Shen, Dinggang
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Publication Optimized biopsy procedures for estimating Gleason Score and prostate cancer volume(2008-09-01) Ou, Yangming; Shen, Dinggang; Fan, Yong; Davatzikos, Christos; Zeng, Jianchao; Sun, LeonProstate biopsy is the gold standard procedure for pre-operatively estimating Gleason Score (GS) and cancer volume (CV), which are two important surrogate markers for prostate cancer aggressiveness. Currently, biopsy estimates GS based on architectural patterns of the sampled tissue at the microscopic level [1] and estimates CV mostly based on the percent positive biopsies. However, underestimations are sometimes observed mainly due to the sampling errors of biopsy [2-5]. This problem is partially alleviated in this paper, where we have developed optimized biopsy procedures that could differentiate between prostate specimens having high and low GS/CV by sampling the spatial cancer distributions at the macro level. Differentiation rates of 81.93% (for GS) and 94.79% (for CV) have been obtained under cross validation in a population of prostatectomy specimens. To the best of our knowledge, the optimized biopsy procedures are the first ones that use (macro-level) spatial cancer distributions to estimate GS and CV. More validations might be needed to reveal its generalization ability.Publication Simultaneous Estimation and Segmentation of T1 Map for Breast Parenchyma Measurement(2007-04-01) Xing, Ye; Ou, Yangming; Englander, Sarah; Schnall, Mitchell D.; Shen, DinggangBreast density has been shown to be an independent risk factor for breast cancer. In order to segment breast parenchyma, which has been proposed as a biomarker of breast cancer risk, we present an integrated algorithm for simultaneous T1 map estimation and segmentation, using a series of magnetic resonance (MR) breast images. The advantage of using this algorithm is that the step of T1 map estimation (E-Step) and the step of T1 map based tissue segmentation (S-Step) can benefit each other. Since the estimated T1 map can be noisy due to the complexity of T1 estimation method, the tentative tissue segmentation results from S-Step can help perform the edge-preserving smoothing on the estimated T1 map in E-Step, thus removing noises and also preserving tissue boundaries. On the other hand, the improved estimation of T1 map from E-Step can help segment breast tissues in a more accurate and less noisy way. Therefore, by repeating these steps, we can simultaneously obtain better results for both T1 map estimation and segmentation. Experimental results show the effectiveness of the proposed algorithm in breast tissue segmentation and parenchyma volume measurement.Publication Sampling the spatial patterns of cancer: Optimized biopsy procedures for estimating prostate cancer volume and Gleason Score(2009-08-01) Ou, Yangming; Shen, Dinggang; Zeng, Jianchao; Davatzikos, Christos; Sun, Leon; Moul, JuddProstate biopsy is the current gold-standard procedure for prostate cancer diagnosis. Existing prostate biopsy procedures have been mostly focusing on detecting cancer presence. However, they often ignore the potential use of biopsy to estimate cancer volume (CV) and Gleason Score (GS, a cancer grade descriptor), the two surrogate markers for cancer aggressiveness and the two crucial factors for treatment planning. To fill up this vacancy, this paper assumes and demonstrates that, by optimally sampling the spatial patterns of cancer, biopsy procedures can be specifically designed for estimating CV and GS. Our approach combines image analysis and machine learning tools in an atlas-based population study that consists of three steps. First, the spatial distributions of cancer in a patient population are learned, by constructing statistical atlases from histological images of prostate specimens with known cancer ground truths. Then, the optimal biopsy locations are determined in a feature selection formulation, so that biopsy outcomes (either cancer presence or absence) at those locations could be used to differentiate, at the best rate, between the existing specimens having different (high vs. low) CV/GS values. Finally, the optimized biopsy locations are utilized to estimate whether a new-coming prostate cancer patient has high or low CV/GS values, based on a binary classification formulation. The estimation accuracy and the generalization ability are evaluated by the classification rates and the associated receiver-operating-characteristic (ROC) curves in cross validations. The optimized biopsy procedures are also designed to be robust to the almost inevitable needle displacement errors in clinical practice, and are found to be robust to variations in the optimization parameters as well as the training populations.Publication Detecting Cognitive States from fMRI Images by Machine Learning and Multivariante Classification(2006-01-01) Fan, Yong; Shen, Dinggang; Davatzikos, ChristosThe major obstacle in building classifiers that robustly detect a particular cognitive state across different subjects using fMRI images has been the high inter-subject functional variability in brain activation patterns. To overcome this obstacle, firstly, the brain regions that are relevant to the problem under study are determined from the training data; then, statistical information of each brain region is extracted to form regional features, which are robust to inter-subject functional variations within the brain region; finally, the regional feature statistical variations across different samples are further alleviated by a PCA technique. To improve the generalization ability and efficiency of the classification, from the extracted regional features, a hybrid feature selection method is utilized to select the most discriminative features, which are used to train a SVM classifier for decoding brain states from fMRI images. The performance of this method is validated in a deception fMRI study. The proposed method yielded better results compared to other commonly used fMRI image classification methods.Publication Classifying spatial patterns of brain activity with machine learning methods: application to lie detection(2005-11-15) Davatzikos, Christos; Ruparel, Kosha; Fan, Yong; Shen, Dinggang; Gur, Ruben; Langleben, Daniel D.; Acharyya, M.; Loughead, JamesPatterns of brain activity during deception have recently been characterized with fMRI on the multi-subject average group level. The clinical value of fMRI in lie detection will be determined by the ability to detect deception in individual subjects, rather than group averages. High-dimensional non-linear pattern classification methods applied to functional magnetic resonance (fMRI) images were used to discriminate between the spatial patterns of brain activity associated with lie and truth. In 22 participants performing a forced-choice deception task, 99% of the true and false responses were discriminated correctly. Predictive accuracy, assessed by cross-validation in participants not included in training, was 88%. The results demonstrate the potential of non-linear machine learning techniques in lie detection and other possible clinical applications of fMRI in individual subjects, and indicate that accurate clinical tests could be based on measurements of brain function with fMRI.Publication Statistically-Constrained High-Dimensional Warping Using Wavelet-Based Priors(2006-06-01) Zue, Zhong; Shen, Dinggang; Davatzikos, ChristosIn this paper, a Statistical Model of Deformation (SMD) that captures the statistical prior distribution of high-dimensional deformations more accurately and effectively than conventional PCA-based statistical shape models is used to regularize deformable registration. SMD utilizes a wavelet-based representation of statistical variation of a deformation field and its Jacobian, and it is able to capture both global and fine shape detail without overconstraining the deformation process. This approach is shown to produce more accurate and robust registration results in MR brain images, relative to the registration methods that use Laplacian-based smoothness constraints of deformation fields. In experiments, we evaluate the SMD-constrained registration by comparing the performance of registration with and without SMD in a specific deformable registration framework. The proposed method can potentially incorporate various registration algorithms to improve their robustness and stability using statistically-based regularization.Publication Registering Histological and MR Images of Prostate for Image-based Cancer Detection(2007-11-01) Ou, Yangming; Feldman, Michael; Tomaszewski, John; Davatzikos, Christos; Zhan, Yiqiang; Shen, DinggangRationale and Objectives Needle biopsy is currently the only way to confirm prostate cancer. To increase prostate cancer diagnostic rate, needles are expected to be deployed at suspicious cancer locations. High contrast MR imaging provides a powerful tool for detecting suspicious cancerous tissues. To do this, MR appearances of cancerous tissue should be characterized and learned from a sufficient number of prostate MR images with known cancer information. However, ground-truth cancer information is only available in histological images. Therefore, it is necessary to warp ground-truth cancerous regions in histological images to MR images by a registration procedure. The objective of this paper is to develop a registration technique for aligning histological and MR images of the same prostate. Material and Methods Five pairs of histological and T2-weighted MR images of radical prostatectomy specimens are collected. For each pair, registration is guided by two sets of correspondences that can be reliably established on prostate boundaries and internal salient blob-like structures of histological and MR images. Results Our developed registration method can accurately register histological and MR images. It yields results comparable to manual registration, in terms of landmark distance and volume overlap. It also outperforms both affine registration and boundary-guided registration methods. Conclusions We have developed a novel method for deformable registration of histological and MR images of the same prostate. Besides the collection of ground-truth cancer information in MR images, the method has other potential applications. An automatic, accurate registration of histological and MR images actually builds a bridge between in vivo anatomical information and ex vivo pathological information, which is valuable for various clinical studies.Publication Non-Rigid Registration between Histological and MR Images of the Prostate: A Joint Segmentation and Registration Framework(2009-06-01) Ou, Yangming; Shen, Dinggang; Feldman, Michael; Tomaszewski, John; Davatzikos, ChristosThis paper presents a 3D non-rigid registration algorithm between histological and MR images of the prostate with cancer. To compensate for the loss of 3D integrity in the histology sectioning process, series of 2D histological slices are first reconstructed into a 3D histological volume. After that, the 3D histology-MRI registration is obtained by maximizing a) landmark similarity and b) cancer region overlap between the two images. The former aims to capture distortions at prostate boundary and internal bloblike structures; and the latter aims to capture distortions specifically at cancer regions. In particular, landmark similarities, the former, is maximized by an annealing process, where correspondences between the automatically-detected boundary and internal landmarks are iteratively established in a fuzzy-to-deterministic fashion. Cancer region overlap, the latter, is maximized in a joint cancer segmentation and registration framework, where the two interleaved problems – segmentation and registration – inform each other in an iterative fashion. Registration accuracy is established by comparing against human-rater-defined landmarks and by comparing with other methods. The ultimate goal of this registration is to warp the histologically-defined cancer ground truth into MRI, for more thoroughly understanding MRI signal characteristics of the prostate cancerous tissue, which will promote the MRI-based prostate cancer diagnosis in the future studies.