Syn3DWound: A Synthetic Dataset for 3D Wound Bed Analysis

Wound management poses a significant challenge, particularly for bedridden patients and the elderly. Accurate diagnostic and healing monitoring can significantly benefit from modern image analysis, providing accurate and precise measurements of wounds. Despite several existing techniques, the shortage of expansive and diverse training datasets remains a significant obstacle to constructing machine learning-based frameworks. This paper introduces Syn3DWound, an open-source dataset of high-fidelity simulated wounds with 2D and 3D annotations. We propose baseline methods and a benchmarking framework for automated 3D morphometry analysis and 2D/3D wound segmentation.

CorticalFlow$^{++}$: Boosting Cortical Surface Reconstruction Accuracy, Regularity, and Interoperability

The problem of Cortical Surface Reconstruction from magnetic resonance imaging has been traditionally addressed using lengthy pipelines of image processing techniques like FreeSurfer, CAT, or CIVET. These frameworks require very long runtimes deemed unfeasible for real-time applications and unpractical for large-scale studies. Recently, supervised deep learning approaches have been introduced to speed up this task cutting down the reconstruction time from hours to seconds. Using the state-of-the-art CorticalFlow model as a blueprint, this paper proposes three modifications to improve its accuracy and interoperability with existing surface analysis tools, while not sacrificing its fast inference time and low GPU memory consumption. First, we employ a more accurate ODE solver to reduce the diffeomorphic mapping approximation error. Second, we devise a routine to produce smoother template meshes avoiding mesh artifacts caused by sharp edges in CorticalFlow's convex-hull based template. Last, we recast pial surface prediction as the deformation of the predicted white surface leading to a one-to-one mapping between white and pial surface vertices. This mapping is essential to many existing surface analysis tools for cortical morphometry. We name the resulting method CorticalFlow$^{++}$. Using large-scale datasets, we demonstrate the proposed changes provide more geometric accuracy and surface regularity while keeping the reconstruction time and GPU memory requirements almost unchanged.

CorticalFlow: A Diffeomorphic Mesh Deformation Module for Cortical Surface Reconstruction

In this paper we introduce CorticalFlow, a new geometric deep-learning model that, given a 3-dimensional image, learns to deform a reference template towards a targeted object. To conserve the template mesh's topological properties, we train our model over a set of diffeomorphic transformations. This new implementation of a flow Ordinary Differential Equation (ODE) framework benefits from a small GPU memory footprint, allowing the generation of surfaces with several hundred thousand vertices. To reduce topological errors introduced by its discrete resolution, we derive numeric conditions which improve the manifoldness of the predicted triangle mesh. To exhibit the utility of CorticalFlow, we demonstrate its performance for the challenging task of brain cortical surface reconstruction. In contrast to current state-of-the-art, CorticalFlow produces superior surfaces while reducing the computation time from nine and a half minutes to one second. More significantly, CorticalFlow enforces the generation of anatomically plausible surfaces; the absence of which has been a major impediment restricting the clinical relevance of such surface reconstruction methods.

MongeNet: Efficient Sampler for Geometric Deep Learning

Recent advances in geometric deep-learning introduce complex computational challenges for evaluating the distance between meshes. From a mesh model, point clouds are necessary along with a robust distance metric to assess surface quality or as part of the loss function for training models. Current methods often rely on a uniform random mesh discretization, which yields irregular sampling and noisy distance estimation. In this paper we introduce MongeNet, a fast and optimal transport based sampler that allows for an accurate discretization of a mesh with better approximation properties. We compare our method to the ubiquitous random uniform sampling and show that the approximation error is almost half with a very small computational overhead.

Going deeper with brain morphometry using neural networks

Brain morphometry from magnetic resonance imaging (MRI) is a consolidated biomarker for many neurodegenerative diseases. Recent advances in this domain indicate that deep convolutional neural networks can infer morphometric measurements within a few seconds. Nevertheless, the accuracy of the devised model for insightful bio-markers (mean curvature and thickness) remains unsatisfactory. In this paper, we propose a more accurate and efficient neural network model for brain morphometry named HerstonNet. More specifically, we develop a 3D ResNet-based neural network to learn rich features directly from MRI, design a multi-scale regression scheme by predicting morphometric measures at feature maps of different resolutions, and leverage a robust optimization method to avoid poor quality minima and reduce the prediction variance. As a result, HerstonNet improves the existing approach by 24.30% in terms of intraclass correlation coefficient (agreement measure) to FreeSurfer silver-standards while maintaining a competitive run-time.