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Register a new userFully Convolutional Networks for Automated Segmentation of Abdominal Adipose Tissue Depots in Multicenter Water-Fat MRI
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Taro Langner
Publication date
2018
fields
Informatics Engineering
and research's language is
English
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Purpose: An approach for the automated segmentation of visceral adipose tissue (VAT) and subcutaneous adipose tissue (SAT) in multicenter water-fat MRI scans of the abdomen was investigated, using two different neural network architectures. Methods: The two fully convolutional network architectures U-Net and V-Net were trained, evaluated and compared on the water-fat MRI data. Data of the study Tellus with 90 scans from a single center was used for a 10-fold cross-validation in which the most successful configuration for both networks was determined. These configurations were then tested on 20 scans of the multicenter study beta-cell function in JUvenile Diabetes and Obesity (BetaJudo), which involved a different study population and scanning device. Results: The U-Net outperformed the used implementation of the V-Net in both cross-validation and testing. In cross-validation, the U-Net reached average dice scores of 0.988 (VAT) and 0.992 (SAT). The average of the absolute quantification errors amount to 0.67% (VAT) and 0.39% (SAT). On the multi-center test data, the U-Net performs only slightly worse, with average dice scores of 0.970 (VAT) and 0.987 (SAT) and quantification errors of 2.80% (VAT) and 1.65% (SAT). Conclusion: The segmentations generated by the U-Net allow for reliable quantification and could therefore be viable for high-quality automated measurements of VAT and SAT in large-scale studies with minimal need for human intervention. The high performance on the multicenter test data furthermore shows the robustness of this approach for data of different patient demographics and imaging centers, as long as a consistent imaging protocol is used.
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Purpose: Development of a fast and fully automated deep learning pipeline (FatSegNet) to accurately identify, segment, and quantify abdominal adipose tissue on Dixon MRI from the Rhineland Study - a large prospective population-based study. Method: FatSegNet is composed of three stages: (i) consistent localization of the abdominal region using two 2D-Competitive Dense Fully Convolutional Networks (CDFNet), (ii) segmentation of adipose tissue on three views by independent CDFNets, and (iii) view aggregation. FatSegNet is trained with 33 manually annotated subjects, and validated by: 1) comparison of segmentation accuracy against a testingset covering a wide range of body mass index (BMI), 2) test-retest reliability, and 3) robustness in a large cohort study. Results: The CDFNet demonstrates increased robustness compared to traditional deep learning networks. FatSegNet dice score outperforms manual raters on the abdominal visceral adipose tissue (VAT, 0.828 vs. 0.788), and produces comparable results on subcutaneous adipose tissue (SAT, 0.973 vs. 0.982). The pipeline has very small test-retest absolute percentage difference and excellent agreement between scan sessions (VAT: APD = 2.957%, ICC=0.998 and SAT: APD= 3.254%, ICC=0.996). Conclusion: FatSegNet can reliably analyze a 3D Dixon MRI in1 min. It generalizes well to different body shapes, sensitively replicates known VAT and SAT volume effects in a large cohort study, and permits localized analysis of fat compartments.
Early and accurate diagnosis of interstitial lung diseases (ILDs) is crucial for making treatment decisions, but can be challenging even for experienced radiologists. The diagnostic procedure is based on the detection and recognition of the different ILD pathologies in thoracic CT scans, yet their manifestation often appears similar. In this study, we propose the use of a deep purely convolutional neural network for the semantic segmentation of ILD patterns, as the basic component of a computer aided diagnosis (CAD) system for ILDs. The proposed CNN, which consists of convolutional layers with dilated filters, takes as input a lung CT image of arbitrary size and outputs the corresponding label map. We trained and tested the network on a dataset of 172 sparsely annotated CT scans, within a cross-validation scheme. The training was performed in an end-to-end and semi-supervised fashion, utilizing both labeled and non-labeled image regions. The experimental results show significant performance improvement with respect to the state of the art.
In this paper, we propose a novel learning based method for automated segmentation of brain tumor in multimodal MRI images, which incorporates two sets of machine -learned and hand crafted features. Fully convolutional networks (FCN) forms the machine learned features and texton based features are considered as hand-crafted features. Random forest (RF) is used to classify the MRI image voxels into normal brain tissues and different parts of tumors, i.e. edema, necrosis and enhancing tumor. The method was evaluated on BRATS 2017 challenge dataset. The results show that the proposed method provides promising segmentations. The mean Dice overlap measure for automatic brain tumor segmentation against ground truth is 0.86, 0.78 and 0.66 for whole tumor, core and enhancing tumor, respectively.
In this paper, we present a conceptually simple, strong, and efficient framework for panoptic segmentation, called Panoptic FCN. Our approach aims to represent and predict foreground things and background stuff in a unified fully convolutional pipeline. In particular, Panoptic FCN encodes each object instance or stuff category into a specific kernel weight with the proposed kernel generator and produces the prediction by convolving the high-resolution feature directly. With this approach, instance-aware and semantically consistent properties for things and stuff can be respectively satisfied in a simple generate-kernel-then-segment workflow. Without extra boxes for localization or instance separation, the proposed approach outperforms previous box-based and -free models with high efficiency on COCO, Cityscapes, and Mapillary Vistas datasets with single scale input. Our code is made publicly available at https://github.com/Jia-Research-Lab/PanopticFCN.
Multiple Sclerosis (MS) is an autoimmune disease that leads to lesions in the central nervous system. Magnetic resonance (MR) images provide sufficient imaging contrast to visualize and detect lesions, particularly those in the white matter. Quantitative measures based on various features of lesions have been shown to be useful in clinical trials for evaluating therapies. Therefore robust and accurate segmentation of white matter lesions from MR images can provide important information about the disease status and progression. In this paper, we propose a fully convolutional neural network (CNN) based method to segment white matter lesions from multi-contrast MR images. The proposed CNN based method contains two convolutional pathways. The first pathway consists of multiple parallel convolutional filter banks catering to multiple MR modalities. In the second pathway, the outputs of the first one are concatenated and another set of convolutional filters are applied. The output of this last pathway produces a membership function for lesions that may be thresholded to obtain a binary segmentation. The proposed method is evaluated on a dataset of 100 MS patients, as well as the ISBI 2015 challenge data consisting of 14 patients. The comparison is performed against four publicly available MS lesion segmentation methods. Significant improvement in segmentation quality over the competing methods is demonstrated on various metrics, such as Dice and false positive ratio. While evaluating on the ISBI 2015 challenge data, our method produces a score of 90.48, where a score of 90 is considered to be comparable to a human rater.
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