Brain Tumor Detection and Segmentation in Multisequence MRI

Tato práce se zabývá detekcí a segmentací mozkového nádoru v multisekvenčních MR obrazech se zaměřením na gliomy vysokého a nízkého stupně malignity. Jsou zde pro tento účel navrženy tři metody. První metoda se zabývá detekcí prezence částí mozkového nádoru v axiálních a koronárních řezech. Jedná se o algoritmus založený na analýze symetrie při různých rozlišeních obrazu, který byl otestován na T1, T2, T1C a FLAIR obrazech. Druhá metoda se zabývá extrakcí oblasti celého mozkového nádoru, zahrnující oblast jádra tumoru a edému, ve FLAIR a T2 obrazech. Metoda je schopna extrahovat mozkový nádor z 2D i 3D obrazů. Je zde opět využita analýza symetrie, která je následována automatickým stanovením intenzitního prahu z nejvíce asymetrických částí. Třetí metoda je založena na predikci lokální struktury a je schopna segmentovat celou oblast nádoru, jeho jádro i jeho aktivní část. Metoda využívá faktu, že většina lékařských obrazů vykazuje vysokou podobnost intenzit sousedních pixelů a silnou korelaci mezi intenzitami v různých obrazových modalitách. Jedním ze způsobů, jak s touto korelací pracovat a používat ji, je využití lokálních obrazových polí. Podobná korelace existuje také mezi sousedními pixely v anotaci obrazu. Tento příznak byl využit v predikci lokální struktury při lokální anotaci polí. Jako klasifikační algoritmus je v této metodě použita konvoluční neuronová síť vzhledem k její známe schopnosti zacházet s korelací mezi příznaky. Všechny tři metody byly otestovány na veřejné databázi 254 multisekvenčních MR obrazech a byla dosáhnuta přesnost srovnatelná s nejmodernějšími metodami v mnohem kratším výpočetním čase (v řádu sekund při použitý CPU), což poskytuje možnost manuálních úprav při interaktivní segmetaci.This work deals with the brain tumor detection and segmentation in multisequence MR images with particular focus on high- and low-grade gliomas. Three methods are propose for this purpose. The first method deals with the presence detection of brain tumor structures in axial and coronal slices. This method is based on multi-resolution symmetry analysis and it was tested for T1, T2, T1C and FLAIR images. The second method deals with extraction of the whole brain tumor region, including tumor core and edema, in FLAIR and T2 images and is suitable to extract the whole brain tumor region from both 2D and 3D. It also uses the symmetry analysis approach which is followed by automatic determination of the intensity threshold from the most asymmetric parts. The third method is based on local structure prediction and it is able to segment the whole tumor region as well as tumor core and active tumor. This method takes the advantage of a fact that most medical images feature a high similarity in intensities of nearby pixels and a strong correlation of intensity profiles across different image modalities. One way of dealing with -- and even exploiting -- this correlation is the use of local image patches. In the same way, there is a high correlation between nearby labels in image annotation, a feature that has been used in the ``local structure prediction'' of local label patches. Convolutional neural network is chosen as a learning algorithm, as it is known to be suited for dealing with correlation between features. All three methods were evaluated on a public data set of 254 multisequence MR volumes being able to reach comparable results to state-of-the-art methods in much shorter computing time (order of seconds running on CPU) providing means, for example, to do online updates when aiming at an interactive segmentation.

Glioma Grading Using Structural Magnetic Resonance Imaging and Molecular Data

A glioma grading method using conventional structural magnetic resonance image (MRI) and molecular data from patients is proposed. The noninvasive grading of glioma tumors is obtained using multiple radiomic texture features including dynamic texture analysis, multifractal detrended fluctuation analysis, and multiresolution fractal Brownian motion in structural MRI. The proposed method is evaluated using two multicenter MRI datasets: (1) the brain tumor segmentation (BRATS-2017) challenge for high-grade versus low-grade (LG) and (2) the cancer imaging archive (TCIA) repository for glioblastoma (GBM) versus LG glioma grading. The grading performance using MRI is compared with that of digital pathology (DP) images in the cancer genome atlas (TCGA) data repository. The results show that the mean area under the receiver operating characteristic curve (AUC) is 0.88 for the BRATS dataset. The classification of tumor grades using MRI and DP images in TCIA/TCGA yields mean AUC of 0.90 and 0.93, respectively. This work further proposes and compares tumor grading performance using molecular alterations (IDH1/2 mutations) along with MRI and DP data, following the most recent World Health Organization grading criteria, respectively. The overall grading performance demonstrates the efficacy of the proposed noninvasive glioma grading approach using structural MRI

Histopathological image analysis : a review

Over the past decade, dramatic increases in computational power and improvement in image analysis algorithms have allowed the development of powerful computer-assisted analytical approaches to radiological data. With the recent advent of whole slide digital scanners, tissue histopathology slides can now be digitized and stored in digital image form. Consequently, digitized tissue histopathology has now become amenable to the application of computerized image analysis and machine learning techniques. Analogous to the role of computer-assisted diagnosis (CAD) algorithms in medical imaging to complement the opinion of a radiologist, CAD algorithms have begun to be developed for disease detection, diagnosis, and prognosis prediction to complement the opinion of the pathologist. In this paper, we review the recent state of the art CAD technology for digitized histopathology. This paper also briefly describes the development and application of novel image analysis technology for a few specific histopathology related problems being pursued in the United States and Europe

Automated Segmentation of Cerebral Aneurysm Using a Novel Statistical Multiresolution Approach

Cerebral Aneurysm (CA) is a vascular disease that threatens the lives of many adults. It a ects almost 1:5 - 5% of the general population. Sub- Arachnoid Hemorrhage (SAH), resulted by a ruptured CA, has high rates of morbidity and mortality. Therefore, radiologists aim to detect it and diagnose it at an early stage, by analyzing the medical images, to prevent or reduce its damages. The analysis process is traditionally done manually. However, with the emerging of the technology, Computer-Aided Diagnosis (CAD) algorithms are adopted in the clinics to overcome the traditional process disadvantages, as the dependency of the radiologist's experience, the inter and intra observation variability, the increase in the probability of error which increases consequently with the growing number of medical images to be analyzed, and the artifacts added by the medical images' acquisition methods (i.e., MRA, CTA, PET, RA, etc.) which impedes the radiologist' s work. Due to the aforementioned reasons, many research works propose di erent segmentation approaches to automate the analysis process of detecting a CA using complementary segmentation techniques; but due to the challenging task of developing a robust reproducible reliable algorithm to detect CA regardless of its shape, size, and location from a variety of the acquisition methods, a diversity of proposed and developed approaches exist which still su er from some limitations. This thesis aims to contribute in this research area by adopting two promising techniques based on the multiresolution and statistical approaches in the Two-Dimensional (2D) domain. The rst technique is the Contourlet Transform (CT), which empowers the segmentation by extracting features not apparent in the normal image scale. While the second technique is the Hidden Markov Random Field model with Expectation Maximization (HMRF-EM), which segments the image based on the relationship of the neighboring pixels in the contourlet domain. The developed algorithm reveals promising results on the four tested Three- Dimensional Rotational Angiography (3D RA) datasets, where an objective and a subjective evaluation are carried out. For the objective evaluation, six performance metrics are adopted which are: accuracy, Dice Similarity Index (DSI), False Positive Ratio (FPR), False Negative Ratio (FNR), speci city, and sensitivity. As for the subjective evaluation, one expert and four observers with some medical background are involved to assess the segmentation visually. Both evaluations compare the segmented volumes against the ground truth data

Radiomic Texture Feature Descriptor to Distinguish Recurrent Brain Tumor From Radiation Necrosis Using Multimodal MRI

Despite multimodal aggressive treatment with chemo-radiation-therapy, and surgical resection, Glioblastoma Multiforme (GBM) may recur which is known as recurrent brain tumor (rBT), There are several instances where benign and malignant pathologies might appear very similar on radiographic imaging. One such illustration is radiation necrosis (RN) (a moderately benign impact of radiation treatment) which are visually almost indistinguishable from rBT on structural magnetic resonance imaging (MRI). There is hence a need for identification of reliable non-invasive quantitative measurements on routinely acquired brain MRI scans: pre-contrast T1-weighted (T1), post-contrast T1-weighted (T1Gd), T2-weighted (T2), and T2 Fluid Attenuated Inversion Recovery (FLAIR) that can accurately distinguish rBT from RN. In this work, sophisticated radiomic texture features are used to distinguish rBT from RN on multimodal MRI for disease characterization. First, stochastic multiresolution radiomic descriptor that captures voxel-level textural and structural heterogeneity as well as intensity and histogram features are extracted. Subsequently, these features are used in a machine learning setting to characterize the rBT from RN from four sequences of the MRI with 155 imaging slices for 30 GBM cases (12 RN, 18 rBT). To reduce the bias in accuracy estimation our model is implemented using Leave-one-out crossvalidation (LOOCV) and stratified 5-fold cross-validation with a Random Forest classifier. Our model offers mean accuracy of 0.967 ± 0.180 for LOOCV and 0.933 ± 0.082 for stratified 5-fold cross-validation using multiresolution texture features for discrimination of rBT from RN in this study. Our findings suggest that sophisticated texture feature may offer better discrimination between rBT and RN in MRI compared to other works in the literature

Medical Image Segmentation Based on Multi-Modal Convolutional Neural Network: Study on Image Fusion Schemes

Image analysis using more than one modality (i.e. multi-modal) has been increasingly applied in the field of biomedical imaging. One of the challenges in performing the multimodal analysis is that there exist multiple schemes for fusing the information from different modalities, where such schemes are application-dependent and lack a unified framework to guide their designs. In this work we firstly propose a conceptual architecture for the image fusion schemes in supervised biomedical image analysis: fusing at the feature level, fusing at the classifier level, and fusing at the decision-making level. Further, motivated by the recent success in applying deep learning for natural image analysis, we implement the three image fusion schemes above based on the Convolutional Neural Network (CNN) with varied structures, and combined into a single framework. The proposed image segmentation framework is capable of analyzing the multi-modality images using different fusing schemes simultaneously. The framework is applied to detect the presence of soft tissue sarcoma from the combination of Magnetic Resonance Imaging (MRI), Computed Tomography (CT) and Positron Emission Tomography (PET) images. It is found from the results that while all the fusion schemes outperform the single-modality schemes, fusing at the feature level can generally achieve the best performance in terms of both accuracy and computational cost, but also suffers from the decreased robustness in the presence of large errors in any image modalities.Comment: Zhe Guo and Xiang Li contribute equally to this wor

Dynamic low-level context for the detection of mild traumatic brain injury.

Mild traumatic brain injury (mTBI) appears as low contrast lesions in magnetic resonance (MR) imaging. Standard automated detection approaches cannot detect the subtle changes caused by the lesions. The use of context has become integral for the detection of low contrast objects in images. Context is any information that can be used for object detection but is not directly due to the physical appearance of an object in an image. In this paper, new low-level static and dynamic context features are proposed and integrated into a discriminative voxel-level classifier to improve the detection of mTBI lesions. Visual features, including multiple texture measures, are used to give an initial estimate of a lesion. From the initial estimate novel proximity and directional distance, contextual features are calculated and used as features for another classifier. This feature takes advantage of spatial information given by the initial lesion estimate using only the visual features. Dynamic context is captured by the proposed posterior marginal edge distance context feature, which measures the distance from a hard estimate of the lesion at a previous time point. The approach is validated on a temporal mTBI rat model dataset and shown to have improved dice score and convergence compared to other state-of-the-art approaches. Analysis of feature importance and versatility of the approach on other datasets are also provided

An Information Theoretic Approach For Feature Selection And Segmentation In Posterior Fossa Tumors

Posterior Fossa (PF) is a type of brain tumor located in or near brain stem and cerebellum. About 55% - 70 % pediatric brain tumors arise in the posterior fossa, compared with only 15% - 20% of adult tumors. For segmenting PF tumors we should have features to study the characteristics of tumors. In literature, different types of texture features such as Fractal Dimension (FD) and Multifractional Brownian Motion (mBm) have been exploited for measuring randomness associated with brain and tumor tissues structures, and the varying appearance of tissues in magnetic resonance images (MRI). For selecting best features techniques such as neural network and boosting methods have been exploited. However, neural network cannot descirbe about the properties of texture features. We explore methods such as information theroetic methods which can perform feature selection based on properties of texture features. The primary contribution of this dissertation is investigating efficacy of different image features such as intensity, fractal texture, and level - set shape in segmentation of PF tumor for pediatric patients. We explore effectiveness of using four different feature selection and three different segmentation techniques respectively to discriminate tumor regions from normal tissue in multimodal brain MRI. Our research suggest that Kullback - Leibler Divergence (KLD) measure for feature ranking and selection and Expectation Maximization (EM) algorithm for feature fusion and tumor segmentation offer the best performance for the patient data in this study. To improve segmentation accuracy, we need to consider abnormalities such as cyst, edema and necrosis which surround tumors. In this work, we exploit features which describe properties of cyst and technique which can be used to segment it. To achieve this goal, we extend the two class KLD techniques to multiclass feature selection techniques, so that we can effectively select features for tumor, cyst and non tumor tissues. We compute segemntation accuracy by computing number of pixels segemented to total number of pixels for the best features. For automated process we integrate the inhomoheneity correction, feature selection using KLD and segmentation in an integrated EM framework. To validate results we have used similarity coefficients for computing the robustness of segmented tumor and cyst