Refactor: Reorganize statistical model workflows and standardize experiment naming (#24)

* Moves heart statistical model creation notebooks from data/KCL-Heart-Model to
experiments/Heart-Create_Statistical_Model with sequential numbering.
* Renames experiment folders to use Title-Case with hyphens for consistency
    - Heart-Model_To_Patient → Heart-Statistical_Model_To_Patient
    - convert_vtk_to_usd_lib → Convert_VTK_To_USD.
* Removes outdated SlicerSALT documentation files and adds input_meshes
directory structure.

Author: aylward

.cursor/rules/project-standards.mdc

@@ -25,20 +25,24 @@ git mv old_name.py new_name.py
 
 ## Documentation
 
-**Do NOT create extra documentation files** describing what was done:
+**NEVER create .md files unless explicitly requested by the user or unless creating a new module in a directory that does not already have a README.md, then a README.md may be created if appropriate.**
 
 ❌ **Don't create**:
 - `MIGRATION.md`
 - `CHANGES.md`
 - `UPDATE_SUMMARY.md`
 - `MODERNIZATION_*.md`
-- Similar meta-documentation files
+- `*_GUIDE.md`
+- `*_EXAMPLE.md`
+- `*_SUMMARY.md`
+- Any other .md files without explicit user request except README.md files for new modules.
 
 ✅ **Do document**:
 - In-code docstrings
 - README files for new modules
 - Inline comments for complex logic
-- API documentation in existing docs
+- Update existing README.md files when needed
+- API documentation in existing docs structure
 
 ## Backward Compatibility
 
@@ -57,6 +61,24 @@ git mv old_name.py new_name.py
 - Use `logging` module instead of `print` statements
 - Follow PEP 8 for Python code
 
+## Python Commands
+
+**Use `py` for running Python on this Windows system:**
+
+```bash
+# Running Python
+py script.py
+
+# Running modules
+py -m pytest tests/
+
+# Python version
+py --version
+```
+
+❌ **Don't use**: `python` (not available in PATH)
+✅ **Do use**: `py` (Python launcher for Windows)
+
 ## Testing
 
 - Test new functionality with Jupyter notebooks in `experiments/`

README.md

@@ -413,17 +413,30 @@ Direct VTK time series to USD conversion for cardiac data:
 - **`0-download_and_convert_4d_to_3d.ipynb`**: Data preparation
 - **`1-heart_vtkseries_to_usd.ipynb`**: VTK series to USD conversion
 
-### 🧠 Heart Model to Patient (`experiments/Heart-Model_To_Patient/`)
+### 🧠 Heart Create Statistical Model (`experiments/Heart-Create_Statistical_Model/`)
 
-Advanced registration between generic anatomical models and patient-specific data:
+Create PCA statistical shape models from population meshes using the KCL Heart Model dataset:
 
-- **`heart_model_to_patient.ipynb`**: Complete model-to-patient registration workflow
+- **`1-input_meshes_to_input_surfaces.ipynb`**: Convert meshes to surfaces
+- **`2-input_surfaces_to_surfaces_aligned.ipynb`**: Align population meshes
+- **`3-registration_based_correspondence.ipynb`**: Compute point correspondences
+- **`4-surfaces_aligned_correspond_to_pca_inputs.ipynb`**: Prepare PCA inputs
+- **`5-compute_pca_model.ipynb`**: Compute PCA model using sklearn
+
+**⚠️ Complete this experiment FIRST** before attempting `Heart-Statistical_Model_To_Patient`.
+
+### 🧠 Heart Statistical Model to Patient (`experiments/Heart-Statistical_Model_To_Patient/`)
+
+Advanced registration between generic anatomical models and patient-specific data using PCA:
+
+- **`heart_model_to_model_icp_itk.ipynb`**: ICP registration for initial alignment
 - **`heart_model_to_model_registration_pca.ipynb`**: PCA-based statistical shape model registration
+- **`heart_model_to_patient.ipynb`**: Complete model-to-patient registration workflow
 
 Uses the `WorkflowRegisterHeartModelToPatient` class for three-stage registration:
 1. ICP-based rough alignment
 2. Mask-to-mask deformable registration
-3. Optional mask-to-image refinement
+3. Optional PCA-constrained shape fitting
 
 ### 🔬 4D CT Reconstruction (`experiments/Reconstruct4DCT/`)
 

data/CHOP-Valve4D/.gitignore

@@ -1,2 +1,3 @@
 Alterra*
 TPV*
+CT