Project-MONAI · aylward · Sep 17, 2026 · Sep 17, 2026 · Sep 17, 2026 · Sep 17, 2026
diff --git a/README.md b/README.md
@@ -26,7 +26,7 @@ diagnosis, treatment planning, or clinical decision-making.
 for users and contributors. Key sections:
 
 - [Installation](https://project-monai.github.io/monai-physio/installation.html) and [Quickstart](https://project-monai.github.io/monai-physio/quickstart.html)
-- [Tutorials](https://project-monai.github.io/monai-physio/tutorials.html) - runnable end-to-end workflows and their datasets
+- [Tutorials](https://project-monai.github.io/monai-physio/tutorials.html) - runnable end-to-end workflows and their datasets. Most numbered tutorials ship multiple organ/dataset variant scripts (heart, lung, duke_heart) that share the same workflow class, so you can see how to adapt a workflow to your own anatomy and data
 - [CLI & Scripts Guide](https://project-monai.github.io/monai-physio/cli_scripts/overview.html) - command-line tools for conversion, segmentation, registration, and USD workflows
 - [API Reference](https://project-monai.github.io/monai-physio/api/index.html) - workflow, registration, segmentation, and USD classes
 - [Developer Guides](https://project-monai.github.io/monai-physio/developer/architecture.html) - architecture, extension points, and implementation conventions
@@ -146,5 +146,8 @@ free for academic and commercial use.  https://docs.omniverse.nvidia.com/ov/late
 ### Non-commercial Licenses (optional)
 * NVIDIA Segment CT MRI AI weights (used in the SegmentNVSegmentCTMRI class,
 are restricted from commercial use. https://github.com/NVIDIA-Medtech/NV-Segment-CTMR
+* NVIDIA Segment CT AI weights (used in the SegmentNVSegmentCT class) are
+released under the NVIDIA Open Model License Agreement, research use only,
+not for clinical use. https://huggingface.co/nvidia/NV-Segment-CT
 * TotalSegmentator includes the optional use of some of their research-only models. Using those models assumes that you have
 the appropriate license key install, otherwise an error occurs.   Those models can be disabled by calling ```set_has_academic_license(False)``` member function of the ```SegmentChestTotalSegmentator``` class.
diff --git a/docs/api/index.rst b/docs/api/index.rst
@@ -53,6 +53,7 @@ By Category
    * :class:`~monai_physio.SegmentHeartSimpleware` - Simpleware cardiac segmentation
    * :class:`~monai_physio.SegmentHeartSimplewareTrimmedBranches` - Simpleware with trimmed great vessels
    * :class:`~monai_physio.SegmentNVSegmentCTMRI` - NV-Segment-CTMR, CT *and* MRI
+   * :class:`~monai_physio.SegmentNVSegmentCT` - NV-Segment-CT, CT only
 
 **Image Registration**
    * :class:`~monai_physio.RegisterImagesBase` - Base registration class

diff --git a/docs/api/segmentation/index.rst b/docs/api/segmentation/index.rst
@@ -15,6 +15,8 @@ MONAI Physio supports multiple segmentation approaches:
 * **Simpleware**: Cardiac-focused segmentation (requires Simpleware Medical)
 * **NV-Segment-CTMR**: Whole-body CT *and* MRI segmentation (345 structures,
   non-commercial license)
+* **NV-Segment-CT**: Whole-body CT-only segmentation (117 structures,
+  weights for research use only, not for clinical use)
 
 All segmentation classes inherit from :class:`SegmentAnatomyBase` and provide consistent interfaces.
 
@@ -26,6 +28,7 @@ Quick Links
    * :doc:`totalsegmentator` - TotalSegmentator implementation
    * :doc:`simpleware` - Simpleware ASCardio cardiac segmentation
    * :doc:`nv_segment_ct_mri` - NVIDIA NV-Segment-CTMR CT/MRI segmentation
+   * :doc:`nv_segment_ct` - NVIDIA NV-Segment-CT CT-only segmentation
 
 Choosing a Method
 =================
@@ -39,6 +42,9 @@ Choosing a Method
 +------------------+------------------+------------------+------------------+
 | NV-Segment-CTMR  | Medium           | Good             | CT and MRI       |
 +------------------+------------------+------------------+------------------+
+| NV-Segment-CT    | Medium           | Good             | CT-only,         |
+|                  |                  |                  | research use     |
++------------------+------------------+------------------+------------------+
 
 Quick Start
 ===========
@@ -64,6 +70,7 @@ Module Documentation
    totalsegmentator
    simpleware
    nv_segment_ct_mri
+   nv_segment_ct
 
 Common Operations
 =================
@@ -120,4 +127,5 @@ See Also
 
 .. rubric:: Navigation
 
-:doc:`../index` | :doc:`base` | :doc:`totalsegmentator` | :doc:`simpleware`
+:doc:`../index` | :doc:`base` | :doc:`totalsegmentator` | :doc:`simpleware` |
+:doc:`nv_segment_ct_mri` | :doc:`nv_segment_ct`
diff --git a/docs/api/segmentation/nv_segment_ct.rst b/docs/api/segmentation/nv_segment_ct.rst
@@ -0,0 +1,99 @@
+=============
+NV-Segment-CT
+=============
+
+.. module:: monai_physio.segment_nv_segment_ct
+.. currentmodule:: monai_physio
+
+``SegmentNVSegmentCT`` runs NVIDIA's NV-Segment-CT model (a VISTA3D
+derivative finetuned on CT scans) and groups its labelmap into the anatomy
+masks used by MONAI Physio workflows. It covers 117 "segment everything"
+classes (132 addressable via label prompt) and supports only automatic
+(label-prompt) segmentation - there is no point-click interactive branch
+exposed here.
+
+.. warning::
+
+   The NV-Segment-CT *weights* are released under the NVIDIA Open Model
+   License Agreement (research use only, not for clinical use); the
+   surrounding bundle code is Apache 2.0. NV-Segment-CTMR's weights carry a
+   different restrictive license (NVIDIA OneWay Non-Commercial License) -
+   both models are research-use-only, just under different named terms, so
+   check the license text for your use case. Use
+   ``SegmentChestTotalSegmentator`` if you need no license restriction at
+   all - its default task set is unrestricted; only its optional
+   ``heartchambers_highres`` and ``tissue_4_types`` tasks
+   (``set_has_academic_license(True)``) require a TotalSegmentator academic
+   license.
+
+Class Reference
+===============
+
+.. autoclass:: SegmentNVSegmentCT
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Basic Usage
+===========
+
+.. code-block:: python
+
+   import itk
+
+   from monai_physio import SegmentNVSegmentCT
+
+   image = itk.imread("chest_ct.nrrd")
+   segmenter = SegmentNVSegmentCT()
+
+   masks = segmenter.segment(image)
+
+   heart = masks["heart"]
+   lungs = masks["lung"]
+   labelmap = masks["labelmap"]
+
+   itk.imwrite(labelmap, "labelmap.nrrd", compression=True)
+
+NV-Segment-CT is CT-only: unlike ``SegmentNVSegmentCTMRI`` there is no
+``set_modality()`` call or MRI code path.
+
+Returned Keys
+=============
+
+For this segmenter, ``segment()`` returns a dictionary with the following
+keys:
+
+* ``labelmap``
+* ``heart``
+* ``major_vessels``
+* ``lung``
+* ``bone``
+* ``soft_tissue``
+* ``other``
+
+Label Ids
+=========
+
+Label ids are the model's own published class indices, used verbatim (see
+``NV-Segment-CT/configs/label_dict.json`` in
+https://github.com/NVIDIA-Medtech/NV-Segment-CTMR), which run to 132. For
+example, 6 is the aorta and 115 the heart. The full group->id mapping is
+available through the segmenter's ``taxonomy`` attribute
+(``segmenter.taxonomy.labels_in_group("heart")``,
+``segmenter.taxonomy.all_labels()``).
+
+Operational Notes
+=================
+
+The first call to ``segment()`` downloads ~872 MB of model weights from
+https://huggingface.co/nvidia/NV-Segment-CT into the Hugging Face cache
+(override the destination with the ``model_cache_dir`` attribute). Inference
+requires a CUDA GPU.
+
+See Also
+========
+
+* :doc:`index`
+* :doc:`nv_segment_ct_mri`
+* :doc:`totalsegmentator`
+* :doc:`../../tutorials`
diff --git a/docs/architecture.rst b/docs/architecture.rst
@@ -28,6 +28,7 @@ Data Flow
    SegmentChestTotalSegmentator / SegmentChestTotalSegmentatorWithContrast
    SegmentHeartSimpleware / SegmentHeartSimplewareTrimmedBranches
    SegmentNVSegmentCTMRI (CT + MRI)
+   SegmentNVSegmentCT (CT only)
           |
           v
    ProcessContours + ProcessTransforms
@@ -165,7 +166,8 @@ Component Boundaries
 Segmentation classes produce anatomy masks or labelmaps from ITK images.
 ``SegmentAnatomyBase`` subclasses (``SegmentChestTotalSegmentator``,
 ``SegmentChestTotalSegmentatorWithContrast``, ``SegmentHeartSimpleware``,
-``SegmentHeartSimplewareTrimmedBranches``, ``SegmentNVSegmentCTMRI``) share the
+``SegmentHeartSimplewareTrimmedBranches``, ``SegmentNVSegmentCTMRI``,
+``SegmentNVSegmentCT``) share the
 same segment/taxonomy interface, so new segmentation methods or anatomy groups
 slot in without touching the workflow layer.
 

diff --git a/docs/assets/tutorial_15_lung.png b/docs/assets/tutorial_15_lung.png
diff --git a/docs/cli_scripts/download_data.rst b/docs/cli_scripts/download_data.rst
@@ -33,6 +33,10 @@ Supported Datasets
        Physio GitHub release. See ``data/TCIA-4DLung/README.md`` for the
        data source, the full-collection manual download, and required
        citation.
+   * - ``PhysicsNeMo-MGN-Lung-Motion``
+     - Pretrained PhysicsNeMo MeshGraphNet checkpoint for lung motion, from
+       the MONAI Physio GitHub release. Used by Lung Tutorial 10 and later
+       when skipping Tutorial 9's training.
 
 Basic Usage
 ===========
@@ -51,12 +55,13 @@ Options
 
 .. code-block:: bash
 
-   monai-physio-download-data [Slicer-Heart-CT|KCL-Heart-Model|CHOP-Valve4D|Chest-CT|TCIA-4DLung] [--directory DIRECTORY]
+   monai-physio-download-data [Slicer-Heart-CT|KCL-Heart-Model|CHOP-Valve4D|Chest-CT|TCIA-4DLung|PhysicsNeMo-MGN-Lung-Motion] [--directory DIRECTORY]
 
 ``data_name``
    Dataset to download. One of ``Slicer-Heart-CT``, ``KCL-Heart-Model``,
-   ``CHOP-Valve4D``, ``Chest-CT``, or ``TCIA-4DLung``. Required - omitting
-   it prints help and exits.
+   ``CHOP-Valve4D``, ``Chest-CT``, ``TCIA-4DLung``, or
+   ``PhysicsNeMo-MGN-Lung-Motion``. Required - omitting it prints help and
+   exits.
 
 ``--directory``
    Directory where the dataset is stored. Defaults to ``data/<data_name>``.
@@ -131,6 +136,22 @@ the download entirely once any case's phase volumes are already present -
 this is a converted tutorial subset; see ``data/TCIA-4DLung/README.md`` for
 how to obtain the full TCIA 4D-Lung collection manually.
 
+For ``PhysicsNeMo-MGN-Lung-Motion``, the command downloads, extracts, and
+reuses:
+
+.. code-block:: text
+
+   tutorials/network_weights/physicsnemo_mgn_lung_motion/mgn_stage_model.pt
+   tutorials/network_weights/physicsnemo_mgn_lung_motion/  (other epoch
+       checkpoints and metadata)
+
+The command uses
+:meth:`monai_physio.download_data.DownloadData.DownloadPhysicsNeMoMGNLungMotionData`,
+which fetches ``physicsnemo_mgn_lung_motion.zip`` from the MONAI Physio
+GitHub release and skips the download once ``mgn_stage_model.pt`` is
+already present. Unlike every other dataset, its default ``--directory`` is
+``tutorials/network_weights``, not ``data/<data_name>``.
+
 See Also
 ========
 
@@ -142,7 +163,10 @@ See Also
   individually and may require registration, so it is manual-only, see
   ``data/DirLab-4DCT/README.md``. ``Duke-Heart-4DLabelmaps``, which drives the
   ten ``duke_heart`` variants, is being released soon; see
-  ``data/Duke-Heart-4DLabelmaps/README.md``.
+  ``data/Duke-Heart-4DLabelmaps/README.md``. ``PhysicsNeMo-MGN-Lung-Motion``
+  is the pretrained-checkpoint shortcut for Lung Tutorial 10 (and everything
+  downstream of it: 11-14), letting a reader skip running Tutorial 9's
+  training themselves.
 * :doc:`byod_tutorials`
 * :doc:`heart_gated_ct`
 * :doc:`overview`
diff --git a/docs/developer/migration_next.md b/docs/developer/migration_next.md
@@ -0,0 +1,39 @@
+# Migration Guide - Unreleased
+
+Breaking changes committed since the last release, and how to update code that
+depends on them.
+
+MONAI Physio prefers compatibility: public APIs are broken only when the change
+is generally beneficial to future users. When a break is unavoidable, the
+project does **not** ship deprecation shims or removed-symbol stubs. Instead,
+substantial changes ship with code that automates the conversion, and every
+break is recorded here in the commit that introduces it.
+
+At release time this file is renamed `migration_<version>.md` and a fresh
+`migration_next.md` is started for the next cycle.
+
+## Entry template
+
+Append one section per breaking change, newest last, using this shape:
+
+````markdown
+## <symbol, module, or CLI flag> - <one-line summary>
+
+**Change:** what moved, was renamed, or changed signature.
+
+**Why:** the benefit to future users that justified the break.
+
+**Before**
+
+```python
+old_call(argument)
+```
+
+**After**
+
+```python
+new_call(argument, required_option="value")
+```
+
+**Automated conversion:** `<path to script or CLI>`, or `None needed`.
+````