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Register a new userSpinal cord gray matter segmentation using deep dilated convolutions
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Added by
Christian Samuel Perone
Publication date
2017
fields
Informatics Engineering
and research's language is
English
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Gray matter (GM) tissue changes have been associated with a wide range of neurological disorders and was also recently found relevant as a biomarker for disability in amyotrophic lateral sclerosis. The ability to automatically segment the GM is, therefore, an important task for modern studies of the spinal cord. In this work, we devise a modern, simple and end-to-end fully automated human spinal cord gray matter segmentation method using Deep Learning, that works both on in vivo and ex vivo MRI acquisitions. We evaluate our method against six independently developed methods on a GM segmentation challenge and report state-of-the-art results in 8 out of 10 different evaluation metrics as well as major network parameter reduction when compared to the traditional medical imaging architectures such as U-Nets.
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Spinal cord tumors lead to neurological morbidity and mortality. Being able to obtain morphometric quantification (size, location, growth rate) of the tumor, edema, and cavity can result in improved monitoring and treatment planning. Such quantification requires the segmentation of these structures into three separate classes. However, manual segmentation of 3-dimensional structures is time-consuming and tedious, motivating the development of automated methods. Here, we tailor a model adapted to the spinal cord tumor segmentation task. Data were obtained from 343 patients using gadolinium-enhanced T1-weighted and T2-weighted MRI scans with cervical, thoracic, and/or lumbar coverage. The dataset includes the three most common intramedullary spinal cord tumor types: astrocytomas, ependymomas, and hemangioblastomas. The proposed approach is a cascaded architecture with U-Net-based models that segments tumors in a two-stage process: locate and label. The model first finds the spinal cord and generates bounding box coordinates. The images are cropped according to this output, leading to a reduced field of view, which mitigates class imbalance. The tumor is then segmented. The segmentation of the tumor, cavity, and edema (as a single class) reached 76.7 $pm$ 1.5% of Dice score and the segmentation of tumors alone reached 61.8 $pm$ 4.0% Dice score. The true positive detection rate was above 87% for tumor, edema, and cavity. To the best of our knowledge, this is the first fully automatic deep learning model for spinal cord tumor segmentation. The multiclass segmentation pipeline is available in the Spinal Cord Toolbox (https://spinalcordtoolbox.com/). It can be run with custom data on a regular computer within seconds.
Dilated Convolutions have been shown to be highly useful for the task of image segmentation. By introducing gaps into convolutional filters, they enable the use of larger receptive fields without increasing the original kernel size. Even though this allows for the inexpensive capturing of features at different scales, the structure of the dilated convolutional filter leads to a loss of information. We hypothesise that inexpensive modifications to Dilated Convolutional Neural Networks, such as additional averaging layers, could overcome this limitation. In this project we test this hypothesis by evaluating the effect of these modifications for a state-of-the art image segmentation system and compare them to existing approaches with the same objective. Our experiments show that our proposed methods improve the performance of dilated convolutions for image segmentation. Crucially, our modifications achieve these results at a much lower computational cost than previous smoothing approaches.
Dilated convolutions are widely used in deep semantic segmentation models as they can enlarge the filters receptive field without adding additional weights nor sacrificing spatial resolution. However, as dilated convolutional filters do not possess positional knowledge about the pixels on semantically meaningful contours, they could lead to ambiguous predictions on object boundaries. In addition, although dilating the filter can expand its receptive field, the total number of sampled pixels remains unchanged, which usually comprises a small fraction of the receptive fields total area. Inspired by the Lateral Inhibition (LI) mechanisms in human visual systems, we propose the dilated convolution with lateral inhibitions (LI-Convs) to overcome these limitations. Introducing LI mechanisms improves the convolutional filters sensitivity to semantic object boundaries. Moreover, since LI-Convs also implicitly take the pixels from the laterally inhibited zones into consideration, they can also extract features at a denser scale. By integrating LI-Convs into the Deeplabv3+ architecture, we propose the Lateral Inhibited Atrous Spatial Pyramid Pooling (LI-ASPP), the Lateral Inhibited MobileNet-V2 (LI-MNV2) and the Lateral Inhibited ResNet (LI-ResNet). Experimental results on three benchmark datasets (PASCAL VOC 2012, CelebAMask-HQ and ADE20K) show that our LI-based segmentation models outperform the baseline on all of them, thus verify the effectiveness and generality of the proposed LI-Convs.
We introduce a fast and efficient convolutional neural network, ESPNet, for semantic segmentation of high resolution images under resource constraints. ESPNet is based on a new convolutional module, efficient spatial pyramid (ESP), which is efficient in terms of computation, memory, and power. ESPNet is 22 times faster (on a standard GPU) and 180 times smaller than the state-of-the-art semantic segmentation network PSPNet, while its category-wise accuracy is only 8% less. We evaluated ESPNet on a variety of semantic segmentation datasets including Cityscapes, PASCAL VOC, and a breast biopsy whole slide image dataset. Under the same constraints on memory and computation, ESPNet outperforms all the current efficient CNN networks such as MobileNet, ShuffleNet, and ENet on both standard metrics and our newly introduced performance metrics that measure efficiency on edge devices. Our network can process high resolution images at a rate of 112 and 9 frames per second on a standard GPU and edge device, respectively.
The spinal cord is frequently affected by atrophy and/or lesions in multiple sclerosis (MS) patients. Segmentation of the spinal cord and lesions from MRI data provides measures of damage, which are key criteria for the diagnosis, prognosis, and longitudinal monitoring in MS. Automating this operation eliminates inter-rater variability and increases the efficiency of large-throughput analysis pipelines. Robust and reliable segmentation across multi-site spinal cord data is challenging because of the large variability related to acquisition parameters and image artifacts. The goal of this study was to develop a fully-automatic framework, robust to variability in both image parameters and clinical condition, for segmentation of the spinal cord and intramedullary MS lesions from conventional MRI data. Scans of 1,042 subjects (459 healthy controls, 471 MS patients, and 112 with other spinal pathologies) were included in this multi-site study (n=30). Data spanned three contrasts (T1-, T2-, and T2*-weighted) for a total of 1,943 volumes. The proposed cord and lesion automatic segmentation approach is based on a sequence of two Convolutional Neural Networks (CNNs). To deal with the very small proportion of spinal cord and/or lesion voxels compared to the rest of the volume, a first CNN with 2D dilated convolutions detects the spinal cord centerline, followed by a second CNN with 3D convolutions that segments the spinal cord and/or lesions. When compared against manual segmentation, our CNN-based approach showed a median Dice of 95% vs. 88% for PropSeg, a state-of-the-art spinal cord segmentation method. Regarding lesion segmentation on MS data, our framework provided a Dice of 60%, a relative volume difference of -15%, and a lesion-wise detection sensitivity and precision of 83% and 77%, respectively. The proposed framework is open-source and readily available in the Spinal Cord Toolbox.
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