Multiple abdominal organ segmentation: an atlas-based fuzzy connectedness approach.

Organ segmentation is an important step in various medical image applications. In this paper, a presegmented atlas is incorporated into the fuzzy connectedness (FC) framework for automatic segmentation of abdominal organs. First, the atlas is registered onto the subject to provide an initial segmentation. Then, a novel method is applied to estimate the necessary FC parameters such as organ intensity features, seeds, and optimal FC threshold automatically and subject adaptively. In order to overcome the intensity overlapping between the neighboring organs, a shape modification approach based on Euclidean distance and watershed segmentation is used. This atlas-based segmentation method has been tested on some abdominal CT and MRI images from Chinese patients. Experimental results indicate the validity of this segmentation method for various image modalities.     

An accurate and efficient bayesian method for automatic segmentation of brain MRI

Automatic three-dimensional (3-D) segmentation of the brain from magnetic resonance (MR) scans is a challenging problem that has received an enormous amount of attention lately. Of the techniques reported in the literature, very few are fully automatic. In this paper, we present an efficient and accurate, fully automatic 3-D segmentation procedure for brain MR scans. It has several salient features; namely, the following. 1) Instead of a single multiplicative bias field that affects all tissue intensities, separate parametric smooth models are used for the intensity of each class. 2) A brain atlas is used in conjunction with a robust registration procedure to find a nonrigid transformation that maps the standard brain to the specimen to be segmented. This transformation is then used to: segment the brain from nonbrain tissue; compute prior probabilities for each class at each voxel location and find an appropriate automatic initialization. 3) Finally, a novel algorithm is presented which is a variant of the expectation-maximization procedure, that incorporates a fast and accurate way to find optimal segmentations, given the intensity models along with the spatial coherence assumption. Experimental results with both synthetic and real data are included, as well as comparisons of the performance of our algorithm with that of other published methods.     

Construction of an abdominal probabilistic atlas and its application in segmentation

There have been significant efforts to build a probabilistic atlas of the brain and to use it for many common applications, such as segmentation and registration. Though the work related to brain atlases can be applied to nonbrain organs, less attention has been paid to actually building an atlas for organs other than the brain. Motivated by the automatic identification of normal organs for applications in radiation therapy treatment planning, we present a method to construct a probabilistic atlas of an abdomen consisting of four organs (i.e., liver, kidneys, and spinal cord). Using 32 noncontrast abdominal computed tomography (CT) scans, 31 were mapped onto one individual scan using thin plate spline as the warping transform and mutual information (MI) as the similarity measure. Except for an initial coarse placement of four control points by the operators, the MI-based registration was automatic. Additionally, the four organs in each of the 32 CT data sets were manually segmented. The manual segmentations were warped onto the "standard" patient space using the same transform computed from their gray scale CT data set and a probabilistic atlas was calculated. Then, the atlas was used to aid the segmentation of low-contrast organs in an additional 20 CT data sets not included in the atlas. By incorporating the atlas information into the Bayesian framework, segmentation results clearly showed improvements over a standard unsupervised segmentation method.     

Automated model-based tissue classification of MR images of the brain

We describe a fully automated method for model-based tissue classification of magnetic resonance (MR) images of the brain. The method interleaves classification with estimation of the model parameters, improving the classification at each iteration. The algorithm is able to segment single- and multispectral MR images, corrects for MR signal inhomogeneities, and incorporates contextual information by means of Markov random Fields (MRF's). A digital brain atlas containing prior expectations about the spatial location of tissue classes is used to initialize the algorithm. This makes the method fully automated and therefore it provides objective and reproducible segmentations. We have validated the technique on simulated as well as on real MR images of the brain.     

Automatic tractography segmentation using a high-dimensional white matter atlas

We propose a new white matter atlas creation method that learns a model of the common white matter structures present in a group of subjects. We demonstrate that our atlas creation method, which is based on group spectral clustering of tractography, discovers structures corresponding to expected white matter anatomy such as the corpus callosum, uncinate fasciculus, cingulum bundles, arcuate fasciculus, and corona radiata. The white matter clusters are augmented with expert anatomical labels and stored in a new type of atlas that we call a high-dimensional white matter atlas. We then show how to perform automatic segmentation of tractography from novel subjects by extending the spectral clustering solution, stored in the atlas, using the Nystrom method. We present results regarding the stability of our method and parameter choices. Finally we give results from an atlas creation and automatic segmentation experiment. We demonstrate that our automatic tractography segmentation identifies corresponding white matter regions across hemispheres and across subjects, enabling group comparison of white matter anatomy.     

Automatic 3-D segmentation of internal structures of the head in MR images using a combination of similarity and free-form transformations: Part II, validation on severely atrophied brains

Studies aimed at quantifying neuroanatomical differences between populations require the volume measurements of individual brain structures. If the study contains a large number of images, manual segmentation is not practical. This study tests the hypothesis that a fully automatic, atlas-based segmentation method can be used to quantify atrophy indexes derived from the brain and cerebellum volumes in normal subjects and chronic alcoholics. This is accomplished by registering an atlas volume with a subject volume, first using a global transformation, and then improving the registration using a local transformation. Segmented structures in the atlas volume are then mapped to the corresponding structures in the subject volume using the combined global and local transformations. This technique has been applied to seven normal and seven alcoholic subjects. Three magnetic resonance volumes were obtained for each subject and each volume was segmented automatically, using the atlas-based method. Accuracy was assessed by manually segmenting regions and measuring the similarity between corresponding regions obtained automatically. Repeatability was determined by comparing volume measurements of segmented structures from each acquisition of the same subject. Results demonstrate that the method is accurate, that the results are repeatable, and that it can provide a method for automatic quantification of brain atrophy, even when the degree of atrophy is large.     

改进的全卷积神经网络的脑肿瘤图像分割

针对现有机器学习算法分割脑肿瘤图像精度不高的问题,提出一种基于改进的全卷积神经网络的脑肿瘤图像分割算法。算法首先将FLAIR、T2和T1C三种模态的MR脑肿瘤图像进行灰度归一化,随后利用灰度图像融合技术得到肿瘤信息更加全面的预处理图像;然后采用融合三次脑肿瘤特征信息的改进全卷积神经网络对预处理图像进行粗分割,并且在每个卷积层后加入批量正则化层以加快网络训练的收敛速度,提高训练模型精度;最后融合全连接条件随机场细化粗分割结果中的脑肿瘤边界。实验结果表明,相较于传统的卷积神经网络脑肿瘤图像分割算法,本算法在分割精度和稳定性上有了较大提升,平均Dice可达91.29%,实时性较好,利用训练模型平均1s内可完成单张脑肿瘤图像的分割。      

Automatic segmentation of hippocampal subfields based on multi-atlas image segmentation techniques

The volume of hippocampal subfields is closely related with early diagnosis of Alzheimer＇s disease. Due to the anatomical complexity of hippocampal subfields, automatic segmentation merely on the content of MR images is extremely difficult. We presented a method which combines multi-atlas image segmentation with extreme learning machine based bias detection and correction technique to achieve a fully automatic segmentation of hippocampal subfields. Symmetric diffeomorphic registration driven by symmetric mutual information energy was implemented in atlas registration, which allows multi-modal image registration and accelerates execution time. An exponential function based label fusion strategy was proposed for the normalized similarity measure case in segmentation combination, which yields better combination accuracy. The test results show that this method is effective, especially for the larger subfields with an overlap of more than 80%, which is competitive with the current methods and is of potential clinical significance.     

Segmenting articular cartilage automatically using a voxel classification approach

We present a fully automatic method for articular cartilage segmentation from magnetic resonance imaging (MRI) which we use as the foundation of a quantitative cartilage assessment. We evaluate our method by comparisons to manual segmentations by a radiologist and by examining the interscan reproducibility of the volume and area estimates. Training and evaluation of the method is performed on a data set consisting of 139 scans of knees with a status ranging from healthy to severely osteoarthritic. This is, to our knowledge, the only fully automatic cartilage segmentation method that has good agreement with manual segmentations, an interscan reproducibility as good as that of a human expert, and enables the separation between healthy and osteoarthritic populations. While high-field scanners offer high-quality imaging from which the articular cartilage have been evaluated extensively using manual and automated image analysis techniques, low-field scanners on the other hand produce lower quality images but to a fraction of the cost of their high-field counterpart. For low-field MRI, there is no well-established accuracy validation for quantitative cartilage estimates, but we show that differences between healthy and osteoarthritic populations are statistically significant using our cartilage volume and surface area estimates, which suggests that low-field MRI analysis can become a useful, affordable tool in clinical studies.     

Differentiation of sCJD and vCJD forms by automated analysis of basal ganglia intensity distribution in multisequence MRI of the brain--definition and evaluation of new MRI-based ratios

We present a method for the analysis of basal ganglia (including the thalamus) for accurate detection of human spongiform encephalopathy in multisequence magnetic resonance imaging (MRI) of the brain. One common feature of most forms of prion protein diseases is the appearance of hyperintensities in the deep grey matter area of the brain in T2-weighted magnetic resonance (MR) images. We employ T1, T2, and Flair-T2 MR sequences for the detection of intensity deviations in the internal nuclei. First, the MR data are registered to a probabilistic atlas and normalized in intensity. Then smoothing is applied with edge enhancement. The segmentation of hyperintensities is performed using a model of the human visual system. For more accurate results, a priori anatomical data from a segmented atlas are employed to refine the registration and remove false positives. The results are robust over the patient data and in accordance with the clinical ground truth. Our method further allows the quantification of intensity distributions in basal ganglia. The caudate nuclei are highlighted as main areas of diagnosis of sporadic Creutzfeldt-Jakob Disease (sCJD), in agreement with the histological data. The algorithm permitted the classification of the intensities of abnormal signals in sCJD patient FLAIR images with a higher hypersignal in caudate nuclei (10/10) and putamen (6/10) than in thalami. Defining normalized MRI measures of the intensity relations between the internal grey nuclei of patients, we robustly differentiate sCJD and variant CJD (vCJD) patients, in an attempt to create an automatic classification tool of human spongiform encephalopathies.     

基于Otsu法自适应阈值的图像分割研究

概述了基于一维Otsu 和二维Otsu 双门限的阈值分割法,提出了基于像素邻域平均灰度的改进的一维Otsu 多门限分割方法,兼有准确性和快速性的优点,并应用于MRI脑图像,实现了多个目标的自动分割,与普通的一维Otsu 法相比具有更好的分割效果.     

基于YCbCr空间对大壁虎脑图谱的分割

确定大壁虎的各种运动行为与脑内控制其运动的具体的皮层组织对应关系是壁虎机器人的制作关键。通过对其脑图谱的制备,可以观察到脑内皮层组织的丰富信息。针对HE染色的大壁虎脑图谱自身的独特性,经过推敲,提出一种基于YCbCr空间的对图谱进行分割的方法。该方法将图谱由RGB空间转换为YCbCr空间,将亮度分量独立出来,不仅解决了拍摄过程中由于光线改变所带来的问题,而且阈值分明,分割彻底,鲁棒性好。其结果表明基于YCbCr空间的分割方法是分割效果非常好的方法。     

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.     

Atlas-based segmentation of pathological MR brain images using a model of lesion growth

We propose a method for brain atlas deformation in the presence of large space-occupying tumors, based on an a priori model of lesion growth that assumes radial expansion of the lesion from its starting point. Our approach involves three steps. First, an affine registration brings the atlas and the patient into global correspondence. Then, the seeding of a synthetic tumor into the brain atlas provides a template for the lesion. The last step is the deformation of the seeded atlas, combining a method derived from optical flow principles and a model of lesion growth. Results show that a good registration is performed and that the method can be applied to automatic segmentation of structures and substructures in brains with gross deformation, with important medical applications in neurosurgery, radiosurgery, and radiotherapy.     

A Hybrid Geometric–Statistical Deformable Model for Automated 3-D Segmentation in Brain MRI

We present a novel 3-D deformable model-based approach for accurate, robust, and automated tissue segmentation of brain MRI data of single as well as multiple magnetic resonance sequences. The main contribution of this study is that we employ an edge-based geodesic active contour for the segmentation task by integrating both image edge geometry and voxel statistical homogeneity into a novel hybrid geometric-statistical feature to regularize contour convergence and extract complex anatomical structures. We validate the accuracy of the segmentation results on simulated brain MRI scans of both single T1-weighted and multiple T1/T2/PD-weighted sequences. We also demonstrate the robustness of the proposed method when applied to clinical brain MRI scans. When compared to a current state-of-the-art region-based level-set segmentation formulation, our white matter and gray matter segmentation resulted in significantly higher accuracy levels with a mean improvement in Dice similarity indexes of 8.55% (p<0.0001) and 10.18% (p<0.0001), respectively.     

Atlas renormalization for improved brain MR image segmentation across scanner platforms

Atlas-based approaches have demonstrated the ability to automatically identify detailed brain structures from 3-D magnetic resonance (MR) brain images. Unfortunately, the accuracy of this type of method often degrades when processing data acquired on a different scanner platform or pulse sequence than the data used for the atlas training. In this paper, we improve the performance of an atlas-based whole brain segmentation method by introducing an intensity renormalization procedure that automatically adjusts the prior atlas intensity model to new input data. Validation using manually labeled test datasets has shown that the new procedure improves the segmentation accuracy (as measured by the Dice coefficient) by 10% or more for several structures including hippocampus, amygdala, caudate, and pallidum. The results verify that this new procedure reduces the sensitivity of the whole brain segmentation method to changes in scanner platforms and improves its accuracy and robustness, which can thus facilitate multicenter or multisite neuroanatomical imaging studies.     

Atlas-based indexing of brain sections via 2-D to 3-D image registration

A 2-D to 3-D nonlinear intensity-based registration method is proposed in which the alignment of histological brain sections with a volumetric brain atlas is performed. First, sparsely cut brain sections were linearly matched with an oblique slice automatically extracted from the atlas. Second, a planar-to-curved surface alignment was employed in order to match each section with its corresponding image overlaid on a curved-surface within the atlas. For the latter, a PDE-based registration technique was developed that is driven by a local normalized-mutual-information similarity measure. We demonstrate the method and evaluate its performance with simulated and real data experiments. An atlas-guided segmentation of mouse brains' hippocampal complex, retrieved from the Mouse Brain Library (MBL) database, is demonstrated with the proposed algorithm.     

基于softmax回归与图割法的脑肿瘤分割算法

从医学图像中分割脑肿瘤区域可以为脑肿瘤的诊断以及放射治疗提供帮助.但肿瘤区域的变化异常且边界非常模糊,因此自动或半自动地分割脑肿瘤非常困难.针对这一问题,本文结合softmax回归和图割法提出一种脑肿瘤分割算法.首先融合多序列核磁共振图像(MRI)并标记训练样本,再用softmax回归训练模型参数并计算每个点属于各个类别的概率,最后将概率融入到图割法中,用最小切/最大流方法得到最终分割结果.实验表明提出的方法可以更好地得到脑肿瘤的边界,并能较准确地分割出脑肿瘤区域.     

Combination Strategies in Multi-Atlas Image Segmentation: Application to Brain MR Data

It has been shown that employing multiple atlas images improves segmentation accuracy in atlas-based medical image segmentation. Each atlas image is registered to the target image independently and the calculated transformation is applied to the segmentation of the atlas image to obtain a segmented version of the target image. Several independent candidate segmentations result from the process, which must be somehow combined into a single final segmentation. Majority voting is the generally used rule to fuse the segmentations, but more sophisticated methods have also been proposed. In this paper, we show that the use of global weights to ponderate candidate segmentations has a major limitation. As a means to improve segmentation accuracy, we propose the generalized local weighting voting method. Namely, the fusion weights adapt voxel-by-voxel according to a local estimation of segmentation performance. Using digital phantoms and MR images of the human brain, we demonstrate that the performance of each combination technique depends on the gray level contrast characteristics of the segmented region, and that no fusion method yields better results than the others for all the regions. In particular, we show that local combination strategies outperform global methods in segmenting high-contrast structures, while global techniques are less sensitive to noise when contrast between neighboring structures is low. We conclude that, in order to achieve the highest overall segmentation accuracy, the best combination method for each particular structure must be selected.      

基于多尺度特征提取的MRI脑肿瘤图像分割研究

针对磁共振成像(magnetic resonance imaging, MRI)脑部肿瘤区域误识别及肿瘤形状 差异较大的问题,提出一种基于多尺度特征提取的 MRI 脑肿瘤图像分割方法。分割模型以 U-Net 为骨干网络,使用密集金字塔卷积(dense pyramidal convolution, DPC)提取多尺度特征, 以适应不同尺寸肿瘤的分割,同时引入条状池化(strip pooling, SP),凭借其能捕获肿瘤中远 距离区域的依赖关系,进一步加强对肿瘤图像的分割能力。提出的方法在 Kaggle_3m 数据 集上进行了实验验证,实验结果表明该方法具有良好的脑部肿瘤分割性能, 其中Dice相似 系数、杰卡德系数分别达到了91.66%,84.38% 。