Purpose In this paper, we investigate a framework for interactive brain tumor segmentation which, at its core, treats the problem of interactive brain tumor segmentation as a machine learning problem.
Although our method is a semi-automatic method, it shares with automatic methods the use of a machine learning classification algorithm, ran on a feature representation of voxels and improved by a spatial dependency model. The main difference is that generalization is performed within each brain, based on the training data provided by the user's interaction. This simplified generalization problem allows us to use a very simple feature space, yielding an interactive segmentation method that is fast and effective. @cite_7 used a similar, semi-automatic, kNN classification method, applied to proton density, T1 and T2 modalities. @cite_8 also proposed a semi-automatic segmentation method that uses instead Quadratic Discriminative Aanalysis to perform multi-class segmentation. However, they did not use the @math voxel positions as features (see ) nor did they deal with label spatial dependency modeling (see ), which we found to play a crucial role in obtaining competitive performances.
@cite_7 @cite_8
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Maximization of mutual information of voxel intensities has been demonstrated to be a very powerful criterion for three-dimensional medical image registration, allowing robust and accurate fully automated affine registration of multimodal images in a variety of applications, without the need for segmentation or other preprocessing of the images. In this paper, we investigate the performance of various optimization methods and multiresolution strategies for maximization of mutual information, aiming at increasing registration speed when matching large high-resolution images. We show that mutual information is a continuous function of the affine registration parameters when appropriate interpolation is used and we derive analytic expressions of its derivatives that allow numerically exact evaluation of its gradient. Various multiresolution gradient- and non-gradient-based optimization strategies, such as Powell, simplex, steepest-descent, conjugate-gradient, quasi-Newton and Levenberg—Marquardt methods, are evaluated for registration of computed tomography (CT) and magnetic resonance images of the brain. Speed-ups of a factor of 3 on average compared to Powell's method at full resolution are achieved with similar precision and without a loss of robustness with the simplex, conjugate-gradient and Levenberg—Marquardt method using a two-level multiresolution scheme. Large data sets such as 2562 × 128 MR and 5122 × 48 CT images can be registered with subvoxel precision in < 5 min CPU time on current workstations. We present a method combining affinity prediction with region agglomeration, which improves significantly upon the state of the art of neuron segmentation from electron microscopy (EM) in accuracy and scalability. Our method consists of a 3D U-Net, trained to predict affinities between voxels, followed by iterative region agglomeration. We train using a structured loss based on Malis, encouraging topologically correct segmentations obtained from affinity thresholding. Our extension consists of two parts: First, we present a quasi-linear method to compute the loss gradient, improving over the original quadratic algorithm. Second, we compute the gradient in two separate passes to avoid spurious gradient contributions in early training stages. Our predictions are accurate enough that simple learning-free percentile-based agglomeration outperforms more involved methods used earlier on inferior predictions. We present results on three diverse EM datasets, achieving relative improvements over previous results of 27, 15, and 250 percent. Our findings suggest that a single method can be applied to both nearly isotropic block-face EM data and anisotropic serial sectioned EM data. The runtime of our method scales linearly with the size of the volume and achieves a throughput of @math ∼ 2.6 seconds per megavoxel, qualifying our method for the processing of very large datasets. Locating Brain tumor segmentation within MR (magnetic resonance) images is integral to the treatment of brain cancer. This segmentation task requires classifying each voxel as either tumor or non-tumor, based on a description of that voxel. Unfortunately, standard classifiers, such as Logistic Regression (LR) and Support Vector Machines (SVM), typically have limited accuracy as they treat voxels as independentand identically distributed(iid). Approaches based on random fields, which are able to incorporate spatial constraints, have recently been applied to brain tumor segmentation with notable performance improvement over iid classifiers. However, previous random field systems involved computationally intractable formulations, which are typically solved using some approximation. Here, we present pseudo-conditional random fields(PCRFs), which achieve accuracy similar to other random fields variants, but are significantly more efficient. We formulate a PCRF as a regularized discriminative classifier that relaxes the classification decision for each voxel by considering the labels and features of neighboring voxels. This paper details a new approach for learning a discriminative model of object classes, incorporating texture, layout, and context information efficiently. The learned model is used for automatic visual understanding and semantic segmentation of photographs. Our discriminative model exploits texture-layout filters, novel features based on textons, which jointly model patterns of texture and their spatial layout. Unary classification and feature selection is achieved using shared boosting to give an efficient classifier which can be applied to a large number of classes. Accurate image segmentation is achieved by incorporating the unary classifier in a conditional random field, which (i) captures the spatial interactions between class labels of neighboring pixels, and (ii) improves the segmentation of specific object instances. Efficient training of the model on large datasets is achieved by exploiting both random feature selection and piecewise training methods. High classification and segmentation accuracy is demonstrated on four varied databases: (i) the MSRC 21-class database containing photographs of real objects viewed under general lighting conditions, poses and viewpoints, (ii) the 7-class Corel subset and (iii) the 7-class Sowerby database used in (Proceeding of IEEE Conference on Computer Vision and Pattern Recognition, vol. 2, pp. 695---702, June 2004), and (iv) a set of video sequences of television shows. The proposed algorithm gives competitive and visually pleasing results for objects that are highly textured (grass, trees, etc.), highly structured (cars, faces, bicycles, airplanes, etc.), and even articulated (body, cow, etc.).