dataset --outdir /path/to/out\n"
             "  seqseg run batch -img_ext .nii.gz "
             "-train_dataset Dataset010_SEQCOROASOCACT\n",
             file=sys.stderr,
@@ -435,9 +436,8 @@ def _cmd_init_dataset(ns: argparse.Namespace) -> None:
         f"  seqseg run batch -data_dir {root}/ -outdir ... -img_ext .nii.gz "
         "-nnunet_results_path ...\n"
         "\nNext (train a new model): also fill centerlines/ and truths/, then:\n"
-        f'  pip install "seqseg[train]"\n'
         f"  seqseg paths init --data-dir {root}/ --outdir ~/seqseg_train\n"
-        "  seqseg train prepare --name MYDATA --dataset-number 999 --modality CT\n"
+        "  seqseg train prepare --name MYDATA --dataset-id 999 --modality CT\n"
     )
 
 
@@ -550,10 +550,7 @@ def _cmd_doctor(ns: argparse.Namespace) -> None:
         try:
             importlib.import_module(modname)
         except ImportError as e:
-            extra = ""
-            if modname == "vascular_segment_sampler":
-                extra = ' — optional; pip install "seqseg[train]"'
-            print(f"  {label}: MISSING ({e}){extra}")
+            print(f"  {label}: MISSING ({e})")
         else:
             print(f"  {label}: OK")
 
@@ -592,19 +589,9 @@ def _cmd_paths_init(ns: argparse.Namespace) -> None:
 
 
 def _cmd_paths_set(ns: argparse.Namespace) -> None:
-    fields = (
-        ns.nnunet_root,
-        ns.nnunet_raw,
-        ns.nnunet_preprocessed,
-        ns.nnunet_results,
-        ns.data_dir,
-        ns.outdir,
-    )
-    if not any(f is not None for f in fields):
+    if not ns.nnunet_root:
         print(
-            "seqseg paths set: provide at least one of "
-            "--nnunet-root, --nnunet-raw, --nnunet-preprocessed, "
-            "--nnunet-results, --data-dir, --outdir",
+            "seqseg paths set: --nnunet-root is required",
             file=sys.stderr,
         )
         sys.exit(2)
@@ -647,6 +634,12 @@ def _cmd_paths_export(_ns: argparse.Namespace) -> None:
 
 
 def _cmd_train_prepare(ns: argparse.Namespace) -> None:
+    if not ns.preprocess_only and not ns.name:
+        print(
+            "seqseg train prepare: --name is required",
+            file=sys.stderr,
+        )
+        sys.exit(2)
     try:
         result = prepare_training_dataset(
             data_dir=ns.data_dir,
@@ -669,14 +662,31 @@ def _cmd_train_prepare(ns: argparse.Namespace) -> None:
             skip_sample=ns.skip_sample,
             skip_convert=ns.skip_convert,
             also_test=ns.also_test,
-            yes=ns.yes,
             verbose=ns.verbose,
             img_ext=ns.img_ext,
             global_volumes=ns.global_volumes,
+            keep_extracted=ns.keep_extracted,
+            configuration=ns.configuration,
+            plans=ns.plans,
+            np=ns.np,
+            preprocess_only=ns.preprocess_only,
         )
     except TrainDependencyError as e:
         print(str(e), file=sys.stderr)
         sys.exit(1)
+    except FileNotFoundError as e:
+        message = str(e)
+        if message.startswith("Sampler config"):
+            print(message, file=sys.stderr)
+            sys.exit(2)
+        if "seqseg train prepare" in message:
+            print(message, file=sys.stderr)
+            sys.exit(1)
+        import traceback
+
+        traceback.print_exc()
+        print(f"seqseg train prepare failed: {e}", file=sys.stderr)
+        sys.exit(1)
     except Exception as e:  # noqa: BLE001
         import traceback
 
@@ -693,8 +703,29 @@ def _cmd_train_prepare(ns: argparse.Namespace) -> None:
         sys.exit(1)
 
     print("\nPrepare complete.")
-    kind = "Whole volumes" if ns.global_volumes else "Patches"
-    print(f"  {kind}: {result.extracted_dir}")
+    if ns.preprocess_only:
+        print(
+            f"  Preprocessed {ns.configuration} from the existing raw dataset."
+        )
+    elif result.removed_staging:
+        print(
+            "  Extracted volumes were linked into nnU-Net raw and the "
+            "temporary folder was removed."
+        )
+    else:
+        kind = "Whole volumes" if ns.global_volumes else "Patches"
+        print(f"  {kind}: {result.extracted_dir}")
+    if not result.preprocessed:
+        print(
+            "  nnU-Net preprocessing was skipped (--skip-convert). "
+            "Re-run prepare without --skip-convert before training."
+        )
+    results = resolve_path("nnunet_results")
+    if results:
+        print(f"  Trained models will be written under: {results}")
+    config_flag = ""
+    if ns.configuration != "3d_fullres":
+        config_flag = f" --configuration {ns.configuration}"
     for name, path in zip(result.dataset_names, result.dataset_dirs):
         try:
             ds_id = dataset_id_from_name(name)
@@ -702,11 +733,12 @@ def _cmd_train_prepare(ns: argparse.Namespace) -> None:
             ds_id = "?"
         print(f"  nnU-Net dataset: {name}")
         print(f"    path: {path}")
-        print(
-            "    next:\n"
-            f"      seqseg train nnunet --dataset-id {ds_id} "
-            "--configuration 3d_fullres --fold 0"
-        )
+        if result.preprocessed:
+            print(
+                "    next:\n"
+                f"      seqseg train nnunet --dataset-id {ds_id}"
+                f"{config_flag} --fold 0"
+            )
 
 
 def _cmd_train_nnunet(ns: argparse.Namespace) -> None:
@@ -729,11 +761,10 @@ def _cmd_train_nnunet(ns: argparse.Namespace) -> None:
             dataset_id,
             configuration=ns.configuration,
             fold=ns.fold,
-            skip_plan=ns.skip_plan,
-            plan_only=ns.plan_only,
-            np=ns.np,
             trainer=ns.trainer,
             plans=ns.plans,
+            cleanup=ns.cleanup,
+            continue_training=ns.continue_training,
         )
     except Exception as e:  # noqa: BLE001
         print(f"seqseg train nnunet failed: {e}", file=sys.stderr)
@@ -921,8 +952,18 @@ def _build_parser() -> argparse.ArgumentParser:
     g1 = gcl_sub.add_parser("single", formatter_class=argparse.ArgumentDefaultsHelpFormatter)
     g1.add_argument("--seg", required=True, type=str)
     g1.add_argument("--out", required=True, type=str)
-    g1.add_argument("--seeds-json", required=True, type=str)
-    g1.add_argument("--case-name", required=True, type=str)
+    g1.add_argument(
+        "--seeds-json",
+        default=None,
+        type=str,
+        help="Dataset seeds.json. Omit to place one seed in each disconnected body",
+    )
+    g1.add_argument(
+        "--case-name",
+        default=None,
+        type=str,
+        help="Case name in seeds.json. Required when --seeds-json is set",
+    )
     g1.add_argument("--config-name", default=None, type=str)
     g1.add_argument("--merge-method", default="clean", type=str)
     g1.add_argument("--directory-data", default=None, type=str)
@@ -932,7 +973,12 @@ def _build_parser() -> argparse.ArgumentParser:
     g2 = gcl_sub.add_parser("batch", formatter_class=argparse.ArgumentDefaultsHelpFormatter)
     g2.add_argument("--seg-dir", required=True, type=str)
     g2.add_argument("--seg-glob", required=True, type=str)
-    g2.add_argument("--seeds-json", required=True, type=str)
+    g2.add_argument(
+        "--seeds-json",
+        default=None,
+        type=str,
+        help="Dataset seeds.json. Omit to place one seed in each disconnected body",
+    )
     g2.add_argument("--out-dir", default=None, type=str)
     g2.add_argument("--config-name", default=None, type=str)
     g2.add_argument("--merge-method", default="clean", type=str)
@@ -998,7 +1044,7 @@ def _build_parser() -> argparse.ArgumentParser:
 
     p_prep = train_sub.add_parser(
         "prepare",
-        help="Prepare patches or whole volumes and convert to nnU-Net DatasetXXX format",
+        help="Extract volumes, write an nnU-Net dataset, and plan/preprocess",
         formatter_class=argparse.ArgumentDefaultsHelpFormatter,
     )
     p_prep.add_argument(
@@ -1014,22 +1060,27 @@ def _build_parser() -> argparse.ArgumentParser:
         "-outdir",
         default=None,
         type=str,
-        help="Directory for extracted patches or whole volumes "
-        "(default: seqseg paths outdir, else ./extracted_data/)",
+        help="Optional scratch directory for extracted patches or whole volumes. "
+        "Default: <parent of nnUNet_raw>/_seqseg_extracted, removed after "
+        "conversion. Pass this to keep extracts or resume with --skip-sample.",
     )
     p_prep.add_argument(
         "--name",
         "-name",
-        required=True,
+        default=None,
         type=str,
-        help="Dataset name stem (e.g. MYDATA → Dataset0XX_MYDATACT)",
+        help="Dataset name stem (e.g. MYDATA → Dataset0XX_MYDATACT). "
+        "Required unless --preprocess-only",
     )
     p_prep.add_argument(
+        "--dataset-id",
         "--dataset-number",
         "-dataset_number",
+        dest="dataset_number",
         required=True,
         type=int,
-        help="nnU-Net dataset id (e.g. 999). Incremented per modality if several",
+        help="nnU-Net dataset id to create (e.g. 999). "
+        "Incremented per modality if several",
     )
     p_prep.add_argument(
         "--modality",
@@ -1041,7 +1092,7 @@ def _build_parser() -> argparse.ArgumentParser:
     p_prep.add_argument(
         "--config-name",
         "-config_name",
-        default="global",
+        default="default_mm",
         type=str,
         help="Sampler YAML name/path (from vascular-segment-sampler)",
     )
@@ -1050,7 +1101,7 @@ def _build_parser() -> argparse.ArgumentParser:
         default=None,
         type=str,
         help="Write DatasetXXX_* here "
-        "(default: seqseg paths nnunet_raw / $nnUNet_raw; else --outdir)",
+        "(default: seqseg paths nnunet_raw / $nnUNet_raw)",
     )
     p_prep.add_argument(
         "--img-ext",
@@ -1101,13 +1152,41 @@ def _build_parser() -> argparse.ArgumentParser:
         action="store_true",
         help="Also convert modality_test folders when present",
     )
-    p_prep.add_argument("--yes", action="store_true", help="Non-interactive confirms")
     p_prep.add_argument("--verbose", action="store_true")
+    p_prep.add_argument(
+        "--keep-extracted",
+        action="store_true",
+        help="Keep <nnunet-root>/_seqseg_extracted after conversion into nnUNet_raw",
+    )
+    p_prep.add_argument(
+        "--configuration",
+        default="3d_fullres",
+        choices=["3d_fullres", "2d", "3d_lowres", "3d_cascade_fullres"],
+        help="nnU-Net configuration to preprocess. Default 3d_fullres",
+    )
+    p_prep.add_argument(
+        "--plans",
+        default="nnUNetPlans",
+        type=str,
+        help="nnU-Net plans name (training -p). Default nnUNetPlans",
+    )
+    p_prep.add_argument(
+        "--np",
+        type=int,
+        default=None,
+        help="Processes for nnU-Net preprocessing. Default: --num-cores",
+    )
+    p_prep.add_argument(
+        "--preprocess-only",
+        action="store_true",
+        help="Preprocess another configuration from an existing raw dataset "
+        "and plans file. Does not extract or convert subvolumes",
+    )
     p_prep.set_defaults(_handler=_cmd_train_prepare, img_ext=None)
 
     p_nn = train_sub.add_parser(
         "nnunet",
-        help="Run nnUNetv2_plan_and_preprocess and/or nnUNetv2_train",
+        help="Train with nnUNetv2_train (--c continues from the latest checkpoint)",
         formatter_class=argparse.ArgumentDefaultsHelpFormatter,
     )
     p_nn.add_argument(
@@ -1120,13 +1199,13 @@ def _build_parser() -> argparse.ArgumentParser:
         "--dataset-name",
         type=str,
         default=None,
-        help="Alternative to --dataset-id (e.g. Dataset0999_MYDATACT)",
+        help="Alternative to --dataset-id (e.g. Dataset999_MYDATACT)",
     )
     p_nn.add_argument(
         "--configuration",
         default="3d_fullres",
         choices=["3d_fullres", "2d", "3d_lowres", "3d_cascade_fullres"],
-        help="nnU-Net configuration for preprocessing (-c) and training",
+        help="nnU-Net configuration to train. Default 3d_fullres",
     )
     p_nn.add_argument(
         "--fold",
@@ -1135,23 +1214,21 @@ def _build_parser() -> argparse.ArgumentParser:
         help="Fold to train (0-4 or all)",
     )
     p_nn.add_argument(
-        "--skip-plan",
+        "--c",
+        "--continue",
+        dest="continue_training",
         action="store_true",
-        help="Skip plan_and_preprocess; only train",
+        help="Continue training from checkpoint_latest.pth (nnU-Net --c)",
     )
+    p_nn.add_argument("--trainer", default="nnUNetTrainer", type=str)
+    p_nn.add_argument("--plans", default="nnUNetPlans", type=str)
     p_nn.add_argument(
-        "--plan-only",
+        "--cleanup",
         action="store_true",
-        help="Only run plan_and_preprocess",
+        help="After training succeeds, delete this dataset's nnUNet_raw and "
+        "nnUNet_preprocessed folders. Leaves nnUNet_results. "
+        "A later --c run needs that preprocessed data.",
     )
-    p_nn.add_argument(
-        "--np",
-        type=int,
-        default=None,
-        help="Processes for plan_and_preprocess (-np)",
-    )
-    p_nn.add_argument("--trainer", default="nnUNetTrainer", type=str)
-    p_nn.add_argument("--plans", default="nnUNetPlans", type=str)
     p_nn.set_defaults(_handler=_cmd_train_nnunet)
 
     paths_p = sub.add_parser(
@@ -1194,10 +1271,15 @@ def _build_parser() -> argparse.ArgumentParser:
 
     p_set = paths_sub.add_parser(
         "set",
-        help="Update one or more saved paths",
+        help="Update saved paths (requires --nnunet-root)",
         formatter_class=argparse.ArgumentDefaultsHelpFormatter,
     )
-    p_set.add_argument("--nnunet-root", default=None, type=str)
+    p_set.add_argument(
+        "--nnunet-root",
+        required=True,
+        type=str,
+        help="Parent directory for nnUNet_raw / preprocessed / results",
+    )
     p_set.add_argument("--nnunet-raw", default=None, type=str)
     p_set.add_argument("--nnunet-preprocessed", default=None, type=str)
     p_set.add_argument("--nnunet-results", default=None, type=str)

{seqseg-2.1.6 → seqseg-2.1.8}/seqseg/config/global.yaml

@@ -14,6 +14,7 @@ TREE_ANALYSIS: False
 
 VOLUME_SIZE_RATIO: 5 # default 5, 5.5 for coronaries, 4 for segs
 MAGN_RADIUS: 1
+ADD_RADIUS: 0 # mm (keep in mm)
 MAX_PERC_ENLARGE: 0.3 # if percent of blood in a given volume goes above this, we try enlarging volume, default 0.33 for coronaries
 MIN_RADIUS: 0.3 # mm (keep in mm)
 MIN_RES: 6

{seqseg-2.1.6 → seqseg-2.1.8}/seqseg/config/global_cereb.yaml

@@ -2,7 +2,7 @@
 # True if we have a segmentation, False if we are predicting
 SEGMENTATION: False # usually False
 
-DEBUG: True
+DEBUG: False
 DEBUG_STEP: 200
 
 ANIMATION: True # to write out animation files