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We present a volumetric mesh-based algorithm for parameterizing the placenta to a flattened template to enable effective visualization of local anatomy and function. MRI shows potential as a research tool as it provides signals directly related to placental function. However, due to the curved and highly variable in vivo shape of the placenta, interpreting and visualizing these images is difficult. We address interpretation challenges by mapping the placenta so that it resembles the familiar ex vivo shape. We formulate the parameterization as an optimization problem for mapping the placental shape represented by a volumetric mesh to a flattened template. We employ the symmetric Dirichlet energy to control local distortion throughout the volume. Local injectivity in the mapping is enforced by a constrained line search during the gradient descent optimization. We validate our method using a research study of 111 placental shapes extracted from BOLD MRI images. Our mapping achieves sub-voxel accuracy in matching the template while maintaining low distortion throughout the volume. We demonstrate how the resulting flattening of the placenta improves visualization of anatomy and function. Our code is freely available at https://github.com/mabulnaga/placenta-flattening ., Comment: Accepted to IEEE TMI ( (c) IEEE). This manuscript expands the MICCAI 2019 paper (arXiv:1903.05044) by developing additional template models and extensions to improve robustness, expanded evaluation on a significantly larger dataset, and experiments and discussion demonstrating utility for clinical research. Code is available at https://github.com/mabulnaga/placenta-flattening

© 2020 Elsevier Ltd Introduction: Before using blood-oxygen-level-dependent magnetic resonance imaging (BOLD MRI) during maternal hyperoxia as a method to detect individual placental dysfunction, it is necessary to understand spatiotemporal variations that represent normal placental function. We investigated the effect of maternal position and Braxton-Hicks contractions on estimates obtained from BOLD MRI of the placenta during maternal hyperoxia. Methods: For 24 uncomplicated singleton pregnancies (gestational age 27–36 weeks), two separate BOLD MRI datasets were acquired, one in the supine and one in the left lateral maternal position. The maternal oxygenation was adjusted as 5 min of room air (21% O2), followed by 5 min of 100% FiO2. After datasets were corrected for signal non-uniformities and motion, global and regional BOLD signal changes in R2* and voxel-wise Time-To-Plateau (TTP) in the placenta were measured. The overall placental and uterine volume changes were determined across time to detect contractions. Results: In mothers without contractions, increases in global placental R2* in the supine position were larger compared to the left lateral position with maternal hyperoxia. Maternal position did not alter global TTP but did result in regional changes in TTP. 57% of the subjects had Braxton-Hicks contractions and 58% of these had global placental R2* decreases during the contraction. Conclusion: Both maternal position and Braxton-Hicks contractions significantly affect global and regional changes in placental R2* and regional TTP. This suggests that both factors must be taken into account in analyses when comparing placental BOLD signals over time within and between individuals.

Although shape correspondence is a central problem in geometry processing, most methods for this task apply only to two-dimensional surfaces. The neglected task of volumetric correspondence--a natural extension relevant to shapes extracted from simulation, medical imaging, and volume rendering--presents unique challenges that do not appear in the two-dimensional case. In this work, we propose a method for mapping between volumes represented as tetrahedral meshes. Our formulation minimizes a distortion energy designed to extract maps symmetrically, i.e., without dependence on the ordering of the source and target domains. We accompany our method with theoretical discussion describing the consequences of this symmetry assumption, leading us to select a symmetrized ARAP energy that favors isometric correspondences. Our final formulation optimizes for near-isometry while matching the boundary. We demonstrate our method on a diverse geometric dataset, producing low-distortion matchings that align closely to the boundary., Accepted to ACM Transactions on Graphics. Our code is available at https://github.com/mabulnaga/symmetric-volume-maps

Standard PolyCube-based hexahedral (hex) meshing methods aim to deform the input domain into an axis-aligned PolyCube volume with integer corners; if this deformation is bijective, then applying the inverse map to the voxelized PolyCube yields a valid hex mesh. A key challenge in these methods is to maintain the bijectivity of the PolyCube deformation, thus reducing the robustness of these algorithms. In this work, we present an interactive pipeline for hex meshing that sidesteps this challenge by using a new representation of PolyCubes as unions of cuboids. We begin by deforming the input tetrahedral mesh into a near-PolyCube domain whose faces are loosely aligned to the major axis directions. We then build a PolyCube by optimizing the layout of a set of cuboids with user guidance to closely fit the deformed domain. Finally, we construct an inversion-free pullback map from the voxelized PolyCube to the input domain while optimizing for mesh quality metrics. We allow extensive user control over each stage, such as editing the voxelized PolyCube, positioning surface vertices, and exploring the trade-off among competing quality metrics, while also providing automatic alternatives. We validate our method on over one hundred shapes, including models that are challenging for past PolyCube-based and frame-field-based methods. Our pipeline reliably produces hex meshes with quality on par with or better than state-of-the-art. We additionally conduct a user study with 21 participants in which the majority prefer hex meshes they make using our tool to the ones from automatic state-of-the-art methods. This demonstrates the need for intuitive interactive hex meshing tools where the user can dictate the priorities of their mesh.

Infarcted brain tissue resulting from acute stroke readily shows up as hyperintense regions within diffusion-weighted magnetic resonance imaging (DWI). It has also been proposed that computed tomography perfusion (CTP) could alternatively be used to triage stroke patients, given improvements in speed and availability, as well as reduced cost. However, CTP has a lower signal to noise ratio compared to MR. In this work, we investigate whether a conditional mapping can be learned by a generative adversarial network to map CTP inputs to generated MR DWI that more clearly delineates hyperintense regions due to ischemic stroke. We detail the architectures of the generator and discriminator and describe the training process used to perform image-to-image translation from multi-modal CT perfusion maps to diffusion weighted MR outputs. We evaluate the results both qualitatively by visual comparison of generated MR to ground truth, as well as quantitatively by training fully convolutional neural networks that make use of generated MR data inputs to perform ischemic stroke lesion segmentation. Segmentation networks trained using generated CT-to-MR inputs result in at least some improvement on all metrics used for evaluation, compared with networks that only use CT perfusion input.

We present a fully convolutional neural network for segmenting ischemic stroke lesions in CT perfusion images for the ISLES 2018 challenge. Treatment of stroke is time sensitive and current standards for lesion identification require manual segmentation, a time consuming and challenging process. Automatic segmentation methods present the possibility of accurately identifying lesions and improving treatment planning. Our model is based on the PSPNet, a network architecture that makes use of pyramid pooling to provide global and local contextual information. To learn the varying shapes of the lesions, we train our network using focal loss, a loss function designed for the network to focus on learning the more difficult samples. We compare our model to networks trained using the U-Net and V-Net architectures. Our approach demonstrates effective performance in lesion segmentation and ranked among the top performers at the challenge conclusion.

We present a volumetric mesh-based algorithm for flattening the placenta to a canonical template to enable effective visualization of local anatomy and function. Monitoring placental function in vivo promises to support pregnancy assessment and to improve care outcomes. We aim to alleviate visualization and interpretation challenges presented by the shape of the placenta when it is attached to the curved uterine wall. To do so, we flatten the volumetric mesh that captures placental shape to resemble the well-studied ex vivo shape. We formulate our method as a map from the in vivo shape to a flattened template that minimizes the symmetric Dirichlet energy to control distortion throughout the volume. Local injectivity is enforced via constrained line search during gradient descent. We evaluate the proposed method on 28 placenta shapes extracted from MRI images in a clinical study of placental function. We achieve sub-voxel accuracy in mapping the boundary of the placenta to the template while successfully controlling distortion throughout the volume. We illustrate how the resulting mapping of the placenta enhances visualization of placental anatomy and function. Our implementation is freely available at https://github.com/mabulnaga/placenta-flattening.

The cerebellum plays an important role in motor control and is also involved in cognitive processes. Cerebellar function is specialized by location, although the exact topographic functional relationship is not fully understood. The spinocerebellar ataxias are a group of neurodegenerative diseases that cause regional atrophy in the cerebellum, yielding distinct motor and cognitive problems. The ability to study the region-specific atrophy patterns can provide insight into the problem of relating cerebellar function to location. In an effort to study these structural change patterns, we developed a toolbox in MATLAB to provide researchers a unique way to visually explore the correlation between cerebellar lobule shape changes and function loss, with a rich set of visualization and analysis modules. In this paper, we outline the functions and highlight the utility of the toolbox. The toolbox takes as input landmark shape representations of subjects’ cerebellar substructures. A principal component analysis is used for dimension reduction. Following this, a linear discriminant analysis and a regression analysis can be performed to find the discriminant direction associated with a specific disease type, or the regression line of a specific functional measure can be generated. The characteristic structural change pattern of a disease type or of a functional score is visualized by sampling points on the discriminant or regression line. The sampled points are used to reconstruct synthetic cerebellar lobule shapes. We showed a few case studies highlighting the utility of the toolbox and we compare the analysis results with the literature.

Cerebellar dysfunction can lead to a wide range of movement disorders. Studying the cerebellar atrophy pattern associated with different cerebellar disease types can potentially help in diagnosis, prognosis, and treatment planning. In this paper, we present a landmark based shape analysis pipeline to classify healthy control and different ataxia types and to visualize the characteristic cerebellar atrophy patterns associated with different types. A highly informative feature representation of the cerebellar structure is constructed by extracting dense homologous landmarks on the boundary surfaces of cerebellar sub-structures. A diagnosis group classifier based on this representation is built using partial least square dimension reduction and regularized linear discriminant analysis. The characteristic atrophy pattern for an ataxia type is visualized by sampling along the discriminant direction between healthy controls and the ataxia type. Experimental results show that the proposed method can successfully classify healthy controls and different ataxia types. The visualized cerebellar atrophy patterns were consistent with the regional volume decreases observed in previous studies, but the proposed method provides intuitive and detailed understanding about changes of overall size and shape of the cerebellum, as well as that of individual lobules.