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+# VSDFullBodyBoneModels
+3D surface models of the bones of the lower body created from CT datasets of the open access VSDFullBody collection.
+![subject-selection](https://github.com/MCM-Fischer/VSDFullBodyBoneModels/assets/43516130/b1e706f4-8b43-42d6-b249-1633aaa28381)
+
+## How to cite
+### Publication
+Fischer, M. C. M. Database of segmentations and surface models of bones of the entire lower body created from cadaver CT scans. *Sci. Data* **10**, 763; [![10.1038/s41597-023-02669-z](https://img.shields.io/badge/DOI-10.1038/s41597--023--02669--z-green.svg)](https://doi.org/10.1038/s41597-023-02669-z) (2023).
+
+### Releases
+- v3.0 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.8316730.svg)](https://doi.org/10.5281/zenodo.8316730) The database contains the bones of the lower extremities of 30 subjects. One duplicate subject (z024) was removed from the database that was part of the previous versions.
+- v2.0 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.4280899.svg)](https://doi.org/10.5281/zenodo.4280899) additionally contains the femora and manually selected femoral landmarks of five experienced raters.
+- v1.0 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3384055.svg)](https://doi.org/10.5281/zenodo.3384055) contains only the bones of the pelvis of 20 subjects of the VSDFullBody database. Additionally, it contains manually selected pelvic landmarks of five experienced raters.
+
+## Usage
+In the Bones folder a MATALB MAT file is stored for each subject containing the triangle meshes of the bones.
+Clone with the recursive option to get the submodules.
+Run the MATLAB or Python example script to plot one of the subjects: `plotBoneModels_example.m` or `plotBoneModels_example.py`.
+
+## Segmentation and reconstruction process
+The surface of each bone was semi-automatically reconstructed by thresholding using 200 Hounsfield units as the lower threshold and the maximum Hunsfield unit value present in the volume data as the upper threshold.
+The thresholding was followed by a manual post-processing procedure using the software 3D Slicer ([slicer.org](https://www.slicer.org)) with default smoothing settings.
+The bones were manually segmented at the joint spaces if necessary. Subsequently, holes in the outer surface of the bones were manually closed.
+The reconstructions were exported as mesh files in the PLY format (see '**[Related data](https://github.com/MCM-Fischer/VSDFullBodyBoneModels#related-data)**') and imported into MATLAB using a conservative decimation and remeshing procedure. 
+The decimator restricted the Hausdorff distance between input and output mesh to 0.05 mm. 
+The adaptive remesher permitted a maximum deviation of 0.05 mm from the input mesh with a minimum edge length of 0.5 mm and a maximal edge length of 100 mm. Number of iterations was set to 10 and back-projection enabled.
+The decimator and remesher are plugins of the software OpenFlipper ([openflipper.org](https://www.openflipper.org)).
+
+## Related data
+- [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.8302448.svg)](https://doi.org/10.5281/zenodo.8302448) CT volume data, segmentations, reconstructions and raw PLY mesh files of each subject linked by a project file (MRML scene file) that can be opened with 3D Slicer ([slicer.org](https://www.slicer.org)).
+- [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.8270364.svg)](https://doi.org/10.5281/zenodo.8270364) Mirror of the full VSDFullBody database as hosted originally by Michael Kistler at [smir.ch](https://www.smir.ch).
+
+## Licenses
+- [![License: CC BY-NC-SA 4.0](https://img.shields.io/badge/License-CC_BY--NC--SA_4.0-lightgrey.svg)](https://creativecommons.org/licenses/by-nc-sa/4.0/) for MAT and XLSX files.
+- [![License: EUPL v1.2](https://img.shields.io/badge/License-EUPL_v1.2-lightgrey.svg)](https://eupl.eu/1.2/en/) for MATLAB and Python source code.
+
+## Related publications
+- v2.0 was used in: Fischer, M. C. M. *et al.* A robust method for automatic identification of femoral landmarks, axes, planes and bone coordinate systems using surface models. *Sci. Rep.* **10**, 20859; [![10.1038/s41598-020-77479-z](https://img.shields.io/badge/DOI-10.1038/s41598--020--77479--z-green.svg)](https://doi.org/10.1038/s41598-020-77479-z) (2020).
+- v1.0 was used in: Fischer, M. C. M. *et al.* A robust method for automatic identification of landmarks on surface models of the pelvis. *Sci. Rep.* **9**, 13322; [![10.1038/s41598-019-49573-4](https://img.shields.io/badge/DOI-10.1038/s41598--019--49573--4-green.svg)](https://doi.org/10.1038/s41598-019-49573-4) (2019).
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