Open-source graphical user interface for the creation of synthetic skeletons for medical image analysis.

Purpose: Deformable medial modeling is an inverse skeletonization approach to representing anatomy in medical images, which can be used for statistical shape analysis and assessment of patient-specific anatomical features such as locally varying thickness. It involves deforming a pre-defined synthetic skeleton, or template, to anatomical structures of the same class. The lack of software for creating such skeletons has been a limitation to more widespread use of deformable medial modeling. Therefore, the objective of this work is to present an open-source user interface (UI) for the creation of synthetic skeletons for a range of medial modeling applications in medical imaging. Approach: A UI for interactive design of synthetic skeletons was implemented in 3D Slicer, an open-source medical image analysis application. The steps in synthetic skeleton design include importation and skeletonization of a 3D segmentation, followed by interactive 3D point placement and triangulation of the medial surface such that the desired branching configuration of the anatomical structure's medial axis is achieved. Synthetic skeleton design was evaluated in five clinical applications. Compatibility of the synthetic skeletons with open-source software for deformable medial modeling was tested, and representational accuracy of the deformed medial models was evaluated. Results: Three users designed synthetic skeletons of anatomies with various topologies: the placenta, aortic root wall, mitral valve, cardiac ventricles, and the uterus. The skeletons were compatible with skeleton-first and boundary-first software for deformable medial modeling. The fitted medial models achieved good representational accuracy with respect to the 3D segmentations from which the synthetic skeletons were generated. Conclusions: Synthetic skeleton design has been a practical challenge in leveraging deformable medial modeling for new clinical applications. This work demonstrates an open-source UI for user-friendly design of synthetic skeletons for anatomies with a wide range of topologies.

Euclidean and Shape-Based Analysis of the Dynamic Mitral Annulus in Children using a Novel Open-Source Framework.

BACKGROUND: The dynamic shape of the normal adult mitral annulus has been shown to be important to mitral valve function. However, annular dynamics of the healthy mitral valve in children have yet to be explored. The aim of this study was to model and quantify the shape and major modes of variation of pediatric mitral valve annuli in four phases of the cardiac cycle using transthoracic echocardiography. METHODS: The mitral valve annuli of 100 children and young adults with normal findings on three-dimensional echocardiography were modeled in four different cardiac phases using the SlicerHeart extension for 3D Slicer. Annular metrics were quantified using SlicerHeart, and optimal normalization to body surface area was explored. Mean annular shapes and the principal components of variation were computed using custom code implemented in a new SlicerHeart module (Annulus Shape Analyzer). Shape was regressed over metrics of age and body surface area, and mean shapes for five age-stratified groups were generated. RESULTS: The ratio of annular height to commissural width of the mitral valve ("saddle shape") changed significantly throughout age for systolic phases (P < .001) but within a narrow range (median range, 0.20-0.25). Annular metrics changed statistically significantly between the diastolic and systolic phases of the cardiac cycle. Visually, the annular shape was maintained with respect to age and body surface area. Principal-component analysis revealed that the pediatric mitral annulus varies primarily in size (mode 1), ratio of annular height to commissural width (mode 2), and sphericity (mode 3). CONCLUSIONS: The saddle-shaped mitral annulus is maintained throughout childhood but varies significantly throughout the cardiac cycle. The major modes of variation in the pediatric mitral annulus are due to size, ratio of annular height to commissural width, and sphericity. The generation of age- and size-specific mitral annular shapes may inform the development of appropriately scaled absorbable or expandable mitral annuloplasty rings for children.

Calculating Relative Lung Perfusion Using Fluoroscopic Sequences and Image Analysis: The Fluoroscopic Flow Calculator.

BACKGROUND: Maldistribution of pulmonary blood flow in patients with congenital heart disease impacts exertional performance and pulmonary artery growth. Currently, measurement of relative pulmonary perfusion can only be performed outside the catheterization laboratory. We sought to develop a tool for measuring relative lung perfusion using readily available fluoroscopy sequences. METHODS: A retrospective cohort study was conducted on patients with conotruncal anomalies who underwent lung perfusion scans and subsequent cardiac catheterizations between 2011 and 2022. Inclusion criteria were nonselective angiogram of pulmonary vasculature, oblique angulation ≤20°, and an adequate view of both lung fields. A method was developed and implemented in 3D Slicer's SlicerHeart extension to calculate the amount of contrast that entered each lung field from the start of contrast injection and until the onset of levophase. The predicted perfusion distribution was compared with the measured distribution of pulmonary blood flow and evaluated for correlation, accuracy, and bias. RESULTS: In total, 32% (79/249) of screened studies met the inclusion criteria. A strong correlation between the predicted flow split and the measured flow split was found (R2=0.83; P<0.001). The median absolute error was 6%, and 72% of predictions were within 10% of the true value. Bias was not systematically worse at either extreme of the flow distribution. The prediction was found to be more accurate for either smaller and younger patients (age 0-2 years), for right ventricle injections, or when less cranial angulations were used (≤20°). In these cases (n=40), the prediction achieved R2=0.87, median absolute error of 5.5%, and 78% of predictions were within 10% of the true flow. CONCLUSIONS: The current study demonstrates the feasibility of a novel method for measuring relative lung perfusion using conventional angiograms. Real-time measurement of lung perfusion at the catheterization laboratory has the potential to reduce unnecessary testing, associated costs, and radiation exposure. Further optimization and validation is warranted.

Modeling of the Tricuspid Valve and Right Ventricle in Hypoplastic Left Heart Syndrome With a Fontan Circulation.

BACKGROUND: In hypoplastic left heart syndrome, tricuspid regurgitation (TR) is associated with circulatory failure and death. We hypothesized that the tricuspid valve (TV) structure of patients with hypoplastic left heart syndrome with a Fontan circulation and moderate or greater TR differs from those with mild or less TR, and that right ventricle volume is associated with TV structure and dysfunction. METHODS: TV of 100 patients with hypoplastic left heart syndrome and a Fontan circulation were modeled using transthoracic 3-dimensional echocardiograms and custom software in SlicerHeart. Associations of TV structure to TR grade and right ventricle function and volume were investigated. Shape parameterization and analysis was used to calculate the mean shape of the TV leaflets, their principal modes of variation, and to characterize associations of TV leaflet shape to TR. RESULTS: In univariate modeling, patients with moderate or greater TR had larger TV annular diameters and area, greater annular distance between the anteroseptal commissure and anteroposterior commissure, greater leaflet billow volume, and more laterally directed anterior papillary muscle angles compared to valves with mild or less TR (all P<0.001). In multivariate modeling greater total billow volume, lower anterior papillary muscle angle, and greater distance between the anteroposterior commissure and anteroseptal commissure were associated with moderate or greater TR (P<0.001, C statistic=0.85). Larger right ventricle volumes were associated with moderate or greater TR (P<0.001). TV shape analysis revealed structural features associated with TR, but also highly heterogeneous TV leaflet structure. CONCLUSIONS: Moderate or greater TR in patients with hypoplastic left heart syndrome with a Fontan circulation is associated with greater leaflet billow volume, a more laterally directed anterior papillary muscle angle, and greater annular distance between the anteroseptal commissure and anteroposterior commissure. However, there is significant heterogeneity of structure in the TV leaflets in regurgitant valves. Given this variability, an image-informed patient-specific approach to surgical planning may be needed to achieve optimal outcomes in this vulnerable and challenging population.

SlicerHeart: An open-source computing platform for cardiac image analysis and modeling.

Cardiovascular disease is a significant cause of morbidity and mortality in the developed world. 3D imaging of the heart's structure is critical to the understanding and treatment of cardiovascular disease. However, open-source tools for image analysis of cardiac images, particularly 3D echocardiographic (3DE) data, are limited. We describe the rationale, development, implementation, and application of SlicerHeart, a cardiac-focused toolkit for image analysis built upon 3D Slicer, an open-source image computing platform. We designed and implemented multiple Python scripted modules within 3D Slicer to import, register, and view 3DE data, including new code to volume render and crop 3DE. In addition, we developed dedicated workflows for the modeling and quantitative analysis of multi-modality image-derived heart models, including heart valves. Finally, we created and integrated new functionality to facilitate the planning of cardiac interventions and surgery. We demonstrate application of SlicerHeart to a diverse range of cardiovascular modeling and simulation including volume rendering of 3DE images, mitral valve modeling, transcatheter device modeling, and planning of complex surgical intervention such as cardiac baffle creation. SlicerHeart is an evolving open-source image processing platform based on 3D Slicer initiated to support the investigation and treatment of congenital heart disease. The technology in SlicerHeart provides a robust foundation for 3D image-based investigation in cardiovascular medicine.

Visualization and Quantification of the Unrepaired Complete Atrioventricular Canal Valve Using Open-Source Software.

BACKGROUND: Repair of complete atrioventricular canal (CAVC) is often complicated by residual left atrioventricular valve regurgitation. The structure of the mitral and tricuspid valves in biventricular hearts has previously been shown to be associated with valve dysfunction. However, the three-dimensional (3D) structure of the entire unrepaired CAVC valve has not been quantified. Understanding the 3D structure of the CAVC may inform optimized repair. METHODS: Novel open-source work flows were created in SlicerHeart for the modeling and quantification of CAVC valves on the basis of 3D echocardiographic images. These methods were applied to model the annulus, leaflets, and papillary muscle (PM) structure of 35 patients (29 with trisomy 21) with CAVC using transthoracic 3D echocardiography. The mean leaflet and annular shapes were calculated and visualized using shape analysis. Metrics of the complete native CAVC valve structure were compared with those of normal mitral valves using the Mann-Whitney U test. Associations between CAVC structure and atrioventricular valve regurgitation were analyzed. RESULTS: CAVC leaflet metrics varied throughout systole. Compared with normal mitral valves, the left CAVC PMs were more acutely angled in relation to the annular plane (P < .001). In addition, the anterolateral PM was laterally and inferiorly rotated in CAVC, while the posteromedial PM was more superiorly and laterally rotated, relative to normal mitral valves (P < .001). Lower native CAVC atrioventricular valve annular height and annular height-to-valve width ratio before repair were both associated with moderate or greater left atrioventricular valve regurgitation after repair (P < .01). CONCLUSIONS: It is feasible to model and quantify 3D CAVC structure using 3D echocardiographic images. The results demonstrate significant variation in CAVC structure across the cohort and differences in annular, leaflet, and PM structure compared with the mitral valve. These tools may be used in future studies to catalyze future research intended to identify structural associations of valve dysfunction and to optimize repair in this vulnerable and complex population.

Statistical shape analysis of the tricuspid valve in hypoplastic left heart sydrome.

Hypoplastic left heart syndrome (HLHS) is a congenital heart disease characterized by incomplete development of the left heart. Children with HLHS undergo a series of operations which result in the tricuspid valve (TV) becoming the only functional atrioventricular valve. Some of those patients develop tricuspid regurgitation which is associated with heart failure and death and necessitates further surgical intervention. Repair of the regurgitant TV, and understanding the connections between structure and function of this valve remains extremely challenging. Adult cardiac populations have used 3D echocardiography (3DE) combined with computational modeling to better understand cardiac conditions affecting the TV. However, these structure-function analyses rely on simplistic point-based techniques that do not capture the leaflet surface in detail, nor do they allow robust comparison of shapes across groups. We propose using statistical shape modeling and analysis of the TV using Spherical Harmonic Representation Point Distribution Models (SPHARM-PDM) in order to generate a reproducible representation, which in turn enables high dimensional low sample size statistical analysis techniques such as principal component analysis and distance weighted discrimination. Our initial results suggest that visualization of the differences in regurgitant vs. non-regurgitant valves can precisely locate populational structural differences as well as how an individual regurgitant valve differs from the mean shape of functional valves. We believe that these results will support the creation of modern image-based modeling tools, and ultimately increase the understanding of the relationship between valve structure and function needed to inform and improve surgical planning in HLHS.

Dynamic Annular Modeling of the Unrepaired Complete Atrioventricular Canal Annulus.

BACKGROUND: Repair of complete atrioventricular canal (CAVC) is often complicated by atrioventricular valve regurgitation, particularly of the left-sided valve. Understanding the 3-dimensional (3D) structure of the atrioventricular canal annulus before repair may help to inform optimized repair. However, the 3D shape and movement of the CAVC annulus has been neither quantified nor rigorously compared with a normal mitral valve annulus. METHODS: The complete annuli of 43 patients with CAVC were modeled in 4 cardiac phases using transthoracic 3D echocardiograms and custom code. The annular structure was compared with the annuli of 20 normal pediatric mitral valves using 3D metrics and statistical shape analysis (Procrustes analysis). RESULTS: The unrepaired CAVC annulus varied in shape significantly throughout the cardiac cycle. Procrustes analysis visually demonstrated that the average normalized CAVC annular shape is more planar than the normal mitral annulus. Quantitatively, the annular height-to-valve width ratio of the native left CAVC atrioventricular valve was significantly lower than that of a normal mitral valve in all systolic phases (P < .001). CONCLUSIONS: The left half of the CAVC annulus is more planar than that of a normal mitral valve with an annular height-to-valve width ratio similar to dysfunctional mitral valves. Given the known importance of annular shape to mitral valve function, further exploration of the association of 3D structure to valve function in CAVC is warranted.

Skeletal model-based analysis of the tricuspid valve in hypoplastic left heart syndrome.

Hypoplastic left heart syndrome (HLHS) is a congenital heart disease characterized by incomplete development of the left heart. Children with HLHS undergo a series of operations which result in the tricuspid valve (TV) becoming the only functional atrioventricular valve. Many HLHS patients develop tricuspid regurgitation and right ventricle enlargement which is associated with heart failure and death without surgical intervention on the valve. Understanding the connections between the geometry of the TV and its function remains extremely challenging and hinders TV repair planning. Traditional analysis methods rely on simple anatomical measures which do not capture information about valve geometry in detail. Recently, surface-based shape representations such as SPHARM-PDM have been shown to be useful for tasks such as discriminating between valves with normal or poor function. In this work we propose to use skeletal representations (s-reps), a more feature-rich geometric representation, for modeling the leaflets of the tricuspid valve. We propose an extension to previous s-rep fitting approaches to incorporate application-specific anatomical landmarks and population information to improve correspondence. We use several traditional statistical shape analysis techniques to evaluate the efficiency of this representation: using principal component analysis (PCA) we observe that it takes fewer modes of variation compared to boundary-based approaches to represent 90% of the population variation, while distance-weighted discrimination (DWD) shows that s-reps provide for more significant classification between valves with less regurgitation and those with more. These results show the power of using s-reps for modeling the relationship between structure and function of the tricuspid valve.

Segmentation of Tricuspid Valve Leaflets From Transthoracic 3D Echocardiograms of Children With Hypoplastic Left Heart Syndrome Using Deep Learning.

Hypoplastic left heart syndrome (HLHS) is a severe congenital heart defect in which the right ventricle and associated tricuspid valve (TV) alone support the circulation. TV failure is thus associated with heart failure, and the outcome of TV valve repair are currently poor. 3D echocardiography (3DE) can generate high-quality images of the valve, but segmentation is necessary for precise modeling and quantification. There is currently no robust methodology for rapid TV segmentation, limiting the clinical application of these technologies to this challenging population. We utilized a Fully Convolutional Network (FCN) to segment tricuspid valves from transthoracic 3DE. We trained on 133 3DE image-segmentation pairs and validated on 28 images. We then assessed the effect of varying inputs to the FCN using Mean Boundary Distance (MBD) and Dice Similarity Coefficient (DSC). The FCN with the input of an annular curve achieved a median DSC of 0.86 [IQR: 0.81-0.88] and MBD of 0.35 [0.23-0.4] mm for the merged segmentation and an average DSC of 0.77 [0.73-0.81] and MBD of 0.6 [0.44-0.74] mm for individual TV leaflet segmentation. The addition of commissural landmarks improved individual leaflet segmentation accuracy to an MBD of 0.38 [0.3-0.46] mm. FCN-based segmentation of the tricuspid valve from transthoracic 3DE is feasible and accurate. The addition of an annular curve and commissural landmarks improved the quality of the segmentations with MBD and DSC within the range of human inter-user variability. Fast and accurate FCN-based segmentation of the tricuspid valve in HLHS may enable rapid modeling and quantification, which in the future may inform surgical planning. We are now working to deploy this network for public use.

Modeling Tool for Rapid Virtual Planning of the Intracardiac Baffle in Double-Outlet Right Ventricle.

PURPOSE: Biventricular repair of double-outlet right ventricle (DORV) necessitates the creation of a complex intracardiac baffle. Creation of the optimal baffle design and placement thereof can be challenging to conceptualize, even with 2-dimensional and 3-dimensional images. This report describes a recently developed methodology for creating virtual baffles to inform intraoperative repair. DESCRIPTION: A total of 3 heart models of DORV were created from cardiac magnetic resonance images. Baffles were created and visualized using custom software. EVALUATION: This report demonstrates application of the tool to virtual planning of the baffle for repair of DORV in 3 cases. Models were examined by a multidisciplinary team, on screen and in virtual reality. Baffles could be rapidly created and revised to facilitate planning of the surgical procedure. CONCLUSIONS: Virtual modeling of the baffle pathway by using cardiac magnetic resonance, creation of physical templates for the baffle, and visualization in virtual reality are feasible and may be beneficial for preoperative planning of complex biventricular repairs in DORV. Further work is needed to demonstrate clinical benefit or improvement in outcomes.

Successful integration of a three-dimensional transthoracic echocardiography-derived model with an electroanatomic mapping system to guide catheter ablation of WPW.

Three-dimensional transthoracic echocardiography (3DE)-derived heart models have not previously been utilized to guide catheter ablation. In this case report, we describe the creation of a 3DE model from transthoracic echocardiography, import of the model into CARTO3, and successful use of the model as a guide during mapping and ablation of a right lateral accessory pathway. We believe this technique represents a valuable alternative to the integration of computed tomography or magnetic resonance imaging-derived anatomic data, and that it has the potential to improve the definition of the atrioventricular valve annuli during catheter ablation of accessory pathways.

Quantitative Imaging Informatics for Cancer Research.

PURPOSE: We summarize Quantitative Imaging Informatics for Cancer Research (QIICR; U24 CA180918), one of the first projects funded by the National Cancer Institute (NCI) Informatics Technology for Cancer Research program. METHODS: QIICR was motivated by the 3 use cases from the NCI Quantitative Imaging Network. 3D Slicer was selected as the platform for implementation of open-source quantitative imaging (QI) tools. Digital Imaging and Communications in Medicine (DICOM) was chosen for standardization of QI analysis outputs. Support of improved integration with community repositories focused on The Cancer Imaging Archive (TCIA). Priorities included improved capabilities of the standard, toolkits and tools, reference datasets, collaborations, and training and outreach. RESULTS: Fourteen new tools to support head and neck cancer, glioblastoma, and prostate cancer QI research were introduced and downloaded over 100,000 times. DICOM was amended, with over 40 correction proposals addressing QI needs. Reference implementations of the standard in a popular toolkit and standalone tools were introduced. Eight datasets exemplifying the application of the standard and tools were contributed. An open demonstration/connectathon was organized, attracting the participation of academic groups and commercial vendors. Integration of tools with TCIA was improved by implementing programmatic communication interface and by refining best practices for QI analysis results curation. CONCLUSION: Tools, capabilities of the DICOM standard, and datasets we introduced found adoption and utility within the cancer imaging community. A collaborative approach is critical to addressing challenges in imaging informatics at the national and international levels. Numerous challenges remain in establishing and maintaining the infrastructure of analysis tools and standardized datasets for the imaging community. Ideas and technology developed by the QIICR project are contributing to the NCI Imaging Data Commons currently being developed.

Three-Dimensional Modeling of Surgically Implanted Stent-Based Valves in the Mitral Position in Children.

PURPOSE: In children with a mitral annulus too small to accommodate traditional prostheses, surgical implantation of stent-based valves is a promising option. However no reliable preoperative methods exist to guide patient selection, device sizing, and positioning. We describe a novel methodology to visualize and quantify device fit in 3-dimensional echocardiogram (3DE)-derived heart models. DESCRIPTION: Heart models were created from existing preoperative 3DEs using custom software. Valve models were virtually implanted into the models, and both device fit and left ventricular outflow tract (LVOT) area were quantified. EVALUATION: The 3DEs of 3 patients who underwent Melody valve placement in the mitral position were retrospectively modeled: 1 with LVOT obstruction, 1 with perivalvar leak, and 1 without complications. In all cases 2-dimensional measurements underestimated 3D annular dimensions, and the patient with clinical LVOT obstruction had the lowest predicted LVOT area-to-aortic area ratio (0.5). CONCLUSIONS: 3DE-based preoperative modeling of surgical implantation of stent-based valves in the mitral position may improve quantification of mitral valve dimensions and inform risk stratification for potential LVOT obstruction.

Open Source Platform for Transperineal In-Bore MRI-Guided Targeted Prostate Biopsy.

OBJECTIVE: Accurate biopsy sampling of the suspected lesions is critical for the diagnosis and clinical management of prostate cancer. Transperineal in-bore MRI-guided prostate biopsy (tpMRgBx) is a targeted biopsy technique that was shown to be safe, efficient, and accurate. Our goal was to develop an open source software platform to support evaluation, refinement, and translation of this biopsy approach. METHODS: We developed SliceTracker, a 3D Slicer extension to support tpMRgBx. We followed modular design of the implementation to enable customization of the interface and interchange of image segmentation and registration components to assess their effect on the processing time, precision, and accuracy of the biopsy needle placement. The platform and supporting documentation were developed to enable the use of software by an operator with minimal technical training to facilitate translation. Retrospective evaluation studied registration accuracy, effect of the prostate segmentation approach, and re-identification time of biopsy targets. Prospective evaluation focused on the total procedure time and biopsy targeting error (BTE). RESULTS: Evaluation utilized data from 73 retrospective and ten prospective tpMRgBx cases. Mean landmark registration error for retrospective evaluation was 1.88 ± 2.63 mm, and was not sensitive to the approach used for prostate gland segmentation. Prospectively, we observed target re-identification time of 4.60 ± 2.40 min and BTE of 2.40 ± 0.98 mm. CONCLUSION: SliceTracker is modular and extensible open source platform for supporting image processing aspects of the tpMRgBx procedure. It has been successfully utilized to support clinical research procedures at our site.

An annotated test-retest collection of prostate multiparametric MRI.

Multiparametric Magnetic Resonance Imaging (mpMRI) is widely used for characterizing prostate cancer. Standard of care use of mpMRI in clinic relies on visual interpretation of the images by an expert. mpMRI is also increasingly used as a quantitative imaging biomarker of the disease. Little is known about repeatability of such quantitative measurements, and no test-retest datasets have been available publicly to support investigation of the technical characteristics of the MRI-based quantification in the prostate. Here we present an mpMRI dataset consisting of baseline and repeat prostate MRI exams for 15 subjects, manually annotated to define regions corresponding to lesions and anatomical structures, and accompanied by region-based measurements. This dataset aims to support further investigation of the repeatability of mpMRI-derived quantitative prostate measurements, study of the robustness and reliability of the automated analysis approaches, and to support development and validation of new image analysis techniques. The manuscript can also serve as an example of the use of DICOM for standardized encoding of the image annotation and quantification results.

Effects of Endurance Training on Detrimental Structural, Cellular, and Functional Alterations in Skeletal Muscles of Heart Failure With Preserved Ejection Fraction.

BACKGROUND: Heart failure with preserved ejection fraction (HFpEF) is underpinned by detrimental skeletal muscle alterations that contribute to disease severity, yet underlying mechanisms and therapeutic treatments remain poorly established. This study used a nonhuman animal model of HFpEF to better understand whether skeletal muscle abnormalities were (1) fiber-type specific and (2) reversible by various exercise training regimes. METHODS AND RESULTS: Lean control rats were compared with obese ZSF1 rats at 20 weeks and then 8 weeks after sedentary, high-intensity interval training, or moderate continuous treadmill exercise. Oxidative soleus and glycolytic extensor digitorum longus (EDL) muscles were assessed for fiber size, capillarity, glycolytic metabolism, autophagy, and contractile function. HFpEF reduced fiber size and capillarity by 20%-50% (P < .05) in both soleus and EDL, but these effects were not reversed by endurance training. In contrast, both endurance training regimes in HFpEF attenuated the elevated lactate dehydrogenase activity observed in the soleus. Autophagy was down-regulated in EDL and up-regulated in soleus (P < .05), with no influence of endurance training. HFpEF impaired contractile forces of both muscles by ∼20% (P < .05), and these were not reversed by training. CONCLUSIONS: Obesity-related HFpEF was associated with detrimental structural, cellular, and functional alterations to both slow-oxidative and fast-glycolytic skeletal muscles that could not be reversed by endurance training.