An Automated Process for 2D and 3D Finite Element Overclosure and Gap Adjustment using Radial Basis Function Networks

In biomechanics, geometries representing complicated organic structures are consistently segmented from sparse volumetric data or morphed from template geometries resulting in initial overclosure between adjacent geometries. In FEA, these overclosures result in numerical instability and inaccuracy as part of contact analysis. Several techniques exist to fix overclosures, but most suffer from several drawbacks. This work introduces a novel automated algorithm in an iterative process to remove overclosure and create a desired minimum gap for 2D and 3D finite element models. The RBF Network algorithm was introduced by its four major steps to remove the initial overclosure. Additionally, the algorithm was validated using two test cases against conventional nodal adjustment. The first case compared the ability of each algorithm to remove differing levels of overclosure between two deformable muscles and the effects on mesh quality. The second case used a non-deformable femur and deformable distal femoral cartilage geometry with initial overclosure to test both algorithms and observe the effects on the resulting contact FEA. The RBF Network in the first case study was successfully able to remove all overclosures. In the second case, the nodal adjustment method failed to create a usable FEA model, while the RBF Network had no such issue. This work proposed an algorithm to remove initial overclosures prior to FEA that has improved performance over conventional nodal adjustment, especially in complicated situations and those involving 3D elements. The work can be included in existing FEA modeling workflows to improve FEA results in situations involving sparse volumetric segmentation and mesh morphing. This algorithm has been implemented in MATLAB, and the source code is publicly available to download at the following GitHub repository: https://github.com/thor-andreassen/femorsComment: 26 Pages, 5 Figures, 2 Table

Characterizing Individual Muscle Force Contributions At Different Running Speeds

Mechanical strategies for increasing speed have been well documented, but there is very little information available on the muscle forces generated to achieve these changes. The purpose of this study is to utilize musculoskeletal modeling to observe the effects of running speed on individual muscle force contributions during the propulsion phase of running. 10 current and former NCAA DI track athletes ran three trails at three different running speeds. Motion capture and ground reaction force data were loaded into Opensim to estimate the individual muscle forces contributing to the net joint torques. Muscle were combined into functional groups and we observed that running speeds had a significant effect on the peak forces generated by the ILPSO, GMAX, RF, SOL, TibPost, and VAS. The SOL and VAS group produced the highest peak forces across all speeds but as speeds increased, saw their percent change decrease from 20% to 9% in the SOL and 43% to 17% in the VAS. The GMAX increased peak forces by 58% from 2 m/s to 4 m/s and another 68% from 4 m/s to 6 m/s. This trend of increased contributions from the hip extensors aligns with the observations made in other studies that found as speeds near 7 m/s, humans alter their running mechanics to a favor a hip focused strategy to increase stride frequency

Three Dimensional Lower Extremity Musculoskeletal Geometry of the Visible Human Female and Male

Abstract Models and simulations of human function impact medicine and medical technology. Particularly, musculoskeletal modeling provides an avenue for insight into the human body, which might not be otherwise possible. However, reaching the ultimate goal of functional multi-scale human models has been slowed by the lack of freely available datasets of anatomical models and geometries. Moreover, female-specific geometries have been neglected with a widespread emphasis on male geometry. To help realize this goal, we have developed and shared complete three-dimensional musculoskeletal geometries extracted from the National Libraries of Medicine Visible Human Female and Male cryosections. Muscle, bone, cartilage, ligament, and fat from the pelvis to the ankle were digitized and exported. These geometries provide a foundation for continued work in human musculoskeletal simulation with high-fidelity deformable tissues that enable a better understanding of normal function and the evaluation of pathologies and treatments. This work is novel as it includes both the male and female Visible Human specimens, outputs at multiple levels of post-processing for maximum data reuse, and is publicly available

Visible Human Male

Files will be available for download upon completion of resulting publications. Objects Available for Download Aligned Cryosection Images: moving proximal to distal in the Visible Human sequences of cryosection images, there are some offsets in the transverse plane that require correction before beginning segmentation. The Visible Human Female images contain some challenging offsets. As correction is a time-consuming process, we have made the corrected images available for download. The corrected scans are available in DICOM, TIFF, .mat, and MHD file formats. Aligned and Rescaled CT Images: the Visible Human CT images are useful for segmentation of tissues that are not as clear in the cryosection images. However, the CT images are not precisely aligned with the cryosection images. We have made available the CT images aligned to the cryosection images also with offsets corrected. CT scans are full scans going from the head-to-toes. The corrected scans are available in DICOM, TIFF, and MHD file formats. Original Segmentation Masks: the 3D models were created using ScanIP by the construction of 3D objects from a series of outlines, or masks, of each object. This was a manual process often requiring subjective decisions when the clarity of the images made the detection of tissue borders challenging. Therefore, we have provided the segmentation masks in 3D Slicer for those that wish to check or alter the masks for creation of unique models. The raw segmentation masks are available in 3D Slicer as NRRD files. Additionally, the segmentations are available as binary label maps in MHD, TIFF, and .mat file formats. Raw 3D Models: the raw 3D models created from ScanIP are provided in STL format in the default edge length of ScanIP, approximately 0.33 mm edge lengths. Providing the raw STL models enables others to apply their own preferred means of post-processing of the objects (e.g., smoothing or lofting) starting from their original state. Smoothed 3D Models: the smoothed and resampled STLs from MeshMixer are provided. These geometries are free of issues resulting from segmentation and each geometry was remeshed to the following target edge lengths: muscle 1.5 mm, bone 1.0 mm, cartilage 0.75 mm, ligament 0.75 mm. Segmentation Masks of Smoothed Models: segmentation masks were created from the smoothed and resampled 3D models to enable transverse inspection of the final product in segmentation software 3D Slicer. Final 3D Models: the goal of the project was to provide 3D models of the tissues that could be used in applications without further processing. The final 3D models were visually inspected to ensure no existing sharp edges and then checked and corrected for any overlap or overclosure. If an overclosure was present, it was removed to provide a gap distance of 0.05 mm using a unique radial basis function-based MATLAB code that is publicly available. Segmentation Masks of Final Models: segmentation masks were created from the final 3D models to enable transverse inspection of the final product in segmentation software 3D Slicer. Folders for Download The complete dataset is very large. For this reason, the datasets have been split into manageable folders for download: Aligned Cryosection DICOM Aligned CT DICOM Aligned Scan Images (.mat, .tif, .ctbl) Original segmentation masks and Aligned scans (.mhd) (Right, Left, or Combined) Original segmentation label maps (.mat, .tif) Original segmentation masks and Aligned scans (3D Slicer) (Right, Left, or Combined, Combined with CT) Smoothed Segmentation masks and Aligned Scans (3D Slicer) (Right, Left, or Combined) Final Segmentation masks and Aligned Scans (3D Slicer) (Right, Left, or Combined) Original 3D STL models (Right, Left, or Combined) Smoothed 3D STL models (Right or Left) Final 3D STL models (Right or Left)https://digitalcommons.du.edu/visiblehuman/1000/thumbnail.jp

Visible Human Female

Files will be available for download upon completion of resulting publications. Objects Available for Download Aligned Cryosection Images: moving proximal to distal in the Visible Human sequences of cryosection images, there are some offsets in the transverse plane that require correction before beginning segmentation. The Visible Human Female images contain some challenging offsets. As correction is a time-consuming process, we have made the corrected images available for download. The corrected scans are available in DICOM, TIFF, .mat, and MHD file formats. Aligned and Rescaled CT Images: the Visible Human CT images are useful for segmentation of tissues that are not as clear in the cryosection images. However, the CT images are not precisely aligned with the cryosection images. We have made available the CT images aligned to the cryosection images also with offsets corrected. CT scans are full scans going from the head-to-toes. The corrected scans are available in DICOM, TIFF, and MHD file formats. Original Segmentation Masks: the 3D models were created using ScanIP by the construction of 3D objects from a series of outlines, or masks, of each object. This was a manual process often requiring subjective decisions when the clarity of the images made the detection of tissue borders challenging. Therefore, we have provided the segmentation masks in 3D Slicer for those that wish to check or alter the masks for creation of unique models. The raw segmentation masks are available in 3D Slicer as NRRD files. Additionally, the segmentations are available as binary label maps in MHD, TIFF, and .mat file formats. Raw 3D Models: the raw 3D models created from ScanIP are provided in STL format in the default edge length of ScanIP, approximately 0.33 mm edge lengths. Providing the raw STL models enables others to apply their own preferred means of post-processing of the objects (e.g., smoothing or lofting) starting from their original state. Smoothed 3D Models: the smoothed and resampled STLs from MeshMixer are provided. These geometries are free of issues resulting from segmentation and each geometry was remeshed to the following target edge lengths: muscle 1.5 mm, bone 1.0 mm, cartilage 0.75 mm, ligament 0.75 mm. Segmentation Masks of Smoothed Models: segmentation masks were created from the smoothed and resampled 3D models to enable transverse inspection of the final product in segmentation software 3D Slicer. Final 3D Models: the goal of the project was to provide 3D models of the tissues that could be used in applications without further processing. The final 3D models were visually inspected to ensure no existing sharp edges and then checked and corrected for any overlap or overclosure. If an overclosure was present, it was removed to provide a gap distance of 0.05 mm using a unique radial basis function-based MATLAB code that is publicly available. Segmentation Masks of Final Models: segmentation masks were created from the final 3D models to enable transverse inspection of the final product in segmentation software 3D Slicer. Folders for Download The complete dataset is very large. For this reason, the datasets have been split into manageable folders for download: Aligned Cryosection DICOM Aligned CT DICOM Aligned Scan Images (.mat, .tif, .ctbl) Original segmentation masks and Aligned scans (.mhd) (Right, Left, or Combined) Original segmentation label maps (.mat, .tif) Original segmentation masks and Aligned scans (3D Slicer) (Right, Left, or Combined, Combined with CT) Smoothed Segmentation masks and Aligned Scans (3D Slicer) (Right, Left, or Combined) Final Segmentation masks and Aligned Scans (3D Slicer) (Right, Left, or Combined) Original 3D STL models (Right, Left, or Combined) Smoothed 3D STL models (Right or Left) Final 3D STL models (Right or Left)https://digitalcommons.du.edu/visiblehuman/1001/thumbnail.jp