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Register a new userAutomated Segmentation of Knee MRI Using Hierarchical Classifiers and Just Enough Interaction Based Learning: Data from Osteoarthritis Initiative
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Added by
Satyananda Kashyap
Publication date
2019
fields
Informatics Engineering
and research's language is
English
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We present a fully automated learning-based approach for segmenting knee cartilage in the presence of osteoarthritis (OA). The algorithm employs a hierarchical set of two random forest classifiers. The first is a neighborhood approximation forest, the output probability map of which is utilized as a feature set for the second random forest (RF) classifier. The output probabilities of the hierarchical approach are used as cost functions in a Layered Optimal Graph Segmentation of Multiple Objects and Surfaces (LOGISMOS). In this work, we highlight a novel post-processing interaction called just-enough interaction (JEI) which enables quick and accurate generation of a large set of training examples. Disjoint sets of 15 and 13 subjects were used for training and tested on another disjoint set of 53 knee datasets. All images were acquired using a double echo steady state (DESS) MRI sequence and are from the osteoarthritis initiative (OAI) database. Segmentation performance using the learning-based cost function showed significant reduction in segmentation errors ($p< 0.05$) in comparison with conventional gradient-based cost functions.
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State-of-the-art automated segmentation algorithms are not 100% accurate especially when segmenting difficult to interpret datasets like those with severe osteoarthritis (OA). We present a novel interactive method called just-enough interaction (JEI), which adds a fast correction step to the automated layered optimal graph segmentation of multiple objects and surfaces (LOGISMOS). After LOGISMOS segmentation in knee MRI, the JEI user interaction does not modify boundary surfaces of the bones and cartilages directly. Local costs of underlying graph nodes are modified instead and the graph is re-optimized, providing globally optimal corrected results. Significant performance improvement ($p ll 0.001$) was observed when comparing JEI-corrected results to the automated. The algorithm was extended from 3D JEI to longitudinal multi-3D (4D) JEI allowing simultaneous visualization and interaction of multiple-time points of the same patient.
A fully automated knee MRI segmentation method to study osteoarthritis (OA) was developed using a novel hierarchical set of random forests (RF) classifiers to learn the appearance of cartilage regions and their boundaries. A neighborhood approximation forest is used first to provide contextual feature to the second-level RF classifier that also considers local features and produces location-specific costs for the layered optimal graph image segmentation of multiple objects and surfaces (LOGISMOS) framework. Double echo steady state (DESS) MRIs used in this work originated from the Osteoarthritis Initiative (OAI) study. Trained on 34 MRIs with varying degrees of OA, the performance of the learning-based method tested on 108 MRIs showed a significant reduction in segmentation errors (emph{p}$<$0.05) compared with the conventional gradient-based and single-stage RF-learned costs. The 3D LOGISMOS was extended to longitudinal-3D (4D) to simultaneously segment multiple follow-up visits of the same patient. As such, data from all time-points of the temporal sequence contribute information to a single optimal solution that utilizes both spatial 3D and temporal contexts. 4D LOGISMOS validation on 108 MRIs from baseline and 12 month follow-up scans of 54 patients showed a significant reduction in segmentation errors (emph{p}$<$0.01) compared to 3D. Finally, the potential of 4D LOGISMOS was further explored on the same 54 patients using 5 annual follow-up scans demonstrating a significant improvement of measuring cartilage thickness (emph{p}$<$0.01) compared to the sequential 3D approach.
Knee osteoarthritis (OA) is the most common musculoskeletal disease without a cure, and current treatment options are limited to symptomatic relief. Prediction of OA progression is a very challenging and timely issue, and it could, if resolved, accelerate the disease modifying drug development and ultimately help to prevent millions of total joint replacement surgeries performed annually. Here, we present a multi-modal machine learning-based OA progression prediction model that utilizes raw radiographic data, clinical examination results and previous medical history of the patient. We validated this approach on an independent test set of 3,918 knee images from 2,129 subjects. Our method yielded area under the ROC curve (AUC) of 0.79 (0.78-0.81) and Average Precision (AP) of 0.68 (0.66-0.70). In contrast, a reference approach, based on logistic regression, yielded AUC of 0.75 (0.74-0.77) and AP of 0.62 (0.60-0.64). The proposed method could significantly improve the subject selection process for OA drug-development trials and help the development of personalized therapeutic plans.
The integrity of articular cartilage is a crucial aspect in the early diagnosis of osteoarthritis (OA). Many novel MRI techniques have the potential to assess compositional changes of the cartilage extracellular matrix. Among these techniques, diffusion tensor imaging (DTI) of cartilage provides a simultaneous assessment of the two principal components of the solid matrix: collagen structure and proteoglycan concentration. DTI, as for any other compositional MRI technique, require a human expert to perform segmentation manually. The manual segmentation is error-prone and time-consuming ($sim$ few hours per subject). We use an ensemble of modified U-Nets to automate this segmentation task. We benchmark our model against a human expert test-retest segmentation and conclude that our model is superior for Patellar and Tibial cartilage using dice score as the comparison metric. In the end, we do a perturbation analysis to understand the sensitivity of our model to the different components of our input. We also provide confidence maps for the predictions so that radiologists can tweak the model predictions as required. The model has been deployed in practice. In conclusion, cartilage segmentation on DW-MRI images with modified U-Nets achieves accuracy that outperforms the human segmenter. Code is available at https://github.com/aakashrkaku/knee-cartilage-segmentation
Knee osteoarthritis (OA) is the most common musculoskeletal disorder. OA diagnosis is currently conducted by assessing symptoms and evaluating plain radiographs, but this process suffers from subjectivity. In this study, we present a new transparent computer-aided diagnosis method based on the Deep Siamese Convolutional Neural Network to automatically score knee OA severity according to the Kellgren-Lawrence grading scale. We trained our method using the data solely from the Multicenter Osteoarthritis Study and validated it on randomly selected 3,000 subjects (5,960 knees) from Osteoarthritis Initiative dataset. Our method yielded a quadratic Kappa coefficient of 0.83 and average multiclass accuracy of 66.71% compared to the annotations given by a committee of clinical experts. Here, we also report a radiological OA diagnosis area under the ROC curve of 0.93. We also present attention maps -- given as a class probability distribution -- highlighting the radiological features affecting the network decision. This information makes the decision process transparent for the practitioner, which builds better trust toward automatic methods. We believe that our model is useful for clinical decision making and for OA research; therefore, we openly release our training codes and the data set created in this study.
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