174 research outputs found
Consistent estimation of shape parameters in statistical shape model by symmetric EM algorithm
In order to fit an unseen surface using statistical shape model (SSM), a correspondence between the unseen surface and the model needs to be established, before the shape parameters can be estimated based on this correspondence. The correspondence and parameter estimation problem can be modeled probabilistically by a Gaussian mixture model (GMM), and solved by expectation-maximization iterative closest points (EM-ICP) algorithm. In this paper, we propose to exploit the linearity of the principal component analysis (PCA) based SSM, and estimate the parameters for the unseen shape surface under the EM-ICP framework. The symmetric data terms are devised to enforce the mutual consistency between the model reconstruction and the shape surface. The a priori shape information encoded in the SSM is also included as regularization. The estimation method is applied to the shape modeling of the hippocampus using a hippocampal SSM
β-amyloid PET harmonisation across longitudinal studies: Application to AIBL, ADNI and OASIS3
INTRODUCTION: The Centiloid scale was developed to harmonise the quantification of β-amyloid (Aβ) PET images across tracers, scanners, and processing pipelines. However, several groups have reported differences across tracers and scanners even after centiloid conversion. In this study, we aim to evaluate the impact of different pre and post-processing harmonisation steps on the robustness of longitudinal Centiloid data across three large international cohort studies.
METHODS: All Aβ PET data in AIBL (N = 3315), ADNI (N = 3442) and OASIS3 (N = 1398) were quantified using the MRI-based Centiloid standard SPM pipeline and the PET-only pipeline CapAIBL. SUVR were converted into Centiloids using each tracer\u27s respective transform. Global Aβ burden from pre-defined target cortical regions in Centiloid units were quantified for both raw PET scans and PET scans smoothed to a uniform 8 mm full width half maximum (FWHM) effective smoothness. For Florbetapir, we assessed the performance of using both the standard Whole Cerebellum (WCb) and a composite white matter (WM)+WCb reference region. Additionally, our recently proposed quantification based on Non-negative Matrix Factorisation (NMF) was applied to all spatially and SUVR normalised images. Correlation with clinical severity measured by the Mini-Mental State Examination (MMSE) and effect size, as well as tracer agreement in
RESULTS: The smoothing to a uniform resolution partially reduced longitudinal variability, but did not improve inter-tracer agreement, effect size or correlation with MMSE. Using a Composite reference region for
CONCLUSIONS: FWHM smoothing has limited impact on longitudinal consistency or outliers. A Composite reference region including subcortical WM should be used for computing both cross-sectional and longitudinal Florbetapir Centiloid. NMF improves Centiloid quantification on all metrics examined
Ea-GANs: Edge-Aware Generative Adversarial Networks for Cross-Modality MR Image Synthesis
Magnetic resonance (MR) imaging is a widely used medical imaging protocol that can be configured to provide different contrasts between the tissues in human body. By setting different scanning parameters, each MR imaging modality reflects the unique visual characteristic of scanned body part, benefiting the subsequent analysis from multiple perspectives. To utilize the complementary information from multiple imaging modalities, cross-modality MR image synthesis has aroused increasing research interest recently. However, most existing methods only focus on minimizing pixel/voxel-wise intensity difference but ignore the textural details of image content structure, which affects the quality of synthesized images. In this paper, we propose edge-aware generative adversarial networks (Ea-GANs) for cross-modality MR image synthesis. Specifically, we integrate edge information, which reflects the textural structure of image content and depicts the boundaries of different objects in images, to reduce this gap. Corresponding to different learning strategies, two frameworks are proposed, i.e., a generator-induced Ea-GAN (gEa-GAN) and a discriminator-induced Ea-GAN (dEa-GAN). The gEa-GAN incorporates the edge information via its generator, while the dEa-GAN further does this from both the generator and the discriminator so that the edge similarity is also adversarially learned. In addition, the proposed Ea-GANs are 3D-based and utilize hierarchical features to capture contextual information. The experimental results demonstrate that the proposed Ea-GANs, especially the dEa-GAN, outperform multiple state-of-the-art methods for cross-modality MR image synthesis in both qualitative and quantitative measures. Moreover, the dEa-GAN also shows excellent generality to generic image synthesis tasks on benchmark datasets about facades, maps, and cityscapes
Atlas selection strategy in multi-atlas segmentation propagation with locally weighted voting using diversity-based MMR re-ranking
In multi-atlas based image segmentation, multiple atlases with label maps are propagated to the query image, and fused into the segmentation result. Voting rule is commonly used classifier fusion method to produce the consensus map. Local weighted voting (LWV) is another method which combines the propagated atlases weighted by local image similarity. When LWV is used, we found that the segmentation accuracy converges slower comparing to simple voting rule. We therefore propose to introduce diversity in addition to image similarity by using Maximal Marginal Relevance (MMR) criteria as a more efficient way to rank and select atlases. We test the MMR re-ranking on a hippocampal atlas set of 138 normal control (NC) subjects and another set of 99 Alzheimer's disease patients provided by ADNI. The result shows that MMR re-ranking performed better than similarity based atlas selection when same number of atlases were selected
Cortical thickness measurement from magnetic resonance images using partial volume estimation
Measurement of the cortical thickness from 3D Magnetic Resonance Imaging (MRI) can aid diagnosis and longitudinal studies of a wide range of neurodegenerative diseases. We estimate the cortical thickness using a Laplacian approach whereby equipotentials analogous to layers of tissue are computed. The thickness is then obtained using an Eulerian approach where partial differential equations (PDE) are solved, avoiding the explicit tracing of trajectories along the streamlines gradient. This method has the advantage of being relatively fast and insure unique correspondence points between the inner and outer boundaries of the cortex. The original method is challenged when the thickness of the cortex is of the same order of magnitude as the image resolution since partial volume (PV) effect is not taken into account at the gray matter (GM) boundaries. We propose a novel way to take into account PV which improves substantially accuracy and robustness. We model PV by computing a mixture of pure Gaussian probability distributions and use this estimate to initialize the cortical thickness estimation. On synthetic phantoms experiments, the errors were divided by three while reproducibility was improved when the same patients was scanned three consecutive times
Bayesian Modeling of Multiple Structural Connectivity Networks During the Progression of Alzheimer's Disease
Alzheimer's disease is the most common neurodegenerative disease. The aim of
this study is to infer structural changes in brain connectivity resulting from
disease progression using cortical thickness measurements from a cohort of
participants who were either healthy control, or with mild cognitive
impairment, or Alzheimer's disease patients. For this purpose, we develop a
novel approach for inference of multiple networks with related edge values
across groups. Specifically, we infer a Gaussian graphical model for each group
within a joint framework, where we rely on Bayesian hierarchical priors to link
the precision matrix entries across groups. Our proposal differs from existing
approaches in that it flexibly learns which groups have the most similar edge
values, and accounts for the strength of connection (rather than only edge
presence or absence) when sharing information across groups. Our results
identify key alterations in structural connectivity which may reflect
disruptions to the healthy brain, such as decreased connectivity within the
occipital lobe with increasing disease severity. We also illustrate the
proposed method through simulations, where we demonstrate its performance in
structure learning and precision matrix estimation with respect to alternative
approaches.Comment: Accepted to Biometrics January 202
A non-rigid registration method for mouse whole body skeleton registration
Micro-CT/PET imaging scanner provides a powerful tool to study tumor in small rodents in response to therapy. Accurate image registration is a necessary step to quantify the characteristics of images acquired in longitudinal studies. Small animal registration is challenging because of the very deformable body of the animal often resulting in different postures despite physical restraints. In this paper, we propose a non-rigid registration approach for the automatic registration of mouse whole body skeletons, which is based on our improved 3D shape context non-rigid registration method. The whole body skeleton registration approach has been tested on 21 pairs of mouse CT images with variations of individuals and time-instances. The experimental results demonstrated the stability and accuracy of the proposed method for automatic mouse whole body skeleton registration
An improved 3D shape context registration method for non-rigid surface registration
3D shape context is a method to define matching points between similar shapes as a pre-processing step to non-rigid registration. The main limitation of the approach is point mismatching, which includes long geodesic distance mismatch and neighbors crossing mismatch. In this paper, we propose a topological structure verification method to correct the long geodesic distance mismatch and a correspondence field smoothing method to correct the neighbors crossing mismatch. A robust 3D shape context model is proposed and further combined with thin-plate spline model for non-rigid surface registration. The method was tested on phantoms and rat hind limb skeletons from micro CT images. The results from experiments on mouse hind limb skeletons indicate that the approach is robust
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
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