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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
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Fetal cortical plate segmentation is essential in quantitative analysis of fetal brain maturation and cortical folding. Manual segmentation of the cortical plate, or manual refinement of automatic segmentations is tedious and time-consuming. Automatic segmentation of the cortical plate, on the other hand, is challenged by the relatively low resolution of the reconstructed fetal brain MRI scans compared to the thin structure of the cortical plate, partial voluming, and the wide range of variations in the morphology of the cortical plate as the brain matures during gestation. To reduce the burden of manual refinement of segmentations, we have developed a new and powerful deep learning segmentation method. Our method exploits new deep attentive modules with mixed kernel convolutions within a fully convolutional neural network architecture that utilizes deep supervision and residual connections. We evaluated our method quantitatively based on several performance measures and expert evaluations. Results show that our method outperforms several state-of-the-art deep models for segmentation, as well as a state-of-the-art multi-atlas segmentation technique. We achieved average Dice similarity coefficient of 0.87, average Hausdorff distance of 0.96 mm, and average symmetric surface difference of 0.28 mm on reconstructed fetal brain MRI scans of fetuses scanned in the gestational age range of 16 to 39 weeks. With a computation time of less than 1 minute per fetal brain, our method can facilitate and accelerate large-scale studies on normal and altered fetal brain cortical maturation and folding.
The UK Biobank is collecting extensive data on health-related characteristics of over half a million volunteers. The biological samples of blood and urine can provide valuable insight on kidney function, with important links to cardiovascular and metabolic health. Further information on kidney anatomy could be obtained by medical imaging. In contrast to the brain, heart, liver, and pancreas, no dedicated Magnetic Resonance Imaging (MRI) is planned for the kidneys. An image-based assessment is nonetheless feasible in the neck-to-knee body MRI intended for abdominal body composition analysis, which also covers the kidneys. In this work, a pipeline for automated segmentation of parenchymal kidney volume in UK Biobank neck-to-knee body MRI is proposed. The underlying neural network reaches a relative error of 3.8%, with Dice score 0.956 in validation on 64 subjects, close to the 2.6% and Dice score 0.962 for repeated segmentation by one human operator. The released MRI of about 40,000 subjects can be processed within two days, yielding volume measurements of left and right kidney. Algorithmic quality ratings enabled the exclusion of outliers and potential failure cases. The resulting measurements can be studied and shared for large-scale investigation of associations and longitudinal changes in parenchymal kidney volume.
Deep learning models have had a great success in disease classifications using large data pools of skin cancer images or lung X-rays. However, data scarcity has been the roadblock of applying deep learning models directly on prostate multiparametric MRI (mpMRI). Although model interpretation has been heavily studied for natural images for the past few years, there has been a lack of interpretation of deep learning models trained on medical images. This work designs a customized workflow for the small and imbalanced data set of prostate mpMRI where features were extracted from a deep learning model and then analyzed by a traditional machine learning classifier. In addition, this work contributes to revealing how deep learning models interpret mpMRI for prostate cancer patients stratification.
The 3D morphology and quantitative assessment of knee articular cartilages (i.e., femoral, tibial, and patellar cartilage) in magnetic resonance (MR) imaging is of great importance for knee radiographic osteoarthritis (OA) diagnostic decision making. However, effective and efficient delineation of all the knee articular cartilages in large-sized and high-resolution 3D MR knee data is still an open challenge. In this paper, we propose a novel framework to solve the MR knee cartilage segmentation task. The key contribution is the adversarial learning based collaborative multi-agent segmentation network. In the proposed network, we use three parallel segmentation agents to label cartilages in their respective region of interest (ROI), and then fuse the three cartilages by a novel ROI-fusion layer. The collaborative learning is driven by an adversarial sub-network. The ROI-fusion layer not only fuses the individual cartilages from multiple agents, but also backpropagates the training loss from the adversarial sub-network to each agent to enable joint learning of shape and spatial constraints. Extensive evaluations are conducted on a dataset including hundreds of MR knee volumes with diverse populations, and the proposed method shows superior performance.
Objective: We evaluate a fully-automated femoral cartilage segmentation model for measuring T2 relaxation values and longitudinal changes using multi-echo spin echo (MESE) MRI. We have open sourced this model and corresponding segmentations. Methods: We trained a neural network to segment femoral cartilage from MESE MRIs. Cartilage was divided into 12 subregions along medial-lateral, superficial-deep, and anterior-central-posterior boundaries. Subregional T2 values and four-year changes were calculated using a musculoskeletal radiologists segmentations (Reader 1) and the models segmentations. These were compared using 28 held out images. A subset of 14 images were also evaluated by a second expert (Reader 2) for comparison. Results: Model segmentations agreed with Reader 1 segmentations with a Dice score of 0.85 +/- 0.03. The models estimated T2 values for individual subregions agreed with those of Reader 1 with an average Spearman correlation of 0.89 and average mean absolute error (MAE) of 1.34 ms. The models estimated four-year change in T2 for individual regions agreed with Reader 1 with an average correlation of 0.80 and average MAE of 1.72 ms. The model agreed with Reader 1 at least as closely as Reader 2 agreed with Reader 1 in terms of Dice score (0.85 vs 0.75) and subregional T2 values. Conclusions: We present a fast, fully-automated model for segmentation of MESE MRIs. Assessments of cartilage health using its segmentations agree with those of an expert as closely as experts agree with one another. This has the potential to accelerate osteoarthritis research.
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