Volume-based features for detection of bladder wall abnormal regions via MR cystography

This paper proposes a framework for detecting the suspected abnormal region of the bladder wall via magnetic resonance (MR) cystography. Volume-based features are used. First, the bladder wall is divided into several layers, based on which a path from each voxel on the inner border to the outer border is found. By using the path length to measure the wall thickness and a bent rate (BR) term to measure the geometry property of the voxels on the inner border, the seed voxels representing the abnormalities on the inner border are determined. Then, by tracing the path from each seed, a weighted BR term is constructed to determine the suspected voxels, which are on the path and inside the bladder wall. All the suspected voxels are grouped together for the abnormal region. This work is significantly different from most of the previous computer-aided bladder tumor detection reports on two aspects. First of all, the T (1)-weighted MR images are used which give better image contrast and texture information for the bladder wall, comparing with the computed tomography images. Second, while most previous reports detected the abnormalities and indicated them on the reconstructed 3-D bladder model by surface rendering, we further determine the possible region of the abnormality inside the bladder wall. This study aims at a noninvasive procedure for bladder tumor detection and abnormal region delineation, which has the potential for further clinical analysis such as the invasion depth of the tumor and virtual cystoscopy diagnosis. Five datasets including two patients and three volunteers were used to test the presented method, all the tumors were detected by the method, and the overlap rates of the regions delineated by the computer against the experts were measured. The results demonstrated the potential of the method for detecting bladder wall abnormal regions via MR cystography.     

多分类CNN的胶质母细胞瘤多模态MR图像分割

为提高胶质母细胞瘤（GBM）多模态磁共振（MR）图像中各肿瘤子区域分割的准确性,提出一种多分类卷积神经网络（CNN）的GBM多模态MR图像自动分割算法.首先在98%缩尾处理和配准GBM多模态MR图像后,利用N4ITK法校正偏移场;其次构建一个主要由4个卷积层、2个池化层和2个全连接层组成的多分类CNN模型,训练后预分割GBM多模态MR图像,将体素分为5类不同的标签;最后移除所有小于200体素的假阳性区域,中值滤波后获得最终分割结果.以Dice相似性系数DSC、阳性预测值PPV和平均Hausdorff距离AHD为评价指标,利用所提出的算法对F-C-GBM数据集中整个肿瘤组织进行分割,获得的DSC、PPV、AHD分别为0.889±0.087、0.859±0.127和1.923.结果表明,该算法能有效提高GBM多模态MR图像分割的性能,可望有临床应用前景.     

Adaptive segmentation of MRI data

Intensity-based classification of MR images has proven problematic, even when advanced techniques are used. Intrascan and interscan intensity inhomogeneities are a common source of difficulty. While reported methods have had some success in correcting intrascan inhomogeneities, such methods require supervision for the individual scan. This paper describes a new method called adaptive segmentation that uses knowledge of tissue intensity properties and intensity inhomogeneities to correct and segment MR images. Use of the expectation-maximization (EM) algorithm leads to a method that allows for more accurate segmentation of tissue types as well as better visualization of magnetic resonance imaging (MRI) data, that has proven to be effective in a study that includes more than 1000 brain scans. Implementation and results are described for segmenting the brain in the following types of images: axial (dual-echo spin-echo), coronal [three dimensional Fourier transform (3-DFT) gradient-echo T1-weighted] all using a conventional head coil, and a sagittal section acquired using a surface coil. The accuracy of adaptive segmentation was found to be comparable with manual segmentation, and closer to manual segmentation than supervised multivariant classification while segmenting gray and white matter.     

Efficient multilevel brain tumor segmentation with integrated bayesian model classification

We present a new method for automatic segmentation of heterogeneous image data that takes a step toward bridging the gap between bottom-up affinity-based segmentation methods and top-down generative model based approaches. The main contribution of the paper is a Bayesian formulation for incorporating soft model assignments into the calculation of affinities, which are conventionally model free. We integrate the resulting model-aware affinities into the multilevel segmentation by weighted aggregation algorithm, and apply the technique to the task of detecting and segmenting brain tumor and edema in multichannel magnetic resonance (MR) volumes. The computationally efficient method runs orders of magnitude faster than current state-of-the-art techniques giving comparable or improved results. Our quantitative results indicate the benefit of incorporating model-aware affinities into the segmentation process for the difficult case of glioblastoma multiforme brain tumor.     

Three-dimensional computer-aided diagnosis scheme for detection ofcolonic polyps

We have developed a three-dimensional (3-D) computer-aided diagnosis scheme for automated detection of colonic polyps in computed tomography (CT) colonographic data sets, and assessed its performance based on colonoscopy as the gold standard. In this scheme, a thick region encompassing the entire colonic wall is extracted from an isotropic volume reconstructed from the CT images in CT colonography. Polyp candidates are detected by first computing of 3-D geometric features that characterize polyps, folds, and colonic walls at each voxel in the extracted colon, and then segmenting of connected components corresponding to suspicious regions by hysteresis thresholding based on these geometric features. We apply fuzzy clustering to these connected components to obtain the polyp candidates. False-positive (FP) detections are then reduced by computation of several 3-D volumetric features characterizing the internal structures of the polyp candidates, followed by the application of discriminant analysis to the feature space generated by these volumetric features. The locations of the polyps detected by our computerized method were compared to the gold standard of conventional colonoscopy. The performance was evaluated based on 43 clinical cases, including 12 polyps determined by colonoscopy. Our computerized scheme was shown to have the potential to detect polyps in CT colonography with a clinically acceptable high sensitivity and a low FP rate.     

Method for segmenting chest CT image data using an anatomicalmodel: preliminary results

Presents an automated, knowledge-based method for segmenting chest computed tomography (CT) datasets. Anatomical knowledge including expected volume, shape, relative position, and X-ray attenuation of organs provides feature constraints that guide the segmentation process. Knowledge is represented at a high level using an explicit anatomical model. The model is stored in a frame-based semantic network and anatomical variability is incorporated using fuzzy sets. A blackboard architecture permits the data representation and processing algorithms in the model domain to be independent of those in the image domain. Knowledge-constrained segmentation routines extract contiguous three-dimensional (3-D) sets of voxels, and their feature-space representations are posted on the blackboard. An inference engine uses fuzzy logic to match image to model objects based on the feature constraints. Strict separation of model and image domains allows for systematic extension of the knowledge base. In preliminary experiments, the method has been applied to a small number of thoracic CT datasets. Based on subjective visual assessment by experienced thoracic radiologists, basic anatomic structures such as the lungs, central tracheobronchial tree, chest wall, and mediastinum were successfully segmented. To demonstrate the extensibility of the system, knowledge was added to represent the more complex anatomy of lung lesions in contact with vessels or the chest wall. Visual inspection of these segmented lesions was also favorable. These preliminary results suggest that use of expert knowledge provides an increased level of automation compared with low-level segmentation techniques. Moreover, the knowledge-based approach may better discriminate between structures of similar attenuation and anatomic contiguity. Further validation is required     

Intraretinal layer segmentation of macular optical coherence tomography images using optimal 3-D graph search

Current techniques for segmenting macular optical coherence tomography (OCT) images have been 2-D in nature. Furthermore, commercially available OCT systems have only focused on segmenting a single layer of the retina, even though each intraretinal layer may be affected differently by disease. We report an automated approach for segmenting (anisotropic) 3-D macular OCT scans into five layers. Each macular OCT dataset consisted of six linear radial scans centered at the fovea. The six surfaces defining the five layers were identified on each 3-D composite image by transforming the segmentation task into that of finding a minimum-cost closed set in a geometric graph constructed from edge/regional information and a priori determined surface smoothness and interaction constraints. The method was applied to the macular OCT scans of 12 patients (24 3-D composite image datasets) with unilateral anterior ischemic optic neuropathy (AION). Using the average of three experts' tracings as a reference standard resulted in an overall mean unsigned border positioning error of 6.1 $pm$ 2.9 $mu$m, a result comparable to the interobserver variability (6.9 $pm$ 3.3 $mu$m). Our quantitative analysis of the automated segmentation results from AION subject data revealed that the inner retinal layer thickness for the affected eye was 24.1 $mu$m (21%) smaller on average than for the unaffected eye $(p≪0.001)$, supporting the need for segmenting the layers separately.      

深度全卷积网络对MRI膀胱图像的分割

大多数膀胱癌患者的膀胱肿瘤组织和膀胱壁组织互相渗透，各自的大小、形状变化多样，位置不固定，且膀胱MRI（Magnetic Resonance Imaging）图像中存在复杂的噪声和伪影，这使得将肿瘤和膀胱壁两者精确分割出来为下一步治疗进行诊断和定量分析成为难题。文中提出一种以U-net作为基础网络框架的深度全卷积网络，用残差网络子模块代替普通的卷积层进行下采样，通过空洞卷积来提取特征图不同感受野的信息，从而对不同尺度的特征图进行并行分支下采样。针对数据集小的问题，提出对图像加入高斯噪声、调节亮度和各向异性扩散滤波三种方法来进行数据扩增。实验结果表明，文中提出的方法对肿瘤分割的DSC（Dice similarity coefficient）值达到了0.9058，对膀胱壁分割的DSC值达到了0.9038，能够达到很好的分割效果。      

Accurate automatic analysis of cardiac cine images

Acquisition of noncontrast agent cine cardiac magnetic resonance (CMR) gated images through the cardiac cycle is, at present, a well-established part of examining cardiac global function. However, regional quantification is less well established. We propose a new automated framework for analyzing the wall thickness and thickening function on these images that consists of three main steps. First, inner and outer wall borders are segmented from their surrounding tissues with a geometric deformable model guided by a special stochastic speed relationship. The latter accounts for Markov-Gibbs shape and appearance models of the object-of-interest and its background. In the second step, point-to-point correspondences between the inner and outer borders are found by solving the Laplace equation and provide initial estimates of the local wall thickness and the thickening function index. Finally, the effects of the segmentation error is reduced and a continuity analysis of the LV wall thickening is performed through iterative energy minimization using a generalized Gauss-Markov random field (GGMRF) image model. The framework was evaluated on 26 datasets from clinical cine CMR images that have been collected from patients with eleven independent studies, with chronic ischemic heart disease and heart damage. The performance evaluation of the proposed segmentation approach, based on the receiver operating characteristic (ROC) and Dice similarity coefficients (DSC) between manually drawn and automatically segmented contours, confirmed a high robustness and accuracy of the proposed segmentation approach. Furthermore, the Bland-Altman plot is used to assess the limit of agreement of our measurements of the global function parameters compared to the ground truth. Importantly, comparative results on the publicly available database (MICCAI 2009 Cardiac MR Left Ventricle Segmentation) demonstrated a superior performance of the proposed segmentation approach over published methods.     

Range image segmentation using surface selection criterion.

In this paper, we address the problem of recovering the true underlying model of a surface while performing the segmentation. First, and in order to solve the model selection problem, we introduce a novel criterion, which is based on minimising strain energy of fitted surfaces. We then evaluate its performance and compare it with many other existing model selection techniques. Using this criterion, we then present a robust range data segmentation algorithm capable of segmenting complex objects with planar and curved surfaces. The presented algorithm simultaneously identifies the type (order and geometric shape) of each surface and separates all the points that are part of that surface. This paper includes the segmentation results of a large collection of range images obtained from objects with planar and curved surfaces. The resulting segmentation algorithm successfully segments various possible types of curved objects. More importantly, the new technique is capable of detecting the association between separated parts of a surface, which has the same Cartesian equation while segmenting a scene. This aspect is very useful in some industrial applications of range data analysis.     

Adaptive model initialization and deformation for automatic segmentation of T1-weighted brain MRI data

A fully automatic, two-step, T1-weighted brain magnetic resonance imaging (MRI) segmentation method is presented. A preliminary mask of parenchyma is first estimated through adaptive image intensity analysis and mathematical morphological operations. It serves as the initial model and probability reference for a level-set algorithm in the second step, which finalizes the segmentation based on both image intensity and geometric information. The Dice coefficient and Euclidean distance between boundaries of automatic results and the corresponding references are reported for both phantom and clinical MR data. For the 28 patient scans acquired at our institution, the average Dice coefficient was 98.2% and the mean Euclidean surface distance measure was 0.074 mm. The entire segmentation for either a simulated or a clinical image volume finishes within 2 min on a modern PC system. The accuracy and speed of this technique allow us to automatically create patient-specific finite element models within the operating room on a timely basis for application in image-guided updating of preoperative scans.     

Prior shape level set segmentation on multistep generated probability maps of MR datasets for fully automatic kidney parenchyma volumetry

Fully automatic 3-D segmentation techniques for clinical applications or epidemiological studies have proven to be a very challenging task in the domain of medical image analysis. 3-D organ segmentation on magnetic resonance (MR) datasets requires a well-designed segmentation strategy due to imaging artifacts, partial volume effects, and similar tissue properties of adjacent tissues. We developed a 3-D segmentation framework for fully automatic kidney parenchyma volumetry that uses Bayesian concepts for probability map generation. The probability map quality is improved in a multistep refinement approach. An extended prior shape level set segmentation method is then applied on the refined probability maps. The segmentation quality is improved by incorporating an exterior cortex edge alignment technique using cortex probability maps. In contrast to previous approaches, we combine several relevant kidney parenchyma features in a sequence of segmentation techniques for successful parenchyma delineation on native MR datasets. Furthermore, the proposed method is able to recognize and exclude parenchymal cysts from the parenchymal volume. We analyzed four different quality measures showing better results for right parenchymal tissue than for left parenchymal tissue due to an incorporated liver part removal in the segmentation framework. The results show that the outer cortex edge alignment approach successfully improves the quality measures.     

Automatic Segmentation and Classification of Multiple Sclerosis in Multichannel MRI

We introduce a multiscale approach that combines segmentation with classification to detect abnormal brain structures in medical imagery, and demonstrate its utility in automatically detecting multiple sclerosis (MS) lesions in 3-D multichannel magnetic resonance (MR) images. Our method uses segmentation to obtain a hierarchical decomposition of a multichannel, anisotropic MR scans. It then produces a rich set of features describing the segments in terms of intensity, shape, location, neighborhood relations, and anatomical context. These features are then fed into a decision forest classifier, trained with data labeled by experts, enabling the detection of lesions at all scales. Unlike common approaches that use voxel-by-voxel analysis, our system can utilize regional properties that are often important for characterizing abnormal brain structures. We provide experiments on two types of real MR images: a multichannel proton-density-, T2-, and T1-weighted dataset of 25 MS patients and a single-channel fluid attenuated inversion recovery (FLAIR) dataset of 16 MS patients. Comparing our results with lesion delineation by a human expert and with previously extensively validated results shows the promise of the approach.     

Automatic segmentation of the caudate nucleus from human brain MR images

We describe a knowledge-driven algorithm to automatically delineate the caudate nucleus (CN) region of the human brain from a magnetic resonance (MR) image. Since the lateral ventricles (LVs) are good landmarks for positioning the CN, the algorithm first extracts the LVs, and automatically localizes the CN from this information guided by anatomic knowledge of the structure. The face validity of the algorithm was tested with 55 high-resolution T1-weighted magnetic resonance imaging (MRI) datasets, and segmentation results were overlaid onto the original image data for visual inspection. We further evaluated the algorithm by comparing automated segmentation results to a "gold standard" established by human experts for these 55 MR datasets. Quantitative comparison showed a high intraclass correlation between the algorithm and expert as well as high spatial overlap between the regions-of-interest (ROIs) generated from the two methods. The mean spatial overlap +/- standard deviation (defined by the intersection of the 2 ROIs divided by the union of the 2 ROIs) was equal to 0.873 +/- 0.0234. The algorithm has been incorporated into a public domain software program written in Java and, thus, has the potential to be of broad benefit to neuroimaging investigators interested in basal ganglia anatomy and function.     

Parametric estimate of intensity inhomogeneities applied to MRI

This paper presents a new approach to the correction of intensity inhomogeneities in magnetic resonance imaging (MRI) that significantly improves intensity-based tissue segmentation. The distortion of the image brightness values by a low-frequency bias field impedes visual inspection and segmentation. The new correction method called parametric bias field correction (PABIC) is based on a simplified model of the imaging process, a parametric model of tissue class statistics, and a polynomial model of the inhomogeneity field. We assume that the image is composed of pixels assigned to a small number of categories with a priori known statistics. Further we assume that the image is corrupted by noise and a low-frequency inhomogeneity field. The estimation of the parametric bias field is formulated as a nonlinear energy minimization problem using an evolution strategy (ES). The resulting bias field is independent of the image region configurations and thus overcomes limitations of methods based on homomorphic filtering. Furthermore, PABIC can correct bias distortions much larger than the image contrast. Input parameters are the intensity statistics of the classes and the degree of the polynomial function. The polynomial approach combines bias correction with histogram adjustment, making it well suited for normalizing the intensity histogram of datasets from serial studies. We present simulations and a quantitative validation with phantom and test images. A large number of MR image data acquired with breast, surface, and head coils, both in two dimensions and three dimensions, have been processed and demonstrate the versatility and robustness of this new bias correction scheme.     

Colonic polyp segmentation in CT colonography-based on fuzzy clustering and deformable models

An automatic method to segment colonic polyps in computed tomography (CT) colonography is presented in this paper. The method is based on a combination of knowledge-guided intensity adjustment, fuzzy c-mean clustering, and deformable models. The computer segmentations were compared with manual segmentations to validate the accuracy of our method. An average 76.3% volume overlap percentage among 105 polyp detections was reported in the validation, which was very good considering the small polyp size. Several experiments were performed to investigate the intraoperator and interoperator repeatability of manual colonic polyp segmentation. The investigation demonstrated that the computer-human repeatability was as good as the interoperator repeatability. The polyp segmentation was also applied in computer-aided detection (CAD) to reduce the number of false positive (FP) detections and provide volumetric features for polyp classification. Our segmentation method was able to eliminate 30% of FP detections. The volumetric features computed from the segmentation can further reduce FP detections by 50% at 80% sensitivity.     

Statistical approach to segmentation of single-channel cerebral MRimages

A statistical model is presented that represents the distributions of major tissue classes in single-channel magnetic resonance (MR) cerebral images. Using the model, cerebral images are segmented into gray matter, white matter, and cerebrospinal fluid (CSF). The model accounts for random noise, magnetic field inhomogeneities, and biological variations of the tissues. Intensity measurements are modeled by a finite Gaussian mixture. Smoothness and piecewise contiguous nature of the tissue regions are modeled by a three-dimensional (3-D) Markov random field (MRF). A segmentation algorithm, based on the statistical model, approximately finds the maximum a posteriori (MAP) estimation of the segmentation and estimates the model parameters from the image data. The proposed scheme for segmentation is based on the iterative conditional modes (ICM) algorithm in which measurement model parameters are estimated using local information at each site, and the prior model parameters are estimated using the segmentation after each cycle of iterations. Application of the algorithm to a sample of clinical MR brain scans, comparisons of the algorithm with other statistical methods, and a validation study with a phantom are presented. The algorithm constitutes a significant step toward a complete data driven unsupervised approach to segmentation of MR images in the presence of the random noise and intensity inhomogeneities     

Shape statistics variational approach for the outer contour segmentation of left ventricle MR images.

Segmentation of left ventricles is one of the important research topics in cardiac magnetic resonance (MR) imaging. The segmentation precision influences the authenticity of ventricular motion reconstruction. In left ventricle MR images, the weak and broken boundary increases the difficulty of segmenting the outer contour precisely. In this paper, we present an improved shape statistics variational approach for the outer contour segmentation of left ventricle MR images. We use the Mumford-Shah model in an object feature space and incorporate the shape statistics and an edge image to the variational framework. The introduction of shape statistics can improve the segmentation with broken boundaries. The edge image can enhance the weak boundary and thus improve the segmentation precision. The generation of the object feature image, which has homogenous "intensities" in the left ventricle, facilitates the application of the Mumford-Shah model. A comparison of mean absolute distance analysis between different contours generated with our algorithm and that generated by hand demonstrated that our method can achieve a higher segmentation precision and a better stability than various approaches. It is a semiautomatic way for the segmentation of the outer contour of the left ventricle in clinical applications.     

带偏场校正和邻域约束的快速MR脑组织分割新方法

 由于部分容积效应(PVE)、图像的偏场(INU)和噪声的存在,脑组织磁共振(MR)图像自动准确的分割是一项具有挑战性的任务.本文提出了一个准确度高并快速鲁棒的二维(2D)和三维(3D)分割算法来将脑部MR图象分割为白质(WM)、灰质(GM)和脑脊液(CSF)三种主要的解剖组织类型.该算法在标准模糊C-均值算法(FCM)的基础上提出了一个新的目标函数,包含偏场校正和邻域约束.在该算法中,采用参数模型表示INU,并且一个类似马尔可夫随机场(MRF)的邻域约束来表示脑组织空间分布一致性信息.本文给出了该算法的模拟和真实脑MR图像的分割结果,同时与其它算法进行了比较.比较结果显示该算法具有较高的准确度和较快的收敛速度.     

Automated segmentation of human brain MR images aided by fuzzy information granulation and fuzzy inference

This paper proposes an automated procedure for segmenting an magnetic resonance (MR) image of a human brain based on fuzzy logic. An MR volumetric image composed of many slice images consists of several parts: gray matter, white matter, cerebrospinal fluid, and others. Generally, the histogram shapes of MR volumetric images are different from person to person. Fuzzy information granulation of the histograms can lead to a series of histogram peaks. The intensity thresholds for segmenting the whole brain of a subject are automatically determined by finding the peaks of the intensity histogram obtained from the MR images. After these thresholds are evaluated by a procedure called region growing, the whole brain can be identified. A segmentation experiment was done on 50 human brain MR volumes. A statistical analysis showed that the automated segmented volumes were similar to the volumes manually segmented by a physician. Next, we describe a procedure for decomposing the obtained whole brain into the left and right cerebral hemispheres, the cerebellum and the brain stem. Fuzzy if-then rules can represent information on the anatomical locations, segmentation boundaries as well as intensities. Evaluation of the inferred result using the region growing method can then lead to the decomposition of the whole brain. We applied this method to 44 MR volumes. The decomposed portions were statistically compared with those manually decomposed by a physician. Consequently, our method can identify the whole brain, the left cerebral hemisphere, the right cerebral hemisphere, the cerebellum and the brain stem with high accuracy and therefore can provide the three dimensional shapes of these regions.