Prediction of biomechanical properties of trabecular bone in MR images with geometric features and support vector regression

Data-Driven Based Characterization of Anisotropic Mechanical Properties for Cancellous Bone From Low-Resolution CT Images

OBJECTIVES

Exploring the anisotropic mechanical behavior of cancellous bone is crucial for in-vivo bone biomechanical analysis. However, it is challenging to characterize anisotropic mechanical behaviors under low-resolution (LR) clinical CT images due to a lack of microstructural information. The data-driven method proposed in this article accurately characterizes the anisotropic mechanical properties of cancellous bone from LR clinical CT images.

METHODS

The trabecular bone cubes of sheep are used to obtain a high-resolution (HR) micro-CT and an LR clinical CT image dataset. First, an auto-encoder model is trained using HR image data. Microstructural features are extracted by the encoder. A fast super-resolution (FSR) model is trained to map LR bone cubes to the features extracted from corresponding HR samples. The pretrained FSR model is used to convert LR clinical CT images to encoded microstructural features. The features are later used to predict target histomorphological parameters, anisotropic elastic tensors, and fabric tensors based on a fully connected neural network.

RESULTS

The data-driven model accurately predicts the elastic tensor and fabric tensor of trabecular bones with LR CT images with 0.6 mm/pixel spatial resolution. It was verified that LR clinical CT images could generate microstructural information using a generative deep-learning model and an up-sampling operation.

SIGNIFICANCE

This study proves that clinical medical images of cancellous bone can be used for analysis of complex mechanical properties using a data-driven method, which is useful for real-time bone defect diagnosis and personalized bone prosthesis design in clinical application.

Clinical applications of artificial intelligence in radiology

The rapid growth of medical imaging has placed increasing demands on radiologists. In this scenario, artificial intelligence (AI) has become an attractive partner, one that may complement case interpretation and may aid in various non-interpretive aspects of the work in the radiological clinic. In this review, we discuss interpretative and non-interpretative uses of AI in the clinical practice, as well as report on the barriers to AI's adoption in the clinic. We show that AI currently has a modest to moderate penetration in the clinical practice, with many radiologists still being unconvinced of its value and the return on its investment. Moreover, we discuss the radiologists' liabilities regarding the AI decisions, and explain how we currently do not have regulation to guide the implementation of explainable AI or of self-learning algorithms.

The promise and limitations of artificial intelligence in musculoskeletal imaging

With the recent developments in deep learning and the rapid growth of convolutional neural networks, artificial intelligence has shown promise as a tool that can transform several aspects of the musculoskeletal imaging cycle. Its applications can involve both interpretive and non-interpretive tasks such as the ordering of imaging, scheduling, protocoling, image acquisition, report generation and communication of findings. However, artificial intelligence tools still face a number of challenges that can hinder effective implementation into clinical practice. The purpose of this review is to explore both the successes and limitations of artificial intelligence applications throughout the muscuskeletal imaging cycle and to highlight how these applications can help enhance the service radiologists deliver to their patients, resulting in increased efficiency as well as improved patient and provider satisfaction.

Artificial intelligence, machine learning and deep learning in musculoskeletal imaging: Current applications

Artificial intelligence is rapidly expanding in all technological fields. The medical field, and especially diagnostic imaging, has been showing the highest developmental potential. Artificial intelligence aims at human intelligence simulation through the management of complex problems. This review describes the technical background of artificial intelligence, machine learning, and deep learning. The first section illustrates the general potential of artificial intelligence applications in the context of request management, data acquisition, image reconstruction, archiving, and communication systems. In the second section, the prospective of dedicated tools for segmentation, lesion detection, automatic diagnosis, and classification of musculoskeletal disorders is discussed.

Quadratic hyper-surface kernel-free least squares support vector regression

We present a novel kernel-free regressor, called quadratic hyper-surface kernel-free least squares support vector regression (QLSSVR), for some regression problems. The task of this approach is to find a quadratic function as the regression function, which is obtained by solving a quadratic programming problem with the equality constraints. Basically, the new model just needs to solve a system of linear equations to achieve the optimal solution instead of solving a quadratic programming problem. Therefore, compared with the standard support vector regression, our approach is much efficient due to kernel-free and solving a set of linear equations. Numerical results illustrate that our approach has better performance than other existing regression approaches in terms of regression criterion and CPU time.

Artificial Intelligence in Musculoskeletal Imaging: Current Status and Future Directions

OBJECTIVE. The objective of this article is to show how artificial intelligence (AI) has impacted different components of the imaging value chain thus far as well as to describe its potential future uses. CONCLUSION. The use of AI has the potential to greatly enhance every component of the imaging value chain. From assessing the appropriateness of imaging orders to helping predict patients at risk for fracture, AI can increase the value that musculoskeletal imagers provide to their patients and to referring clinicians by improving image quality, patient centricity, imaging efficiency, and diagnostic accuracy.

Impaired bone healing at tooth extraction sites in CD24-deficient mice: A pilot study

AIM

To use a micro-computed tomography (micro-CT) to quantify bone healing at maxillary first molar extraction sites, and test the hypothesis that bone healing is impaired in CD24-knockout mice as compared with wild-type C57BL/6J mice.

MATERIALS AND METHODS

Under ketamine-xylazine general anaesthesia, mice had either extraction of the right maxillary first molar tooth or sham operation. Mice were sacrificed 1 (n = 12/group), 2 (n = 6/group) or 4 (n = 6/group) weeks postoperatively. The right maxillae was disected. Micro-CT was used to quantify differences in bone microstructural features at extrction sites, between CD24-knockout mice and wild-type mice.

RESULTS

CD24-Knockout mice displayed impaired bone healing at extraction sites that was manifested as decreased trabecular bone density, and decreased number and thickness of trabeculae.

CONCLUSIONS

This pilot study suggests that CD24 plays an important role in extraction socket bone healing and may be used as a novel biomarker of bone quality and potential therapeutic target to improve bone healing and density following alveolar bone injury.

Identifying HIV Associated Neurocognitive Disorder Using Large-Scale Granger Causality Analysis on Resting-State Functional MRI

We investigate the applicability of large-scale Granger Causality (lsGC) for extracting a measure of multivariate information flow between pairs of regional brain activities from resting-state functional MRI (fMRI) and test the effectiveness of these measures for predicting a disease state. Such pairwise multivariate measures of interaction provide high-dimensional representations of connectivity profiles for each subject and are used in a machine learning task to distinguish between healthy controls and individuals presenting with symptoms of HIV Associated Neurocognitive Disorder (HAND). Cognitive impairment in several domains can occur as a result of HIV infection of the central nervous system. The current paradigm for assessing such impairment is through neuropsychological testing. With fMRI data analysis, we aim at non-invasively capturing differences in brain connectivity patterns between healthy subjects and subjects presenting with symptoms of HAND. To classify the extracted interaction patterns among brain regions, we use a prototype-based learning algorithm called Generalized Matrix Learning Vector Quantization (GMLVQ). Our approach to characterize connectivity using lsGC followed by GMLVQ for subsequent classification yields good prediction results with an accuracy of 87% and an area under the ROC curve (AUC) of up to 0.90. We obtain a statistically significant improvement (p<0.01) over a conventional Granger causality approach (accuracy = 0.76, AUC = 0.74). High accuracy and AUC values using our multivariate method to connectivity analysis suggests that our approach is able to better capture changes in interaction patterns between different brain regions when compared to conventional Granger causality analysis known from the literature.

Investigating Changes in Resting-State Connectivity from Functional MRI Data in Patients with HIV Associated Neurocognitive Disorder Using MCA and Machine Learning

Infection of the brain by the Human Immunodeficiency Virus (HIV) causes irreversible damage to the synaptic connections resulting in cognitive impairment. Patients with HIV infection, showing signs of impairment in multiple cognitive domains, as assessed by neuropsychological testing, are said to exhibit symptoms of HIV Associated Neurocognitive Disorder (HAND). In this study, we use resting-state functional MRI (fMRI) data to distinguish between healthy subjects and subjects with symptoms of HAND. To this end, we first establish a measure of interaction between pairs of regional time-series by quantifying their non-linear functional connectivity using Mutual Connectivity Analysis (MCA). Subsequently, we use a classifier to distinguish patterns of interaction between healthy and diseased individuals. Our results, quantified as the mean Area under the ROC curve (AUC) over 75 iterations, indicate that, using fMRI data, we can discriminate between the two cohorts well (AUC > 0.8). Specifically, we find that MCA (mean AUC = 0.89) based connectivity features perform significantly better (p < 0.05) when compared to cross-correlation (mean AUC = 0.82) at the classification task. A higher AUC using our approach suggests that such a nonlinear approach is better able to capture connectivity changes between brain regions and has potential for the development of novel neuro-imaging biomarkers.

Classification of micro-CT images using 3D characterization of bone canal patterns in human osteogenesis imperfecta

Few studies have analyzed the microstructural properties of bone in cases of Osteogenenis Imperfecta (OI), or 'brittle bone disease'. Current approaches mainly focus on bone mineral density measurements as an indirect indicator of bone strength and quality. It has been shown that bone strength would depend not only on composition but also structural organization. This study aims to characterize 3D structure of the cortical bone in high-resolution micro CT images. A total of 40 bone fragments from 28 subjects (13 with OI and 15 healthy controls) were imaged using micro tomography using a synchrotron light source (SRμCT). Minkowski functionals - volume, surface, curvature, and Euler characteristics - describing the topological organization of the bone were computed from the images. The features were used in a machine learning task to classify between healthy and OI bone. The best classification performance (mean AUC - 0.96) was achieved with a combined 4-dimensional feature of all Minkowski functionals. Individually, the best feature performance was seen using curvature (mean AUC - 0.85), which characterizes the edges within a binary object. These results show that quantitative analysis of cortical bone microstructure, in a computer-aided diagnostics framework, can be used to distinguish between healthy and OI bone with high accuracy.

Using Large-Scale Granger Causality to Study Changes in Brain Network Properties in the Clinically Isolated Syndrome (CIS) Stage of Multiple Sclerosis

Clinically Isolated Syndrome (CIS) is often considered to be the first neurological episode associated with Multiple sclerosis (MS). At an early stage the inflammatory demyelination occurring in the CNS can manifest as a change in neuronal metabolism, with multiple asymptomatic white matter lesions detected in clinical MRI. Such damage may induce topological changes of brain networks, which can be captured by advanced functional MRI (fMRI) analysis techniques. We test this hypothesis by capturing the effective relationships of 90 brain regions, defined in the Automated Anatomic Labeling (AAL) atlas, using a large-scale Granger Causality (lsGC) framework. The resulting networks are then characterized using graph-theoretic measures that quantify various network topology properties at a global as well as at a local level. We study for differences in these properties in network graphs obtained for 18 subjects (10 male and 8 female, 9 with CIS and 9 healthy controls). Global network properties captured trending differences with modularity and clustering coefficient (p<0.1). Additionally, local network properties, such as local efficiency and the strength of connections, captured statistically significant (p<0.01) differences in some regions of the inferior frontal and parietal lobe. We conclude that multivariate analysis of fMRI time-series can reveal interesting information about changes occurring in the brain in early stages of MS.

Mutual Connectivity Analysis (MCA) Using Generalized Radial Basis Function Neural Networks for Nonlinear Functional Connectivity Network Recovery in Resting-State Functional MRI

We investigate the applicability of a computational framework, called mutual connectivity analysis (MCA), for directed functional connectivity analysis in both synthetic and resting-state functional MRI data. This framework comprises of first evaluating non-linear cross-predictability between every pair of time series prior to recovering the underlying network structure using community detection algorithms. We obtain the non-linear cross-prediction score between time series using Generalized Radial Basis Functions (GRBF) neural networks. These cross-prediction scores characterize the underlying functionally connected networks within the resting brain, which can be extracted using non-metric clustering approaches, such as the Louvain method. We first test our approach on synthetic models with known directional influence and network structure. Our method is able to capture the directional relationships between time series (with an area under the ROC curve = 0.92 ± 0.037) as well as the underlying network structure (Rand index = 0.87 ± 0.063) with high accuracy. Furthermore, we test this method for network recovery on resting-state fMRI data, where results are compared to the motor cortex network recovered from a motor stimulation sequence, resulting in a strong agreement between the two (Dice coefficient = 0.45). We conclude that our MCA approach is effective in analyzing non-linear directed functional connectivity and in revealing underlying functional network structure in complex systems.

Detecting Altered connectivity patterns in HIV associated neurocognitive impairment using Mutual Connectivity Analysis

The use of functional Magnetic Resonance Imaging (fMRI) has provided interesting insights into our understanding of the brain. In clinical setups these scans have been used to detect and study changes in the brain network properties in various neurological disorders. A large percentage of subjects infected with HIV present cognitive deficits, which are known as HIV associated neurocognitive disorder (HAND). In this study we propose to use our novel technique named Mutual Connectivity Analysis (MCA) to detect differences in brain networks in subjects with and without HIV infection. Resting state functional MRI scans acquired from 10 subjects (5 HIV+ and 5 HIV-) were subject to standard pre-processing routines. Subsequently, the average time-series for each brain region of the Automated Anatomic Labeling (AAL) atlas are extracted and used with the MCA framework to obtain a graph characterizing the interactions between them. The network graphs obtained for different subjects are then compared using Network-Based Statistics (NBS), which is an approach to detect differences between graphs edges while controlling for the family-wise error rate when mass univariate testing is performed. Applying this approach on the graphs obtained yields a single network encompassing 42 nodes and 65 edges, which is significantly different between the two subject groups. Specifically connections to the regions in and around the basal ganglia are significantly decreased. Also some nodes corresponding to the posterior cingulate cortex are affected. These results are inline with our current understanding of pathophysiological mechanisms of HIV associated neurocognitive disease (HAND) and other HIV based fMRI connectivity studies. Hence, we illustrate the applicability of our novel approach with network-based statistics in a clinical case-control study to detect differences connectivity patterns.

Investigating Changes in Brain Network Properties in HIV-Associated Neurocognitive Disease (HAND) using Mutual Connectivity Analysis (MCA)

About 50% of subjects infected with HIV present deficits in cognitive domains, which are known collectively as HIV associated neurocognitive disorder (HAND). The underlying synaptodendritic damage can be captured using resting state functional MRI, as has been demonstrated by a few earlier studies. Such damage may induce topological changes of brain connectivity networks. We test this hypothesis by capturing the functional interdependence of 90 brain network nodes using a Mutual Connectivity Analysis (MCA) framework with non-linear time series modeling based on Generalized Radial Basis function (GRBF) neural networks. The network nodes are selected based on the regions defined in the Automated Anatomic Labeling (AAL) atlas. Each node is represented by the average time series of the voxels of that region. The resulting networks are then characterized using graph-theoretic measures that quantify various network topology properties at a global as well as at a local level. We tested for differences in these properties in network graphs obtained for 10 subjects (6 male and 4 female, 5 HIV+ and 5 HIV-). Global network properties captured some differences between these subject cohorts, though significant differences were seen only with the clustering coefficient measure. Local network properties, such as local efficiency and the degree of connections, captured significant differences in regions of the frontal lobe, precentral and cingulate cortex amongst a few others. These results suggest that our method can be used to effectively capture differences occurring in brain network connectivity properties revealed by resting-state functional MRI in neurological disease states, such as HAND.

Large-Scale Granger Causality Analysis on Resting-State Functional MRI

We demonstrate an approach to measure the information flow between each pair of time series in resting-state functional MRI (fMRI) data of the human brain and subsequently recover its underlying network structure. By integrating dimensionality reduction into predictive time series modeling, large-scale Granger Causality (lsGC) analysis method can reveal directed information flow suggestive of causal influence at an individual voxel level, unlike other multivariate approaches. This method quantifies the influence each voxel time series has on every other voxel time series in a multivariate sense and hence contains information about the underlying dynamics of the whole system, which can be used to reveal functionally connected networks within the brain. To identify such networks, we perform non-metric network clustering, such as accomplished by the Louvain method. We demonstrate the effectiveness of our approach to recover the motor and visual cortex from resting state human brain fMRI data and compare it with the network recovered from a visuomotor stimulation experiment, where the similarity is measured by the Dice Coefficient (DC). The best DC obtained was 0.59 implying a strong agreement between the two networks. In addition, we thoroughly study the effect of dimensionality reduction in lsGC analysis on network recovery. We conclude that our approach is capable of detecting causal influence between time series in a multivariate sense, which can be used to segment functionally connected networks in the resting-state fMRI.

Assessing vertebral fracture risk on volumetric quantitative computed tomography by geometric characterization of trabecular bone structure

The current clinical standard for measuring Bone Mineral Density (BMD) is dual X-ray absorptiometry, however more recently BMD derived from volumetric quantitative computed tomography has been shown to demonstrate a high association with spinal fracture susceptibility. In this study, we propose a method of fracture risk assessment using structural properties of trabecular bone in spinal vertebrae. Experimental data was acquired via axial multi-detector CT (MDCT) from 12 spinal vertebrae specimens using a whole-body 256-row CT scanner with a dedicated calibration phantom. Common image processing methods were used to annotate the trabecular compartment in the vertebral slices creating a circular region of interest (ROI) that excluded cortical bone for each slice. The pixels inside the ROI were converted to values indicative of BMD. High dimensional geometrical features were derived using the scaling index method (SIM) at different radii and scaling factors (SF). The mean BMD values within the ROI were then extracted and used in conjunction with a support vector machine to predict the failure load of the specimens. Prediction performance was measured using the root-mean-square error (RMSE) metric and determined that SIM combined with mean BMD features (RMSE = 0.82 ± 0.37) outperformed MDCT-measured mean BMD (RMSE = 1.11 ± 0.33) (p < 10^-4). These results demonstrate that biomechanical strength prediction in vertebrae can be significantly improved through the use of SIM-derived texture features from trabecular bone.

Volumetric quantitative characterization of human patellar cartilage with topological and geometrical features on phase-contrast X-ray computed tomography

Phase-contrast X-ray computed tomography (PCI-CT) has attracted significant interest in recent years for its ability to provide significantly improved image contrast in low absorbing materials such as soft biological tissue. In the research context of cartilage imaging, previous studies have demonstrated the ability of PCI-CT to visualize structural details of human patellar cartilage matrix and capture changes to chondrocyte organization induced by osteoarthritis. This study evaluates the use of geometrical and topological features for volumetric characterization of such chondrocyte patterns in the presence (or absence) of osteoarthritic damage. Geometrical features derived from the scaling index method (SIM) and topological features derived from Minkowski Functionals were extracted from 1392 volumes of interest (VOI) annotated on PCI-CT images of ex vivo human patellar cartilage specimens. These features were subsequently used in a machine learning task with support vector regression to classify VOIs as healthy or osteoarthritic; classification performance was evaluated using the area under the receiver operating characteristic curve (AUC). Our results show that the classification performance of SIM-derived geometrical features (AUC: 0.90 ± 0.09) is significantly better than Minkowski Functionals volume (AUC: 0.54 ± 0.02), surface (AUC: 0.72 ± 0.06), mean breadth (AUC: 0.74 ± 0.06) and Euler characteristic (AUC: 0.78 ± 0.04) (p < 10(-4)). These results suggest that such geometrical features can provide a detailed characterization of the chondrocyte organization in the cartilage matrix in an automated manner, while also enabling classification of cartilage as healthy or osteoarthritic with high accuracy. Such features could potentially serve as diagnostic imaging markers for evaluating osteoarthritis progression and its response to different therapeutic intervention strategies.

Volumetric Characterization of Human Patellar Cartilage Matrix on Phase Contrast X-Ray Computed Tomography

Phase contrast X-ray computed tomography (PCI-CT) has recently emerged as a novel imaging technique that allows visualization of cartilage soft tissue, subsequent examination of chondrocyte patterns, and their correlation to osteoarthritis. Previous studies have shown that 2D texture features are effective at distinguishing between healthy and osteoarthritic regions of interest annotated in the radial zone of cartilage matrix on PCI-CT images. In this study, we further extend the texture analysis to 3D and investigate the ability of volumetric texture features at characterizing chondrocyte patterns in the cartilage matrix for purposes of classification. Here, we extracted volumetric texture features derived from Minkowski Functionals and gray-level co-occurrence matrices (GLCM) from 496 volumes of interest (VOI) annotated on PCI-CT images of human patellar cartilage specimens. The extracted features were then used in a machine-learning task involving support vector regression to classify ROIs as healthy or osteoarthritic. Classification performance was evaluated using the area under the receiver operating characteristic (ROC) curve (AUC). The best classification performance was observed with GLCM features correlation (AUC = 0.83 ± 0.06) and homogeneity (AUC = 0.82 ± 0.07), which significantly outperformed all Minkowski Functionals (p < 0.05). These results suggest that such quantitative analysis of chondrocyte patterns in human patellar cartilage matrix involving GLCM-derived statistical features can distinguish between healthy and osteoarthritic tissue with high accuracy.

Investigating the use of mutual information and non-metric clustering for functional connectivity analysis on resting-state functional MRI

Functional MRI (fMRI) is currently used to investigate structural and functional connectivity in human brain networks. To this end, previous studies have proposed computational methods that involve assumptions that can induce information loss, such as assumed linear coupling of the fMRI signals or requiring dimension reduction. This study presents a new computational framework for investigating the functional connectivity in the brain and recovering network structure while reducing the information loss inherent in previous methods. For this purpose, pair-wise mutual information (MI) was extracted from all pixel time series within the brain on resting-state fMRI data. Non-metric topographic mapping of proximity (TMP) data was subsequently applied to recover network structure from the pair-wise MI analysis. Our computational framework is demonstrated in the task of identifying regions of the primary motor cortex network on resting state fMRI data. For ground truth comparison, we also localized regions of the primary motor cortex associated with hand movement in a task-based fMRI sequence with a finger-tapping stimulus function. The similarity between our pair-wise MI clustering results and the ground truth is evaluated using the dice coefficient. Our results show that non-metric clustering with the TMP algorithm, as performed on pair-wise MI analysis, was able to detect the primary motor cortex network and achieved a dice coefficient of 0.53 in terms of overlap with the ground truth. Thus, we conclude that our computational framework can extract and visualize valuable information concerning the underlying network structure between different regions of the brain in resting state fMRI.

Characterizing Trabecular Bone structure for Assessing Vertebral Fracture Risk on Volumetric Quantitative Computed Tomography

While the proximal femur is preferred for measuring bone mineral density (BMD) in fracture risk estimation, the introduction of volumetric quantitative computed tomography has revealed stronger associations between BMD and spinal fracture status. In this study, we propose to capture properties of trabecular bone structure in spinal vertebrae with advanced second-order statistical features for purposes of fracture risk assessment. For this purpose, axial multi-detector CT (MDCT) images were acquired from 28 spinal vertebrae specimens using a whole-body 256-row CT scanner with a dedicated calibration phantom. A semi-automated method was used to annotate the trabecular compartment in the central vertebral slice with a circular region of interest (ROI) to exclude cortical bone; pixels within were converted to values indicative of BMD. Six second-order statistical features derived from gray-level co-occurrence matrices (GLCM) and the mean BMD within the ROI were then extracted and used in conjunction with a generalized radial basis functions (GRBF) neural network to predict the failure load of the specimens; true failure load was measured through biomechanical testing. Prediction performance was evaluated with a root-mean-square error (RMSE) metric. The best prediction performance was observed with GLCM feature 'correlation' (RMSE = 1.02 ± 0.18), which significantly outperformed all other GLCM features (p < 0.01). GLCM feature correlation also significantly outperformed MDCT-measured mean BMD (RMSE = 1.11 ± 0.17) (p < 10^-4). These results suggest that biomechanical strength prediction in spinal vertebrae can be significantly improved through characterization of trabecular bone structure with GLCM-derived texture features.

Functional Connectivity Analysis in Resting State fMRI with Echo-State Networks and Non-Metric Clustering for Network Structure Recovery

Echo state networks (ESN) are recurrent neural networks where the hidden layer is replaced with a fixed reservoir of neurons. Unlike feed-forward networks, neuron training in ESN is restricted to the output neurons alone thereby providing a computational advantage. We demonstrate the use of such ESNs in our mutual connectivity analysis (MCA) framework for recovering the primary motor cortex network associated with hand movement from resting state functional MRI (fMRI) data. Such a framework consists of two steps - (1) defining a pair-wise affinity matrix between different pixel time series within the brain to characterize network activity and (2) recovering network components from the affinity matrix with non-metric clustering. Here, ESNs are used to evaluate pair-wise cross-estimation performance between pixel time series to create the affinity matrix, which is subsequently subject to non-metric clustering with the Louvain method. For comparison, the ground truth of the motor cortex network structure is established with a task-based fMRI sequence. Overlap between the primary motor cortex network recovered with our model free MCA approach and the ground truth was measured with the Dice coefficient. Our results show that network recovery with our proposed MCA approach is in close agreement with the ground truth. Such network recovery is achieved without requiring low-pass filtering of the time series ensembles prior to analysis, an fMRI preprocessing step that has courted controversy in recent years. Thus, we conclude our MCA framework can allow recovery and visualization of the underlying functionally connected networks in the brain on resting state fMRI.

Nonlinear Functional Connectivity Network Recovery in the Human Brain with Mutual Connectivity Analysis (MCA): Convergent Cross-Mapping and Non-Metric Clustering

We explore a computational framework for functional connectivity analysis in resting-state functional MRI (fMRI) data acquired from the human brain for recovering the underlying network structure and understanding causality between network components. Termed mutual connectivity analysis (MCA), this framework involves two steps, the first of which is to evaluate the pair-wise cross-prediction performance between fMRI pixel time series within the brain. In a second step, the underlying network structure is subsequently recovered from the affinity matrix using non-metric network clustering approaches, such as the so-called Louvain method. Finally, we use convergent cross-mapping (CCM) to study causality between different network components. We demonstrate our MCA framework in the problem of recovering the motor cortex network associated with hand movement from resting state fMRI data. Results are compared with a ground truth of active motor cortex regions as identified by a task-based fMRI sequence involving a finger-tapping stimulation experiment. Our results regarding causation between regions of the motor cortex revealed a significant directional variability and were not readily interpretable in a consistent manner across subjects. However, our results on whole-slice fMRI analysis demonstrate that MCA-based model-free recovery of regions associated with the primary motor cortex and supplementary motor area are in close agreement with localization of similar regions achieved with a task-based fMRI acquisition. Thus, we conclude that our MCA methodology can extract and visualize valuable information concerning the underlying network structure between different regions of the brain in resting state fMRI.

Computer-aided diagnosis for phase-contrast X-ray computed tomography: quantitative characterization of human patellar cartilage with high-dimensional geometric features

Phase-contrast computed tomography (PCI-CT) has shown tremendous potential as an imaging modality for visualizing human cartilage with high spatial resolution. Previous studies have demonstrated the ability of PCI-CT to visualize (1) structural details of the human patellar cartilage matrix and (2) changes to chondrocyte organization induced by osteoarthritis. This study investigates the use of high-dimensional geometric features in characterizing such chondrocyte patterns in the presence or absence of osteoarthritic damage. Geometrical features derived from the scaling index method (SIM) and statistical features derived from gray-level co-occurrence matrices were extracted from 842 regions of interest (ROI) annotated on PCI-CT images of ex vivo human patellar cartilage specimens. These features were subsequently used in a machine learning task with support vector regression to classify ROIs as healthy or osteoarthritic; classification performance was evaluated using the area under the receiver-operating characteristic curve (AUC). SIM-derived geometrical features exhibited the best classification performance (AUC, 0.95 ± 0.06) and were most robust to changes in ROI size. These results suggest that such geometrical features can provide a detailed characterization of the chondrocyte organization in the cartilage matrix in an automated and non-subjective manner, while also enabling classification of cartilage as healthy or osteoarthritic with high accuracy. Such features could potentially serve as imaging markers for evaluating osteoarthritis progression and its response to different therapeutic intervention strategies.

Bone mineral density and donor age are not predictive of femoral ring allograft bone mechanical strength

While metal or plastic interbody spinal fusion devices are manufactured to appropriate mechanical standards, mechanical properties of commercially prepared structural allograft bone remain relatively unassessed. Robust models predicting compressive load to failure of structural allograft bone based on easily measured variables would be useful. Three hundred twenty seven femoral rings from 34 cadaver femora were tested to failure in axial compression. Predictive variables included age, gender, bone mineral density (BMD), position along femoral shaft, maximum/minimum wall thickness, outer/inner diameter, and area. We used support vector regression and 10-fold cross-validation to develop robust nonlinear predictive models for load to failure. Model performance was measured by the root-mean-squared-deviation (RMSD) and correlation coefficients (r). A polynomial model using all variables had RMSD = 7.92, r = 0.84, indicating excellent performance. A model using all variables except BMD was essentially unchanged (RMSD = 8.12, r = 0.83). Eliminating both age and BMD produced a model with RMSD = 8.41, r = 0.82, again essentially unchanged. Compressive strength of structural allograft bone can be estimated using easily measured geometric parameters, without including BMD or age. As DEXA is costly and cumbersome, and setting upper age-limits for potential donors reduces the supply, our results may prove helpful to increase the quality and availability of structural allograft.

Using Anisotropic 3D Minkowski Functionals for Trabecular Bone Characterization and Biomechanical Strength Prediction in Proximal Femur Specimens

The ability of Anisotropic Minkowski Functionals (AMFs) to capture local anisotropy while evaluating topological properties of the underlying gray-level structures has been previously demonstrated. We evaluate the ability of this approach to characterize local structure properties of trabecular bone micro-architecture in ex vivo proximal femur specimens, as visualized on multi-detector CT, for purposes of biomechanical bone strength prediction. To this end, volumetric AMFs were computed locally for each voxel of volumes of interest (VOI) extracted from the femoral head of 146 specimens. The local anisotropy captured by such AMFs was quantified using a fractional anisotropy measure; the magnitude and direction of anisotropy at every pixel was stored in histograms that served as a feature vectors that characterized the VOIs. A linear multi-regression analysis algorithm was used to predict the failure load (FL) from the feature sets; the predicted FL was compared to the true FL determined through biomechanical testing. The prediction performance was measured by the root mean square error (RMSE) for each feature set. The best prediction performance was obtained from the fractional anisotropy histogram of AMF Euler Characteristic (RMSE = 1.01 ± 0.13), which was significantly better than MDCT-derived mean BMD (RMSE = 1.12 ± 0.16, p<0.05). We conclude that such anisotropic Minkowski Functionals can capture valuable information regarding regional trabecular bone quality and contribute to improved bone strength prediction, which is important for improving the clinical assessment of osteoporotic fracture risk.

Investigating the use of texture features for analysis of breast lesions on contrast-enhanced cone beam CT

Cone beam computed tomography (CBCT) has found use in mammography for imaging the entire breast with sufficient spatial resolution at a radiation dose within the range of that of conventional mammography. Recently, enhancement of lesion tissue through the use of contrast agents has been proposed for cone beam CT. This study investigates whether the use of such contrast agents improves the ability of texture features to differentiate lesion texture from healthy tissue on CBCT in an automated manner. For this purpose, 9 lesions were annotated by an experienced radiologist on both regular and contrast-enhanced CBCT images using two-dimensional (2D) square ROIs. These lesions were then segmented, and each pixel within the lesion ROI was assigned a label - lesion or non-lesion, based on the segmentation mask. On both sets of CBCT images, four three-dimensional (3D) Minkowski Functionals were used to characterize the local topology at each pixel. The resulting feature vectors were then used in a machine learning task involving support vector regression with a linear kernel (SVRlin) to classify each pixel as belonging to the lesion or non-lesion region of the ROI. Classification performance was assessed using the area under the receiver-operating characteristic (ROC) curve (AUC). Minkowski Functionals derived from contrast-enhanced CBCT images were found to exhibit significantly better performance at distinguishing between lesion and non-lesion areas within the ROI when compared to those extracted from CBCT images without contrast enhancement (p < 0.05). Thus, contrast enhancement in CBCT can improve the ability of texture features to distinguish lesions from surrounding healthy tissue.

Predicting the Biomechanical Strength of Proximal Femur Specimens with Minkowski Functionals and Support Vector Regression

Regional trabecular bone quality estimation for purposes of femoral bone strength prediction is important for improving the clinical assessment of osteoporotic fracture risk. In this study, we explore the ability of 3D Minkowski Functionals derived from multi-detector computed tomography (MDCT) images of proximal femur specimens in predicting their corresponding biomechanical strength. MDCT scans were acquired for 50 proximal femur specimens harvested from human cadavers. An automated volume of interest (VOI)-fitting algorithm was used to define a consistent volume in the femoral head of each specimen. In these VOIs, the trabecular bone micro-architecture was characterized by statistical moments of its BMD distribution and by topological features derived from Minkowski Functionals. A linear multi-regression analysis and a support vector regression (SVR) algorithm with a linear kernel were used to predict the failure load (FL) from the feature sets; the predicted FL was compared to the true FL determined through biomechanical testing. The prediction performance was measured by the root mean square error (RMSE) for each feature set. The best prediction result was obtained from the Minkowski Functional surface used in combination with SVR, which had the lowest prediction error (RMSE = 0.939 ± 0.345) and which was significantly lower than mean BMD (RMSE = 1.075 ± 0.279, p<0.005). Our results indicate that the biomechanical strength prediction can be significantly improved in proximal femur specimens with Minkowski Functionals extracted from on MDCT images used in conjunction with support vector regression.

Improving bone strength prediction in human proximal femur specimens through geometrical characterization of trabecular bone microarchitecture and support vector regression

We investigate the use of different trabecular bone descriptors and advanced machine learning tech niques to complement standard bone mineral density (BMD) measures derived from dual-energy x-ray absorptiometry (DXA) for improving clinical assessment of osteoporotic fracture risk. For this purpose, volumes of interest were extracted from the head, neck, and trochanter of 146 ex vivo proximal femur specimens on multidetector computer tomography. The trabecular bone captured was characterized with (1) statistical moments of the BMD distribution, (2) geometrical features derived from the scaling index method (SIM), and (3) morphometric parameters, such as bone fraction, trabecular thickness, etc. Feature sets comprising DXA BMD and such supplemental features were used to predict the failure load (FL) of the specimens, previously determined through biomechanical testing, with multiregression and support vector regression. Prediction performance was measured by the root mean square error (RMSE); correlation with measured FL was evaluated using the coefficient of determination R2. The best prediction performance was achieved by a combination of DXA BMD and SIM-derived geometric features derived from the femoral head (RMSE: 0.869 ± 0.121, R2: 0.68 ± 0.079), which was significantly better than DXA BMD alone (RMSE: 0.948 ± 0.119, R2: 0.61 ± 0.101) (p < 10-4). For multivariate feature sets, SVR outperformed multiregression (p < 0.05). These results suggest that supplementing standard DXA BMD measurements with sophisticated femoral trabecular bone characterization and supervised learning techniques can significantly improve biomechanical strength prediction in proximal femur specimens.

Phase contrast imaging X-ray computed tomography: Quantitative characterization of human patellar cartilage matrix with topological and geometrical features

Current assessment of cartilage is primarily based on identification of indirect markers such as joint space narrowing and increased subchondral bone density on x-ray images. In this context, phase contrast CT imaging (PCI-CT) has recently emerged as a novel imaging technique that allows a direct examination of chondrocyte patterns and their correlation to osteoarthritis through visualization of cartilage soft tissue. This study investigates the use of topological and geometrical approaches for characterizing chondrocyte patterns in the radial zone of the knee cartilage matrix in the presence and absence of osteoarthritic damage. For this purpose, topological features derived from Minkowski Functionals and geometric features derived from the Scaling Index Method (SIM) were extracted from 842 regions of interest (ROI) annotated on PCI-CT images of healthy and osteoarthritic specimens of human patellar cartilage. The extracted features were then used in a machine learning task involving support vector regression to classify ROIs as healthy or osteoarthritic. Classification performance was evaluated using the area under the receiver operating characteristic (ROC) curve (AUC). The best classification performance was observed with high-dimensional geometrical feature vectors derived from SIM (0.95 ± 0.06) which outperformed all Minkowski Functionals (p < 0.001). These results suggest that such quantitative analysis of chondrocyte patterns in human patellar cartilage matrix involving SIM-derived geometrical features can distinguish between healthy and osteoarthritic tissue with high accuracy.