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Register a new userSegmentation-based Method combined with Dynamic Programming for Brain Midline Delineation
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The midline related pathological image features are crucial for evaluating the severity of brain compression caused by stroke or traumatic brain injury (TBI). The automated midline delineation not only improves the assessment and clinical decision making for patients with stroke symptoms or head trauma but also reduces the time of diagnosis. Nevertheless, most of the previous methods model the midline by localizing the anatomical points, which are hard to detect or even missing in severe cases. In this paper, we formulate the brain midline delineation as a segmentation task and propose a three-stage framework. The proposed framework firstly aligns an input CT image into the standard space. Then, the aligned image is processed by a midline detection network (MD-Net) integrated with the CoordConv Layer and Cascade AtrousCconv Module to obtain the probability map. Finally, we formulate the optimal midline selection as a pathfinding problem to solve the problem of the discontinuity of midline delineation. Experimental results show that our proposed framework can achieve superior performance on one in-house dataset and one public dataset.
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Brain lesion segmentation provides a valuable tool for clinical diagnosis, and convolutional neural networks (CNNs) have achieved unprecedented success in the task. Data augmentation is a widely used strategy that improves the training of CNNs, and the design of the augmentation method for brain lesion segmentation is still an open problem. In this work, we propose a simple data augmentation approach, dubbed as CarveMix, for CNN-based brain lesion segmentation. Like other mix-based methods, such as Mixup and CutMix, CarveMix stochastically combines two existing labeled images to generate new labeled samples. Yet, unlike these augmentation strategies based on image combination, CarveMix is lesion-aware, where the combination is performed with an attention on the lesions and a proper annotation is created for the generated image. Specifically, from one labeled image we carve a region of interest (ROI) according to the lesion location and geometry, and the size of the ROI is sampled from a probability distribution. The carved ROI then replaces the corresponding voxels in a second labeled image, and the annotation of the second image is replaced accordingly as well. In this way, we generate new labeled images for network training and the lesion information is preserved. To evaluate the proposed method, experiments were performed on two brain lesion datasets. The results show that our method improves the segmentation accuracy compared with other simple data augmentation approaches.
In recent years, deep learning based methods have shown success in essential medical image analysis tasks such as segmentation. Post-processing and refining the results of segmentation is a common practice to decrease the misclassifications originating from the segmentation network. In addition to widely used methods like Conditional Random Fields (CRFs) which focus on the structure of the segmented volume/area, a graph-based recent approach makes use of certain and uncertain points in a graph and refines the segmentation according to a small graph convolutional network (GCN). However, there are two drawbacks of the approach: most of the edges in the graph are assigned randomly and the GCN is trained independently from the segmentation network. To address these issues, we define a new neighbor-selection mechanism according to feature distances and combine the two networks in the training procedure. According to the experimental results on pancreas segmentation from Computed Tomography (CT) images, we demonstrate improvement in the quantitative measures. Also, examining the dynamic neighbors created by our method, edges between semantically similar image parts are observed. The proposed method also shows qualitative enhancements in the segmentation maps, as demonstrated in the visual results.
Brain tumor segmentation is a challenging problem in medical image analysis. The goal of brain tumor segmentation is to generate accurate delineation of brain tumor regions with correctly located masks. In recent years, deep learning methods have shown very promising performance in solving various computer vision problems, such as image classification, object detection and semantic segmentation. A number of deep learning based methods have been applied to brain tumor segmentation and achieved impressive system performance. Considering state-of-the-art technologies and their performance, the purpose of this paper is to provide a comprehensive survey of recently developed deep learning based brain tumor segmentation techniques. The established works included in this survey extensively cover technical aspects such as the strengths and weaknesses of different approaches, pre- and post-processing frameworks, datasets and evaluation metrics. Finally, we conclude this survey by discussing the potential development in future research work.
Magnetic resonance (MR) imaging is an essential diagnostic tool in clinical medicine. Recently, a variety of deep learning methods have been applied to segmentation tasks in medical images, with promising results for computer-aided diagnosis. For MR images, effectively integrating different pulse sequences is important to optimize performance. However, the best way to integrate different pulse sequences remains unclear. In this study, we evaluate multiple architectural features and characterize their effects in the task of metastasis segmentation. Specifically, we consider (1) different pulse sequence integration schemas, (2) different modes of weight sharing for parallel network branches, and (3) a new approach for enabling robustness to missing pulse sequences. We find that levels of integration and modes of weight sharing that favor low variance work best in our regime of small data (n = 100). By adding an input-level dropout layer, we could preserve the overall performance of these networks while allowing for inference on inputs with missing pulse sequence. We illustrate not only the generalizability of the network but also the utility of this robustness when applying the trained model to data from a different center, which does not use the same pulse sequences. Finally, we apply network visualization methods to better understand which input features are most important for network performance. Together, these results provide a framework for building networks with enhanced robustness to missing data while maintaining comparable performance in medical imaging applications.
In fetal Magnetic Resonance Imaging, Super Resolution Reconstruction (SRR) algorithms are becoming popular tools to obtain high-resolution 3D volume reconstructions from low-resolution stacks of 2D slices, acquired at different orientations. To be effective, these algorithms often require accurate segmentation of the region of interest, such as the fetal brain in suspected pathological cases. In the case of Spina Bifida, Ebner, Wang et al. (NeuroImage, 2020) combined their SRR algorithm with a 2-step segmentation pipeline (2D localisation followed by a 2D segmentation network). However, if the localisation step fails, the second network is not able to recover a correct brain mask, thus requiring manual corrections for an effective SRR. In this work, we aim at improving the fetal brain segmentation for SRR in Spina Bifida. We hypothesise that a well-trained single-step UNet can achieve accurate performance, avoiding the need of a 2-step approach. We propose a new tool for fetal brain segmentation called MONAIfbs, which takes advantage of the Medical Open Network for Artificial Intelligence (MONAI) framework. Our network is based on the dynamic UNet (dynUNet), an adaptation of the nnU-Net framework. When compared to the original 2-step approach proposed in Ebner-Wang, and the same Ebner-Wang approach retrained with the expanded dataset available for this work, the dynUNet showed to achieve higher performance using a single step only. It also showed to reduce the number of outliers, as only 28 stacks obtained Dice score less than 0.9, compared to 68 for Ebner-Wang and 53 Ebner-Wang expanded. The proposed dynUNet model thus provides an improvement of the state-of-the-art fetal brain segmentation techniques, reducing the need for manual correction in automated SRR pipelines. Our code and our trained model are made publicly available at https://github.com/gift-surg/MONAIfbs.
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