arXiv subjects

Matthew Daemer

Publications and source records attributed to Matthew Daemer.

7 recordsLinked to original sources

arXiv2026

Open-Source Framework for the Visualization, Quantification, and Analysis of 4D Flow and High-Dimensional Magnetic Resonance Images

Background: Four-dimensional (4D) flow cardiovascular magnetic resonance (CMR) captures 3D anatomy and blood velocity across the cardiac cycle, but current post-processing software is closed, varies across platforms, and sits outside open-source image-computing frameworks. We developed an open-source framework for the import, visualization, and quantification of 4D flow and other high-dimensional CMR within SlicerHeart, an extension for 3D Slicer. Methods: Import 4D Flow reads vendor DICOM, applies preprocessing, and stores velocities as a time-resolved vector field; Analyze 4D Flow provides measurement planes, streamline and Doppler-like visualization, segmentation propagation, and quantification. Underlying both, we extended the Insight Toolkit to store five- and higher-dimensional arrays. Flow quantification was compared with a commercial package (cvi42) and 2D phase contrast in 13 patients with congenital heart disease across 108 paired regions of interest (Bland-Altman analysis and intraclass correlation coefficients, ICCs). Consensus-recommended processing methods were also implemented as an open-source library with an automated test suite of analytic and CFD phantoms and clinical acquisitions. Results: The modules integrate with 3D Slicer's segmentation, registration, and rendering tools and export velocity fields and geometry for computational modeling. Agreement with cvi42 was close: forward volume bias -0.1 mL (95% limits of agreement 2.2 to -2.3; ICC 0.997), effective volume per minute bias -0.015 L/min (0.21 to -0.24; ICC 0.994). Against 2D phase contrast, forward volume bias (-2.2 mL) and mean absolute percentage error (21.8%) matched cvi42 (-2.1 mL; 21.3%). Conclusions: This open, extensible framework brings 4D flow CMR into an established image-computing ecosystem and agrees closely with a commercial reference; every step can be inspected, reproduced, and improved.

q-bio.QM↗

arXiv2026

An Open-Source Web-Based Viewer for Disseminating Image-Derived Models

Patient-specific 3-dimensional (3D) models are increasingly central to planning surgery and catheter-based intervention in children with congenital heart disease (CHD), whose anatomy is often atypical and variable. These models inform care only when the surgeons and interventional cardiologists who make treatment decisions can rotate, crop, and measure them directly. Desktop modeling applications require local installation, capable hardware, and training. Commercial web-based viewers are portable but closed, and, in our experience, cannot display volume rendering, time-resolved (e.g., 4-dimensional) data, or the custom workflows centers build for CHD. Because CHD populations are small and heterogeneous, such workflows are unlikely to be prioritized commercially, and end users have no means to add them. To address these limitations, we developed the SlicerHeart Viewer, an open-source module that presents a simplified interface to a complete 3D Slicer/SlicerHeart session running on a server. Clinicians access models created by clinical modeling services from any device through a web browser. Because 3D Slicer runs underneath, volume rendering, time-resolved data, and any SlicerHeart workflow, including those developed for CHD, are available without modification. The module is independent of the hosting environment; we chose internal servers behind institutional single sign-on, and a cloud-hosted option is in development. Over one year at a single pediatric center, nearly all of 82 modeled cases were shared through the Viewer with clinicians from five specialties, with cases loading in 5 to 10 seconds. The approach is not specific to CHD and is deployable at other centers.

q-bio.QM↗

arXiv2026

A geometric feature tracking approach for noninvasive patient specific estimation of leaflet strain from 3D images of heart valves

Valvular heart disease is prevalent and a major contributor to heart failure. Valve leaflet strain is a promising metric for evaluating the mechanics underlying the initiation and progression of valvular pathology. However, generalizable methods for noninvasively quantifying valvular strain from clinically acquired patient images remain limited. To address this limitation, we developed a geometric feature-tracking framework to quantify in vivo leaflet strain from 3DE images. The method integrates a cohort-derived geometric reference atlas to establish geometric correspondence and introduces a novel distance-weighted coherent point drift algorithm for non-rigid registration. We evaluated performance against a finite element benchmark model and compared the approach with conventional point-based tracking methods. The framework was applied to pediatric and adult patient datasets (N = 31) across variable valve morphologies. The proposed method demonstrated greater accuracy in quantifying anatomical alignment and leaflet strain than conventional point-based approaches. Validation against the finite element benchmark confirmed improved strain estimation. The framework achieved reliable inter-phase tracking of valve deformation across diverse morphologies in pediatric and adult patients. Analysis identified a consistent distribution pattern of the 1st principal strain associated with leaflet billow (prolapse). This feature-tracking framework provides a generalizable method for noninvasive quantification of atrioventricular valve leaflet strain from clinical 3DE images. Characterization of biomechanical strain patterns may improve prognostic assessment and support longitudinal evaluation of valvular heart disease. Further investigation of the biomechanical signatures of heart valve disease has the potential to enhance prognostic assessment and longitudinal evaluation of valvular heart disease.

q-bio.QM↗

arXiv2026

Biomechanically Informed Image Registration for Patient-Specific Aortic Valve Strain Analysis

Aortic valve (AV) biomechanics play a critical role in maintaining normal cardiac function. Pathological variations, particularly in bicuspid aortic valves, alter leaflet loading, increase strain, and accelerate disease progression. Accurate patient-specific characterization of valve geometry and deformation is therefore essential for predicting disease progression and guiding durable repair. Current imaging and computational methods often fail to capture rapid valve motion and complex patient-specific features, limiting precise biomechanical assessment. To address these limitations, we developed an image registration framework coupled with the finite element method (FEM) to improve AV tracking and biomechanical evaluation. The valve geometries derived from 4D echocardiography and CT were used to simulate AV closure and generate intermediate deformation states. These FEM-generated states facilitated leaflet tracking, while image registration corrected misalignment between simulations and imaging data. In 20 patients, FEM-augmented registration improved accuracy by 40% compared with direct registration. This improvement enabled more reliable strain estimation by measuring leaflet deformation directly from imaging and reducing uncertainties associated with boundary conditions and material assumptions. Areal, Green-Lagrange, and deviatoric strains were quantified in adult trileaflet/bicuspid valves, as well as pediatric patients, revealing distinct deformation patterns across valve groups. Convergence in mean deviatoric strain between adult trileaflet and pediatric valves suggests volumetric deformation underlies age- and size-related differences in AV mechanics. The FEM-augmented registration enhances tracking and biomechanical evaluation accuracy, providing clinically relevant insights into patient-specific AV deformation to support individualized medical and intervention planning.

q-bio.QM↗

arXiv2025

Simulation of Repair on Dynamic Patient-Specific Left Atrioventricular Valve Models

Purpose: To develop and evaluate a dynamic, image-derived patient-specific physical simulation platform for the assessment of left atrioventricular valve (LAVV) repair strategies in pediatric patients with repaired atrioventricular canal defects. Methods: 3D transesophageal echocardiographic images of two patients with regurgitant LAVVs were identified from an institutional database. Custom code in SlicerHeart was used to segment leaflets, define the annulus, and generate patient-specific valve molds. Silicone valve models were fabricated and tested in a pulse duplicator under simulated physiological conditions. Five unrepaired valves were analyzed for manufacturing consistency, and multiple surgical repair techniques were compared for two patient-specific models. Results: Manufacturing variability was low in annular metrics (CV for annular circumference: 2.1; commissural distance: 4.1; annulus height: 14.7) but higher in leaflet closure metrics (billow height: 11.1%; billow volume: 18.9%; tenting height: 45.9%; tenting volume: 73.5%). In Patient 1, cleft closure and an Alfieri stitch both eliminated the regurgitant orifice area, but the Alfieri stitch resulted in elevated mean pressure gradient (17 mmHg vs. 4-9 mmHg for other repairs) and deteriorated with repeated loading. In Patient 2, no repair eliminated regurgitation entirely; however, combining an 11 mm patch augmentation with commissuroplasty reduced regurgitant area to 0.147 cm2, the smallest observed among tested strategies. Conclusion: This study demonstrates the feasibility of a dynamic physical simulation platform for preclinical LAVV repair evaluation. This proof-of-concept work highlights the platform potential for refining repair strategies before clinical application, which may be particularly relevant in small and heterogeneous populations with congenital heart disease.

physics.med-ph↗

arXiv2025

Geodesic-based Predictive Shape Modeling of the Right Ventricle in Patients with Hypoplastic Left Heart Syndrome

Hypoplastic left heart syndrome (HLHS) is characterized by severe underdevelopment of left ventricle requiring staged surgical reconstruction (stages) to allow the right ventricle (RV) alone to support the circulation. In this setting changes in RV size and shape over time reflect adaptations to single-ventricle physiology, dysfunction of the associated tricuspid valve (TV), and are associated with circulatory failure. As such, an accurate prediction of the RV shape of a patient would inform understanding of both RV and TV failure, as well as clinical prognosis and associated decision making. We present a geodesic-based predictive shape modeling framework applied a cohort of RVs obtained from 15 HLHS patients at three individual time points. Reasonable predictions on stage 1 RV shapes can generated using pre-stage 1 RV shapes and two predictors from prior clinical and demographic measures. Our results demonstrate the future potential for a data-driven method to predict how the morphology of the RV of an individual patient will change in size and shape over time. Future studies will seek to expand the training sample size and integrate more comprehensive demographic and morphological data into the proposed predictive model.

physics.med-ph↗

arXiv2024

FEBio FINESSE: An open-source finite element simulation approach to estimate in vivo heart valve strains using shape enforcement

Finite element simulations are an enticing tool to evaluate heart valve function in healthy and diseased patients; however, patient-specific simulations derived from 3D echocardiography are hampered by several technical challenges. In this work, we present an open-source method to enforce matching between finite element simulations and in vivo image-derived heart valve geometry in the absence of patient-specific material properties, leaflet thickness, and chordae tendineae structures. We evaluate FEBio Finite Element Simulations with Shape Enforcement (FINESSE) using three synthetic test cases covering a wide range of model complexity. Our results suggest that FINESSE can be used to not only enforce finite element simulations to match an image-derived surface, but to also estimate the first principal leaflet strains within +/- 0.03 strain. Key FINESSE considerations include: (i) appropriately defining the user-defined penalty, (ii) omitting the leaflet commissures to improve simulation convergence, and (iii) emulating the chordae tendineae behavior via prescribed leaflet free edge motion or a chordae emulating force. We then use FINESSE to estimate the in vivo valve behavior and leaflet strains for three pediatric patients. In all three cases, FINESSE successfully matched the target surface with median errors similar to or less than the smallest voxel dimension. Further analysis revealed valve-specific findings, such as the tricuspid valve leaflet strains of a 2-day old patient with HLHS being larger than those of two 13-year old patients. The development of this open source pipeline will enable future studies to begin linking in vivo leaflet mechanics with patient outcomes

physics.med-ph↗