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Li JN, Zhang SW, Qiang YR, Zhou QY. A novel cross-layer dual encoding-shared decoding network framework with spatial self-attention mechanism for hippocampus segmentation. Comput Biol Med 2023; 167:107584. [PMID: 37883852 DOI: 10.1016/j.compbiomed.2023.107584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 09/21/2023] [Accepted: 10/15/2023] [Indexed: 10/28/2023]
Abstract
Accurate segmentation of the hippocampus from the brain magnetic resonance images (MRIs) is a crucial task in the neuroimaging research, since its structural integrity is strongly related to several neurodegenerative disorders, such as Alzheimer's disease (AD). Automatic segmentation of the hippocampus structures is challenging due to the small volume, complex shape, low contrast and discontinuous boundaries of hippocampus. Although some methods have been developed for the hippocampus segmentation, most of them paid too much attention to the hippocampus shape and volume instead of considering the spatial information. Additionally, the extracted features are independent of each other, ignoring the correlation between the global and local information. In view of this, here we proposed a novel cross-layer dual Encoding-Shared Decoding network framework with Spatial self-Attention mechanism (called ESDSA) for hippocampus segmentation in human brains. Considering that the hippocampus is a relatively small part in MRI, we introduced the spatial self-attention mechanism in ESDSA to capture the spatial information of hippocampus for improving the segmentation accuracy. We also designed a cross-layer dual encoding-shared decoding network to effectively extract the global information of MRIs and the spatial information of hippocampus. The spatial features of hippocampus and the features extracted from the MRIs were combined to realize the hippocampus segmentation. Results on the baseline T1-weighted structural MRI data show that the performance of our ESDSA is superior to other state-of-the-art methods, and the dice similarity coefficient of ESDSA achieves 89.37%. In addition, the dice similarity coefficient of the Spatial Self-Attention mechanism (SSA) strategy and the dual Encoding-Shared Decoding (ESD) strategy is 9.47%, 5.35% higher than that of the baseline U-net, respectively, indicating that the strategies of SSA and ESD can effectively enhance the segmentation accuracy of human brain hippocampus.
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Affiliation(s)
- Jia-Ni Li
- MOE Key Laboratory of Information Fusion Technology, School of Automation, Northwestern Polytechnical University, Xi'an 710072, China.
| | - Shao-Wu Zhang
- MOE Key Laboratory of Information Fusion Technology, School of Automation, Northwestern Polytechnical University, Xi'an 710072, China.
| | - Yan-Rui Qiang
- MOE Key Laboratory of Information Fusion Technology, School of Automation, Northwestern Polytechnical University, Xi'an 710072, China.
| | - Qin-Yi Zhou
- MOE Key Laboratory of Information Fusion Technology, School of Automation, Northwestern Polytechnical University, Xi'an 710072, China.
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Huang J, Vong CM, Chen CLP, Zhou Y. Accurate and Efficient Large-Scale Multi-Label Learning With Reduced Feature Broad Learning System Using Label Correlation. IEEE TRANSACTIONS ON NEURAL NETWORKS AND LEARNING SYSTEMS 2023; 34:10240-10253. [PMID: 35436203 DOI: 10.1109/tnnls.2022.3165299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Multi-label learning for large-scale data is a grand challenge because of a large number of labels with a complex data structure. Hence, the existing large-scale multi-label methods either have unsatisfactory classification performance or are extremely time-consuming for training utilizing a massive amount of data. A broad learning system (BLS), a flat network with the advantages of succinct structures, is appropriate for addressing large-scale tasks. However, existing BLS models are not directly applicable for large-scale multi-label learning due to the large and complex label space. In this work, a novel multi-label classifier based on BLS (called BLS-MLL) is proposed with two new mechanisms: kernel-based feature reduction module and correlation-based label thresholding. The kernel-based feature reduction module contains three layers, namely, the feature mapping layer, enhancement nodes layer, and feature reduction layer. The feature mapping layer employs elastic network regularization to solve the randomness of features in order to improve performance. In the enhancement nodes layer, the kernel method is applied for high-dimensional nonlinear conversion to achieve high efficiency. The newly constructed feature reduction layer is used to further significantly improve both the training efficiency and accuracy when facing high-dimensionality with abundant or noisy information embedded in large-scale data. The correlation-based label thresholding enables BLS-MLL to generate a label-thresholding function for effective conversion of the final decision values to logical outputs, thus, improving the classification performance. Finally, experimental comparisons among six state-of-the-art multi-label classifiers on ten datasets demonstrate the effectiveness of the proposed BLS-MLL. The results of the classification performance show that BLS-MLL outperforms the compared algorithms in 86% of cases with better training efficiency in 90% of cases.
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Chen X, Xie H, Li Z, Cheng G, Leng M, Wang FL. Information fusion and artificial intelligence for smart healthcare: a bibliometric study. Inf Process Manag 2023. [DOI: 10.1016/j.ipm.2022.103113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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4
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Li Y, Qiu Z, Fan X, Liu X, Chang EIC, Xu Y. Integrated 3d flow-based multi-atlas brain structure segmentation. PLoS One 2022; 17:e0270339. [PMID: 35969596 PMCID: PMC9377636 DOI: 10.1371/journal.pone.0270339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 06/09/2022] [Indexed: 11/18/2022] Open
Abstract
MRI brain structure segmentation plays an important role in neuroimaging studies. Existing methods either spend much CPU time, require considerable annotated data, or fail in segmenting volumes with large deformation. In this paper, we develop a novel multi-atlas-based algorithm for 3D MRI brain structure segmentation. It consists of three modules: registration, atlas selection and label fusion. Both registration and label fusion leverage an integrated flow based on grayscale and SIFT features. We introduce an effective and efficient strategy for atlas selection by employing the accompanying energy generated in the registration step. A 3D sequential belief propagation method and a 3D coarse-to-fine flow matching approach are developed in both registration and label fusion modules. The proposed method is evaluated on five public datasets. The results show that it has the best performance in almost all the settings compared to competitive methods such as ANTs, Elastix, Learning to Rank and Joint Label Fusion. Moreover, our registration method is more than 7 times as efficient as that of ANTs SyN, while our label transfer method is 18 times faster than Joint Label Fusion in CPU time. The results on the ADNI dataset demonstrate that our method is applicable to image pairs that require a significant transformation in registration. The performance on a composite dataset suggests that our method succeeds in a cross-modality manner. The results of this study show that the integrated 3D flow-based method is effective and efficient for brain structure segmentation. It also demonstrates the power of SIFT features, multi-atlas segmentation and classical machine learning algorithms for a medical image analysis task. The experimental results on public datasets show the proposed method’s potential for general applicability in various brain structures and settings.
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Affiliation(s)
- Yeshu Li
- School of Computer Science and Engineering, Beihang University, Beijing, China
| | - Ziming Qiu
- Electrical and Computer Engineering, Tandon School of Engineering, New York University, Brooklyn, NY, United States of America
| | - Xingyu Fan
- Bioengineering College, Chongqing University, Chongqing, China
| | - Xianglong Liu
- School of Computer Science and Engineering, Beihang University, Beijing, China
| | | | - Yan Xu
- School of Biological Science and Medical Engineering, State Key Laboratory of Software Development Environment, Key Laboratory of Biomechanics, Mechanobiology of Ministry of Education and Beijing Advanced Innovation Centre for Biomedical Engineering, Beihang University, Beijing, China
- Microsoft Research, Beijing, China
- * E-mail:
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Wei J, Wu Z, Wang L, Bui TD, Qu L, Yap PT, Xia Y, Li G, Shen D. A cascaded nested network for 3T brain MR image segmentation guided by 7T labeling. PATTERN RECOGNITION 2022; 124:108420. [PMID: 38469076 PMCID: PMC10927017 DOI: 10.1016/j.patcog.2021.108420] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/13/2024]
Abstract
Accurate segmentation of the brain into gray matter, white matter, and cerebrospinal fluid using magnetic resonance (MR) imaging is critical for visualization and quantification of brain anatomy. Compared to 3T MR images, 7T MR images exhibit higher tissue contrast that is contributive to accurate tissue delineation for training segmentation models. In this paper, we propose a cascaded nested network (CaNes-Net) for segmentation of 3T brain MR images, trained by tissue labels delineated from the corresponding 7T images. We first train a nested network (Nes-Net) for a rough segmentation. The second Nes-Net uses tissue-specific geodesic distance maps as contextual information to refine the segmentation. This process is iterated to build CaNes-Net with a cascade of Nes-Net modules to gradually refine the segmentation. To alleviate the misalignment between 3T and corresponding 7T MR images, we incorporate a correlation coefficient map to allow well-aligned voxels to play a more important role in supervising the training process. We compared CaNes-Net with SPM and FSL tools, as well as four deep learning models on 18 adult subjects and the ADNI dataset. Our results indicate that CaNes-Net reduces segmentation errors caused by the misalignment and improves segmentation accuracy substantially over the competing methods.
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Affiliation(s)
- Jie Wei
- National Engineering Laboratory for Integrated Aero-Space-Ground-Ocean Big Data Application Technology, School of Computer Science and Engineering, Northwestern Polytechnical University, Xi’an 710072, China
- Department of Radiology and BRIC, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Zhengwang Wu
- Department of Radiology and BRIC, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Li Wang
- Department of Radiology and BRIC, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Toan Duc Bui
- Department of Radiology and BRIC, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Liangqiong Qu
- Department of Biomedical Data Science at Stanford University, Stanford, CA 94305, USA
| | - Pew-Thian Yap
- Department of Radiology and BRIC, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Yong Xia
- National Engineering Laboratory for Integrated Aero-Space-Ground-Ocean Big Data Application Technology, School of Computer Science and Engineering, Northwestern Polytechnical University, Xi’an 710072, China
| | - Gang Li
- Department of Radiology and BRIC, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Dinggang Shen
- School of Biomedical Engineering, ShanghaiTech University, Shanghai 201210, China
- Shanghai United Imaging Intelligence Co., Ltd., Shanghai 200232, China
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Kazemivash B, Calhoun VD. A novel 5D brain parcellation approach based on spatio-temporal encoding of resting fMRI data from deep residual learning. J Neurosci Methods 2022; 369:109478. [PMID: 35031344 PMCID: PMC9394484 DOI: 10.1016/j.jneumeth.2022.109478] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 12/15/2021] [Accepted: 01/06/2022] [Indexed: 10/19/2022]
Abstract
OBJECTIVE Brain parcellation is an essential aspect of computational neuroimaging research and deals with segmenting the brain into (possibly overlapping) sub-regions employed to study brain anatomy or function. In the context of functional parcellation, brain organization which is often measured via temporal metrics such as coherence, is highly dynamic. This dynamic aspect is ignored in most research, which typically applies anatomically based, fixed regions for each individual, and can produce misleading results. METHODS In this work, we propose a novel spatio-temporal-network (5D) brain parcellation scheme utilizing a deep residual network to predict the probability of each voxel belonging to a brain network at each point in time. RESULTS We trained 53 4D brain networks and evaluate the ability of these networks to capture spatial and temporal dynamics as well as to show sensitivity to individual or group-level variation (in our case with age). CONCLUSION The proposed system generates informative spatio-temporal networks that vary not only across individuals but also over time and space. SIGNIFICANCE The dynamic 5D nature of the developed approach provides a powerful framework that expands on existing work and has potential to identify novel and typically ignored findings when studying the healthy and disordered brain.
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Affiliation(s)
- Behnam Kazemivash
- Department of Computer Science, Georgia State University, Atlanta, GA 30332, USA.
| | - Vince D. Calhoun
- Tri-Institutional Center for Translational Research in Neuroimaging and Data Science (TReNDS), Georgia State University, Georgia Institute of Technology, and Emory University, Atlanta GA 30303
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Prakash J, Wang V, Quinn RE, Mitchell CS. Unsupervised Machine Learning to Identify Separable Clinical Alzheimer's Disease Sub-Populations. Brain Sci 2021; 11:977. [PMID: 34439596 PMCID: PMC8392842 DOI: 10.3390/brainsci11080977] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 07/10/2021] [Accepted: 07/20/2021] [Indexed: 11/20/2022] Open
Abstract
Heterogeneity among Alzheimer's disease (AD) patients confounds clinical trial patient selection and therapeutic efficacy evaluation. This work defines separable AD clinical sub-populations using unsupervised machine learning. Clustering (t-SNE followed by k-means) of patient features and association rule mining (ARM) was performed on the ADNIMERGE dataset from the Alzheimer's Disease Neuroimaging Initiative (ADNI). Patient sociodemographics, brain imaging, biomarkers, cognitive tests, and medication usage were included for analysis. Four AD clinical sub-populations were identified using between-cluster mean fold changes [cognitive performance, brain volume]: cluster-1 represented least severe disease [+17.3, +13.3]; cluster-0 [-4.6, +3.8] and cluster-3 [+10.8, -4.9] represented mid-severity sub-populations; cluster-2 represented most severe disease [-18.4, -8.4]. ARM assessed frequently occurring pharmacologic substances within the 4 sub-populations. No drug class was associated with the least severe AD (cluster-1), likely due to lesser antecedent disease. Anti-hyperlipidemia drugs associated with cluster-0 (mid-severity, higher volume). Interestingly, antioxidants vitamin C and E associated with cluster-3 (mid-severity, higher cognition). Anti-depressants like Zoloft associated with most severe disease (cluster-2). Vitamin D is protective for AD, but ARM identified significant underutilization across all AD sub-populations. Identification and feature characterization of four distinct AD sub-population "clusters" using standard clinical features enhances future clinical trial selection criteria and cross-study comparative analysis.
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Affiliation(s)
- Jayant Prakash
- Laboratory for Pathology Dynamics, Department of Biomedical Engineering, Georgia Institute of Technology and Emory University School of Medicine, Atlanta, GA 30332, USA; (J.P.); (V.W.); (R.E.Q.III)
- Department of Computer Science, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Velda Wang
- Laboratory for Pathology Dynamics, Department of Biomedical Engineering, Georgia Institute of Technology and Emory University School of Medicine, Atlanta, GA 30332, USA; (J.P.); (V.W.); (R.E.Q.III)
| | - Robert E. Quinn
- Laboratory for Pathology Dynamics, Department of Biomedical Engineering, Georgia Institute of Technology and Emory University School of Medicine, Atlanta, GA 30332, USA; (J.P.); (V.W.); (R.E.Q.III)
- Department of Computer Science, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Cassie S. Mitchell
- Laboratory for Pathology Dynamics, Department of Biomedical Engineering, Georgia Institute of Technology and Emory University School of Medicine, Atlanta, GA 30332, USA; (J.P.); (V.W.); (R.E.Q.III)
- Center for Machine Learning, Georgia Institute of Technology, Atlanta, GA 30332, USA
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Zargari Khuzani A, Heidari M, Shariati SA. COVID-Classifier: an automated machine learning model to assist in the diagnosis of COVID-19 infection in chest X-ray images. Sci Rep 2021; 11:9887. [PMID: 33972584 PMCID: PMC8110795 DOI: 10.1038/s41598-021-88807-2] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 02/04/2021] [Indexed: 02/07/2023] Open
Abstract
Chest-X ray (CXR) radiography can be used as a first-line triage process for non-COVID-19 patients with pneumonia. However, the similarity between features of CXR images of COVID-19 and pneumonia caused by other infections makes the differential diagnosis by radiologists challenging. We hypothesized that machine learning-based classifiers can reliably distinguish the CXR images of COVID-19 patients from other forms of pneumonia. We used a dimensionality reduction method to generate a set of optimal features of CXR images to build an efficient machine learning classifier that can distinguish COVID-19 cases from non-COVID-19 cases with high accuracy and sensitivity. By using global features of the whole CXR images, we successfully implemented our classifier using a relatively small dataset of CXR images. We propose that our COVID-Classifier can be used in conjunction with other tests for optimal allocation of hospital resources by rapid triage of non-COVID-19 cases.
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Affiliation(s)
- Abolfazl Zargari Khuzani
- Department of Electrical and Computer Engineering, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Morteza Heidari
- School of Electrical and Computer Engineering, The University of Oklahoma, Norman, OK, USA
| | - S Ali Shariati
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, USA.
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A Fully Automatic Procedure for Brain Tumor Segmentation from Multi-Spectral MRI Records Using Ensemble Learning and Atlas-Based Data Enhancement. APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app11020564] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The accurate and reliable segmentation of gliomas from magnetic resonance image (MRI) data has an important role in diagnosis, intervention planning, and monitoring the tumor’s evolution during and after therapy. Segmentation has serious anatomical obstacles like the great variety of the tumor’s location, size, shape, and appearance and the modified position of normal tissues. Other phenomena like intensity inhomogeneity and the lack of standard intensity scale in MRI data represent further difficulties. This paper proposes a fully automatic brain tumor segmentation procedure that attempts to handle all the above problems. Having its foundations on the MRI data provided by the MICCAI Brain Tumor Segmentation (BraTS) Challenges, the procedure consists of three main phases. The first pre-processing phase prepares the MRI data to be suitable for supervised classification, by attempting to fix missing data, suppressing the intensity inhomogeneity, normalizing the histogram of observed data channels, generating additional morphological, gradient-based, and Gabor-wavelet features, and optionally applying atlas-based data enhancement. The second phase accomplishes the main classification process using ensembles of binary decision trees and provides an initial, intermediary labeling for each pixel of test records. The last phase reevaluates these intermediary labels using a random forest classifier, then deploys a spatial region growing-based structural validation of suspected tumors, thus achieving a high-quality final segmentation result. The accuracy of the procedure is evaluated using the multi-spectral MRI records of the BraTS 2015 and BraTS 2019 training data sets. The procedure achieves high-quality segmentation results, characterized by average Dice similarity scores of up to 86%.
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Li MM, Li BZ. A Novel Active Contour Model for Noisy Image Segmentation based on Adaptive Fractional Order Differentiation. IEEE TRANSACTIONS ON IMAGE PROCESSING : A PUBLICATION OF THE IEEE SIGNAL PROCESSING SOCIETY 2020; PP:9520-9531. [PMID: 33048677 DOI: 10.1109/tip.2020.3029443] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The images used in various practices are often disturbed by noise, such as Gaussian noise, speckled noise, and salt and pepper noise. Images with noise are one of the challenges for segmentation, since the noise may cause inaccurate segmented results. To cope with the effect of noise on images during segmentation, a novel active contour model is proposed in this paper. The newly proposed model consists of fitting term, regularization term and penalty term. The fitting term is designed using a Gaussian kernel function and fractional order differentiation with an adaptively defined fractional order, which applies different orders to different pixels. The regularization term is applied to maintain the smoothness of curves. In order to ensure stable evolution of curves, a penalty term is added into the proposed model. Comparison experiments are conducted to show the effectiveness and efficiency of the proposed model.
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Zhang L, Wang M, Liu M, Zhang D. A Survey on Deep Learning for Neuroimaging-Based Brain Disorder Analysis. Front Neurosci 2020; 14:779. [PMID: 33117114 PMCID: PMC7578242 DOI: 10.3389/fnins.2020.00779] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Accepted: 06/02/2020] [Indexed: 12/12/2022] Open
Abstract
Deep learning has recently been used for the analysis of neuroimages, such as structural magnetic resonance imaging (MRI), functional MRI, and positron emission tomography (PET), and it has achieved significant performance improvements over traditional machine learning in computer-aided diagnosis of brain disorders. This paper reviews the applications of deep learning methods for neuroimaging-based brain disorder analysis. We first provide a comprehensive overview of deep learning techniques and popular network architectures by introducing various types of deep neural networks and recent developments. We then review deep learning methods for computer-aided analysis of four typical brain disorders, including Alzheimer's disease, Parkinson's disease, Autism spectrum disorder, and Schizophrenia, where the first two diseases are neurodegenerative disorders and the last two are neurodevelopmental and psychiatric disorders, respectively. More importantly, we discuss the limitations of existing studies and present possible future directions.
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Affiliation(s)
- Li Zhang
- College of Computer Science and Technology, Nanjing Forestry University, Nanjing, China
- College of Computer Science and Technology, Nanjing University of Aeronautics and Astronautics, Nanjing, China
| | - Mingliang Wang
- College of Computer Science and Technology, Nanjing University of Aeronautics and Astronautics, Nanjing, China
| | - Mingxia Liu
- Department of Radiology and Biomedical Research Imaging Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Daoqiang Zhang
- College of Computer Science and Technology, Nanjing University of Aeronautics and Astronautics, Nanjing, China
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Sun L, Shao W, Zhang D, Liu M. Anatomical Attention Guided Deep Networks for ROI Segmentation of Brain MR Images. IEEE TRANSACTIONS ON MEDICAL IMAGING 2020; 39:2000-2012. [PMID: 31899417 DOI: 10.1109/tmi.2019.2962792] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Brain region-of-interest (ROI) segmentation based on structural magnetic resonance imaging (MRI) scans is an essential step for many computer-aid medical image analysis applications. Due to low intensity contrast around ROI boundary and large inter-subject variance, it has been remaining a challenging task to effectively segment brain ROIs from structural MR images. Even though several deep learning methods for brain MR image segmentation have been developed, most of them do not incorporate shape priors to take advantage of the regularity of brain structures, thus leading to sub-optimal performance. To address this issue, we propose an anatomical attention guided deep learning framework for brain ROI segmentation of structural MR images, containing two subnetworks. The first one is a segmentation subnetwork, used to simultaneously extract discriminative image representation and segment ROIs for each input MR image. The second one is an anatomical attention subnetwork, designed to capture the anatomical structure information of the brain from a set of labeled atlases. To utilize the anatomical attention knowledge learned from atlases, we develop an anatomical gate architecture to fuse feature maps derived from a set of atlas label maps and those from the to-be-segmented image for brain ROI segmentation. In this way, the anatomical prior learned from atlases can be explicitly employed to guide the segmentation process for performance improvement. Within this framework, we develop two anatomical attention guided segmentation models, denoted as anatomical gated fully convolutional network (AG-FCN) and anatomical gated U-Net (AG-UNet), respectively. Experimental results on both ADNI and LONI-LPBA40 datasets suggest that the proposed AG-FCN and AG-UNet methods achieve superior performance in ROI segmentation of brain MR images, compared with several state-of-the-art methods.
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